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Nasser F, Gaudreau A, Lubega S, Zaker A, Xia X, Mer AS, D'Costa VM. Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter. Emerg Microbes Infect 2024; 13:2320929. [PMID: 38530969 DOI: 10.1080/22221751.2024.2320929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.
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Affiliation(s)
- Farah Nasser
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Avery Gaudreau
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Shareefah Lubega
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Arvin Zaker
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Xuhua Xia
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
- Department of Biology, University of Ottawa, Ottawa, Canada
| | - Arvind S Mer
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Vanessa M D'Costa
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
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Uea-Anuwong T, Stephan R, Stevens MJ, Boss S, Lugsomya K, Kiu LH, Kamali M, Gröhn YT, Nekouei O, Magouras I. Isolation of community-associated methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 30 from house rats ( Rattus tanezumi) in Hong Kong. One Health 2024; 19:100861. [PMID: 39157653 PMCID: PMC11327950 DOI: 10.1016/j.onehlt.2024.100861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 07/17/2024] [Indexed: 08/20/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is of major public health concern due to its resistance to multiple antibiotics. This resistance has been observed in various settings, including hospitals and communities, and has been detected in both animals and humans. Although peridomestic rat species (Rattus spp.) are well described reservoirs of several human pathogens and antimicrobial resistant bacteria, little is known about their role in MRSA epidemiology. In order to investigate whether Rattus spp. in Hong Kong are potential carriers of MRSA, 221 rats were caught from various ecological areas and nasopharyngeal samples were cultured on MRSA selective media. Genotypic characteristics of MRSA were confirmed by whole genome sequencing. Two clonal sequence type (ST) 30 MRSA isolates, harbouring mecA on staphylococcal chromosome cassette (SCC) mec type IVc, were cultured from two house rats (Rattus tanezumi) caught in two densely populated urban areas. To the best of the authors' knowledge, this is the first detection of community-associated (CA)-MRSA strain ST30 SCCmec IVc in peridomestic rodents in Hong Kong and globally. Our finding indicates that house rats can be carriers of MRSA strains that are widely distributed in the community.
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Affiliation(s)
- Theethawat Uea-Anuwong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Marc J.A. Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Sara Boss
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Kittitat Lugsomya
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Lam Hoi Kiu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Maedeh Kamali
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yrjö Tapio Gröhn
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Omid Nekouei
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Applied One Health Research and Policy Advice, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ioannis Magouras
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Applied One Health Research and Policy Advice, City University of Hong Kong, Hong Kong Special Administrative Region, China
- Veterinary Public Health Institute, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Joishy TK, Bhattacharya A, Singh CT, Mukherjee AK, Khan MR. Probiotic and anti-inflammatory properties of Lactiplantibacillus plantarum MKTJ24 isolated from an artisanal fermented fish of North-east India. N Biotechnol 2024; 83:121-132. [PMID: 39111568 DOI: 10.1016/j.nbt.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/21/2024] [Accepted: 07/27/2024] [Indexed: 08/13/2024]
Abstract
The study aimed to isolate and characterize lactic acid bacteria from various traditional fermented fish products from North East India, including Xindol, Hentak, and Ngari, which hold significant dietary importance for the indigenous tribes. Additionally, the study sought to examine their untargeted metabolomic profiles. A total of 43 strains of Bacillus, Priestia, Staphylococcus, Pediococcus, and Lactiplantibacillus were isolated, characterized by 16 S rRNA gene and tested for probiotic properties. Five strains passed pH and bile salt tests with strain dependent antimicrobial activity, which exhibited moderate autoaggregation and hydrophobicity properties. Lactiplantibacillus plantarum MKTJ24 exhibited the highest hydrophobicity (42 %), which was further confirmed by adhesion assay in HT-29 cell lines (100 %). Lactiplantibacillus plantarum MKTJ24 treatment in LPS-stimulated HT-29 cells up-regulated expression of mucin genes compared to LPS-treated cells. Treatment of RAW 264.7 cells with Lactiplantibacillus plantarum MKTJ24 decreased LPS-induced reactive oxygen species (ROS) and nitric oxide (NO) productions. Further, genome analysis of Lactiplantibacillus plantarum MKTJ24 revealed the presence of several probiotic markers and immunomodulatory genes. The genome was found to harbor plantaricin operon involved in bacteriocin production. A pangenome analysis using all the publicly available L. plantarum genomes specifically isolated from fermented fish products identified 120 unique genes in Lactiplantibacillus plantarum MKTJ24. Metabolomic analysis indicated dominance of ascorbic acids, pentafluropropionate, cyclopropaneacetic acid, florobenzylamine, and furanone in Xindol. This study suggests that Lactiplantibacillus plantarum MKTJ24 has potential probiotic and immunomodulatory properties that could be used in processing traditional fermented fish products on an industrial scale to improve their quality and enhance functional properties.
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Affiliation(s)
- Tulsi K Joishy
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Anupam Bhattacharya
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Chingtham Thanil Singh
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-202002, India
| | - Ashis K Mukherjee
- Microbial Biotechnology and Protein Research Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Mojibur R Khan
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India.
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Siderius NL, Sapula SA, Hart BJ, Hutchings JL, Venter H. Enterobacter adelaidei sp. nov. Isolation of an extensively drug resistant strain from hospital wastewater in Australia and the global distribution of the species. Microbiol Res 2024; 288:127867. [PMID: 39163716 DOI: 10.1016/j.micres.2024.127867] [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: 05/16/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 08/22/2024]
Abstract
BACKGROUND Enterobacter species are included among the normal human gut microflora and persist in a diverse range of other environmental niches. They have become important opportunistic nosocomial pathogens known to harbour plasmid-mediated multi-class antimicrobial resistance (AMR) determinants. Global AMR surveillance of Enterobacterales isolates shows the genus is second to Klebsiella in terms of frequency of carbapenem resistance. Enterobacter taxonomy is confusing and standard species identification methods are largely inaccurate or insufficient. There are currently 27 named species and a total of 46 taxa in the genus distinguishable via average nucleotide identity (ANI) calculation between pairs of genomic sequences. Here we describe an Enterobacter strain, ECC3473, isolated from the wastewater of an Australian hospital whose species could not be determined by standard methods nor by ribosomal RNA gene multi-locus typing. AIM To characterise ECC3473 in terms of phenotypic and genotypic antimicrobial resistance, biochemical characteristics and taxonomy as well as to determine the global distribution of the novel species to which it belongs. METHODS Standard broth dilution and disk diffusion were used to determine phenotypic AMR. The strain's complete genome, including plasmids, was obtained following long- and short read sequencing and a novel long/short read hybrid assembly and polishing, and the genomic basis of AMR was determined. Phylogenomic analysis and quantitative measures of relatedness (ANI, digital DNA-DNA hybridisation, and difference in G+C content) were used to study the taxonomic relationship between ECC3473 and Enterobacter type-strains. NCBI and PubMLST databases and the literature were searched for additional members of the novel species to determine its global distribution. RESULTS ECC3473 is one of 21 strains isolated globally belonging to a novel Enterobacter species for which the name, Enterobacter adelaidei sp. nov. is proposed. The novel species was found to be resilient in its capacity to persist in contaminated water and adaptable in its ability to accumulate multiple transmissible AMR determinants. CONCLUSION E. adelaidei sp. nov. may become increasingly important to the dissemination of AMR.
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Affiliation(s)
- Naomi L Siderius
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Sylvia A Sapula
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Bradley J Hart
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Joshua L Hutchings
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Henrietta Venter
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
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Bertrans-Tubau L, Martínez-Campos S, Lopez-Doval J, Abril M, Ponsá S, Salvadó V, Hidalgo M, Pico-Tomàs A, Balcazar JL, Proia L. Nature-based bioreactors: Tackling antibiotic resistance in urban wastewater treatment. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 22:100445. [PMID: 39055482 PMCID: PMC11269294 DOI: 10.1016/j.ese.2024.100445] [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: 02/05/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
The overuse and misuse of antibiotics have accelerated the selection of antibiotic-resistant bacteria, significantly impacting human, animal, and environmental health. As aquatic environments are vulnerable to antibiotic resistance, suitable management practices should be adopted to tackle this phenomenon. Here we show an effective, nature-based solution for reducing antibiotic resistance from actual wastewater. We utilize a bioreactor that relies on benthic (biofilms) and planktonic microbial communities to treat secondary effluent from a small urban wastewater treatment plant (<10,000 population equivalent). This treated effluent is eventually released into the local aquatic ecosystem. We observe high removal efficiency for genes that provide resistance to commonly used antibiotic families, as well as for mobile genetic elements that could potentially aid in their spread. Importantly, we notice a buildup of sulfonamide (sul1 and sul2) and tetracycline (tet(C), tet(G), and tetR) resistance genes specifically in biofilms. This advancement marks the initial step in considering this bioreactor as a nature-based, cost-effective tertiary treatment option for small UWWTPs facing antibiotic resistance challenges.
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Affiliation(s)
- Lluís Bertrans-Tubau
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Sergio Martínez-Campos
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Julio Lopez-Doval
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Meritxell Abril
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Sergio Ponsá
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
| | - Victoria Salvadó
- Chemistry Department, University of Girona. Campus Montilivi, 17005, Girona, Spain
| | - Manuela Hidalgo
- Chemistry Department, University of Girona. Campus Montilivi, 17005, Girona, Spain
| | - Anna Pico-Tomàs
- Catalan Institute Water Research (ICRA-CERCA), Emili Grahit 101, 17003, Girona, Spain
| | - Jose Luis Balcazar
- Catalan Institute Water Research (ICRA-CERCA), Emili Grahit 101, 17003, Girona, Spain
- University of Girona, 17004, Girona, Spain
| | - Lorenzo Proia
- BETA Technological Centre- University of Vic- Central University of Catalunya (BETA- UVIC- UCC), Carretera de Roda 70, 08500, Vic, Barcelona, Spain
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Yao S, Yu J, Zhang T, Xie J, Yan C, Ni X, Guo B, Cui C. Comprehensive analysis of distribution characteristics and horizontal gene transfer elements of bla NDM-1-carrying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:173907. [PMID: 38906294 DOI: 10.1016/j.scitotenv.2024.173907] [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: 04/01/2024] [Revised: 06/08/2024] [Accepted: 06/08/2024] [Indexed: 06/23/2024]
Abstract
The worldwide dissemination of New Delhi metallo-β-lactamase-1 (NDM-1), which mediates resistance to almost all clinical β-lactam antibiotics, is a major public health problem. The global distribution, species, sources, and potential transfer risk of blaNDM-1-carrying bacteria are unclear. Results of a comprehensive analysis of literature in 2010-2022 showed that a total of 6002 blaNDM-1 carrying bacteria were widely distributed around 62 countries with a high trend in the coastal areas. Opportunistic pathogens or pathogens like Klebsiella sp., Escherichia sp., Acinetobacter sp. and Pseudomonas sp. were the four main species indicating the potential microbial risk. Source analysis showed that 86.45 % of target bacteria were isolated from the source of hospital (e.g., Hospital patients and wastewater) and little from surface water (5.07 %) and farms (3.98 %). A plasmid-encoded blaNDM-1Acinetobacter sp. with the resistance mechanisms of antibiotic efflux pump, antibiotic target change and antibiotic degradation was isolated from the wastewater of a typical tertiary hospital. Insertion sequences (IS3 and IS30) located in the adjacent 5 kbp of blaNDM-1-bleMBL gene cluster indicating the transposon-mediated horizontal gene transfer risk. These results showed that the worldwide spread of blaNDM-1-carrying bacteria and its potential horizontal gene transfer risk deserve good control.
