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Nguinkal JA, Zoclanclounon YAB, Molina A, Roba A, Nyakio NM, Lokamar PN, Nzoyikorera N, Ihorimbere T, Nyandwi J, Aguer MA, Maror JA, Lokore ML, Francis MF, Mapunda LA, Beyanga M, Muyigi T, Pimundu G, Nabadda SN, Kabalisa E, Umuringa JD, Tare IM, Lagu HI, Achol E, May J, Affara M, Gehre F. Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community. BMC Public Health 2024; 24:1500. [PMID: 38840103 PMCID: PMC11151545 DOI: 10.1186/s12889-024-18990-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
The East African Community (EAC) grapples with many challenges in tackling infectious disease threats and antimicrobial resistance (AMR), underscoring the importance of regional and robust pathogen genomics capacities. However, a significant disparity exists among EAC Partner States in harnessing bacterial pathogen sequencing and data analysis capabilities for effective AMR surveillance and outbreak response. This study assesses the current landscape and challenges associated with pathogen next-generation sequencing (NGS) within EAC, explicitly focusing on World Health Organization (WHO) AMR-priority pathogens. The assessment adopts a comprehensive approach, integrating a questionnaire-based survey amongst National Public Health Laboratories (NPHLs) with an analysis of publicly available metadata on bacterial pathogens isolated in the EAC countries. In addition to the heavy reliance on third-party organizations for bacterial NGS, the findings reveal a significant disparity among EAC member States in leveraging bacterial pathogen sequencing and data analysis. Approximately 97% (n = 4,462) of publicly available high-quality bacterial genome assemblies of samples collected in the EAC were processed and analyzed by external organizations, mainly in Europe and North America. Tanzania led in-country sequencing efforts, followed by Kenya and Uganda. The other EAC countries had no publicly available samples or had all their samples sequenced and analyzed outside the region. Insufficient local NGS sequencing facilities, limited bioinformatics expertise, lack of adequate computing resources, and inadequate data-sharing mechanisms are among the most pressing challenges that hinder the EAC's NPHLs from effectively leveraging pathogen genomics data. These insights emphasized the need to strengthen microbial pathogen sequencing and data analysis capabilities within the EAC to empower these laboratories to conduct pathogen sequencing and data analysis independently. Substantial investments in equipment, technology, and capacity-building initiatives are crucial for supporting regional preparedness against infectious disease outbreaks and mitigating the impact of AMR burden. In addition, collaborative efforts should be developed to narrow the gap, remedy regional imbalances, and harmonize NGS data standards. Supporting regional collaboration, strengthening in-country genomics capabilities, and investing in long-term training programs will ultimately improve pathogen data generation and foster a robust NGS-driven AMR surveillance and outbreak response in the EAC, thereby supporting global health initiatives.
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Affiliation(s)
- Julien A Nguinkal
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
| | | | - Andrea Molina
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Animal Science School, University of Costa Rica, San José, Costa Rica
| | - Abdi Roba
- Department of Disease Surveillance and Epidemic Response, Ministry of Health, Nairobi, Kenya
| | - Ndia M Nyakio
- Department of Disease Surveillance and Epidemic Response, Ministry of Health, Nairobi, Kenya
| | - Peter N Lokamar
- Department of Disease Surveillance and Epidemic Response, Ministry of Health, Nairobi, Kenya
| | - Néhémie Nzoyikorera
- National Reference Laboratory, National Institute of Public Health, Bujumbura, Burundi
| | - Théogène Ihorimbere
- National Reference Laboratory, National Institute of Public Health, Bujumbura, Burundi
| | - Joseph Nyandwi
- National Reference Laboratory, National Institute of Public Health, Bujumbura, Burundi
| | - Mamdouh A Aguer
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - James A Maror
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - Michael Lasuba Lokore
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | | | - Lawrence A Mapunda
- National Public Health Laboratory, Ministry of Health, Dar es Salam, Tanzania
| | - Medard Beyanga
- National Public Health Laboratory, Ministry of Health, Dar es Salam, Tanzania
| | - Tonny Muyigi
- Central Public Health Laboratories, National Health Laboratories, Ministry of Health, Kampala, Uganda
| | - Godfrey Pimundu
- Central Public Health Laboratories, National Health Laboratories, Ministry of Health, Kampala, Uganda
| | - Susan N Nabadda
- Central Public Health Laboratories, National Health Laboratories, Ministry of Health, Kampala, Uganda
| | - Emmanuel Kabalisa
- Biomedical Services Department, Biomedical Centre Rwanda, Kigali, Rwanda
| | | | | | - Hakim I Lagu
- Health Department, East African Community (EAC), Arusha, Tanzania
| | - Emmanuel Achol
- Health Department, East African Community (EAC), Arusha, Tanzania
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Muna Affara
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Florian Gehre
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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Muturi P, Wachira P, Wagacha M, Mbae C, Kavai S, Mugo M, Muhammed M, González JF, Kariuki S, Gunn JS. Salmonella Typhi Haplotype 58 (H58) Biofilm Formation and Genetic Variation in Typhoid Fever Patients with Gallstones in an Endemic Setting in Kenya. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.03.24308409. [PMID: 38883710 PMCID: PMC11177912 DOI: 10.1101/2024.06.03.24308409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
The causative agent of typhoid fever, Salmonella enterica serovar Typhi, is a human restricted pathogen. Human carriers, 90% of whom have gallstones in their gallbladder, continue to shed the pathogen after treatment. The genetic mechanisms involved in establishing the carrier state are poorly understood, but S. Typhi is thought to undergo specific genetic changes within the gallbladder as an adaptive mechanism. In the current study, we aimed to identify biofilm forming ability and the genetic differences in longitudinal clinical S. Typhi isolates from asymptomatic carriers with gallstones in Nairobi, Kenya. Whole genome sequences were analyzed from 22 S. Typhi isolates, 20 from stool and 2 from blood samples, all genotype 4.3.1 (H58). Nineteen strains were from four patients also diagnosed with gallstones, of whom, three had typhoid symptoms and continued to shed S. Typhi after treatment. All isolates had point mutations in the quinolone resistance determining region (QRDR) and only sub-lineage 4.3.1.2EA3 encoded multidrug resistance genes. There was no variation in antimicrobial resistance patterns among strains from the same patient/household. Non-multidrug resistant (MDR), isolates formed significantly stronger biofilms in vitro than the MDR isolates, p<0.001. A point mutation within the treB gene (treB A383T) was observed in strains isolated after clinical resolution from patients living in 75% of the households. Missense mutations in Vi capsular polysaccharide genes, tviE P263S was also observed in 18% of the isolates. This study provides insights into the role of typhoid carriage, biofilm formation, AMR genes and genetic variations in S. Typhi from asymptomatic carriers.
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Affiliation(s)
- Peter Muturi
- Centre for Microbiology Research, Kenya Medical Research Institute
- Department of Biology, University of Nairobi, Kenya
| | | | | | - Cecilia Mbae
- Centre for Microbiology Research, Kenya Medical Research Institute
| | - Susan Kavai
- Centre for Microbiology Research, Kenya Medical Research Institute
| | - Michael Mugo
- Centre for Microbiology Research, Kenya Medical Research Institute
| | | | - Juan F. González
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Drugs for Neglected Diseases initiative Eastern Africa, Nairobi, Kenya
| | - John S. Gunn
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
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53
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Chen Z, Grim CJ, Ramachandran P, Meng J. Advancing metagenome-assembled genome-based pathogen identification: unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing. Microbiol Spectr 2024; 12:e0011724. [PMID: 38687063 DOI: 10.1128/spectrum.00117-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Oxford Nanopore sequencing is one of the high-throughput sequencing technologies that facilitates the reconstruction of metagenome-assembled genomes (MAGs). This study aimed to assess the potential of long-read assembly algorithms in Oxford Nanopore sequencing to enhance the MAG-based identification of bacterial pathogens using both simulated and mock communities. Simulated communities were generated to mimic those on fresh spinach and in surface water. Long reads were produced using R9.4.1+SQK-LSK109 and R10.4 + SQK-LSK112, with 0.5, 1, and 2 million reads. The simulated bacterial communities included multidrug-resistant Salmonella enterica serotypes Heidelberg, Montevideo, and Typhimurium in the fresh spinach community individually or in combination, as well as multidrug-resistant Pseudomonas aeruginosa in the surface water community. Real data sets of the ZymoBIOMICS HMW DNA Standard were also studied. A bioinformatic pipeline (MAGenie, freely available at https://github.com/jackchen129/MAGenie) that combines metagenome assembly, taxonomic classification, and sequence extraction was developed to reconstruct draft MAGs from metagenome assemblies. Five assemblers were evaluated based on a series of genomic analyses. Overall, Flye outperformed the other assemblers, followed by Shasta, Raven, and Unicycler, while Canu performed least effectively. In some instances, the extracted sequences resulted in draft MAGs and provided the locations and structures of antimicrobial resistance genes and mobile genetic elements. Our study showcases the viability of utilizing the extracted sequences for precise phylogenetic inference, as demonstrated by the consistent alignment of phylogenetic topology between the reference genome and the extracted sequences. R9.4.1+SQK-LSK109 was more effective in most cases than R10.4+SQK-LSK112, and greater sequencing depths generally led to more accurate results.IMPORTANCEBy examining diverse bacterial communities, particularly those housing multiple Salmonella enterica serotypes, this study holds significance in uncovering the potential of long-read assembly algorithms to improve metagenome-assembled genome (MAG)-based pathogen identification through Oxford Nanopore sequencing. Our research demonstrates that long-read assembly stands out as a promising avenue for boosting precision in MAG-based pathogen identification, thus advancing the development of more robust surveillance measures. The findings also support ongoing endeavors to fine-tune a bioinformatic pipeline for accurate pathogen identification within complex metagenomic samples.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
| | - Christopher J Grim
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
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Kolte B, Nübel U. Genetic determinants of resistance to antimicrobial therapeutics are rare in publicly available Clostridioides difficile genome sequences. J Antimicrob Chemother 2024; 79:1320-1328. [PMID: 38598696 PMCID: PMC11144481 DOI: 10.1093/jac/dkae101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
OBJECTIVES To determine the frequencies and clonal distributions of putative genetic determinants of resistance to antimicrobials applied for treatment of Clostridioides difficile infection (CDI), as documented in the genomic record. METHODS We scanned 26 557 C. difficile genome sequences publicly available from the EnteroBase platform for plasmids, point mutations and gene truncations previously reported to reduce susceptibility to vancomycin, fidaxomicin or metronidazole, respectively. We measured the antimicrobial susceptibility of 143 selected C. difficile isolates. RESULTS The frequency of mutations causing reduced susceptibility to vancomycin and metronidazole, respectively, increased strongly after 2000, peaking at up to 52% of all sequenced C. difficile genomes. However, both mutations declined sharply more recently, reflecting major changes in CDI epidemiology. We detected mutations associated with fidaxomicin resistance in several major genotypes, but found no evidence of international spread of resistant clones. The pCD-METRO plasmid, conferring metronidazole resistance, was detected in a single previously unreported C. difficile isolate, recovered from a hospital patient in Germany in 2008. The pX18-498 plasmid, putatively associated with decreased vancomycin susceptibility, was confined to related, recent isolates from the USA. Phenotype measurements confirmed that most of those genetic features were useful predictors of antibiotic susceptibility, even though ranges of MICs typically overlapped among isolates with and without specific mutations. CONCLUSIONS Genomic data suggested that resistance to therapeutic antimicrobial drugs is rare in C. difficile. Public antimicrobial resistance marker databases were not equipped to detect most of the genetic determinants relevant to antibiotic therapy of CDI.