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Affiliation(s)
- Shijie Yao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaqin Yu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Tianyang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Jianhao Xie
- Children's Hospital of Fudan University, Shanghai 200233, China
| | - Chicheng Yan
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xuan Ni
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bingbing Guo
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Shanghai environmental protection key laboratory on environmental standard and risk management of chemical pollutants, East China University of Science & Technology, Shanghai 200237, China.
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Pei Y, Lei A, Yang S, Chen H, Liu X, Liu L, Kang X. Biodegradation and bioaugmentation of tetracycline by Providencia stuartii TX2: Performance, degradation pathway, genetic background, key enzymes, and application risk assessment. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135231. [PMID: 39032181 DOI: 10.1016/j.jhazmat.2024.135231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024]
Abstract
The antibiotic tetracycline (TC) is an emerging pollutant frequently detected in various environments. Biodegradation is a crucial approach for eliminating TC contamination. However, only a few efficient TC-degrading bacteria have been isolated, and the molecular mechanisms of TC degradation, as well as their application potential, remain poorly understood. This study isolated a novel TC-degrading bacterium, Providencia stuartii TX2, from the intestine of black soldier fly larvae. TX2 exhibited remarkable performance, degrading 72.17 % of 400 mg/L TC within 48 h. Genomic analysis of TX2 unveiled the presence of antibiotic resistance genes and TC degradation enzymes. Transcriptomic analysis highlighted the roles of proteins related to efflux pumps, enzymatic transformation, adversity resistance, and unknown functions. Three TC degradation pathways were proposed, with TC being transformed into 27 metabolites through epimerization, hydroxylation, oxygenation, ring opening, and de-grouping, reducing TC toxicity. Additionally, TX2 significantly enhanced TC biodegradation in four TC-contaminated environmental samples and reduced antibiotic resistance genes and mobile genetic elements in chicken manure. This research provides insights into the survival and biodegradation mechanisms of Providencia stuartii TX2 and evaluates its potential for environmental bioremediation.
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Affiliation(s)
- Yaxin Pei
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, School of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China.
| | - Aojie Lei
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
| | - Sen Yang
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
| | - Hongge Chen
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
| | - Xinyu Liu
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
| | - Liangwei Liu
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), School of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
| | - Xiangtao Kang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, School of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, 450046, China
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Howe S, Wei X, Kovac J, Zhao J. Draft genome sequence of Ruoffia tabacinasalis isolated from a bovine nasal swab: a novel member of the bovine nasal microbiota. Microbiol Resour Announc 2024; 13:e0008724. [PMID: 39082814 PMCID: PMC11385104 DOI: 10.1128/mra.00087-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 06/08/2024] [Indexed: 09/11/2024] Open
Abstract
We report the isolation and draft genome sequence of Ruoffia tabacinasalis, a novel member of the bovine nasal microbiota. The genome, which is estimated to be 90.5% complete, is composed of one contig comprising 2,363,349 bp with a GC content of 36.66%.
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Affiliation(s)
- Samantha Howe
- Department of Animal Science, University of Arkansas, Fayetteville, Arkansas, USA
| | - Xiaoyuan Wei
- Department of Food Science, Pennsylvania State University, State College, Pennsylvania, USA
| | - Jasna Kovac
- Department of Food Science, Pennsylvania State University, State College, Pennsylvania, USA
| | - Jiangchao Zhao
- Department of Animal Science, University of Arkansas, Fayetteville, Arkansas, USA
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Lin L, Li L, Yang X, Hou L, Wu D, Wang B, Ma B, Liao X, Yan X, Gad M, Su J, Liu Y, Liu K, Hu A. Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135730. [PMID: 39243538 DOI: 10.1016/j.jhazmat.2024.135730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 08/26/2024] [Accepted: 08/31/2024] [Indexed: 09/09/2024]
Abstract
Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.
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Affiliation(s)
- Laichang Lin
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Laiyi Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyong Yang
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, China
| | - Liyuan Hou
- Department of Civil and Environmental Engineering, Utah State University, Logan, UT 84322, United States; Utah Water Research Laboratory, 1600 Canyon Road, Logan, UT 84321, United States
| | - Dong Wu
- Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, China
| | - Binhao Wang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin Liao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuhang Yan
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Life Sciences, Hebei University, Baoding 071002, China
| | - Mahmoud Gad
- Water Pollution Research Department, National Research Centre, Cairo 12622, Egypt
| | - Jianqiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yongqin Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Hitch TCA, Wylensek D, Bisdorf K, Buhl EM, Treichel N, Abt B, Overmann J, Clavel T. Harmonious naming across nomenclature codes exemplified by the description of bacterial isolates from the mammalian gut. Syst Appl Microbiol 2024; 47:126543. [PMID: 39163745 DOI: 10.1016/j.syapm.2024.126543] [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: 01/31/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 08/22/2024]
Abstract
A dual system for naming prokaryotes is currently in place based on the well-established International Code of Nomenclature of Prokaryotes (ICNP) and the newly created Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Whilst recent creation of the SeqCode opened an avenue to accelerate the naming of uncultured taxa, the existence of two codes increases the risk of species being assigned multiple validly published names. In this work we present a workflow that aims to limit conflicts by firstly naming novel cultured taxa under the SeqCode, and secondly under the ICNP, enhancing the traceability of the taxa across the two codes. To exemplify this workflow, we describe four novel taxa isolated from the intestine of pigs: Intestinicryptomonas porci gen. nov., sp. nov. (strain CLA-KB-P66T, genome accession GCA_033971905.1TS) within a novel family, Intestinicryptomonaceae; Grylomicrobium aquisgranensis gen. nov., sp. nov. (CLA-KB-P133T, GCA_033971865.1TS); Absicoccus intestinalis sp. nov. (CLA-KB-P134T, GCA_033971885.1TS); and Mesosutterella porci sp. nov. (oilRF-744- wt-GAM-9T, GCF_022134585.1TS).
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Affiliation(s)
- Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - David Wylensek
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Kevin Bisdorf
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany; Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Eva M Buhl
- Electron Microscopy Facility, Institute of Pathology, RWTH University Hospital, Aachen, Germany
| | - Nicole Treichel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Birte Abt
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany; Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany.
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11
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Sola F, Ayala D, Pulido M, Ayala R, López-Cerero L, Hernández I, Ruiz D. ginmappeR: an unified approach for integrating gene and protein identifiers across biological sequence databases. BIOINFORMATICS ADVANCES 2024; 4:vbae129. [PMID: 39262905 PMCID: PMC11387618 DOI: 10.1093/bioadv/vbae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/09/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024]
Abstract
Summary The proliferation of biological sequence data, due to developments in molecular biology techniques, has led to the creation of numerous open access databases on gene and protein sequencing. However, the lack of direct equivalence between identifiers across these databases difficults data integration. To address this challenge, we introduce ginmappeR, an integrated R package facilitating the translation of gene and protein identifiers between databases. By providing a unified interface, ginmappeR streamlines the integration of diverse data sources into biological workflows, so it enhances efficiency and user experience. Availability and implementation from Bioconductor: https://bioconductor.org/packages/ginmappeR.
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Affiliation(s)
- Fernando Sola
- SCORE Lab, DEAL, University of Seville, ETSII, 41012 Seville, Spain
| | - Daniel Ayala
- SCORE Lab, DEAL, University of Seville, ETSII, 41012 Seville, Spain
| | - Marina Pulido
- Department of Microbiology, University of Seville, 41009 Seville, Spain
- Institute of Biomedicine of Seville, Virgen Macarena University Hospital, CSIC, University of Seville, 41013 Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain
| | - Rafael Ayala
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0411, Japan
| | - Lorena López-Cerero
- Department of Microbiology, University of Seville, 41009 Seville, Spain
- Institute of Biomedicine of Seville, Virgen Macarena University Hospital, CSIC, University of Seville, 41013 Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain
| | - Inma Hernández
- SCORE Lab, DEAL, University of Seville, ETSII, 41012 Seville, Spain
| | - David Ruiz
- SCORE Lab, DEAL, University of Seville, ETSII, 41012 Seville, Spain
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12
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Zhang X, Xu D, Usman S, Li Y, Liang Y, Bai J, Guo X. Heterofermentative Lentilactobacillus buchneri and low dry matter reduce high-risk antibiotic resistance genes in corn silage by regulating pathogens and mobile genetic element. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135700. [PMID: 39241365 DOI: 10.1016/j.jhazmat.2024.135700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/02/2024] [Accepted: 08/28/2024] [Indexed: 09/09/2024]
Abstract
The study of antibiotic resistance in the silage microbiome has attracted initial attention. However, the influences of lactic acid bacteria inoculants and dry matter (DM) content on antibiotic resistance genes (ARGs) reduction in whole-plant corn silage remain poorly studied. This study accessed the ARGs' risk and transmission mechanism in whole-plant corn silage with different DM levels and treated with Lactiplantibacillus plantarum or Lentilactobacillus buchneri. The macrolide and tetracycline were the main ARGs in corn silage. The dominant species (Lent. buchneri and Lactobacillus acetotolerans) were the main ARGs carriers in whole-plant corn silage. The application of Lent. buchneri increased total ARGs abundance regardless of corn DM. Whole-plant corn silage with 30 % DM reduced the abundances of integrase and plasmid compared with 40 % DM. The correlation and structural equation model analysis demonstrated that bacterial community succession, resulting from changes in DM content, was the primary driving factor influencing the ARGs distribution in whole-plant corn silage. Interestingly, whole-plant corn silage inoculated with Lent. buchneri reduced abundances of high-risk ARGs (mdtG, mepA, tetM, mecA, vatE and tetW) by regulating pathogens (Escherichia coli), mobile genetic elements (MGEs) genes (IS3 and IS1182), and this effect was more pronounced at 30 % DM level. In summary, although whole-plant corn silage inoculated with Lent. buchneri increased the total ARGs abundance at both DM levels, it decreased the abundance of high-risk ARGs by reducing the abundances of the pathogens and MGEs, and this effect was more noticeable at 30 % DM level.
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Affiliation(s)
- Xia Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China; College of Animal Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Dongmei Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China; Probiotics and Life Health Research Institute, Lanzhou University, Lanzhou 730000, PR China
| | - Samaila Usman
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China; Probiotics and Life Health Research Institute, Lanzhou University, Lanzhou 730000, PR China
| | - Yue Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China; Probiotics and Life Health Research Institute, Lanzhou University, Lanzhou 730000, PR China
| | - Ying Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China; Probiotics and Life Health Research Institute, Lanzhou University, Lanzhou 730000, PR China
| | - Jie Bai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China; Probiotics and Life Health Research Institute, Lanzhou University, Lanzhou 730000, PR China
| | - Xusheng Guo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China; Probiotics and Life Health Research Institute, Lanzhou University, Lanzhou 730000, PR China.
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13
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Ferriol-González C, Concha-Eloko R, Bernabéu-Gimeno M, Fernández-Cuenca F, Cañada-García JE, García-Cobos S, Sanjuán R, Domingo-Calap P. Targeted phage hunting to specific Klebsiella pneumoniae clinical isolates is an efficient antibiotic resistance and infection control strategy. Microbiol Spectr 2024:e0025424. [PMID: 39194291 DOI: 10.1128/spectrum.00254-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 08/06/2024] [Indexed: 08/29/2024] Open
Abstract
Klebsiella pneumoniae is one of the most threatening multi-drug-resistant pathogens today, with phage therapy being a promising alternative for personalized treatments. However, the intrinsic capsule diversity in Klebsiella spp. poses a substantial barrier to the phage host range, complicating the development of broad-spectrum phage-based treatments. Here, we have isolated and genomically characterized phages capable of infecting each of the acquired 77 reference serotypes of Klebsiella spp., including capsular types widespread among high-risk K. pneumoniae clones causing nosocomial infections. We demonstrated the possibility of isolating phages for all capsular types in the collection, revealing high capsular specificity among taxonomically related phages, in contrast to a few phages that exhibited broad-spectrum infection capabilities. To decipher the determinants of the specificity of these phages, we focused on their receptor-binding proteins, with particular attention to depolymerases. We also explored the possibility of designing a broad-spectrum phage cocktail based on phages isolated in reference capsular-type strains and determining the ability to lyse relevant clinical isolates. A combination of 12 phages capable of infecting 55% of the reference Klebsiella spp. serotypes was tested on a panel of carbapenem-resistant K. pneumoniae clinical isolates. Thirty-one percent of isolates were susceptible to the phage cocktail. However, our results suggest that in a highly variable encapsulated bacterial host, phage hunting must be directed to the specific Klebsiella isolates. This work is a step forward in the understanding of the complexity of phage-host interactions and highlights the importance of implementing precise and phage-specific strategies to treat K. pneumoniae infections worldwide.IMPORTANCEThe emergence of resistant bacteria is a serious global health problem. In the absence of effective treatments, phages are a personalized and effective therapeutic alternative. However, little is still known about phage-host interactions, which are key to implementing effective strategies. Here, we focus on the study of Klebsiella pneumoniae, a highly pathogenic encapsulated bacterium. The complexity and variability of the capsule, where in most cases phage receptors are found, make it difficult for phage-based treatments. Here, we isolated a large collection of Klebsiella phages against all the reference strains and in a cohort of clinical isolates. Our results suggest that clinical isolates represent a challenge, especially high-risk clones. Thus, we propose targeted phage hunting as an effective strategy to implement phage-derived therapies. Our results are a step forward for new phage-based strategies to control K. pneumoniae infections, highlighting the importance of understanding phage-host interactions to design personalized treatments against Klebsiella spp.
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Affiliation(s)
- Celia Ferriol-González
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Robby Concha-Eloko
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Mireia Bernabéu-Gimeno
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Felipe Fernández-Cuenca
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen Macarena-CSIC-Universidad de Sevilla, Sevilla, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier E Cañada-García
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia García-Cobos
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Sanjuán
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
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14
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Li L, Miao W, Li Z, Huang L, Hau E, Khan MF, Liu Q, Zeng Q, Cui K. Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods. Genes (Basel) 2024; 15:1081. [PMID: 39202441 PMCID: PMC11353964 DOI: 10.3390/genes15081081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/06/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Milking methods have significant impacts on the microbiological composition, which could affect the quality of raw buffalo milk. Hence, the current study was conducted on the impact of milking methods on microorganisms in buffalo tank raw milk from 15 farms in Guangxi, China. The farms were divided into two groups based on the milking method: mechanical milking (MM, n = 6) and hand milking (HM, n = 9). Somatic cell counts, bacterial cell counts and nutrients of the raw buffalo milk samples were analyzed. The comparison of raw buffalo milk samples was analyzed using metagenomic sequencing to detect any differences between the two groups. There was no significant difference in the basic nutritional compositions and somatic cell count of raw buffalo milk between the two milking methods. However, the HM samples had significantly higher bacterial counts and diversity compared to the MM samples. The results showed that Staphylococcus spp., Klebsiella spp., Streptococcus spp., and Pseudomonas spp. were the major microbes present in canned raw buffalo milk. However, the differences between the two milking methods were the relative abundance of core microorganisms and their potential mastitis-causing genera, including the content of antibiotic-resistance genes and virulence genes. Our study revealed that Staphylococcus spp. and Streptococcus spp. were significantly more abundant in the MM group, while Klebsiella spp. was more abundant in the HM group. Regardless of the milking method used, Pseudomonas spp. was identified as the primary genus contributing to antibiotic resistance and virulence genes in canned raw buffalo milk. These findings affirm that there are differences in the microbial and genomic levels in canned raw milk. To prove the functional roles of the discovered genes and how these genes affect milk quality, further research and experimental validation are necessary.
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Affiliation(s)
- Ling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (L.L.); (W.M.); (Z.L.); (Q.L.)
- Guangxi Zhuang Autonomous Region Buffalo Milk Quality and Safety Control Technology Engineering Research Center, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China; (L.H.); (E.H.)
| | - Wenhao Miao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (L.L.); (W.M.); (Z.L.); (Q.L.)
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (L.L.); (W.M.); (Z.L.); (Q.L.)
- Guangxi Zhuang Autonomous Region Buffalo Milk Quality and Safety Control Technology Engineering Research Center, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China; (L.H.); (E.H.)
| | - Li Huang
- Guangxi Zhuang Autonomous Region Buffalo Milk Quality and Safety Control Technology Engineering Research Center, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China; (L.H.); (E.H.)
| | - Enghuan Hau
- Guangxi Zhuang Autonomous Region Buffalo Milk Quality and Safety Control Technology Engineering Research Center, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China; (L.H.); (E.H.)
| | | | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (L.L.); (W.M.); (Z.L.); (Q.L.)
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Qingkun Zeng
- Guangxi Zhuang Autonomous Region Buffalo Milk Quality and Safety Control Technology Engineering Research Center, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China; (L.H.); (E.H.)
| | - Kuiqing Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China; (L.L.); (W.M.); (Z.L.); (Q.L.)
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
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15
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NAKAJIMA K, KASUYA K, SENBA H, TAGAMI K, KINOSHITA Y, NIWA H. Genetic analysis based on next generation sequencing of Streptococcus equi subsp. equi isolated from horses imported into Japan. J Vet Med Sci 2024; 86:828-832. [PMID: 38897953 PMCID: PMC11300130 DOI: 10.1292/jvms.23-0342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 05/09/2024] [Indexed: 06/21/2024] Open
Abstract
Strangles is a globally widespread, commonly diagnosed and important infectious disease of equids caused by Streptococcus equi subsp. equi. We performed whole genome sequencing of 19 S. equi isolates collected from imported horses at the Japanese border. Of these isolates, 15 isolates were obtained from clinical cases and 4 were from subclinical cases. The 19 isolates were grouped into 3 Bayesian analysis of population structure (BAPS) groups by the core genome single nucleotide polymorphism analysis corresponding to exporting country, SeM typing, or exporter of the horses. The 19 isolates possessed same pathogenic genes regardless of clinical status in imported horses and no antimicrobial resistance genes. The disease status of the horses may rather reflect the prior exposure of animals with sub-clinical infection to S. equi.
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Affiliation(s)
- Kei NAKAJIMA
- Moji Branch Shinmoji Quarantine Facility, Animal Quarantine
Service, MAFF, Fukuoka, Japan
| | - Kazufumi KASUYA
- Microbiological Examination Division, Laboratory Department,
Animal Quarantine Service, MAFF, Kanagawa, Japan
| | - Hironobu SENBA
- Pathological and Physiochemical Examination Division,
Laboratory Department, Animal Quarantine Service, MAFF, Kanagawa, Japan
| | - Katsunori TAGAMI
- Moji Branch Shinmoji Quarantine Facility, Animal Quarantine
Service, MAFF, Fukuoka, Japan
| | - Yuta KINOSHITA
- Microbiology Division, Equine Research Institute, Japan
Racing Association, Tochigi, Japan
| | - Hidekazu NIWA
- Microbiology Division, Equine Research Institute, Japan
Racing Association, Tochigi, Japan
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16
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Huang B, Ge L, Xiang D, Tan G, Liu L, Yang L, Jing Y, Liu Q, Chen W, Li Y, He H, Sun H, Pan Q, Yi K. Isolation, characterization, and genomic analysis of a lytic bacteriophage, PQ43W, with the potential of controlling bacterial wilt. Front Microbiol 2024; 15:1396213. [PMID: 39149212 PMCID: PMC11324598 DOI: 10.3389/fmicb.2024.1396213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/17/2024] [Indexed: 08/17/2024] Open
Abstract
Bacterial wilt (BW) is a devastating plant disease caused by the soil-borne bacterium Ralstonia solanacearum species complex (Rssc). Numerous efforts have been exerted to control BW, but effective, economical, and environmentally friendly approaches are still not available. Bacteriophages are a promising resource for the control of bacterial diseases, including BW. So, in this study, a crop BW pathogen of lytic bacteriophage was isolated and named PQ43W. Biological characterization revealed PQ43W had a short latent period of 15 min, 74 PFU/cell of brust sizes, and good stability at a wide range temperatures and pH but a weak resistance against UV radiation. Sequencing revealed phage PQ43W contained a circular double-stranded DNA genome of 47,156 bp with 65 predicted open reading frames (ORFs) and genome annotation showed good environmental security for the PQ43W that no tRNA, antibiotic resistance, or virulence genes contained. Taxonomic classification showed PQ43W belongs to a novel genus of subfamily Kantovirinae under Caudoviricetes. Subsequently, a dose of PQ43W for phage therapy in controlling crop BW was determined: 108 PFU*20 mL per plant with non-invasive irrigation root application twice by pot experiment. Finally, a field experiment of PQ43W showed a significantly better control effect in crop BW than the conventional bactericide Zhongshengmycin. Therefore, bacteriophage PQ43W is an effective bio-control resource for controlling BW diseases, especially for crop cultivation.