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Affiliation(s)
- Baban Kolte
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Microbial Genome Research, Inhoffenstr. 7B, 38124, Braunschweig, Germany
- Technical University Braunschweig, Institute of Microbiology, Braunschweig, Germany
| | - Ulrich Nübel
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Microbial Genome Research, Inhoffenstr. 7B, 38124, Braunschweig, Germany
- Technical University Braunschweig, Institute of Microbiology, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
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Pellegrinetti TA, de Cássia Mesquita da Cunha I, Chaves MGD, Freitas ASD, Passos GS, Silva AVRD, Cotta SR, Tsai SM, Mendes LW. Genomic insights of Fictibacillus terranigra sp. nov., a versatile metabolic bacterium from Amazonian Dark Earths. Braz J Microbiol 2024; 55:1817-1828. [PMID: 38358421 PMCID: PMC11153436 DOI: 10.1007/s42770-024-01268-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
The Amazon rainforest, a hotspot for biodiversity, is a crucial research area for scientists seeking novel microorganisms with ecological and biotechnological significance. A key region within the Amazon rainforest is the Amazonian Dark Earths (ADE), noted for supporting diverse plant and microbial communities, and its potential as a blueprint for sustainable agriculture. This study delineates the isolation, morphological traits, carbon source utilization, and genomic features of Fictibacillus terranigra CENA-BCM004, a candidate novel species of the Fictibacillus genus isolated from ADE. The genome of Fictibacillus terranigra was sequenced, resulting in 16 assembled contigs, a total length of 4,967,627 bp, and a GC content of 43.65%. Genome annotation uncovered 3315 predicted genes, encompassing a wide range of genes linked to various metabolic pathways. Phylogenetic analysis indicated that CENA-BCM004 is a putative new species, closely affiliated with other unidentified Fictibacillus species and Bacillus sp. WQ 8-8. Moreover, this strain showcased a multifaceted metabolic profile, revealing its potential for diverse biotechnological applications. It exhibited capabilities to antagonize pathogens, metabolize multiple sugars, mineralize organic matter compounds, and solubilize several minerals. These insights substantially augment our comprehension of microbial diversity in ADE and underscore the potential of Fictibacillus terranigra as a precious resource for biotechnological endeavors. The genomic data generated from this study will serve as a foundational resource for subsequent research and exploration of the biotechnological capabilities of this newly identified species.
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Affiliation(s)
- Thierry Alexandre Pellegrinetti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Izadora de Cássia Mesquita da Cunha
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
- Luiz de Queiroz College of Agriculture (ESALQ), University of Sao Paulo, Piracicaba, Brazil
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Anderson Santos de Freitas
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Gabriel Schimmelpfeng Passos
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Ana Vitória Reina da Silva
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Simone Raposo Cotta
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil.
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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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Monte DFM, de Oliveira CJB. Global distribution of colistin- and carbapenem-resistant Citrobacter freundii. Diagn Microbiol Infect Dis 2024; 109:116248. [PMID: 38574443 DOI: 10.1016/j.diagmicrobio.2024.116248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
Affiliation(s)
- Daniel F M Monte
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil.
| | - Celso José Bruno de Oliveira
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil
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Cersosimo LM, Worley JN, Bry L. Approaching toxigenic Clostridia from a One Health perspective. Anaerobe 2024; 87:102839. [PMID: 38552896 PMCID: PMC11180571 DOI: 10.1016/j.anaerobe.2024.102839] [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: 12/31/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. Their prevalence in diverse ecosystems requires a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs and as commensals or infecting pathogens in human and animal populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jay N Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; National Center for Biotechnology Information, NIH, Bethesda, MD, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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Zhang Y, Quensen J, Chen B, Li H, Tiedje J, Sun W, Qian X. Paenalcaligenes faecalis sp. nov., a novel species of the family Alcaligenaceae isolated from chicken faeces. Int J Syst Evol Microbiol 2024; 74. [PMID: 38896454 DOI: 10.1099/ijsem.0.006429] [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: 06/21/2024] Open
Abstract
A Gram-negative, motile, rod-shaped aerobic and alkalogenic bacterium, designated as strain YLCF04T, was isolated from chicken faeces. Its growth was optimal at 28 °C (range, 10-40 °C), pH 8 (range, pH 6-9) and in 1 % (w/v) NaCl (range, 0-10 %). It was classified to the genus Paenalcaligenes and was most closely related to Paenalcaligenes hominis CCUG 53761AT (97.5 % similarity) based on 16S rRNA gene sequence analysis. Average nucleotide identity and digital DNA-DNA hybridization values between YLCF04T and P. hominis CCUG 53761AT were 76.3 and 18.2 %, respectively. Strain YLCF04T has a genome size of 2.7 Mb with DNA G+C content of 46.3 mol%. Based on its phylogenetic, genomic, phenotypic and biochemical characteristics, strain YLCF04T represents a novel species of the genus Paenalcaligenes, for which the name Paenalcaligenes faecalis sp. nov. is proposed. The type strain is YLCF04T (=CCTCC AB 2022359T= KCTC 92789T).
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Affiliation(s)
- Yiran Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - John Quensen
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Bo Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Hailong Li
- Xi'an Environmental Monitoring Station, Xi'an, Shaanxi, 710119, PR China
| | - James Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Wei Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling,Shaanxi, 712100, PR China
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Zhang J, Tang A, Jin T, Sun D, Guo F, Lei H, Lin L, Shu W, Yu P, Li X, Li B. A panoramic view of the virosphere in three wastewater treatment plants by integrating viral-like particle-concentrated and traditional non-concentrated metagenomic approaches. IMETA 2024; 3:e188. [PMID: 38898980 PMCID: PMC11183165 DOI: 10.1002/imt2.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 06/21/2024]
Abstract
Wastewater biotreatment systems harbor a rich diversity of microorganisms, and the effectiveness of biotreatment systems largely depends on the activity of these microorganisms. Specifically, viruses play a crucial role in altering microbial behavior and metabolic processes throughout their infection phases, an aspect that has recently attracted considerable interest. Two metagenomic approaches, viral-like particle-concentrated (VPC, representing free viral-like particles) and non-concentrated (NC, representing the cellular fraction), were employed to assess their efficacy in revealing virome characteristics, including taxonomy, diversity, host interactions, lifestyle, dynamics, and functional genes across processing units of three wastewater treatment plants (WWTPs). Our findings indicate that each approach offers unique insights into the viral community and functional composition. Their combined use proved effective in elucidating WWTP viromes. We identified nearly 50,000 viral contigs, with Cressdnaviricota and Uroviricota being the predominant phyla in the VPC and NC fractions, respectively. Notably, two pathogenic viral families, Asfarviridae and Adenoviridae, were commonly found in these WWTPs. We also observed significant differences in the viromes of WWTPs processing different types of wastewater. Additionally, various phage-derived auxiliary metabolic genes (AMGs) were active at the RNA level, contributing to the metabolism of the microbial community, particularly in carbon, sulfur, and phosphorus cycling. Moreover, we identified 29 virus-carried antibiotic resistance genes (ARGs) with potential for host transfer, highlighting the role of viruses in spreading ARGs in the environment. Overall, this study provides a detailed and integrated view of the virosphere in three WWTPs through the application of VPC and NC metagenomic approaches. Our findings enhance the understanding of viral communities, offering valuable insights for optimizing the operation and regulation of wastewater treatment systems.
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Affiliation(s)
- Jiayu Zhang
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
- Research Center for Eco‐Environmental EngineeringDongguan University of TechnologyDongguanChina
| | - Aixi Tang
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Tao Jin
- Guangdong Magigene Biotechnology Co., Ltd.ShenzhenChina
| | - Deshou Sun
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
- Shenzhen Tongchen Biotechnology Co., LimitedShenzhenChina
| | - Fangliang Guo
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Huaxin Lei
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Lin Lin
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Wensheng Shu
- Guangdong Magigene Biotechnology Co., Ltd.ShenzhenChina
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life SciencesSouth China Normal UniversityGuangzhouChina
| | - Pingfeng Yu
- College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
| | - Xiaoyan Li
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Bing Li
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
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Saleem F, Ameer A, Star-Shirko B, Keating C, Gundogdu O, Ijaz UZ, Javed S. Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan. Data Brief 2024; 54:110552. [PMID: 38882194 PMCID: PMC11177053 DOI: 10.1016/j.dib.2024.110552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 06/18/2024] Open
Abstract
This article focuses the recovery of prokaryotic organisms including bacteria and archaea from 9 different groups of chicken raised in different farm setups in Pakistan. The groups comprise of three different breeds (Broilers, White Layers, and Black Australorp) of chicken raised in different farming setups that include antibiotic-free control, commercial (open and controlled shed), and backyard farms. We have recovered 569 Metagenomics-Assembled Genomes (MAGs) with a completeness of ≥50 % and contamination of ≤10 %. For each MAG, functional annotations were obtained that include KEGG modules, carbohydrate active enzymes (CAZymes), peptidases, geochemical cycles, antibiotic resistance genes, stress genes, and virulence genes. Furthermore, two different sets of Single Copy Genes (SCGs) were used to construct the phylogenetic trees. Based on the reconstructed phylogeny, phylogenetic gain of each MAG is calculated to give an account of novelty.
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Affiliation(s)
- Farrukh Saleem
- Department of Biosciences, COMSATS University Islamabad, Pakistan
| | - Aqsa Ameer
- Department of Biosciences, COMSATS University Islamabad, Pakistan
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow, United Kingdom
| | - Banaz Star-Shirko
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ciara Keating
- Department of Engineering, Durham University, Durham, DH1 3LE, United Kingdom
- School of Biodiversity, One Health, and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ozan Gundogdu
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Umer Zeeshan Ijaz
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow, United Kingdom
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
- College of Science and Engineering, University of Galway, Ireland
| | - Sundus Javed
- Department of Biosciences, COMSATS University Islamabad, Pakistan
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Liou JS, Zhang WL, Hsu LW, Chen CC, Wang YT, Mori K, Hidaka K, Hamada M, Huang L, Watanabe K, Huang CH. Faecalibacterium taiwanense sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2024; 74:006413. [PMID: 38848117 PMCID: PMC11261667 DOI: 10.1099/ijsem.0.006413] [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: 02/23/2024] [Accepted: 05/26/2024] [Indexed: 06/09/2024] Open
Abstract
Two Gram-stain-negative, straight rods, non-motile, asporogenous, catalase-negative and obligately anaerobic butyrate-producing strains, HLW78T and CYL33, were isolated from faecal samples of two healthy Taiwanese adults. Phylogenetic analyses of 16S rRNA and DNA mismatch repair protein MutL (mutL) gene sequences revealed that these two novel strains belonged to the genus Faecalibacterium. On the basis of 16S rRNA and mutL gene sequence similarities, the type strains Faecalibacterium butyricigenerans AF52-21T(98.3-98.1 % and 79.0-79.5 % similarity), Faecalibacterium duncaniae A2-165T(97.8-97.9 % and 70.9-80.1 %), Faecalibacterium hattorii APC922/41-1T(97.1-97.3 % and 80.3-80.5 %), Faecalibacterium longum CM04-06T(97.8-98.0% and 78.3 %) and Faecalibacterium prausnitzii ATCC 27768T(97.3-97.4 % and 82.7-82.9 %) were the closest neighbours to the novel strains HLW78T and CYL33. Strains HLW78T and CYL33 had 99.4 % both the 16S rRNA and mutL gene sequence similarities, 97.9 % average nucleotide identity (ANI), 96.3 % average amino acid identity (AAI), and 80.5 % digital DNA-DNA hybridization (dDDH) values, indicating that these two strains are members of the same species. Phylogenomic tree analysis indicated that strains HLW78T and CYL33 formed an independent robust cluster together with F. prausnitzii ATCC 27768T. The ANI, AAI and dDDH values between strain HLW78T and its closest neighbours were below the species delineation thresholds of 77.6-85.1 %, 71.4-85.2 % and 28.3-30.9 %, respectively. The two novel strains could be differentiated from the type strains of their closest Faecalibacterium species based on their cellular fatty acid compositions, which contained C18 : 1 ω7c and lacked C15 : 0 and C17 : 1 ω6c, respectively. Phenotypic, chemotaxonomic and genotypic test results demonstrated that the two novel strains HLW78T and CYL33 represented a single, novel species within the genus Faecalibacterium, for which the name Faecalibacterium taiwanense sp. nov. is proposed. The type strain is HLW78T (=BCRC 81397T=NBRC 116372T).