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Affiliation(s)
- Binbin Huang
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, China
| | - Long Ge
- Qingdao NABT PhagePharm Co., Ltd., Qingdao, China
| | - Dong Xiang
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Ge Tan
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Lijia Liu
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Lei Yang
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Yongfeng Jing
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Qingshu Liu
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, China
| | - Wu Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Ye Li
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, China
| | - Haoxin He
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Huzhi Sun
- Qingdao NABT PhagePharm Co., Ltd., Qingdao, China
| | - Qiang Pan
- Qingdao NABT PhagePharm Co., Ltd., Qingdao, China
- Institute of Special Food, Qingdao Agricultural University, Qingdao, China
| | - Ke Yi
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
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17
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Kumari K, Aggarwal Y, Singh RP. Molecular characterization and in-depth genomic analysis to unravel the pathogenic features of an environmental isolate Enterobacter sp. S-33. Int Microbiol 2024; 27:1095-1110. [PMID: 38044418 DOI: 10.1007/s10123-023-00461-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/05/2023]
Abstract
Enterobacter species represent widely distributed opportunistic pathogens, commonly associated with plants and humans. In the present study, we performed a detailed molecular characterization as well as genomic study of a type VI secretion system (T6SS) bacterium belonging to member of the family Enterobacteriaceae and named Enterobacter sp. S-33. The comparative sequence analysis of the 16S rRNA gene showed that the strain was closely related to other Enterobacter species. The complete genome of the strain with a genome size of 4.6 Mbp and GC-content of 55.63% was obtained through high-quality sequencing. The genomic analysis with online tools unravelled the various genes belonging to the bacterial secretion system, antibiotic resistance, virulence, efflux pumps, etc. The isolate showed the motility behavior that contributes to Enterobacter persistence in a stressed environment and further supports infections. PCR amplification and further sequencing confirmed the presence of drug-efflux genes acrA, acrB, and outer membrane genes, viz. OmpA, OmpC, and OmpF. The cell surface hydrophobicity and co-aggregation assay against different bacterial strains illustrated its putative pathogenic nature. Genome mining identified various biosynthetic gene clusters (BGCs) corresponding to non-ribosomal proteins (NRPS), siderophore, and arylpolyene production. Briefly, genome sequencing and detailed characterization of environmental Enterobacter isolate will assist in understanding the epidemiology of Enterobacter species, and the further prevention and treatment of infectious diseases caused by these broad-host range species.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Yogender Aggarwal
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
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18
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Asad M, Hassan A, Wang W, Alonazi WB, Khan MS, Ogunyemi SO, Ibrahim M, Bin L. An integrated in silico approach for the identification of novel potential drug target and chimeric vaccine against Neisseria meningitides strain 331401 serogroup X by subtractive genomics and reverse vaccinology. Comput Biol Med 2024; 178:108738. [PMID: 38870724 DOI: 10.1016/j.compbiomed.2024.108738] [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: 01/25/2024] [Revised: 05/15/2024] [Accepted: 06/08/2024] [Indexed: 06/15/2024]
Abstract
Neisseria meningitidis, commonly known as the meningococcus, leads to substantial illness and death among children and young adults globally, revealing as either epidemic or sporadic meningitis and/or septicemia. In this study, we have designed a novel peptide-based chimeric vaccine candidate against the N. meningitidis strain 331,401 serogroup X. Through rigorous analysis of subtractive genomics, two essential cytoplasmic proteins, namely UPI000012E8E0(UDP-3-O-acyl-GlcNAc deacetylase) and UPI0000ECF4A9(UDP-N-acetylglucosamine acyltransferase) emerged as potential drug targets. Additionally, using reverse vaccinology, the outer membrane protein UPI0001F4D537 (Membrane fusion protein MtrC) identified by subcellular localization and recognized for its known indispensable role in bacterial survival was identified as a novel chimeric vaccine target. Following a careful comparison of MHC-I, MHC-II, T-cell, and B-cell epitopes, three epitopes derived from UPI0001F4D537 were linked with three types of linkers-GGGS, EAAAK, and the essential PADRE-for vaccine construction. This resulted in eight distinct vaccine models (V1-V8). Among them V1 model was selected as the final vaccine construct. It exhibits exceptional immunogenicity, safety, and enhanced antigenicity, with 97.7 % of its residues in the Ramachandran plot's most favored region. Subsequently, the vaccine structure was docked with the TLR4/MD2 complex and six different HLA allele receptors using the HADDOCK server. The docking resulted in the lowest HADDOCK score of 39.3 ± 9.0 for TLR/MD2. Immune stimulation showed a strong immune response, including antibodies creation and the activation of B-cells, T Cytotoxic cells, T Helper cells, Natural Killer cells, and interleukins. Furthermore, the vaccine construct was successfully expressed in the Escherichia coli system by reverse transcription, optimization, and ligation in the pET-28a (+) vector for the expression study. The current study proposes V1 construct has the potential to elicit both cellular and humoral responses, crucial for the developing an epitope-based vaccine against N. meningitidis strain 331,401 serogroup X.
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Affiliation(s)
- Muhammad Asad
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Ahmad Hassan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Weiyu Wang
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Wadi B Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh, Saudi Arabia
| | | | - Solabomi Olaitan Ogunyemi
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Muhammad Ibrahim
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan.
| | - Li Bin
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
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19
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Sukumar S, Rahmanyar Z, El Jurf HQ, Akil WS, Hussain J, Martin FE, Ekanayake K, Martinez E. Mapping the oral resistome: a systematic review. J Med Microbiol 2024; 73:001866. [PMID: 39133536 PMCID: PMC11318793 DOI: 10.1099/jmm.0.001866] [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: 02/22/2024] [Accepted: 07/17/2024] [Indexed: 08/13/2024] Open
Abstract
Studying individual ecological niches within the oral cavity is a logical first step to understanding the distribution of antimicrobial resistance genes (ARGs); however, it is not representative of the whole oral resistome. The aim of our systematic review was to provide a map of the oral resistome by reviewing the composition of individual niches. A total of 580 papers were retrieved from a search of all English language publications investigating the presence of oral ARGs in five electronic databases between January 2015 and August 2023. Fifteen studies [10 PCR and 5 next-generation sequencing (NGS)] were included in this review. The heterogeneity of methods precluded meta-analysis. ARGs are present throughout the oral cavity with 158 unique ARGs identified across 6 locations - supra and sub-gingival biofilm, mucosa, oropharynx, root canal system (RCS) and saliva. The supragingival biofilm had the highest resistome richness, while the RCS had the least. Tetracycline was the dominant antimicrobial resistance (AMR) class found. Three core genes were identified - tet(M), tet(O) and ermB.This review highlights the necessity of NGS studies to comprehensively characterize the oral resistome in its entirety. This is the logical foundation for future 'omics studies to truly understand the scope of the resistome and its contribution to AMR.
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Affiliation(s)
- Smitha Sukumar
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2000, Australia
| | - Zalmay Rahmanyar
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2000, Australia
| | - Hagaar Q. El Jurf
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2000, Australia
| | - William S. Akil
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2000, Australia
| | - Jafar Hussain
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2000, Australia
| | - F. Elizabeth Martin
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2000, Australia
| | - Kanchana Ekanayake
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2000, Australia
| | - Elena Martinez
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2000, Australia
- Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, 2145, Australia
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20
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Abdelhamed H, Mannan SB, Riman MM, Tekedar HC, Lawrence ML. Comparative analysis of three plasmids from Plesiomonas shigelloides strain MS-17-188 and their role in antimicrobial resistance. JAC Antimicrob Resist 2024; 6:dlae109. [PMID: 39035015 PMCID: PMC11258559 DOI: 10.1093/jacamr/dlae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
Background Plesiomonas shigelloides strain MS-17-188 was isolated from a deceased catfish from East Mississippi and showed resistance to florfenicol, tetracyclines and a sulphonamide. WGS of strain MS-17-188 revealed three plasmids (pPSMS-171881, pPSMS-171882 and pPSMS-171883). Objectives To accurately determine the impact of three plasmids found in P. shigelloides strain MS-17-188 on the dissemination of antibiotic resistance genes and to provide insights into the molecular structure of these plasmids. Methods The genetic features of these plasmids in terms of genes associated with antimicrobial resistance (AMR), virulence, transfer, maintenance and replication were identified using bioinformatic tools. Additionally, we investigated the in vitro mobilization and stability of plasmid-mediated resistance. The Comprehensive Antibiotic Resistance Database and Virulence Factors Database were used to detect the AMR genes and virulence genes of P. shigelloides plasmids. Moreover, plasmid mobility was evaluated by a filter-mating assay using strain MS-17-188 as a donor and azide-resistant Escherichia coli J53 as a recipient strain. A stability experiment was conducted to explore the persistence of plasmid-mediated antibiotic resistance in strain MS-17-188 in the absence and presence of selection. Results pPSMS-171881 harboured multidrug efflux complex (adeF) and two genes responsible for arsenic resistance (arsB and arsC). pPSMS-171882 had a region of 7085 bp encoding type IV secretion system proteins. pPSMS-171883 carried the tetracycline resistance genes tet(A) and tet(R), and a phenicol resistance gene (floR), which were flanked by two transposable elements and mobilization proteins, suggesting that there is a conjugative mechanism by which this plasmid can be mobilized. Results from the stability experiment indicated that pPSMS-171883 is lost over time in the absence of selective pressure. Moreover, pPSMS-171883 is more stable in P. shigelloides at growth temperatures of 30°C and 37°C compared with 40°C and 43°C. After intraperitoneal injection in catfish, P. shigelloides strain MS-17-188 resulted in no mortalities. Conclusions This is the first study to report plasmid-mediated AMR in Plesiomonas isolated from cultured fish, which needs continued monitoring. This study will provide an understanding of the genetic mechanisms of AMR and virulence of P. shigelloides.
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Affiliation(s)
- Hossam Abdelhamed
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Shahnewaj Bin Mannan
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Munshi Mustafiz Riman
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Hasan C Tekedar
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Mark L Lawrence
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
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21
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Chanchaithong P, Chueahiran S, Pinpimai K, Sroithongkham P, Leelapsawas C, Indra R, Yindee J, Chuanchuen R. Chromosomal and plasmid localization of ileS2 in high-level mupirocin-resistant Staphylococcus pseudintermedius and Staphylococcus aureus isolated from canine and feline origins. J Antimicrob Chemother 2024; 79:1856-1864. [PMID: 38863334 DOI: 10.1093/jac/dkae172] [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: 12/05/2023] [Accepted: 05/11/2024] [Indexed: 06/13/2024] Open
Abstract
OBJECTIVES To characterize the mobile genetic elements and genetic localization of ileS2 in high-level mupirocin-resistant (Hi-MupR) methicillin-resistant Staphylococcus pseudintermedius (MRSP) and MRSA isolates recovered from canine and feline clinical samples. METHODS The identification of bacterial species and presence of mecA and ileS2 genes in MRSP and MRSA isolates were performed using MALDI-TOF MS and PCR, respectively. Antimicrobial resistance (AMR) phenotypes were determined by broth microdilution assays. The genome characteristics, ileS2-containing elements and staphylococcal cassette chromosome mec (SCCmec) were illustrated using complete circular genomes obtained from hybrid assembly of Illumina short-reads and Oxford Nanopore Technologies long-reads. These were analysed through phylogenetic and bioinformatics approaches. RESULTS A total of 18 MRSP clinical isolates and four MRSA clinical isolates exhibited the Hi-MupR phenotype and carried multiple AMR genes, including mecA and ileS2 genes. MRSP ST182-SCCmec V (n = 6) and ST282-ΨSCCmec57395-t10 (n = 4) contained the ileS2 transposable unit associated with IS257 on the chromosome. Three MRSA ST398-SCCmec V-t034/t4652 isolates carried ∼42 kb pSK41-like ileS2 plasmids, whereas similar ileS2 plasmids lacking tra genes were found in MRSP ST282-ΨSCCmec57395-t72/t21 isolates. Furthermore, a new group of ileS2 plasmids, carried by MRSP ST45-ΨSCCmec57395, ST433-ΨSCCmecKW21-t05 and ST2165-SCCmec IV-t06, and by one MRSA ST398-SCCmec V-t034 strain, shared the plasmid backbone with the cfr/fexA-carrying plasmid pM084526_1 in MRSA ST398. CONCLUSIONS This study provides the first evidence of ileS2 integration into the S. pseudintermedius chromosome, which is a rare occurrence in staphylococcal species, and plasmids played a pivotal role in dissemination of ileS2 in both staphylococcal species.
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Affiliation(s)
- 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
| | - Surawit Chueahiran
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Komkiew Pinpimai
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Parinya Sroithongkham
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chavin Leelapsawas
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Rusmin Indra
- 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
| | - Rungtip Chuanchuen
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
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Naidoo Y, Pierneef RE, Cowan DA, Valverde A. Characterization of the soil resistome and mobilome in Namib Desert soils. Int Microbiol 2024; 27:967-975. [PMID: 37968548 PMCID: PMC11300574 DOI: 10.1007/s10123-023-00454-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: 08/16/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.
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Affiliation(s)
- Yashini Naidoo
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria, 0110, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Angel Valverde
- IRNASA-CSIC, Cordel de Merinas, 37008, Salamanca, Spain.
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Corrigan A, McCooey P, Taylor-Pickard J, Stockdale S, Murphy R. Breaking the Cycle: A Yeast Mannan-Rich Fraction Beneficially Modulates Egg Quality and the Antimicrobial Resistome Associated with Layer Hen Caecal Microbiomes under Commercial Conditions. Microorganisms 2024; 12:1562. [PMID: 39203404 PMCID: PMC11356413 DOI: 10.3390/microorganisms12081562] [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: 07/16/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024] Open
Abstract
Antibiotics and antibiotic growth promoters have been extensively employed in poultry farming to enhance growth performance, maintain bird health, improve nutrient uptake efficiency, and mitigate enteric diseases at both sub-therapeutic and therapeutic doses. However, the extensive use of antimicrobials in poultry farming has led to the emergence of antimicrobial resistance (AMR) in microbial reservoirs, representing a significant global public health concern. In response, non-antibiotic dietary interventions, such as yeast mannan-rich fraction (MRF), have emerged as a promising alternative to modulate the gut microbiota and combat the AMR crisis. This study investigated whether a yeast mannan-rich fraction containing feed supplement impacted the performance of laying hens, their microbiomes, and the associated carriage of antimicrobial resistance genes under commercial conditions. High-throughput DNA sequencing was utilised to profile the bacterial community and assess changes in the antibiotic resistance genomes detected in the metagenome, the "resistome", in response to MRF supplementation. It was found that supplementation favourably influenced laying hen performance and microbial composition. Notably, there was a compositional shift in the MRF supplemented group associated with a lower relative abundance of pathobionts, e.g., Escherichia, Brachyspira and Trueperella, and their AMR-encoded genes, relative to beneficial microbes. Overall, the findings further demonstrate the ability of prebiotics to improve laying hen performance through changes associated with their microbiome and resistome.
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Affiliation(s)
- Aoife Corrigan
- Alltech Bioscience Centre, A86 X006 Dunboyne, Co. Meath, Ireland; (P.M.); (R.M.)
| | - Paula McCooey
- Alltech Bioscience Centre, A86 X006 Dunboyne, Co. Meath, Ireland; (P.M.); (R.M.)
| | | | - Stephen Stockdale
- Novogene (UK) Company Ltd., 25 Cambridge Science Park, Cambridge CB4 0FW, UK;
- BioFigR, Ballyvoloon, P24 N524 Cobh, Cork, Ireland
| | - Richard Murphy
- Alltech Bioscience Centre, A86 X006 Dunboyne, Co. Meath, Ireland; (P.M.); (R.M.)
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24
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Judd M, Wira J, Place AR, Bachvaroff T. Long-Read Sequencing Unlocks New Insights into the Amphidinium carterae Microbiome. Mar Drugs 2024; 22:342. [PMID: 39195458 DOI: 10.3390/md22080342] [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: 06/21/2024] [Revised: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
Dinoflagellates are one of the largest groups of marine microalgae and exhibit diverse trophic strategies. Some dinoflagellates can produce secondary metabolites that are known to be toxic, which can lead to ecologically harmful blooms. Amphidinium carterae is one species of dinoflagellate that produces toxic compounds and is used as a model for dinoflagellate studies. The impact of the microbiome on A. carterae growth and metabolite synthesis is not yet fully understood, nor is the impact of bacterial data on sequencing and assembly. An antibiotic cocktail was previously shown to eliminate 16S amplification from the dinoflagellate culture. Even with drastically reduced bacterial numbers during antibiotic treatment, bacterial sequences were still present. In this experiment, we used novel Nanopore long-read sequencing techniques on A. carterae cultures to assemble 15 full bacterial genomes ranging from 2.9 to 6.0 Mb and found that the use of antibiotics decreased the percentage of reads mapping back to bacteria. We also identified shifts in the microbiome composition and identified a potentially deleterious bacterial species arising in the absence of the antibiotic treatment. Multiple antibiotic resistance genes were identified, as well as evidence that the bacterial population does not contribute to toxic secondary metabolite synthesis.
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Affiliation(s)
- Miranda Judd
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Jens Wira
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Allen R Place
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Tsvetan Bachvaroff
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
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25
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Mudhluli TE, Kujawska M, Mueller J, Felsl A, Truppel BA, Hall LJ, Chitsike I, Gomo E, Zhou DT. Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort. BMC Genomics 2024; 25:718. [PMID: 39054474 PMCID: PMC11271062 DOI: 10.1186/s12864-024-10618-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024] Open
Abstract
INTRODUCTION Our understanding of particular gut microbiota members such as Bifidobacterium and Enterococcus in low-middle-income countries remains very limited, particularly early life strain-level beneficial traits. This study addresses this gap by exploring a collection of bacterial strains isolated from the gut of Zimbabwean infants; comparing their genomic characteristics with strains isolated from infants across North America, Europe, and other regions of Africa. MATERIALS AND METHOD From 110 infant stool samples collected in Harare, Zimbabwe, 20 randomly selected samples were used to isolate dominant early-life gut microbiota members Bifidobacterium and Enterococcus. Isolated strains were subjected to whole genome sequencing and bioinformatics analysis including functional annotation of carbohydrates, human milk oligosaccharide (HMO) and protein degradation genes and clusters, and the presence of antibiotic resistance genes (ARGs). RESULTS The study observed some location-based clustering within the main five identified taxonomic groups. Furthermore, there were varying and overall species-specific numbers of genes belonging to different GH families encoded within the analysed dataset. Additionally, distinct strain- and species-specific variances were identified in the potential of Bifidobacterium for metabolizing HMOs. Analysis of putative protease activity indicated a consistent presence of gamma-glutamyl hydrolases in Bifidobacterium, while Enterococcus genomes exhibited a high abundance of aspartyl peptidases. Both genera harboured resistance genes against multiple classes of antimicrobial drugs, with Enterococcus genomes containing a higher number of ARGs compared to Bifidobacterium, on average. CONCLUSION This study identified promising probiotic strains within Zimbabwean isolates, offering the potential for early-life diet and microbial therapies. However, the presence of antibiotic resistance genes in infant-associated microbes raises concerns for infection risk and next-stage probiotic development. Further investigation in larger cohorts, particularly in regions with limited existing data on antibiotic and probiotic use, is crucial to validate these initial insights. IMPACT STATEMENT This research represents the first investigation of its kind in the Zimbabwean context, focusing on potential probiotic strains within the early-life gut microbiota. By identifying local probiotic strains, this research can contribute to the development of probiotic interventions that are tailored to the Zimbabwean population, which can help address local health challenges and promote better health outcomes for infants. Another essential aspect of the study is the investigation of antimicrobial resistance genes present in Zimbabwean bacterial strains. Antimicrobial resistance is a significant global health concern, and understanding the prevalence and distribution of resistance genes in different regions can help inform public health policies and interventions.
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Affiliation(s)
- Taona Emmah Mudhluli
- Faculty of Medicine and Health Sciences, Department of Laboratory Diagnostic and Investigative Sciences, Medical Laboratory Sciences Unit, University of Zimbabwe, Box A 178, Avondale, Harare, Zimbabwe.