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Affiliation(s)
- Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Wei-Ling Zhang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Li-Wen Hsu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei 11561, Taiwan, ROC
| | - Koji Mori
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kohei Hidaka
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, No. 50, Lane 155, Sec 3, Keelung Rd., Taipei 10673, Taiwan, ROC
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
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Scherrer S, Biggel M, Schneeberger M, Cernela N, Rademacher F, Schmitt S, Stephan R. Genetic diversity and antimicrobial susceptibility of Streptococcus suis from diseased Swiss pigs collected between 2019 - 2022. Vet Microbiol 2024; 293:110084. [PMID: 38608374 DOI: 10.1016/j.vetmic.2024.110084] [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: 01/16/2024] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Streptococcus suis is an important pathogen causing severe disease in pigs and humans, giving rise to economic losses in the pig production industry. Out of 65 S. suis isolates collected from diseased pigs in Switzerland between 2019 and 2022, 57 isolates were thoroughly examined by phenotypic and whole genome sequence (WGS) based characterization. The isolates' genomes were sequenced allowing for a comprehensive analysis of their distribution in terms of serovar, sequence type (ST), clonal complex (CC), and classical virulence markers. Antimicrobial resistance (AMR) genes were screened, and phenotypic susceptibility to eight classes of antimicrobial agents was examined. Serovar 6, devoid of any resistance genes, was found to be most prevalent, followed by serovars 1, 3, 1/2, and 9. Thirty STs were identified, with ST1104 being the most prevalent. Serovar 2 and serovar 1/2 were associated with CC1, potentially containing the most virulent variants. Based on single nucleotide polymorphism (SNP) analyses, fifteen isolates belonged to one of seven putative transmission clusters each consisting of two or three isolates. High phenotypic AMR rates were detected for tetracyclines (80%) and macrolides (35%) and associated with the resistance genes tet(O) and erm(B), respectively. In contrast, susceptibility to β-lactam antibiotics and phenicols was high. Determination of phenotypic AMR profiling, including the minimum inhibitory concentrations (MICs) of the tested antimicrobial agents, sets a baseline for future studies. The study provides valuable insights into the genetic diversity and antimicrobial susceptibility of Swiss S. suis isolates, facilitating the identification of emerging clones relevant to public health concerns.
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Affiliation(s)
- Simone Scherrer
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland.
| | - Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Marianne Schneeberger
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Fenja Rademacher
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Sarah Schmitt
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Roger Stephan
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland; Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
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Davies AR, Chisnall T, Akter S, Afrad MMH, Sadekuzzaman M, Badhy SC, Hasan MZ, Rahman MT, Smith RP, Card RM, Brum E, Chowdhury MGA. Genomic characterisation of Escherichia coli isolated from poultry at retail through Sink Surveillance in Dhaka, Bangladesh reveals high levels of multi-drug resistance. Front Microbiol 2024; 15:1418476. [PMID: 38873136 PMCID: PMC11169737 DOI: 10.3389/fmicb.2024.1418476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024] Open
Abstract
The surveillance of antimicrobial resistance (AMR) in commensal Escherichia coli from livestock at slaughter is widely employed to assess the potential for risk to humans. There is currently a limited understanding of AMR in Bangladesh poultry at retail in live bird markets, with studies focussing solely on phenotypic characterisation of resistance. To address this evidence gap we performed antimicrobial susceptibility testing and whole genome sequencing on E. coli obtained from chickens from live bird markets in Dhaka in 2018 (n = 38) and 2020 (n = 45). E. coli were isolated from caeca samples following ISO guidelines and sequenced using short and long read methods. Multidrug resistance was extremely common (n = 77) and there was excellent concordance between AMR phenotype and the presence of corresponding AMR genes or mutations. There was considerable genomic diversity, with 43 different sequence types detected. Public health considerations included the high occurrence of resistance to ciprofloxacin (n = 75) associated with plasmid-residing qnrS or mutations in the gyrA and parC chromosomal genes; and the detection of a tigecycline resistant isolate harbouring tet(X4) on an IncHI1A/B-IncFIA mosaic plasmid. Thirty-nine isolates were resistant to azithromycin and harboured mphA, with a significant increase in the incidence of resistance between 2018 and 2020. Although azithromycin is banned for veterinary use in Bangladesh it remains an important treatment option for humans. Interestingly, mphA confers high-level resistance to azithromycin and erythromycin, and the latter is commonly used on poultry farms in Bangladesh. Seven isolates were colistin resistant and carried mcr1. For two isolates hybrid assemblies revealed that mcr1 resided on a highly conserved IncHI2 plasmid that had 93% nucleotide identity to a plasmid from the published genome of an E. coli isolate of Bangladeshi human origin. Six isolates had resistance to third generation cephalosporins, associated with plasmid-residing bla CTX-M-55, bla CTX-M-65, or bla DHA-1. By employing phenotypic and genomic approaches for AMR surveillance we have provided new insights into the potential for One Health AMR linkages in Bangladesh. Employing similar approaches in human and environmental sectors will help inform the One Health approach to addressing AMR, and generate evidence to support mitigation measures such as improved antimicrobial stewardship.
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Affiliation(s)
- Alistair R. Davies
- FAO Reference Centre for AMR, Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Thomas Chisnall
- FAO Reference Centre for AMR, Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Shamima Akter
- Central Disease Investigation Laboratory (CDIL), Dhaka, Bangladesh
| | - Md. Mohibul Hassan Afrad
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Dhaka, Bangladesh
| | | | | | - Md. Zakiul Hasan
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Dhaka, Bangladesh
| | - Md. Taifur Rahman
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Dhaka, Bangladesh
| | - Richard P. Smith
- WOAH Collaborating Centre for Risk Analysis & Modelling, Department of Epidemiological Sciences, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Roderick M. Card
- FAO Reference Centre for AMR, Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Eric Brum
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Dhaka, Bangladesh
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Wei HL, Liao YS, Chen BH, Teng RH, Wang YW, Chang JH, Chiou CS. Antimicrobial resistance and genetic relatedness among Campylobacter coli and Campylobacter jejuni from humans and retail chicken meat in Taiwan. J Glob Antimicrob Resist 2024; 38:27-34. [PMID: 38821444 DOI: 10.1016/j.jgar.2024.05.013] [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: 10/22/2023] [Revised: 04/19/2024] [Accepted: 05/17/2024] [Indexed: 06/02/2024] Open
Abstract
OBJECTIVES Campylobacter is a significant zoonotic pathogen primarily transmitted through poultry. Our study aimed to assess antimicrobial resistance and genetic relationships among Campylobacter isolates from retail chicken meat and humans in Taiwan. METHODS Campylobacter isolates were analysed using whole-genome sequencing to investigate their antimicrobial resistance, genetic determinants of resistance, and genotypes. RESULTS Campylobacter coli and Campylobacter jejuni accounted for 44.9% and 55.1% of chicken meat isolates, and 11.4% and 88.6% of human isolates, respectively. C. coli displayed significantly higher resistance levels. Furthermore, isolates from chicken meat exhibited higher levels of resistance to most tested antimicrobials compared to isolates from humans. Multidrug resistance was observed in 96.3% of C. coli and 43.3% of C. jejuni isolates from chicken meat and 80.6% of C. coli and 15.8% of C. jejuni isolates from humans. Macrolide resistance was observed in 85.5% of C. coli isolates, primarily attributed to the erm(B) rather than the A2075G mutation in 23S rRNA. Among the 511 genomes, we identified 133 conventional MLST sequence types, indicating significant diversity among Campylobacter strains. Notably, hierarchical Core-genome multilocus sequence typing clustering, including HC0, HC5, and HC10, revealed a significant proportion of closely related isolates from chicken meat and humans. CONCLUSIONS Our research highlights significant associations in antimicrobial resistance and genetic relatedness between Campylobacter isolates from chicken meat and humans in Taiwan. The genetic analysis data suggest that campylobacteriosis outbreaks may occur more frequently in Taiwan than previously assumed. Our study emphasizes the need for strategies to control multidrug-resistant strains and enhance outbreak prevention.
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Affiliation(s)
- Hsiao-Lun Wei
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Ying-Shu Liao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Bo-Han Chen
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Ru-Hsiou Teng
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - You-Wun Wang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Jui-Hsien Chang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Chien-Shun Chiou
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan.
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Otero-Olarra JE, Díaz-Cárdenas G, Aguilera-Arreola MG, Curiel-Quesada E, Pérez-Valdespino A. Aeromonas trota Is Highly Refractory to Acquire Exogenous Genetic Material. Microorganisms 2024; 12:1091. [PMID: 38930473 PMCID: PMC11206119 DOI: 10.3390/microorganisms12061091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Aeromonas trota is sensitive to most antibiotics and the sole species of this genus susceptible to ampicillin. This susceptibility profile could be related to its inability to acquire exogenous DNA. In this study, A. trota isolates were analyzed to establish their capacity to incorporate foreign DNA. Fourteen strains were identified as A. trota by multilocus phylogenetic analysis (MLPA). Minimal inhibitory concentrations of antibiotics (MIC) were assessed, confirming the susceptibility to most antibiotics tested. To explore their capacity to be transformed, A. trota strains were used as recipients in different horizontal transfer assays. Results showed that around fifty percent of A. trota strains were able to incorporate pBAMD1-2 and pBBR1MCS-3 plasmids after conjugal transfer. In all instances, conjugation frequencies were very low. Interestingly, several isoforms of plasmid pBBR1MCS-3 were observed in transconjugants. Strains could not receive pAr-32, a native plasmid from A. salmonicida. A. trota strains were unable to receive DNA by means of electroporation, natural transformation or vesiduction. These results confirm that A. trota species are extremely refractory to horizontal gene transfer, which could be associated to plasmid instability resulting from oligomerization or to the presence of defense systems against exogenous genetic material in their genomes. To explain the poor results of horizontal gene transfer (HGT), selected genomes were sequenced and analyzed, revealing the presence of defense systems, which could prevent the stable incorporation of exogenous DNA in A. trota.
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Affiliation(s)
- Jorge Erick Otero-Olarra
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.E.O.-O.); (G.D.-C.)
| | - Gilda Díaz-Cárdenas
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.E.O.-O.); (G.D.-C.)
| | - Ma Guadalupe Aguilera-Arreola
- Department of Microbiology, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico;
| | - Everardo Curiel-Quesada
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.E.O.-O.); (G.D.-C.)
| | - Abigail Pérez-Valdespino
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.E.O.-O.); (G.D.-C.)
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Kim JH, Dong J, Le BH, Lonergan ZR, Gu W, Girke T, Zhang W, Newman DK, Martins-Green M. Pseudomonas aeruginosa Activates Quorum Sensing, Antioxidant Enzymes and Type VI Secretion in Response to Oxidative Stress to Initiate Biofilm Formation and Wound Chronicity. Antioxidants (Basel) 2024; 13:655. [PMID: 38929094 PMCID: PMC11200925 DOI: 10.3390/antiox13060655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/29/2024] [Accepted: 05/13/2024] [Indexed: 06/28/2024] Open
Abstract
Pseudomonas aeruginosa (PA) is an opportunistic pathogen frequently isolated from cutaneous chronic wounds. How PA, in the presence of oxidative stress (OS), colonizes chronic wounds and forms a biofilm is still unknown. The purpose of this study is to investigate the changes in gene expression seen when PA is challenged with the high levels of OS present in chronic wounds. We used a biofilm-forming PA strain isolated from the chronic wounds of our murine model (RPA) and performed a qPCR to obtain gene expression patterns as RPA developed a biofilm in vitro in the presence of high levels of OS, and then compared the findings in vivo, in our mouse model of chronic wounds. We found that the planktonic bacteria under OS conditions overexpressed quorum sensing genes that are important for the bacteria to communicate with each other, antioxidant stress genes important to reduce OS in the microenvironment for survival, biofilm formation genes and virulence genes. Additionally, we performed RNAseq in vivo and identified the activation of novel genes/pathways of the Type VI Secretion System (T6SS) involved in RPA pathogenicity. In conclusion, RPA appears to survive the high OS microenvironment in chronic wounds and colonizes these wounds by turning on virulence, biofilm-forming and survival genes. These findings reveal pathways that may be promising targets for new therapies aimed at disrupting PA-containing biofilms immediately after debridement to facilitate the treatment of chronic human wounds.