- Faculty of Medicine and Health Science, Department of Biochemistry, Midlands State University, P. Bag 9055, Senga Road, Gweru, Zimbabwe.
| | - Magdalena Kujawska
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Julia Mueller
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Angela Felsl
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Bastian-Alexander Truppel
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
- BioSciences Building, APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Lindsay J Hall
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
- Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 42TT, UK
| | - Inam Chitsike
- Faculty of Medicine and Health Sciences, Department of Family Health, Paediatrics Unit, University of Zimbabwe, Box A 178, Avondale, Harare, Zimbabwe
| | - Exnevia Gomo
- Faculty of Medicine and Health Sciences, Department of Laboratory Diagnostic and Investigative Sciences, Medical Laboratory Sciences Unit, University of Zimbabwe, Box A 178, Avondale, Harare, Zimbabwe
| | - Danai Tavonga Zhou
- Faculty of Medicine and Health Sciences, Department of Laboratory Diagnostic and Investigative Sciences, Medical Laboratory Sciences Unit, University of Zimbabwe, Box A 178, Avondale, Harare, Zimbabwe
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26
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Ye L, Zhang L, Li X, Huang Y, Zhang B, Yang X, Tan W, Li X, Zhang X. De novo genome assembly and functional insights of the first commercial pink Auricularia cornea. Genomics 2024; 116:110902. [PMID: 39053612 DOI: 10.1016/j.ygeno.2024.110902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/08/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
A pioneering pink cultivar of Auricularia cornea, first commercially cultivated in 2022, lacks genomic data, hindering research in genetic breeding, gene discovery, and product development. Here, we report the de novo assembly of the pink A. cornea Fen-A1 genome and provide a detailed functional annotation. The genome is 73.17 Mb in size, contains 86 scaffolds (N50 ∼ 5.49 Mb), 59.09% GC content and encodes 19,120 predicted genes with a BUSCO completeness of 92.60%. Comparative genomic analysis reveals the phylogenetic relatedness of Fen-A1 and remarkable gene family dynamics. Putative genes were found mapped to 3 antibiotic-related, 36 light-dependent and 25 terpene metabolites. In addition, 789 CAZymes genes were classified, revealing the dynamics of quality loss due to postharvest refrigeration. Overall, our work is the first report on a pink A. cornea genome and provides a comprehensive insight into its complex functions.
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Affiliation(s)
- Lei Ye
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Lingzi Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Huang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China; Luzhou Laojiao Co., Ltd, Luzhou 646000, China
| | - Bo Zhang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Xuezhen Yang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Wei Tan
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Xiaolin Li
- Sichuan Institute of Edible Fungi, Chengdu 610066, China; Luzhou Laojiao Co., Ltd, Luzhou 646000, China.
| | - Xiaoping Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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27
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Xiang Y, Zhu K, Min K, Zhang Y, Liu J, Liu K, Han Y, Li X, Du X, Wang X, Huang Y, Li X, Peng Y, Yang C, Liu H, Liu H, Li X, Wang H, Wang C, Wang Q, Jia H, Yang M, Wang L, Wu Y, Cui Y, Chen F, Yang H, Baker S, Xu X, Yang J, Song H, Qiu S. Characterization of a Salmonella enterica serovar Typhimurium lineage with rough colony morphology and multidrug resistance. Nat Commun 2024; 15:6123. [PMID: 39033143 PMCID: PMC11271444 DOI: 10.1038/s41467-024-50331-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of salmonellosis, and the emergence of multidrug-resistant pathovariants has become a growing concern. Here, we investigate a distinct rough colony variant exhibiting a strong biofilm-forming ability isolated in China. Whole-genome sequencing on 2,212 Chinese isolates and 1,739 publicly available genomes reveals the population structure and evolutionary history of the rough colony variants. Characterized by macro, red, dry, and rough (mrdar) colonies, these variants demonstrate enhanced biofilm formation at 28 °C and 37 °C compared to typical rdar colonies. The mrdar variants exhibit extensive multidrug resistance, with significantly higher resistance to at least five classes of antimicrobial agents compared to non-mrdar variants. This resistance is primarily conferred by an IncHI2 plasmid harboring 19 antimicrobial resistance genes. Phylogenomic analysis divides the global collections into six lineages. The majority of mrdar variants belong to sublineage L6.5, which originated from Chinese smooth colony strains and possibly emerged circa 1977. Among the mrdar variants, upregulation of the csgDEFG operons is observed, probably due to a distinct point mutation (-44G > T) in the csgD gene promoter. Pangenome and genome-wide association analyses identify 87 specific accessory genes and 72 distinct single nucleotide polymorphisms associated with the mrdar morphotype.
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Affiliation(s)
- Ying Xiang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Kunpeng Zhu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
- Kaifeng Center for Disease Control and Prevention, Kaifeng, China
| | - Kaiyuan Min
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yaowen Zhang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
- Daxing Center for Disease Control and Prevention, Beijing, China
| | - Jiangfeng Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Kangkang Liu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Yiran Han
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xinge Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xinying Du
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xin Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Ying Huang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xinping Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Yuqian Peng
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Chaojie Yang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Hongbo Liu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Hongbo Liu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xiaoying Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Hui Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Chao Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Qi Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Huiqun Jia
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Mingjuan Yang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Ligui Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China.
| | - Juntao Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.
| | - Hongbin Song
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China.
| | - Shaofu Qiu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China.
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Trinh P, Teichman S, Roberts MC, Rabinowitz PM, Willis AD. A cross-sectional comparison of gut metagenomes between dairy workers and community controls. BMC Genomics 2024; 25:708. [PMID: 39033279 DOI: 10.1186/s12864-024-10562-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases. RESULTS Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). CONCLUSIONS This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.
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Affiliation(s)
- Pauline Trinh
- Department of Biostatistics, University of Washington, Seattle, USA
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Sarah Teichman
- Department of Statistics, University of Washington, Seattle, USA
| | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Peter M Rabinowitz
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, USA.
- Department of Statistics, University of Washington, Seattle, USA.
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da Silva Santos D, Freitas NSA, de Morais MA, Mendonça AA. Liquorilactobacillus: A Context of the Evolutionary History and Metabolic Adaptation of a Bacterial Genus from Fermentation Liquid Environments. J Mol Evol 2024:10.1007/s00239-024-10189-6. [PMID: 39017924 DOI: 10.1007/s00239-024-10189-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024]
Abstract
In the present work, we carried out a comparative genomic analysis to trace the evolutionary trajectory of the bacterial species that make up the Liquorilactobacillus genus, from the identification of genes and speciation/adaptation mechanisms in their unique characteristics to the identification of the pattern grouping these species. We present phylogenetic relationships between Liquorilactobacillus and related taxa such as Bacillus, basal lactobacilli and Ligilactobacillus, highlighting evolutionary divergences and lifestyle transitions across different taxa. The species of this genus share a core genome of 1023 genes, distributed in all COGs, which made it possible to characterize it as Liquorilactobacillus sensu lato: few amino acid auxotrophy, low genes number for resistance to antibiotics and general and specific cellular reprogramming mechanisms for environmental responses. These species were divided into four clades, with diversity being enhanced mainly by the diversity of genes involved in sugar metabolism. Clade 1 presented lower (< 70%) average amino acid identity with the other clades, with exclusive or absent genes, and greater distance in the genome compared to clades 2, 3 and 4. The data pointed to an ancestor of clades 2, 3 and 4 as being the origin of the genus Ligilactobacillus, while the species of clade 1 being closer to the ancestral Bacillus. All these traits indicated that the species of clade 1 could be soon separated in a distinct genus.
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Affiliation(s)
- Dayane da Silva Santos
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | | | - Marcos Antonio de Morais
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil.
| | - Allyson Andrade Mendonça
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil.
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Zhang J, Xu J, Shen S, Ding L, Yang W, Tang C, Shi Q, Zhao H, Guo Y, Han R, Hu F. Comparison of three colloidal gold immunoassays and GeneXpert Carba-R for the detection of Klebsiella pneumoniae blaKPC-2 variants. J Clin Microbiol 2024; 62:e0015424. [PMID: 38809033 PMCID: PMC11250111 DOI: 10.1128/jcm.00154-24] [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: 01/29/2024] [Accepted: 05/05/2024] [Indexed: 05/30/2024] Open
Abstract
The increasing use of ceftazidime-avibactam has led to the emergence of a wide range of ceftazidime-avibactam-resistant blaKPC-2 variants. Particularly, the conventional carbapenemase phenotypic assay exhibited a high false-negative rate for KPC-2 variants. In this study, three colloidal gold immunoassays, including the Gold Mountainriver CGI test, Dynamiker CGI test and NG-Test CARBA5, and GeneXpert Carba-R, were used to detect the presence of KPC-2 carbapenemase and its various variants in 42 Klebsiella pneumoniae strains. These strains covered blaKPC-2 (13/42) and 16 other blaKPC-2 variants including blaKPC-12 (1/42), blaKPC-23 (1/42), blaKPC-25 (1/42), blaKPC-33 (6/42), blaKPC-35 (1/42), blaKPC-44 (1/42), blaKPC-71 (1/42), blaKPC-76 (8/42), blaKPC-78 (1/42), blaKPC-79 (1/42), blaKPC-100 (1/42), blaKPC-127 (1/42), blaKPC-128 (1/42), blaKPC-144 (1/42), blaKPC-157 (2/42), and blaKPC-180 (1/42). For KPC-2 strains, all four assays showed 100% negative percentage agreement (NPA) and 100% positive percentage agreement (PPA) with sequencing results. For all 16 KPC-2 variants, GeneXpert Carba-R showed 100% NPA and 100% PPA, and the three colloidal gold immunoassays showed 100% NPA, while the PPAs of the Gold Mountainriver CGI test, Dynamiker CGI test, and NG-Test CARBA5 were 87.5%, 87.5%, and 68.8%, respectively. We also found a correlation between the mutation site in the amino acid of the variants and false-negative results by colloidal gold immunoassays. In conclusion, the GeneXpert Carba-R has been proven to be a reliable method in detecting KPC-2 and its variants, and the colloidal gold immunoassay tests offer a practical and cost-effective approach for their detection. For the sample with a negative result by a colloidal gold immunoassay test but not matching the drug-resistant phenotype, it is recommended to retest using another type of kit or the GeneXpert Carba-R assay, which can significantly improve the accuracy of detection.
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Affiliation(s)
- Jinghao Zhang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
- Joint Laboratory of Hospital & Enterprise for Pathogen Diagnosis of Drug-resistant Bacterial Infections and Innovative Drug R & D, Shanghai, China
| | - Jieli Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
- Joint Laboratory of Hospital & Enterprise for Pathogen Diagnosis of Drug-resistant Bacterial Infections and Innovative Drug R & D, Shanghai, China
- Department of Laboratory Medicine, GuiPing People's Hospital, Guangxi, China
| | - Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
- Joint Laboratory of Hospital & Enterprise for Pathogen Diagnosis of Drug-resistant Bacterial Infections and Innovative Drug R & D, Shanghai, China
| | - Li Ding
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
- Joint Laboratory of Hospital & Enterprise for Pathogen Diagnosis of Drug-resistant Bacterial Infections and Innovative Drug R & D, Shanghai, China
| | - Weiwei Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
- Joint Laboratory of Hospital & Enterprise for Pathogen Diagnosis of Drug-resistant Bacterial Infections and Innovative Drug R & D, Shanghai, China
| | - Chengkang Tang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
- Joint Laboratory of Hospital & Enterprise for Pathogen Diagnosis of Drug-resistant Bacterial Infections and Innovative Drug R & D, Shanghai, China
| | - Qingyu Shi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
- Joint Laboratory of Hospital & Enterprise for Pathogen Diagnosis of Drug-resistant Bacterial Infections and Innovative Drug R & D, Shanghai, China
| | - Hu Zhao
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Yan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
- Joint Laboratory of Hospital & Enterprise for Pathogen Diagnosis of Drug-resistant Bacterial Infections and Innovative Drug R & D, Shanghai, China
| | - Renru Han
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
- Joint Laboratory of Hospital & Enterprise for Pathogen Diagnosis of Drug-resistant Bacterial Infections and Innovative Drug R & D, Shanghai, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
- Joint Laboratory of Hospital & Enterprise for Pathogen Diagnosis of Drug-resistant Bacterial Infections and Innovative Drug R & D, Shanghai, China
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Jin X, Zhang L, Cao Y, Dai Z, Ge X, Cai R, Wang R, Hu Z. Antibiotic resistance characterization, virulence factors and molecular characteristics of Bacillus species isolated from probiotic preparations in China. J Glob Antimicrob Resist 2024:S2213-7165(24)00124-3. [PMID: 38996868 DOI: 10.1016/j.jgar.2024.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 05/30/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
OBJECTIVES The aim of this study was to determine the phenotypic and molecular characteristics of antibiotic-resistant Bacillus spp. isolated from probiotic preparations in China. METHODS Bacillus strains were isolated from probiotic preparations and then identified using 16S rDNA sequencing. Drug sensitivity tests were conducted to determine their susceptibility to seven antibiotics. Whole genome sequencing was performed on the most resistant strains, followed by analysis of their molecular characteristics, resistance genes, and virulence factors. RESULTS In total, we isolated 21 suspected Bacillus species from seven compound probiotics, which were identified by 16S rDNA as 12 Bacillus licheniformis, six Bacillus subtilis and three Bacillus cereus. The determination of antimicrobial susceptibility showed widespread resistance to chloramphenicol (95.2%), erythromycin (85.7%) and gentamicin (42.9%). Whole genome sequencing of seven resistant strains revealed that J-6-A (Bacillus subtilis) and J-7-A (Bacillus cereus) contained a plasmid. The resistance gene analysis revealed that each strain contained more than ten resistance genes, among which J-7-A was the most. The streptomycin resistance gene strA was detected in all strains. The chloramphenicol resistance genes ykkC and ykkD were found in J-1-A to J-5-A and were first reported in Bacillus subtilis. The erythrocin resistance gene ermD was detected in strains J-1-A to J-4-A. There were also more than 15 virulence factors and gene islands (GIs) involved in each strain. CONCLUSIONS These results confirm the potential safety risks of probiotics and remind us to carefully select probiotic preparations containing strains of Bacillus species, especially Bacillus cereus, to avoid the potential spread of resistance and pathogenicity.
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Affiliation(s)
- Xin Jin
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China.
| | - Ling Zhang
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Yu Cao
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Zhen Dai
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Xiaoming Ge
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Rui Cai
- Jiangsu Province Hospital of Chinese Medicine, Jiangsu, Nanjing, China
| | - Ruirong Wang
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
| | - Ziyan Hu
- Nanjing Institute for Food and Drug Control, Jiangsu, Nanjing, China
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Lyytinen OL, Dapuliga C, Wallinger D, Patpatia S, Audu BJ, Kiljunen SJ. Three novel Enterobacter cloacae bacteriophages for therapeutic use from Ghanaian natural waters. Arch Virol 2024; 169:156. [PMID: 38967872 PMCID: PMC11226500 DOI: 10.1007/s00705-024-06081-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 05/15/2024] [Indexed: 07/06/2024]
Abstract
Infections caused by multidrug-resistant (MDR) bacteria are a growing global concern. Enterobacter cloacae complex (ECC) species are particularly adept at developing antibiotic resistance. Phage therapy is proposed as an alternative treatment for pathogens that no longer respond to antibiotics. Unfortunately, ECC phages are understudied when compared to phages of many other bacterial species. In this Ghanaian-Finnish study, we isolated two ECC strains from ready-to-eat food samples and three novel phages from natural waters against these strains. We sequenced the genomic DNA of the novel Enterobacter phages, fGh-Ecl01, fGh-Ecl02, and fGh-Ecl04, and assessed their therapeutic potential. All of the phages were found to be lytic, easy to propagate, and lacking any toxic, integrase, or antibiotic resistance genes and were thus considered suitable for therapy purposes. They all were found to be related to T4-type viruses: fGh-Ecl01 and fGh-Ecl04 to karamviruses and fGh-Ecl02 to agtreviruses. Testing of Finnish clinical ECC strains showed promising susceptibility to these novel phages. As many as 61.1% of the strains were susceptible to fGh-Ecl01 and fGh-Ecl04, and 7.4% were susceptible to fGh-Ecl02. Finally, we investigated the susceptibility of the newly isolated ECC strains to three antibiotics - meropenem, ciprofloxacin, and cefepime - in combination with the novel phages. The use of phages and antibiotics together had synergistic effects. When using an antibiotic-phage combination, even low concentrations of antibiotics fully inhibited the growth of bacteria.
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Affiliation(s)
- O L Lyytinen
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - C Dapuliga
- Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - D Wallinger
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - S Patpatia
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - B J Audu
- National Veterinary Research Institute, Vom, Nigeria
| | - S J Kiljunen
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
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Robb AR, Ure R, Chaput DL, Foster G. Emergence of novel methicillin resistant Staphylococcus pseudintermedius lineages revealed by whole genome sequencing of isolates from companion animals and humans in Scotland. PLoS One 2024; 19:e0305211. [PMID: 38968222 PMCID: PMC11226068 DOI: 10.1371/journal.pone.0305211] [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: 09/14/2023] [Accepted: 05/24/2024] [Indexed: 07/07/2024] Open
Abstract
Staphylococcus pseudintermedius is an opportunistic pathogen in dogs, and infection in humans is increasingly found, often linked to contact with dogs. We conducted a retrospective genotyping and antimicrobial susceptibility testing study of 406 S. pseudintermedius isolates cultured from animals (dogs, cats and an otter) and humans across Scotland, from 2007 to 2020. Seventy-five sequence types (STs) were identified, among the 130 isolates genotyped, with 59 seen only once. We observed the emergence of two methicillin resistant Staphylococcus pseudintermedius (MRSP) clones in Scotland: ST726, a novel locally-evolving clone, and ST551, first reported in 2015 in Poland, possibly linked to animal importation to Scotland from Central Europe. While ST71 was the most frequent S. pseudintermedius strain detected, other lineages that have been replacing ST71 in other countries, in addition to ST551, were detected. Multidrug resistance (MDR) was detected in 96.4% of MRSP and 8.4% of MSSP. A single MRSP isolate was resistant to mupirocin. Continuous surveillance for the emergence and dissemination of novel MDR MRSP in animals and humans and changes in antimicrobial susceptibility in S. pseudintermedius is warranted to minimise the threat to animal and human health.
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Affiliation(s)
- Andrew R. Robb
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
| | - Roisin Ure
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
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Sundaresan AK, Gangwar J, Murugavel A, Malli Mohan GB, Ramakrishnan J. Complete genome sequence, phenotypic correlation and pangenome analysis of uropathogenic Klebsiella spp. AMB Express 2024; 14:78. [PMID: 38965152 PMCID: PMC11224175 DOI: 10.1186/s13568-024-01737-w] [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: 04/08/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Urinary tract infections (UTI) by antibiotic resistant and virulent K. pneumoniae are a growing concern. Understanding the genome and validating the genomic profile along with pangenome analysis will facilitate surveillance of high-risk clones of K. pneumoniae to underpin management strategies toward early detection. The present study aims to correlate resistome with phenotypic antimicrobial resistance and virulome with pathogenicity in Klebsiella spp. The present study aimed to perform complete genome sequences of Klebsiella spp. and to analyse the correlation of resistome with phenotypic antimicrobial resistance and virulome with pathogenicity. To understand the resistome, pangenome and virulome in the Klebsiella spp, the ResFinder, CARD, IS Finder, PlasmidFinder, PHASTER, Roary, VFDB were used. The phenotypic susceptibility profiling identified the uropathogenic kp3 to exhibit multi drug resistance. The resistome and in vitro antimicrobial profiling showed concordance with all the tested antibiotics against the study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA and magA genes. To the best of our knowledge, this is the first report on the presence of ste, stf, stc and sti major fimbrial operons of Salmonella enterica serotype Typhimurium in K. pneumoniae genome. The study identifies the discordance of virulome and virulence in Klebsiella spp. The complete genome analysis and phenotypic correlation identify uropathogenic K. pneumoniae kp3 as a carbapenem-resistant and virulent pathogen. The Pangenome of K. pneumoniae was open suggesting high genetic diversity. Diverse K serotypes were observed. Sequence typing reveals the prevalence of K. pneumoniae high-risk clones in UTI catheterised patients. The study also highlights the concordance of resistome and in vitro susceptibility tests. Importantly, the study identifies the necessity of virulome and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high-risk K. pneumoniae clones.
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Affiliation(s)
- Abhirami Krishnamoorthy Sundaresan
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Jaya Gangwar
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Aravind Murugavel
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Ganesh Babu Malli Mohan
- Microbial Omics Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
- Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Georgia, Athens, United States of America
| | - Jayapradha Ramakrishnan
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India.
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Jin H, Yan Z, Ge X, Wang Q, Wang H, Du X, Liu H, Yang C, Xiang Y, Tian S, Qiu S, Zhou Y. Genomic and Phenotypic Analysis of bla KPC-2 Associated Carbapenem Resistance in Klebsiella aerogenes: Insights into Clonal Spread and Resistance Mechanisms Across Hospital Departments in Beijing. Infect Drug Resist 2024; 17:2735-2749. [PMID: 38974314 PMCID: PMC11227833 DOI: 10.2147/idr.s458182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/29/2024] [Indexed: 07/09/2024] Open
Abstract
Purpose This study conducted an phenotypic and whole-genome sequencing analysis with Klebsiella aerogenes to elucidate its clinical epidemiological characteristics, antimicrobial resistance (AMR) phenotype, biofilm formation ability and hemolytic activity testing, AMR genes and phylogenetic relationships, so as to provide a further understanding of the intra-hospital strain transmission. Methods Samples were collected from a hospital in Beijing between 2020 and 2022. All strains underwent bacterial identification, antimicrobial susceptibility testing (AST) using the VITEK-2 compact system. Biofilm formation ability and hemolytic activity were tested. Second-generation sequencing was applied to all strains, with those carrying the bla KPC gene were selected for third-generation sequencing. Whole-genome analysis identified resistance genes, plasmid types, MLST typing, and phylogenetic relationships. Plasmids were assembled to detect plasmid structures and AMR gene location. Results Among the 42 K. aerogenes isolates, 21 were carbapenem-resistant K. aerogenes (CRKA). All strains exhibited strong biofilm formation and no hemolytic activity. Most were sourced from sputum (83.3%). CRKA demonstrated extensive resistance to antibiotics, particularly β-lactamase inhibitors and Cefotetan. This resistance pattern was closely associated with the presence of an IncFII(pHN7A8) plasmid, which carried multiple resistance genes, including bla KPC-2, bla CTX-M-65, bla TEM-1, rmtB and a large number of mobile elements. The majority of CRKA strains clustered within the same branch of the phylogenetic tree, exhibiting minimal single nucleotide polymorphism (0-13 SNPs) differences, and they shared the same sequence type (ST292), resistance genes, and plasmids, originating from different departments, suggesting clonal transmission among the hospital. Conclusion Our research reveals that the clonal transmission of CRKA occurs across various departments within the hospital. The widespread resistance observed in CRKA, attributed to the presence of bla KPC and ESBLs genes, underscores the need for heightened vigilance to prevent the further dissemination of CRKA within the hospital and, potentially, throughout the wider community.