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Affiliation(s)
- Jane H. Kim
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
| | - Julianna Dong
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
| | - Brandon H. Le
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Zachery R. Lonergan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Weifeng Gu
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
| | - Thomas Girke
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Wei Zhang
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Manuela Martins-Green
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
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Sroithongkham P, Nittayasut N, Yindee J, Nimsamer P, Payungporn S, Pinpimai K, Ponglowhapan S, Chanchaithong P. Multidrug-resistant Escherichia coli causing canine pyometra and urinary tract infections are genetically related but distinct from those causing prostatic abscesses. Sci Rep 2024; 14:11848. [PMID: 38782931 PMCID: PMC11116460 DOI: 10.1038/s41598-024-62028-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Despite extensive characterisation of uropathogenic Escherichia coli (UPEC) causing urinary tract infections (UTIs), the genetic background of non-urinary extraintestinal pathogenic E. coli (ExPEC) in companion animals remains inadequately understood. In this study, we characterised virulence traits of 104 E. coli isolated from canine pyometra (n = 61) and prostatic abscesses (PAs) (n = 38), and bloodstream infections (BSIs) in dogs (n = 2), and cats (n = 3). A stronger association with UPEC of pyometra strains in comparison to PA strains was revealed. Notably, 44 isolates exhibited resistance to third-generation cephalosporins and/or fluoroquinolones, 15 were extended-spectrum ß-lactamase-producers. Twelve multidrug-resistant (MDR) strains, isolated from pyometra (n = 4), PAs (n = 5), and BSIs (n = 3), along with 7 previously characterised UPEC strains from dogs and cats, were sequenced. Genomic characteristics revealed that MDR E. coli associated with UTIs, pyometra, and BSIs belonged to international high-risk E. coli clones, including sequence type (ST) 38, ST131, ST617, ST648, and ST1193. However, PA strains belonged to distinct lineages, including ST12, ST44, ST457, ST744, and ST13037. The coreSNPs, cgMLST, and pan-genome illustrated intra-clonal variations within the same ST from different sources. The high-risk ST131 and ST1193 (phylogroup B2) contained high numbers of ExPEC virulence genes on pathogenicity islands, predominating in pyometra and UTI. Hybrid MDR/virulence IncF multi-replicon plasmids, containing aerobactin genes, were commonly found in non-B2 phylogroups from all sources. These findings offer genomic insights into non-urinary ExPEC, highlighting its potential for invasive infections in pets beyond UTIs, particularly with regards to high-risk global clones.
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Affiliation(s)
- Parinya Sroithongkham
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Naiyaphat Nittayasut
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jitrapa Yindee
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pattaraporn Nimsamer
- Department of Biochemistry, Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sunchai Payungporn
- Department of Biochemistry, Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Komkiew Pinpimai
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Suppawiwat Ponglowhapan
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pattrarat Chanchaithong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Chulalongkorn University, Bangkok, 10330, Thailand.
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69
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Franklin AM, Weller DL, Durso LM, Bagley M, Davis BC, Frye JG, Grim CJ, Ibekwe AM, Jahne MA, Keely SP, Kraft AL, McConn BR, Mitchell RM, Ottesen AR, Sharma M, Strain EA, Tadesse DA, Tate H, Wells JE, Williams CF, Cook KL, Kabera C, McDermott PF, Garland JL. A one health approach for monitoring antimicrobial resistance: developing a national freshwater pilot effort. FRONTIERS IN WATER 2024; 6:10.3389/frwa.2024.1359109. [PMID: 38855419 PMCID: PMC11157689 DOI: 10.3389/frwa.2024.1359109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Antimicrobial resistance (AMR) is a world-wide public health threat that is projected to lead to 10 million annual deaths globally by 2050. The AMR public health issue has led to the development of action plans to combat AMR, including improved antimicrobial stewardship, development of new antimicrobials, and advanced monitoring. The National Antimicrobial Resistance Monitoring System (NARMS) led by the United States (U.S) Food and Drug Administration along with the U.S. Centers for Disease Control and U.S. Department of Agriculture has monitored antimicrobial resistant bacteria in retail meats, humans, and food animals since the mid 1990's. NARMS is currently exploring an integrated One Health monitoring model recognizing that human, animal, plant, and environmental systems are linked to public health. Since 2020, the U.S. Environmental Protection Agency has led an interagency NARMS environmental working group (EWG) to implement a surface water AMR monitoring program (SWAM) at watershed and national scales. The NARMS EWG divided the development of the environmental monitoring effort into five areas: (i) defining objectives and questions, (ii) designing study/sampling design, (iii) selecting AMR indicators, (iv) establishing analytical methods, and (v) developing data management/analytics/metadata plans. For each of these areas, the consensus among the scientific community and literature was reviewed and carefully considered prior to the development of this environmental monitoring program. The data produced from the SWAM effort will help develop robust surface water monitoring programs with the goal of assessing public health risks associated with AMR pathogens in surface water (e.g., recreational water exposures), provide a comprehensive picture of how resistant strains are related spatially and temporally within a watershed, and help assess how anthropogenic drivers and intervention strategies impact the transmission of AMR within human, animal, and environmental systems.
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Affiliation(s)
- Alison M. Franklin
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Daniel L. Weller
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lisa M. Durso
- U.S. Department of Agriculture, Agricultural Research Service (USDA, ARS), Agroecosystem Management Research, Lincoln, NE, United States
| | - Mark Bagley
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Benjamin C. Davis
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Jonathan G. Frye
- USDA ARS, U.S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, Athens, GA, United States
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Abasiofiok M. Ibekwe
- USDA, ARS, Agricultural Water Efficiency and Salinity Research Unit, Riverside, CA, United States
| | - Michael A. Jahne
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Scott P. Keely
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Autumn L. Kraft
- Oak Ridge Institute for Science and Education, USDA, ARS, Beltsville, MD, United States
| | - Betty R. McConn
- Oak Ridge Institute for Science and Education, USDA, ARS, Beltsville, MD, United States
| | - Richard M. Mitchell
- Environmental Protection Agency, Office of Water, Washington, DC, United States
| | - Andrea R. Ottesen
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Manan Sharma
- USDA, ARS Environmental Microbial and Food Safety Laboratory, Beltsville, MD, United States
| | - Errol A. Strain
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Daniel A. Tadesse
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Heather Tate
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jim E. Wells
- USDA, ARS, U.S. Meat Animal Research Center, Meat Safety and Quality, Clay Center, NE, United States
| | - Clinton F. Williams
- USDA, ARS, US Arid-Land Agricultural Research Center, Maricopa, AZ, United States
| | - Kim L. Cook
- USDA, ARS Nutrition, Food Safety and Quality National Program Staff, Beltsville, MD, United States
| | - Claudine Kabera
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Patrick F. McDermott
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jay L. Garland
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
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70
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Sabtcheva S, Stoikov I, Ivanov IN, Donchev D, Lesseva M, Georgieva S, Teneva D, Dobreva E, Christova I. Genomic Characterization of Carbapenemase-Producing Enterobacter hormaechei, Serratia marcescens, Citrobacter freundii, Providencia stuartii, and Morganella morganii Clinical Isolates from Bulgaria. Antibiotics (Basel) 2024; 13:455. [PMID: 38786183 PMCID: PMC11117914 DOI: 10.3390/antibiotics13050455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Carbapenemase-producing Enterobacter spp. Serratia marcescens, Citrobacter freundii, Providencia spp., and Morganella morganii (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation experiments, we sought to elucidate the genomic characteristics and transferability of resistance genes in clinical CP-ESCPM isolates from Bulgaria. Among the 36 sequenced isolates, NDM-1 (12/36), VIM-4 (11/36), VIM-86 (8/36), and OXA-48 (7/36) carbapenemases were identified; two isolates carried both NDM-1 and VIM-86. The majority of carbapenemase genes were found on self-conjugative plasmids. IncL plasmids were responsible for the spread of OXA-48 among E. hormaechei, C. freundii, and S. marcescens. IncM2 plasmids were generally associated with the spread of NDM-1 in C. freundii and S. marcescens, and also of VIM-4 in C. freundii. IncC plasmids were involved in the spread of the recently described VIM-86 in P. stuartii isolates. IncC plasmids carrying blaNDM-1 and blaVIM-86 were observed too. blaNDM-1 was also detected on IncX3 in S. marcescens and on IncT plasmid in M. morganii. The significant resistance transfer rates we observed highlight the role of the ESCPM group as a reservoir of resistance determinants and stress the need for strengthening infection control measures.
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Affiliation(s)
- Stefana Sabtcheva
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
| | - Ivan Stoikov
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Ivan N. Ivanov
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Deyan Donchev
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Magdalena Lesseva
- Department of Microbiology, University Multiprofile Hospital for Active Treatment and Emergency Medicine “N. I. Pirogov”, 1606 Sofia, Bulgaria;
| | - Sylvia Georgieva
- Laboratory for Clinical Microbiology, National Oncology Center, 1797 Sofia, Bulgaria; (I.S.); (S.G.)
| | - Deana Teneva
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Elina Dobreva
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
| | - Iva Christova
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.N.I.); (D.D.); (D.T.); (E.D.); (I.C.)
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71
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Le DQ, Nguyen SH, Nguyen TT, Nguyen CH, Ho TH, Vo NS, Nguyen T, Nguyen HA, Cao MD. AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance. BMC Bioinformatics 2024; 25:193. [PMID: 38755527 PMCID: PMC11100100 DOI: 10.1186/s12859-024-05792-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at https://github.com/amromics/amrviz .
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Affiliation(s)
- Duc Quang Le
- AMROMICS JSC, Nghe An, Vietnam.
- Faculty of IT, Hanoi University of Civil Engineering, Hanoi, Vietnam.
| | | | - Tam Thi Nguyen
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Canh Hao Nguyen
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Tho Huu Ho
- Department of Medical Microbiology, The 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Nam S Vo
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
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72
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Souza SSR, Smith JT, Marcovici MM, Eckhardt EM, Hansel NB, Martin IW, Andam CP. Demographic fluctuations in bloodstream Staphylococcus aureus lineages configure the mobile gene pool and antimicrobial resistance. NPJ ANTIMICROBIALS AND RESISTANCE 2024; 2:14. [PMID: 38725655 PMCID: PMC11076216 DOI: 10.1038/s44259-024-00032-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/08/2024] [Indexed: 05/12/2024]
Abstract
Staphylococcus aureus in the bloodstream causes high morbidity and mortality, exacerbated by the spread of multidrug-resistant and methicillin-resistant S. aureus (MRSA). We aimed to characterize the circulating lineages of S. aureus from bloodstream infections and the contribution of individual lineages to resistance over time. Here, we generated 852 high-quality short-read draft genome sequences of S. aureus isolates from patient blood cultures in a single hospital from 2010 to 2022. A total of 80 previously recognized sequence types (ST) and five major clonal complexes are present in the population. Two frequently detected lineages, ST5 and ST8 exhibited fluctuating demographic structures throughout their histories. The rise and fall in their population growth coincided with the acquisition of antimicrobial resistance, mobile genetic elements, and superantigen genes, thus shaping the accessory genome structure across the entire population. These results reflect undetected selective events and changing ecology of multidrug-resistant S. aureus in the bloodstream.
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Affiliation(s)
- Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
| | - Joshua T. Smith
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Michael M. Marcovici
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
| | - Elissa M. Eckhardt
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Nicole B. Hansel
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Isabella W. Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
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73
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Mileto I, Merla C, Corbella M, Gaiarsa S, Kuka A, Ghilotti S, De Cata P, Baldanti F, Cambieri P. Bloodstream Infection Caused by Erysipelothrix rhusiopathiae in an Immunocompetent Patient. Microorganisms 2024; 12:942. [PMID: 38792772 PMCID: PMC11124489 DOI: 10.3390/microorganisms12050942] [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: 03/15/2024] [Revised: 04/26/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Erysipelothrix rhusiopathiae is a facultative anaerobe Gram-positive bacillus, which is considered a zoonotic pathogen. E. rhusiopathiae causes erysipeloid, mainly in occupational groups such as veterinarians, slaughterhouse workers, farmers, and fishermen. Two cutaneous forms (localised and generalised) and a septicaemic form have been described. Here, we report the isolation of a strain of E. rhusiopathiae from a 56-year-old immunocompetent obese male admitted to Fondazione IRCCS Policlinico San Matteo Pavia (Italy). Blood cultures were collected and Gram-positive bacilli were observed. E. rhusiopathiae grew and was identified. Antimicrobial susceptibility tests were performed and interpreted with EUCAST breakpoints (PK-PD). The strain was susceptible to all the antibiotics tested, while it was intrinsically resistant to vancomycin. The clinical diagnosis of E. rhusiopathiae can be challenging, due to the broad spectrum of symptoms and potential side effects, including serious systemic infections such as heart diseases. In the case described, bacteraemia caused by E. rhusiopathiae was detected in a immunocompetent patient. Bacteraemia caused by E. rhusiopathiae is rare in immunocompetent people and blood cultures were proven to be essential for the diagnosis and underdiagnosis of this pathogen, which is possible due to its resemblance to other clinical manifestations.
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Affiliation(s)
- Irene Mileto
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
- Specialization School of Microbiology and Virology, University of Pavia, 27100 Pavia, Italy
| | - Cristina Merla
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marta Corbella
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Stefano Gaiarsa
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Angela Kuka
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
- Specialization School of Microbiology and Virology, University of Pavia, 27100 Pavia, Italy
| | - Stefania Ghilotti
- Department of General Medicine, Istituti Clinici Maugeri IRCCS, 27100 Pavia, Italy
| | - Pasquale De Cata
- Department of General Medicine, Istituti Clinici Maugeri IRCCS, 27100 Pavia, Italy
| | - Fausto Baldanti
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy
| | - Patrizia Cambieri
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Zhong T, Wu H, Hu J, Liu Y, Zheng Y, Li N, Sun Z, Yin XF, He QY, Sun X. Two synonymous single-nucleotide polymorphisms promoting fluoroquinolone resistance of Escherichia coli in the environment. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133849. [PMID: 38432089 DOI: 10.1016/j.jhazmat.2024.133849] [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: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
Single-nucleotide polymorphism (SNP) is one of the core mechanisms that respond to antibiotic resistance of Escherichia coli (E. coli), which is a major issue in environmental pollution. A specific type of SNPs, synonymous SNPs, have been generally considered as the "silent" SNPs since they do not change the encoded amino acid. However, the impact of synonymous SNPs on mRNA splicing, nucleo-cytoplasmic export, stability, and translation was gradually discovered in the last decades. Figuring out the mechanism of synonymous SNPs in regulating antibiotic resistance is critical to improve antimicrobial therapy strategies in clinics and biological treatment strategies of antibiotic-resistant E. coli-polluted materials. With our newly designed antibiotic resistant SNPs prediction algorithm, Multilocus Sequence Type based Identification for Phenotype-single nucleotide polymorphism Analysis (MIPHA), and in vivo validation, we identified 2 important synonymous SNPs 522 G>A and 972 C>T, located at hisD gene, which was previously predicted as a fluoroquinolone resistance-related gene without a detailed mechanism in the E. coli samples with environmental backgrounds. We first discovered that hisD causes gyrA mutation via the upregulation of sbmC and its downstream gene umuD. Moreover, those 2 synonymous SNPs of hisD cause its own translational slowdown and further reduce the expression levels of sbmC and its downstream gene umuD, making the fluoroquinolone resistance determining region of gyrA remains unmutated, ultimately causing the bacteria to lose their ability to resist drugs. This study provided valuable insight into the role of synonymous SNPs in mediating antibiotic resistance of bacteria and a new perspective for the treatment of environmental pollution caused by drug-resistant bacteria.
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Affiliation(s)
- Tairan Zhong
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Haiming Wu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jiehua Hu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Yun Liu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Yundan Zheng
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Nan Li
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Zhenghua Sun
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xing-Feng Yin
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Yu He
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China.
| | - Xuesong Sun
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China.
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75
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Langelier C, Lu D, Kalantar K, Chu V, Glascock A, Guerrero E, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones A, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani P, Pickering A, Raphenya A, Alcock B, McArthur A. Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline. RESEARCH SQUARE 2024:rs.3.rs-4271356. [PMID: 38746293 PMCID: PMC11092797 DOI: 10.21203/rs.3.rs-4271356/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the CZ ID AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.
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Affiliation(s)
| | - Dan Lu
- Chan Zuckerberg Initiative
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Toyting J, Nuanmuang N, Utrarachkij F, Supha N, Thongpanich Y, Leekitcharoenphon P, Aarestrup FM, Sato T, Thapa J, Nakajima C, Suzuki Y. Genomic analysis of Salmonella isolated from canal water in Bangkok, Thailand. Microbiol Spectr 2024; 12:e0421623. [PMID: 38563788 PMCID: PMC11064549 DOI: 10.1128/spectrum.04216-23] [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: 12/20/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Antimicrobial resistance (AMR) poses an escalating global public health threat. Canals are essential in Thailand, including the capital city, Bangkok, as agricultural and daily water sources. However, the characteristic and antimicrobial-resistance properties of the bacteria in the urban canals have never been elucidated. This study employed whole genome sequencing to characterize 30 genomes of a causal pathogenic bacteria, Salmonella enterica, isolated from Bangkok canal water between 2016 and 2020. The dominant serotype was Salmonella Agona. In total, 35 AMR genes and 30 chromosomal-mediated gene mutations were identified, in which 21 strains carried both acquired genes and mutations associated with fluoroquinolone resistance. Virulence factors associated with invasion, adhesion, and survival during infection were detected in all study strains. 75.9% of the study stains were multidrug-resistant and all the strains harbored the necessary virulence factors associated with salmonellosis. One strain carried 20 resistance genes, including mcr-3.1, mutations in GyrA, ParC, and ParE, and typhoid toxin-associated genes. Fifteen plasmid replicon types were detected, with Col(pHAD28) being the most common type. Comparative analysis of nine S. Agona from Bangkok and 167 from public databases revealed that specific clonal lineages of S. Agona might have been circulating between canal water and food sources in Thailand and globally. These findings provide insight into potential pathogens in the aquatic ecosystem and support the inclusion of environmental samples into comprehensive AMR surveillance initiatives as part of a One Health approach. This approach aids in comprehending the rise and dissemination of AMR and devising sustainable intervention strategies.IMPORTANCEBangkok is the capital city of Thailand and home to a large canal network that serves the city in various ways. The presence of pathogenic and antimicrobial-resistant Salmonella is alarming and poses a significant public health risk. The present study is the first characterization of the genomic of Salmonella strains from Bangkok canal water. Twenty-two of 29 strains (75.9%) were multidrug-resistant Salmonella and all the strains carried essential virulence factors for pathogenesis. Various plasmid types were identified in these strains, potentially facilitating the horizontal transfer of AMR genes. Additional investigations indicated a potential circulation of S. Agona between canal water and food sources in Thailand. The current study underscores the role of environmental water in an urban city as a reservoir of pathogens and these data obtained can serve as a basis for public health risk assessment and help shape intervention strategies to combat AMR challenges in Thailand.
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Affiliation(s)
- Jirachaya Toyting
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Narong Nuanmuang
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Fuangfa Utrarachkij
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Neunghatai Supha
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Yuwanda Thongpanich
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Toyotaka Sato
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Research Support, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Research Support, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan
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Urbanowicz P, Izdebski R, Biedrzycka M, Gniadkowski M. VIM-type metallo-β-lactamase (MBL)-encoding genomic islands in Pseudomonas spp. in Poland: predominance of clc-like integrative and conjugative elements (ICEs). J Antimicrob Chemother 2024; 79:1030-1037. [PMID: 38488311 DOI: 10.1093/jac/dkae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/23/2024] [Indexed: 05/03/2024] Open
Abstract
OBJECTIVES To characterize VIM-type metallo-β-lactamase (MBL)-encoding genomic islands (GIs) in Pseudomonas aeruginosa and P. putida group isolates from Polish hospitals from 2001-2015/16. METHODS Twelve P. aeruginosa and 20 P. putida group isolates producing VIM-like MBLs were selected from a large collection of these based on epidemiological and typing data. The organisms represented all major epidemic genotypes of these species spread in Poland with chromosomally located blaVIM gene-carrying integrons. The previously determined short-read sequences were complemented by long-read sequencing in this study. The comparative structural analysis of the GIs used a variety of bioinformatic tools. RESULTS Thirty different GIs with blaVIM integrons were identified in the 32 isolates, of which 24 GIs from 26 isolates were integrative and conjugative elements (ICEs) of the clc family. These in turn were dominated by 21 variants of the GI2/ICE6441 subfamily with a total of 19 VIM integrons, each inserted in the same position within the ICE's Tn21-like transposon Tn4380. The three other ICEs formed a novel ICE6705 subfamily, lacking Tn4380 and having different VIM integrons located in another site of the elements. The remaining six non-ICE GIs represented miscellaneous structures. The presence of various integrons in the same ICE sublineage, and of the same integron in different GIs, indicated circulation and recombination of the integron-carrying genetic platforms across Pseudomonas species/genotypes. CONCLUSIONS Despite the general diversity of the blaVIM-carrying GIs in Pseudomonas spp. in Poland, a clear predominance of broadly spread and rapidly evolving clc-type ICEs was documented, confirming their significant role in antimicrobial resistance epidemiology.
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Affiliation(s)
- P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, Warsaw 00-725, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, Warsaw 00-725, Poland
| | - M Biedrzycka
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, Warsaw 00-725, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, Warsaw 00-725, Poland
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78
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Chen Z, Toro M, Moreno-Switt AI, Adell AD, Delgado-Suárez EJ, Bonelli RR, Oliveira CJB, Reyes-Jara A, Huang X, Albee B, Grim CJ, Allard M, Tallent SM, Brown EW, Bell RL, Meng J. Unveiling the genomic landscape of Salmonella enterica serotypes Typhimurium, Newport, and Infantis in Latin American surface waters: a comparative analysis. Microbiol Spectr 2024; 12:e0004724. [PMID: 38546218 PMCID: PMC11064523 DOI: 10.1128/spectrum.00047-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/06/2024] [Indexed: 05/03/2024] Open
Abstract
Surface waters are considered ecological habitats where Salmonella enterica can persist and disseminate to fresh produce production systems. This study aimed to explore the genomic profiles of S. enterica serotypes Typhimurium, Newport, and Infantis from surface waters in Chile, Mexico, and Brazil collected between 2019 and 2022. We analyzed the whole genomes of 106 S. Typhimurium, 161 S. Newport, and 113 S. Infantis isolates. Our phylogenetic analysis exhibited distinct groupings of isolates by their respective countries except for a notable case involving a Chilean S. Newport isolate closely related to two Mexican isolates, showing 4 and 13 single nucleotide polymorphisms of difference, respectively. The patterns of the most frequently detected antimicrobial resistance genes varied across countries and serotypes. A strong correlation existed between integron carriage and genotypic multidrug resistance (MDR) across serotypes in Chile and Mexico (R > 0.90, P < 0.01), while integron(s) were not detected in any of the Brazilian isolates. By contrast, we did not identify any strong correlation between plasmid carriage and genotypic MDR across diverse countries and serotypes.IMPORTANCEUnveiling the genomic landscape of S. enterica in Latin American surface waters is pivotal for ensuring public health. This investigation sheds light on the intricate genomic diversity of S. enterica in surface waters across Chile, Mexico, and Brazil. Our research also addresses critical knowledge gaps, pioneering a comprehensive understanding of surface waters as a reservoir for multidrug-resistant S. enterica. By integrating our understanding of integron carriage as biomarkers into broader MDR control strategies, we can also work toward targeted interventions that mitigate the emergence and dissemination of MDR in S. enterica in surface waters. Given its potential implications for food safety, this study emphasizes the critical need for informed policies and collaborative initiatives to address the risks associated with S. enterica in surface waters.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
| | - Magaly Toro
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Andrea I. Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Aiko D. Adell
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Facultad de Agronomía y Sistemas Naturales, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andrés Bello, Santiago, Chile
| | - Enrique J. Delgado-Suárez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad de Nacional Autónoma de México, Mexico City, Mexico
| | - Raquel R. Bonelli
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Angélica Reyes-Jara
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Xinyang Huang
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
| | - Brett Albee
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Sandra M. Tallent
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Eric W. Brown
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Rebecca L. Bell
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
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Yano H, Hayashi W, Kawakami S, Aoki S, Anzai E, Zuo H, Kitamura N, Hirabayashi A, Kajihara T, Kayama S, Sugawara Y, Yahara K, Sugai M. Nationwide genome surveillance of carbapenem-resistant Pseudomonas aeruginosa in Japan. Antimicrob Agents Chemother 2024; 68:e0166923. [PMID: 38564665 PMCID: PMC11064530 DOI: 10.1128/aac.01669-23] [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: 12/19/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Japan is a country with an approximate 10% prevalence rate of carbapenem-resistant Pseudomonas aeruginosa (CRPA). Currently, a comprehensive overview of the genotype and phenotype patterns of CRPA in Japan is lacking. Herein, we conducted genome sequencing and quantitative antimicrobial susceptibility testing for 382 meropenem-resistant CRPA isolates that were collected from 78 hospitals across Japan from 2019 to 2020. CRPA exhibited susceptibility rates of 52.9%, 26.4%, and 88.0% against piperacillin-tazobactam, ciprofloxacin, and amikacin, respectively, whereas 27.7% of CRPA isolates was classified as difficult-to-treat resistance P. aeruginosa. Of the 148 sequence types detected, ST274 (9.7%) was predominant, followed by ST235 (7.6%). The proportion of urine isolates in ST235 was higher than that in other STs (P = 0.0056, χ2 test). Only 4.1% of CRPA isolates carried the carbapenemase genes: blaGES (2) and blaIMP (13). One ST235 isolate carried the novel blaIMP variant blaIMP-98 in the chromosome. Regarding chromosomal mutations, 87.1% of CRPA isolates possessed inactivating or other resistance mutations in oprD, and 28.8% showed mutations in the regulatory genes (mexR, nalC, and nalD) for the MexAB-OprM efflux pump. Additionally, 4.7% of CRPA isolates carried a resistance mutation in the PBP3-encoding gene ftsI. The findings from this study and other surveillance studies collectively demonstrate that CRPA exhibits marked genetic diversity and that its multidrug resistance in Japan is less prevailed than in other regions. This study contributes a valuable data set that addresses a gap in genotype/phenotype information regarding CRPA in the Asia-Pacific region, where the epidemiological background markedly differs between regions.
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Affiliation(s)
- Hirokazu Yano
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Wataru Hayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Sayoko Kawakami
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Sadao Aoki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Eiko Anzai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Hui Zuo
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Norikazu Kitamura
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Aki Hirabayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Toshiki Kajihara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Shizuo Kayama
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Yo Sugawara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
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80
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Anglemyer A, Ren X, Gilkison C, Kumbaroff Z, Morgan J, DuBray K, Tiong A, Reingold A, Walls T. The impact of pneumococcal serotype replacement on the effectiveness of a national immunization program: a population-based active surveillance cohort study in New Zealand. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024; 46:101082. [PMID: 38745973 PMCID: PMC11091704 DOI: 10.1016/j.lanwpc.2024.101082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024]
Abstract
Background In Aotearoa New Zealand (NZ) PCV7 was introduced in 2008, then PCV10 in 2011 and PCV13 in 2014. In 2017 PCV10 was re-introduced, replacing PCV13. In the present study, we investigate the resultant rapidly changing invasive pneumococcal disease (IPD) epidemiology. Methods We compare the IPD incidence rate ratio (IRR) in NZ (2022 versus 2020) with other countries, and describe the IPD epidemiology (including trends in overall IPD and serotype 19A, and antimicrobial resistance) within NZ. Additionally, we performed a genomic-epidemiology investigation identifying the most common 19A sequence types and associated risk factors. Findings Though IPD incidence rates have increased in the US and Australia (2021-22) after declines in 2020, in NZ the incidence rate is the highest since 2011 with a significantly higher IRR than US (p < 0.01). Incidence rates among children <2 and adults 65 or over in 2022 are the highest since 2009, driven by significant increases of serotype 19A (p = 0.01). Māori and Pacific peoples are experiencing the highest rates since 2009. Further, penicillin resistance among 19A isolates has increased from 39% (2012) to 84% (2021) (p = 0.02). Genomic sequencing identified the more virulent ST-2062 as most common among 19A isolates sequenced, increasing from 5% (2010) to 55% (2022). Interpretation With very high incidence rates of IPD in NZ, inadequate protection against 19A, increasing resistance, and a more virulent 19A clade, targeted public health campaigns and increased PCV13 availability are needed. Funding The NZ Ministry of Health funds IPD surveillance and typing in NZ.
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Affiliation(s)
- Andrew Anglemyer
- Health Intelligence Team, Institute of Environmental Science and Research, Porirua, New Zealand
- Department of Preventive and Social Medicine, University of Otago, Dunedin, New Zealand
| | - Xiaoyun Ren
- Invasive Pathogens Laboratory, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Charlotte Gilkison
- Health Intelligence Team, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Zoe Kumbaroff
- Health Intelligence Team, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Julie Morgan
- Invasive Pathogens Laboratory, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Kara DuBray
- Department of Paediatrics, Dunedin Hospital, Dunedin, New Zealand
| | - Audrey Tiong
- Invasive Pathogens Laboratory, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Arthur Reingold
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Tony Walls
- Department of Paediatrics, University of Otago, Christchurch, New Zealand
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81
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Lim C, Coombs GW, Daley DA, Shoby P, Mowlaboccus S. Whole-genome sequencing identifies MprF mutations in a genetically diverse population of daptomycin non-susceptible Staphylococcus aureus in Australia. Int J Antimicrob Agents 2024; 63:107144. [PMID: 38494147 DOI: 10.1016/j.ijantimicag.2024.107144] [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: 07/31/2023] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
OBJECTIVES Daptomycin is one of the few last-line antimicrobials available for the treatment of multidrug-resistant Staphylococcus aureus infections. An increasing number of daptomycin non-susceptible S. aureus infections has been reported worldwide, including Australia. Resistance to daptomycin is multifactorial and involves chromosomal mutations in genes encoding proteins involved in cell membrane and cell wall synthesis. METHODS In this study, we performed broth microdilution (BMD) to determine the daptomycin minimum inhibitory concentration (MIC) of 66 clinical isolates of S. aureus previously reported as daptomycin non-susceptible by the VITEKⓇ 2. We used whole-genome sequencing to characterise the isolates and screened the genomes for mutations associated with daptomycin non-susceptibility. RESULTS Only 56 of the 66 isolates had a daptomycin MIC >1 mg/L by BMD. Although the 66 isolates were polyclonal, ST22 was the predominant sequence type and one-third of the isolates were multidrug resistant. Daptomycin non-susceptibility was primarily associated with MprF mutations-at least one MprF mutation was identified in the 66 isolates. Twelve previously reported MprF mutations associated with daptomycin non-susceptibility were identified in 83% of the isolates. Novel MprF mutations identified included P314A, P314F, P314T, S337T, L341V, F349del, and T423R. CONCLUSIONS Daptomycin non-susceptible S. aureus causing infections in Australia are polyclonal and harbour MprF mutation(s). The identification of multidrug-resistant daptomycin non-susceptible S. aureus is a public health concern.
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Affiliation(s)
- Candice Lim
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Australia; Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Australia
| | - Denise A Daley
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Australia
| | - Princy Shoby
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Australia
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Australia; Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Australia; School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia.
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82
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Long H, Zhao F, Feng Y, Zong Z. Global distribution of bla CMY-42, a gene mediating reduced susceptibility to aztreonam-avibactam and ceftazidime-avibactam, in Escherichia coli. Int J Antimicrob Agents 2024; 63:107141. [PMID: 38484805 DOI: 10.1016/j.ijantimicag.2024.107141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/12/2024] [Accepted: 03/08/2024] [Indexed: 04/07/2024]
Affiliation(s)
- Haiyan Long
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Feifei Zhao
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Yu Feng
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China; Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China.
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83
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Vaz CSL, da Fonseca FN, Voss-Rech D, Morés MAZ, Coldebella A, Cantão ME. Wild-type lytic bacteriophages against Salmonella Heidelberg: Further characterization and effect of prophylactic therapy in broiler chickens. Res Vet Sci 2024; 171:105247. [PMID: 38554611 DOI: 10.1016/j.rvsc.2024.105247] [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: 07/18/2023] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
To characterize wild-type bacteriophages and their effect on Salmonella Heidelberg intestinal colonization in broilers, phages combined in a cocktail were continuously delivered via drinking water since the first day after hatching. After challenge with a field strain, broilers were evaluated at regular intervals for S. Heidelberg and bacteriophages in tissues and cecum, and gross and microscopic lesions in organs. Phages were highly virulent against S. Heidelberg by efficiency of plating. One-step growth curves exhibited eclipse period from 20 to 25 min, whereas the lowest latent period and higher burst size found were 45 min and 54 PFU/cell, respectively. Bacteriophage whole genomic sequencing analyses revealed a lack of genes related to lysogeny, antimicrobial resistance, and virulence factors. Relevant gross or microscopic lesions were absent in tissues analyzed from treated broilers. Although numerically stable bacteriophage concentrations were detected in the cecal contents of treated broilers, no significant difference was found for the S. Heidelberg cecal load in comparison to the untreated group and for the prevalence of positive tissues throughout the evaluated period. The phages produced turbid plaques against some S. Heidelberg re-isolated from treated broilers, suggesting the evolving of a resistant subpopulation. Overall, the results provide new evidence of the safety and in vitro replication of such phages in S. Heidelberg. Nevertheless, continuous administration of the phage suspension most likely induced the development of bacteriophage-resistant mutants, which might have affected the in vivo effect. Therefore, a putative administration protocol should be based on other strategies, such as short-term therapy at pre-harvest age.
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Affiliation(s)
| | | | - Daiane Voss-Rech
- Embrapa Suínos e Aves, BR 153, Km 110, PO box 321, Concórdia, Santa Catarina 89715899, Brazil
| | | | - Arlei Coldebella
- Embrapa Suínos e Aves, BR 153, Km 110, PO box 321, Concórdia, Santa Catarina 89715899, Brazil
| | - Maurício Egídio Cantão
- Embrapa Suínos e Aves, BR 153, Km 110, PO box 321, Concórdia, Santa Catarina 89715899, Brazil
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84
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Quiñonero-Coronel MDM, Devos DP, Garcillán-Barcia MP. Specificities and commonalities of the Planctomycetes plasmidome. Environ Microbiol 2024; 26:e16638. [PMID: 38733104 DOI: 10.1111/1462-2920.16638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.
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Affiliation(s)
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD, CSIC-Universidad Pablo de Olavide), Sevilla, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, CSIC-Universidad de Cantabria), Cantabria, Spain
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85
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Oyelade AA, Ikhimiukor OO, Nwadike BI, Fagade OE, Adelowo OO. Assessing the risk of exposure to antimicrobial resistance at public beaches: Genome-based insights into the resistomes, mobilomes and virulomes of beta-lactams resistant Enterobacteriaceae from recreational beaches in Lagos, Nigeria. Int J Hyg Environ Health 2024; 258:114347. [PMID: 38492327 DOI: 10.1016/j.ijheh.2024.114347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/18/2024] [Accepted: 03/02/2024] [Indexed: 03/18/2024]
Abstract
The role of recreational water use in the acquisition and transmission of antimicrobial resistance (AMR) is under-explored in low- and middle-income countries (LMICs). We used whole genome sequence analysis to provide insights into the resistomes, mobilomes and virulomes of 14 beta-lactams resistant Enterobacterales isolated from water and wet-sand at four recreational beaches in Lagos, Nigeria. Carriage of multiple beta-lactamase genes was detected in all isolates except two, including six isolates carrying blaNDM-1. Most detected antibiotic resistance genes (ARGs) were located within a diverse landscape of plasmids, insertion sequences and transposons including the presence of ISKpn14 upstream of blaNDM-1 in a first report in Africa. Virulence genes involved in adhesion and motility as well as secretion systems are particularly abundant in the genomes of the isolates. Our results confirmed the four beaches are contaminated with bacteria carrying clinically relevant ARGs associated with mobile genetic elements (MGE) which could promote the transmission of ARGs at the recreational water-human interface.
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Affiliation(s)
- Abolade A Oyelade
- New Jersey Department of Health, Public Health and Environmental Laboratories, New Jersey, USA
| | - Odion O Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA
| | - Blessing I Nwadike
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Obasola E Fagade
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Olawale O Adelowo
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria.
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86
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Ghaly TM, Gillings MR, Rajabal V, Paulsen IT, Tetu SG. Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange. Front Microbiol 2024; 15:1338026. [PMID: 38741746 PMCID: PMC11089894 DOI: 10.3389/fmicb.2024.1338026] [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: 11/14/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Plant microbiomes play important roles in plant health and fitness. Bacterial horizontal gene transfer (HGT) can influence plant health outcomes, driving the spread of both plant growth-promoting and phytopathogenic traits. However, community dynamics, including the range of genetic elements and bacteria involved in this process are still poorly understood. Integrons are genetic elements recently shown to be abundant in plant microbiomes, and are associated with HGT across broad phylogenetic boundaries. They facilitate the spread of gene cassettes, small mobile elements that collectively confer a diverse suite of adaptive functions. Here, we analysed 5,565 plant-associated bacterial genomes to investigate the prevalence and functional diversity of integrons in this niche. We found that integrons are particularly abundant in the genomes of Pseudomonadales, Burkholderiales, and Xanthomonadales. In total, we detected nearly 9,000 gene cassettes, and found that many could be involved in plant growth promotion or phytopathogenicity, suggesting that integrons might play a role in bacterial mutualistic or pathogenic lifestyles. The rhizosphere was enriched in cassettes involved in the transport and metabolism of diverse substrates, suggesting that they may aid in adaptation to this environment, which is rich in root exudates. We also found that integrons facilitate cross-species HGT, which is particularly enhanced in the phyllosphere. This finding may provide an ideal opportunity to promote plant growth by fostering the spread of genes cassettes relevant to leaf health. Together, our findings suggest that integrons are important elements in plant microbiomes that drive HGT, and have the potential to facilitate plant host adaptation.
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Affiliation(s)
- Timothy M. Ghaly
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | | | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
| | - Ian T. Paulsen
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
| | - Sasha G. Tetu
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
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87
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Nitz AA, Johnson DL, Lupiyaningdyah P, Meinzer MA, Ramsey JS, Robinson CM, Valencia Amores CS, Pickett BE. Secondary analysis of Staphylococcus aureus whole genomes reveals diverse antimicrobial resistance profiles. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.000903. [PMID: 38741934 PMCID: PMC11089388 DOI: 10.17912/micropub.biology.000903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
Antimicrobial resistance (AMR) in microorganisms is an ongoing threat to human health across the globe. To better characterize the AMR profiles of six strains of Staphylococcus aureus , we performed a secondary analysis that consisted of the following steps: 1) download fastq files from the Sequence Read Archive, 2) perform a de novo genome assembly from the sequencing reads, 3) annotate the assembled contigs, 4) predict the presence of antimicrobial resistance genes. We predicted the presence of 75 unique genes that conferred resistance against 22 unique antimicrobial compounds.
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Affiliation(s)
- Alyssa A Nitz
- Brigham Young University, Provo, Utah, United States
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88
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Loos D, Filho APDC, Dutilh BE, Barber AE, Panagiotou G. A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists. Cell Rep 2024; 43:114046. [PMID: 38581683 DOI: 10.1016/j.celrep.2024.114046] [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: 07/28/2023] [Revised: 12/22/2023] [Accepted: 03/19/2024] [Indexed: 04/08/2024] Open
Abstract
Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.
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Affiliation(s)
- Daniel Loos
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Ailton Pereira da Costa Filho
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Bas E Dutilh
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany; Institute of Biodiversity, Friedrich Schiller University, Jena, Germany; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Amelia E Barber
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany.
| | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
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89
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Gomathinayagam S, Kodiveri Muthukaliannan G. Dynamics of antibiotic resistance genes in plasmids and bacteriophages. Crit Rev Microbiol 2024:1-10. [PMID: 38651513 DOI: 10.1080/1040841x.2024.2339262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
This brief review explores the intricate interplay between bacteriophages and plasmids in the context of antibiotic resistance gene (ARG) dissemination. Originating from studies in the late 1950s, the review traces the evolution of knowledge regarding extrachromosomal factors facilitating horizontal gene transfer and adaptation in bacteria. Analyzing the gene repertoires of plasmids and bacteriophages, the study highlights their contributions to bacterial evolution and adaptation. While plasmids encode essential and accessory genes influencing host characteristics, bacteriophages carry auxiliary metabolic genes (AMGs) that augment host metabolism. The debate on phages carrying ARGs is explored through a critical evaluation of various studies, revealing contrasting findings from researchers. Additionally, the review addresses the interplay between prophages and plasmids, underlining their similarities and divergences. Based on the available literature evidence, we conclude that plasmids generally encode ARGs while bacteriophages typically do not contain ARGs. But extra-chromosomaly present prophages with plasmid characteristics can encode and disseminate ARGs.
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90
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Rao RSP, Ghate SD, Pinto L, Suravajhala P, Patil P, Shetty P, Ahsan N. Extent of Virulence and Antibiotic Resistance Genes in Helicobacter pylori and Campylobacteria. Curr Microbiol 2024; 81:154. [PMID: 38652129 DOI: 10.1007/s00284-024-03653-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/26/2024] [Indexed: 04/25/2024]
Abstract
Helicobacter pylori, a member of the clade campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence and antibiotic resistance genes in H. pylori in relation to other campylobacteria remains unclear. Using the virulence and comprehensive antibiotic resistance databases, we explored all available 354 complete genomes of H. pylori and compared it with 90 species of campylobacteria for virulence and antibiotic resistance genes/proteins. On average, H. pylori had 129 virulence genes, highest among Helicobacter spp. and 71 antibiotic resistance genes, one of the lowest among campylobacteria. Just 2.6% of virulence genes were shared by all campylobacterial members, whereas 9.4% were unique to H. pylori. The cytotoxin-associated genes (cags) seemed to be exclusive to H. pylori. Majority of the isolates from Asia and South America were cag2-negative and many antibiotic resistance genes showed isolate-specific patterns of occurrence. Just 15 (8.8%) antibiotic resistance genes, but 103 (66%) virulence genes including 25 cags were proteomically identified in H. pylori. Arcobacterial members showed large variation in the number of antibiotic resistance genes and there was a positive relation with the genome size. Large repository of antibiotic resistance genes in campylobacteria and a unique set of virulence genes might have important implications in shaping the course of virulence and antibiotic resistance in H. pylori.
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Affiliation(s)
- R Shyama Prasad Rao
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India.
| | - Sudeep D Ghate
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India.
| | - Larina Pinto
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India
| | - Prakash Patil
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
| | - Praveenkumar Shetty
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
- Department of Biochemistry, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
| | - Nagib Ahsan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK, USA
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91
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Wang YT, Lin YC, Hsieh YH, Lin YT, Hamada M, Chen CC, Liou JS, Lee AY, Zhang WL, Chen YT, Huang CH. Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk. Pathogens 2024; 13:343. [PMID: 38668298 PMCID: PMC11055063 DOI: 10.3390/pathogens13040343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
A novel coagulase-negative Staphylococcus strain (H164T) was isolated from soymilk in Taiwan. Comparative sequence analysis of the 16S rRNA gene revealed that the H164T strain is a member of the genus Staphylococcus. We used multilocus sequence analysis (MLSA) and phylogenomic analyses to demonstrate that the novel strain was closely related to Staphylococcus gallinarum, Staphylococcus nepalensis, Staphylococcus cohnii, and Staphylococcus urealyuticus. The average nucleotide identity and digital DNA-DNA hybridization values between H164T and its closest relatives were <95% and <70%, respectively. The H164T strain could also be distinguished from its closest relatives by the fermentation of d-fructose, d-maltose, d-trehalose, and d-mannitol, as well as by the activities of α-glucosidase and alkaline phosphatase. The major cellular fatty acids were C15:0 iso and C15:0 anteiso, and the predominant menaquinones were MK-7 and MK-8, respectively. The major cellular fatty acids and predominant menaquinones were C15:0 iso and C15:0 anteiso and MK-7 and MK-8, respectively. In conclusion, this strain represents a novel species, named Staphylococcus hsinchuensis sp. nov., with the type strain H164T (=BCRC 81404T = NBRC 116174T).
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Affiliation(s)
- Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei 115021, Taiwan;
| | - Yu-Chun Lin
- Taiwan Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (Y.-C.L.)
- Fisheries Research Institute, Ministry of Agriculture, Keelung 202008, Taiwan
| | - Yi-Huei Hsieh
- Taiwan Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (Y.-C.L.)
| | - Yu-Tzu Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404328, Taiwan;
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu 292-0818, Chiba, Japan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
| | - Ai-Yun Lee
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
| | - Wei-Ling Zhang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
| | - Yung-Tsung Chen
- Department of Food Science, National Taiwan Ocean University, Keelung 202301, Taiwan;
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan (A.-Y.L.)
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92
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Lu D, Kalantar KL, Chu VT, Glascock AL, Guerrero ES, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones AE, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani PM, Pickering AJ, Raphenya AR, Alcock BP, McArthur AG, Langelier CR. Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589250. [PMID: 38645206 PMCID: PMC11030322 DOI: 10.1101/2024.04.12.589250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.
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Affiliation(s)
- Dan Lu
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | - Victoria T. Chu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Nina Bernick
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | - Kirsty Ewing
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | | | - Erin Hoops
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | - Ann E. Jones
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | - Ryan Lim
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | | | | | | | | | - Peter M. Mourani
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children’s, Little Rock, AR, USA
| | - Amy J. Pickering
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- University of California, Berkeley, Berkeley, CA, USA
| | - Amogelang R. Raphenya
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Brian P. Alcock
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Andrew G. McArthur
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Charles R. Langelier
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
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93
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Jiménez-Edeza M, Galván-Gordillo SV, Pacheco-Arjona R, Castañeda-Ruelas GM. Genomic Approach of Listeria monocytogenes Strains Isolated from Deli-Meats in Mexico. Curr Microbiol 2024; 81:145. [PMID: 38632127 DOI: 10.1007/s00284-024-03680-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/28/2024] [Indexed: 04/19/2024]
Abstract
Listeria monocytogenes is a foodborne pathogen that causes listeriosis worldwide. In México, L. monocytogenes has been identified as a hazard of deli-meats. However, the genomic analysis that supports the transmission of L. monocytogenes strains via deli-meats and its role as a source for virulence and resistance genes is lacking. Here, we present four high-quality genome drafts of L. monocytogenes strains isolated from deli-meats in Mexico. In silico typing was used to determine the serotype, lineage, clonal complexes (CC), and multilocus sequence (ST). Also, comparative genomics were performed to explore the diversity, virulence, mobile elements, antimicrobial resistant and stress survival traits. The genome sequence size of these strains measured 3.05 ± 0.07 Mb with a mean value of 37.9%G+C. All strains belonged to linage I, which was divided into two groups: 4b, CC2, ST1 (n = 3) and 1/2b, CC5, ST5 (n = 1). The pangenome and core genome contained 3493 and 2625 genes, respectively. The strains harbor the L. monocytogenes pathogenicity island-1 (LIPI-1) and the same multidrug resistance pattern (fosX, norB, mprF, lin) via in silico analysis. Comparative analysis delineated the genomes as essentially syntenic, whose genomic differences were due to phage insertion. These results expand what is known about the biology of the L. monocytogenes strains isolated from deli-meats in Mexico and warns of the risk that these strains belong to epidemic linage and harbor virulence genes linked to human disease.
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Affiliation(s)
- Maribel Jiménez-Edeza
- Laboratorio de Investigación y Diagnóstico Microbiológico, Facultad de Ciencias Químico Biológicas, Programa Regional de Posgrado en Biotecnología, Universidad Autónoma de Sinaloa, 80013, Sinaloa, Mexico
| | | | - Ramón Pacheco-Arjona
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Yucatán, 97315, Yucatan, Mexico
| | - Gloria Marisol Castañeda-Ruelas
- Laboratorio de Investigación y Diagnóstico Microbiológico, Facultad de Ciencias Químico Biológicas, Programa Regional de Posgrado en Biotecnología, Universidad Autónoma de Sinaloa, 80013, Sinaloa, Mexico.
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94
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Ridley RS, Conrad RE, Lindner BG, Woo S, Konstantinidis KT. Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes. Sci Rep 2024; 14:8798. [PMID: 38627476 PMCID: PMC11021508 DOI: 10.1038/s41598-024-59279-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.
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Affiliation(s)
- Rodney S Ridley
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Roth E Conrad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Seongwook Woo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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95
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Rodrigues IC, Ribeiro-Almeida M, Silveira L, Prata JC, de Carvalho AP, Roque C, Gomes JP, Borges V, Pista Â, Martins da Costa P. Unveiling a Listeria monocytogenes Outbreak in a Rabbit Farm: Clinical Manifestation, Antimicrobial Resistance, Genomic Insights and Environmental Investigation. Microorganisms 2024; 12:785. [PMID: 38674729 PMCID: PMC11051769 DOI: 10.3390/microorganisms12040785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Listeria monocytogenes poses a threat to both human and animal health. This work describes an L. monocytogenes outbreak in a Portuguese rabbit farm, detailing the isolates' clinical manifestations, necropsy findings, and phenotypic and genomic profiles. Clinical signs, exclusively observed in does, included lethargy and reproductive signs. Post-mortem examination of does revealed splenomegaly, hepatomegaly with a reticular pattern, pulmonary congestion, and haemorrhagic lesions in the uterus, with thickening of the uterine wall and purulent greyish exudates. Positive L. monocytogenes samples were identified in fattening and maternity units across different samples, encompassing does and environmental samples. Core-genome Multi Locus Sequence Typing (cgMLST) analysis confirmed the outbreak, with the 16 sequenced isolates (lineage II, CC31, and ST325) clustering within a ≤2 allelic difference (AD) threshold. Antimicrobial susceptibility testing for five antibiotics revealed that 15 out of 19 outbreak isolates were resistant to sulfamethoxazole-trimethoprim (SXT). Concordantly, all SXT-resistant sequenced isolates were found to exclusively harbour a plasmid containing a trimethoprim-resistance gene (dfrD), along with loci linked to resistance to lincosamides (lnuG), macrolides (mphB), and polyether ionophores (NarAB operon). All sequenced outbreak isolates carried the antibiotic resistance-related genes tetM, fosX, lin, norB, lmrB, sul, and mprF. The outbreak cluster comprises isolates from does and the environment, which underscores the ubiquitous presence of L. monocytogenes and emphasizes the importance of biosecurity measures. Despite limited data on listeriosis in rabbit farming, this outbreak reveals its significant impact on animal welfare and production.
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Affiliation(s)
- Inês C. Rodrigues
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (M.R.-A.); (J.C.P.); (A.P.d.C.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Marisa Ribeiro-Almeida
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (M.R.-A.); (J.C.P.); (A.P.d.C.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4099-002 Porto, Portugal
| | - Leonor Silveira
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; (L.S.); (C.R.); (Â.P.)
| | - Joana C. Prata
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (M.R.-A.); (J.C.P.); (A.P.d.C.)
- i4HB—Institute for Health and Bioeconomy, University Institute of Health Sciences, Advanced Polytechnic and University Cooperative (CESPU), 4585-116 Gandra, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Translational Toxicology Research Laboratory, University Institute of Health Sciences (1H-TOXRUN, IUCS-CESPU), 4585-116 Gandra, Portugal
| | - André Pinto de Carvalho
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (M.R.-A.); (J.C.P.); (A.P.d.C.)
- NANTA Portugal, S.A., Rua da Estação, N° 157, 4630-221 Marco de Canaveses, Portugal
| | - Carla Roque
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; (L.S.); (C.R.); (Â.P.)
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; (J.P.G.); (V.B.)
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; (J.P.G.); (V.B.)
| | - Ângela Pista
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; (L.S.); (C.R.); (Â.P.)
| | - Paulo Martins da Costa
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (I.C.R.); (M.R.-A.); (J.C.P.); (A.P.d.C.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
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96
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Long DR, Bryson-Cahn C, Waalkes A, Holmes EA, Penewit K, Tavolaro C, Bellabarba C, Zhang F, Chan JD, Fang FC, Lynch JB, Salipante SJ. Contribution of the patient microbiome to surgical site infection and antibiotic prophylaxis failure in spine surgery. Sci Transl Med 2024; 16:eadk8222. [PMID: 38598612 DOI: 10.1126/scitranslmed.adk8222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
Despite modern antiseptic techniques, surgical site infection (SSI) remains a leading complication of surgery. However, the origins of SSI and the high rates of antimicrobial resistance observed in these infections are poorly understood. Using instrumented spine surgery as a model of clean (class I) skin incision, we prospectively sampled preoperative microbiomes and postoperative SSI isolates in a cohort of 204 patients. Combining multiple forms of genomic analysis, we correlated the identity, anatomic distribution, and antimicrobial resistance profiles of SSI pathogens with those of preoperative strains obtained from the patient skin microbiome. We found that 86% of SSIs, comprising a broad range of bacterial species, originated endogenously from preoperative strains, with no evidence of common source infection among a superset of 1610 patients. Most SSI isolates (59%) were resistant to the prophylactic antibiotic administered during surgery, and their resistance phenotypes correlated with the patient's preoperative resistome (P = 0.0002). These findings indicate the need for SSI prevention strategies tailored to the preoperative microbiome and resistome present in individual patients.
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Affiliation(s)
- Dustin R Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Chloe Bryson-Cahn
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Elizabeth A Holmes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Celeste Tavolaro
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carlo Bellabarba
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Fangyi Zhang
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jeannie D Chan
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Pharmacy, Harborview Medical Center, University of Washington School of Pharmacy, Seattle, WA 98104, USA
| | - Ferric C Fang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Clinical Microbiology Laboratory, Harborview Medical Center, Seattle, WA 98104, USA
| | - John B Lynch
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
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97
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Khasapane NG, Nkhebenyane J, Mnisi Z, Kwenda S, Thekisoe O. Comprehensive whole genome analysis of Staphylococcus aureus isolates from dairy cows with subclinical mastitis. Front Microbiol 2024; 15:1376620. [PMID: 38650877 PMCID: PMC11033518 DOI: 10.3389/fmicb.2024.1376620] [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: 01/26/2024] [Accepted: 03/19/2024] [Indexed: 04/25/2024] Open
Abstract
Staphylococcus species are the primary cause of mastitis in dairy cows across the world. Staphylococcus aureus has recently become a pathogen that is zoonotic and multidrug resistant. This study aimed to sequence whole genomes of 38 S. aureus isolates from 55 subclinical mastitis dairy cows of 7 small-scale farmers in the Free State Province, South Africa and document and their antimicrobial and virulence genes. The 38 isolates were grouped by the in silico multi-locus sequencing types (MLST) into seven sequence types (STs), that is (ST 97, 352, 152, 243) and three new STs (ST8495, ST8500, and ST8501). Thirty-three S. aureus isolates were divided into 7 core single-nucleotide polymorphism (SNP) clusters. Among the 9 distinct spa-types that were detected, Spa-types t2883 accounted for the majority of isolates at 12 (31.57%), followed by t416 with 11 (28.94%) and t2844 with 5 (13.15%). The data also revealed the identification of four (4) plasmids, with Rep_N (rep20) accounting for the majority of isolates with 17 (44.73%), followed by Inc18 (repUS5) with 2 (5.26%). These isolates included 11 distinct antimicrobial resistance genes and 23 genes linked to bacterial virulence. Surprisingly, no methicillin resistance associated genes were detected in these isolates. Genome data of the current study will contribute to understanding epidemiology S. aureus genotypes and ultimately aid in developing treatment and control plans to stop the spread of mastitis in the Free State province and South Africa as a whole.
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Affiliation(s)
- Ntelekwane George Khasapane
- Department of Life Sciences, Centre for Applied Food Safety and Biotechnology, Central University of Technology, Bloemfontein, South Africa
| | - Jane Nkhebenyane
- Department of Life Sciences, Centre for Applied Food Safety and Biotechnology, Central University of Technology, Bloemfontein, South Africa
| | - Zamantungwa Mnisi
- Clinvet International, Study Operations, Bloemfontein, South Africa
- Vectors and Vector-Borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Oriel Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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98
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Tathode MS, Bonomo MG, Zappavigna S, Mang SM, Bocchetti M, Camele I, Caraglia M, Salzano G. Whole-genome analysis suggesting probiotic potential and safety properties of Pediococcus pentosaceus DSPZPP1, a promising LAB strain isolated from traditional fermented sausages of the Basilicata region (Southern Italy). Front Microbiol 2024; 15:1268216. [PMID: 38638895 PMCID: PMC11024341 DOI: 10.3389/fmicb.2024.1268216] [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: 07/27/2023] [Accepted: 03/07/2024] [Indexed: 04/20/2024] Open
Abstract
Introduction Many lactic acid bacteria (LAB) strains are currently gaining attention in the food industry and various biological applications because of their harmless and functional properties. Given the growing consumer demand for safe food, further research into potential probiotic bacteria is beneficial. Therefore, we aimed to characterize Pediococcus pentosaceus DSPZPP1, a LAB strain isolated from traditional fermented sausages from the Basilicata region of Southern Italy. Methods In this study, we analyzed the whole genome of the P. pentosaceus DSPZPP1 strain and performed in silico characterization to evaluate its applicability for probiotics and use in the food industry. Results and Discussion The whole-genome assembly and functional annotations revealed many interesting characteristics of the DSPZPP1 strain. Sequencing raw reads were assembled into a draft genome of size 1,891,398 bp, with a G + C content of 37.3%. Functional annotation identified 1930 protein-encoding genes and 58 RNAs including tRNA, tmRNA, and 16S, 23S, and 5S rRNAs. The analysis shows the presence of genes that encode water-soluble B-group vitamins such as biotin, folate, coenzyme A, and riboflavin. Furthermore, the analysis revealed that the DSPZPP1 strain can synthesize class II bacteriocin, penocin A, adding importance to the food industry for bio-enriched food. The DSPZPP1 genome does not show the presence of plasmids, and no genes associated with antimicrobial resistance and virulence were found. In addition, two intact bacteriophages were identified. Importantly, the lowest probability value in pathogenicity analysis indicates that this strain is non-pathogenic to humans. 16 s rRNA-based phylogenetic analysis and comparative analysis based on ANI and Tetra reveal that the DSPZPP1 strain shares the closest evolutionary relationship with P. pentosaceus DSM 20336 and other Pediococcus strains. Analysis of carbohydrate active enzymes (CAZymes) identified glycosyl transferases (GT) as a main class of enzymes followed by glycoside hydrolases (GH). Our study shows several interesting characteristics of the isolated DSPZPP1 strain from fermented Italian sausages, suggesting its potential use as a promising probiotic candidate and making it more appropriate for selection as a future additive in biopreservation.
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Affiliation(s)
- Madhura S. Tathode
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Maria Grazia Bonomo
- Department of Science, Università degli Studi della Basilicata, Potenza, Italy
- Spinoff TNcKILLERS, Potenza, Italy
| | - Silvia Zappavigna
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Stefania Mirela Mang
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), Università degli Studi della Basilicata, Potenza, Italy
| | - Marco Bocchetti
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, Ariano Irpino, Italy
| | - Ippolito Camele
- School of Agricultural, Forestry, Food and Environmental Sciences (SAFE), Università degli Studi della Basilicata, Potenza, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, Ariano Irpino, Italy
| | - Giovanni Salzano
- Department of Science, Università degli Studi della Basilicata, Potenza, Italy
- Spinoff TNcKILLERS, Potenza, Italy
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99
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Zhang Y, Nair S, Zhang Z, Zhao J, Zhao H, Lu L, Chang L, Jiao N. Adverse Environmental Perturbations May Threaten Kelp Farming Sustainability by Exacerbating Enterobacterales Diseases. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5796-5810. [PMID: 38507562 DOI: 10.1021/acs.est.3c09921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Globally kelp farming is gaining attention to mitigate land-use pressures and achieve carbon neutrality. However, the influence of environmental perturbations on kelp farming remains largely unknown. Recently, a severe disease outbreak caused extensive kelp mortality in Sanggou Bay, China, one of the world's largest high-density kelp farming areas. Here, through in situ investigations and simulation experiments, we find indications that an anomalously dramatic increase in elevated coastal seawater light penetration may have contributed to dysbiosis in the kelp Saccharina japonica's microbiome. This dysbiosis promoted the proliferation of opportunistic pathogenic Enterobacterales, mainly including the genera Colwellia and Pseudoalteromonas. Using transcriptomic analyses, we revealed that high-light conditions likely induced oxidative stress in kelp, potentially facilitating opportunistic bacterial Enterobacterales attack that activates a terrestrial plant-like pattern recognition receptor system in kelp. Furthermore, we uncover crucial genotypic determinants of Enterobacterales dominance and pathogenicity within kelp tissue, including pathogen-associated molecular patterns, potential membrane-damaging toxins, and alginate and mannitol lysis capability. Finally, through analysis of kelp-associated microbiome data sets under the influence of ocean warming and acidification, we conclude that such Enterobacterales favoring microbiome shifts are likely to become more prevalent in future environmental conditions. Our study highlights the need for understanding complex environmental influences on kelp health and associated microbiomes for the sustainable development of seaweed farming.
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Affiliation(s)
- Yongyu Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, Shandong, China
| | - Shailesh Nair
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, Shandong, China
| | - Zenghu Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, Shandong, China
| | - Jiulong Zhao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao 266101, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, Shandong, China
| | - Hanshuang Zhao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, Shandong, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longfei Lu
- Weihai Changqing Ocean Science Technology Co., Ltd., Rongcheng 264300, China
| | - Lirong Chang
- Weihai Changqing Ocean Science Technology Co., Ltd., Rongcheng 264300, China
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361100, China
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100
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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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