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Affiliation(s)
- Hang Jin
- School of Public Health, Zhengzhou University, Zhengzhou, People’s Republic of China
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Chinese PLA, Beijing, People’s Republic of China
| | - Zhongqiang Yan
- Department of Disease Prevention and Control, The Second Medical Center of PLA General Hospital, Beijing, People’s Republic of China
| | - Xin Ge
- School of Public Health, Anhui Medical University, Hefei, People’s Republic of China
| | - Qi Wang
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Chinese PLA, Beijing, People’s Republic of China
| | - Hui Wang
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Chinese PLA, Beijing, People’s Republic of China
| | - Xinying Du
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Chinese PLA, Beijing, People’s Republic of China
| | - Hongbo Liu
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Chinese PLA, Beijing, People’s Republic of China
| | - Chaojie Yang
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Chinese PLA, Beijing, People’s Republic of China
| | - Ying Xiang
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Chinese PLA, Beijing, People’s Republic of China
| | - Sai Tian
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Chinese PLA, Beijing, People’s Republic of China
| | - Shaofu Qiu
- School of Public Health, Zhengzhou University, Zhengzhou, People’s Republic of China
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Chinese PLA, Beijing, People’s Republic of China
| | - Yu Zhou
- Department of Clinical Laboratory, National Clinical Research Center for Geriatric Diseases, The Second Medical Center of Chinese PLA General Hospital, Beijing, People’s Republic of China
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Kim BH, Ashrafudoulla M, Shaila S, Park HJ, Sul JD, Park SH, Ha SD. Isolation, characterization, and application of bacteriophage on Vibrio parahaemolyticus biofilm to control seafood contamination. Int J Antimicrob Agents 2024; 64:107194. [PMID: 38723695 DOI: 10.1016/j.ijantimicag.2024.107194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 04/07/2024] [Accepted: 05/03/2024] [Indexed: 06/03/2024]
Abstract
OBJECTIVE This study intended to isolate a Vibrio-particular phage from the natural environment, analyse its characteristics and genome sequence, and investigate its reduction effect on V. parahaemolyticus biofilm as a biocontrol agent in squid and mackerel. METHODS Among 21 phages, phage CAU_VPP01, isolated from beach mud, was chosen for further experiments based on host range and EOP tests. When examining the reduction effect of phage CAU_VPP01 against Vibrio parahaemolyticus biofilms on surfaces (stainless steel [SS] and polyethylene terephthalate [PET]) and food surfaces (squid and mackerel). RESULTS The phage showed the most excellent reduction effect at a multiplicity-of-infection (MOI) 10. Three-dimensional images acquired with confocal laser scanning microscopy (CLSM) analysis were quantified using COMSTAT, which showed that biomass, average thickness, and roughness coefficient decreased when treated with the phage. Colour and texture analysis confirmed that the quality of squid and mackerel was maintained after the phage treatment. Finally, a comparison of gene expression levels determined by qRT-PCR analysis showed that the phage treatment induced a decrease in the gene expression of flaA, vp0962, andluxS, as examples. CONCLUSION This study indicated that Vibrio-specific phage CAU_VPP01 effectively controlled V. parahaemolyticus biofilms under various conditions and confirmed that the isolated phage could possibly be used as an effective biocontrol weapon in the seafood manufacturing industry.
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Affiliation(s)
- Byoung Hu Kim
- Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea; Food Quality Technology Center, Food Safety division, Pulmuone Co. Ltd., Cheongju, Republic of Korea
| | - Md Ashrafudoulla
- Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea; National Institute of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Shanjida Shaila
- Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea
| | - Hyung Jin Park
- College of Sport Sciences, Chung-Ang University, Anseong-Si, Republic of Korea
| | - Jeong Dug Sul
- College of Sport Sciences, Chung-Ang University, Anseong-Si, Republic of Korea
| | - Si Hong Park
- Food Science and Technology, Oregon State University, Corvallis, OR, USA
| | - Sang-Do Ha
- Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea.
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Aleksandrova EV, Wu KJY, Tresco BIC, Syroegin EA, Killeavy EE, Balasanyants SM, Svetlov MS, Gregory ST, Atkinson GC, Myers AG, Polikanov YS. Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it. Nat Chem Biol 2024; 20:867-876. [PMID: 38238495 PMCID: PMC11325235 DOI: 10.1038/s41589-023-01525-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 12/11/2023] [Indexed: 01/30/2024]
Abstract
The bacterial ribosome is an essential drug target as many clinically important antibiotics bind and inhibit its functional centers. The catalytic peptidyl transferase center (PTC) is targeted by the broadest array of inhibitors belonging to several chemical classes. One of the most abundant and clinically prevalent resistance mechanisms to PTC-acting drugs in Gram-positive bacteria is C8-methylation of the universally conserved A2503 nucleobase by Cfr methylase in 23S ribosomal RNA. Despite its clinical importance, a sufficient understanding of the molecular mechanisms underlying Cfr-mediated resistance is currently lacking. Here, we report a set of high-resolution structures of the Cfr-modified 70S ribosome containing aminoacyl- and peptidyl-transfer RNAs. These structures reveal an allosteric rearrangement of nucleotide A2062 upon Cfr-mediated methylation of A2503 that likely contributes to the reduced potency of some PTC inhibitors. Additionally, we provide the structural bases behind two distinct mechanisms of engaging the Cfr-methylated ribosome by the antibiotics iboxamycin and tylosin.
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Affiliation(s)
- Elena V Aleksandrova
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Kelvin J Y Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ben I C Tresco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Egor A Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Erin E Killeavy
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Samson M Balasanyants
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Maxim S Svetlov
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Steven T Gregory
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Gemma C Atkinson
- Department of Experimental Medicine, Lund University, Lund, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
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AlJindan R, Mahmoud N, AlEraky DM, Almandil NB, AbdulAzeez S, Borgio JF. Phenomics and genomic features of Enterococcus avium IRMC1622a isolated from a clinical sample of hospitalized patient. J Infect Public Health 2024; 17:102463. [PMID: 38833914 DOI: 10.1016/j.jiph.2024.05.051] [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: 12/08/2023] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Enterococcus avium (E. avium) is a Gram-positive nosocomial pathogen that is commonly isolated from the alimentary tract. The objective of this functional genomics study was to identify the resistant genes by analyzing the genome of E. avium IRMC1622a, a type of bacteria found in feces collected from a patient at a Saudi Arabian tertiary hospital. METHODS The bacterial strain IRMC1622a was identified by 16 S rRNA sequencing as Enterococcus sp. The resistance phenomics were performed using VITEK® 2, and morphological analysis was achieved using a scanning electron microscope (SEM). Finally, the whole bacterial genome of the bacterial strain IRMC1622a was subjected to sequencing during October 2023 using Oxford Nanopore long-read sequencing technology, and mining for resistant genes. RESULTS The results of antimicrobial resistant phenomics indicated that the IRMC1622a strain was sensitive to all tested antimicrobial agents except for erythromycin, and the same result was confirmed by genomic analysis in addition to other classes of antibiotics. SEM showed E. avium IRMC1622a is ovoid shape, in single cells (L 1.2797 ± 0.1490 µm), in pairs (L 1.7333 ± 0.1054 µm), and in chains (L 2.44033 ± 0.1978 µm). The E. avium IRMC1622a genome has 14 (in CARD) antimicrobial resistance genes that were identified with several mechanisms of antimicrobial resistance, such as the efflux pump and conferring antibiotic resistance. The present study revealed that the E. avium IRMC1622a genome contains a high number of genes associated with virulence factors, and 14 matched pathogenic protein families and predicted as human pathogen (probability score 0.855). We report two (ISEnfa4 and ISEfa5) mobile genetic elements for the first time in the E. avium genome. CONCLUSIONS The study concludes that E. avium IRMC1622a is susceptible to all tested antibacterials except erythromycin. The IRMC1622a has 14 genes encoding antimicrobial resistance mechanisms, including the efflux pump and conferring antibiotic resistance. This could indicate a potential rise in E. avium resistance in healthcare facilities. These observations may raise concerns regarding E. avium resistance in healthcare. We need more research to understand the pathophysiology of E. avium, which leads to hospital-acquired infections.
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Affiliation(s)
- Reem AlJindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Nehal Mahmoud
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Doaa M AlEraky
- Department of Biomedical Sciences, College of Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates
| | - Noor B Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
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Madhukar MK, Singh N, Iyer VR, Sowpati DT, Tallapaka KB, Mishra RK, Moharir SC. Antimicrobial resistance landscape in a metropolitan city context using open drain wastewater-based metagenomic analysis. ENVIRONMENTAL RESEARCH 2024; 252:118556. [PMID: 38503380 DOI: 10.1016/j.envres.2024.118556] [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: 12/10/2023] [Revised: 02/22/2024] [Accepted: 02/24/2024] [Indexed: 03/21/2024]
Abstract
One Health concept recognizes the inextricable interactions of diverse ecosystems and their subsequent effect on human, animal and plant health. Antimicrobial resistance (AMR) is a major One Health concern and is predicted to cause catastrophes if appropriate measures are not implemented. To understand the AMR landscape in a south Indian metropolitan city, metagenomic analysis of open drains was performed. The data suggests that in January 2022, macrolide class of antibiotics contributed the highest resistance of 40.1% in the city, followed by aminoglycoside- 24.4%, tetracycline- 11.3% and lincosamide- 6.7%. The 'mutations in the 23S rRNA gene conferring resistance to macrolide antibiotics' were the major contributor of resistance with a prevalence of 39.7%, followed by '16s rRNA with mutation conferring resistance to aminoglycoside antibiotics'- 22.2%, '16S rRNA with mutation conferring resistance to tetracycline derivatives'- 9.2%, and '23S rRNA with mutation conferring resistance to lincosamide antibiotics'- 6.7%. The most prevalent antimicrobial resistance gene (ARG) 'mutations in the 23S rRNA gene conferring resistance to macrolide antibiotics' was present in multiple pathogens including Escherichia coli, Campylobacter jejuni, Acinetobacter baumannii, Streptococcus pneumoniae, Pseudomonas aeruginosa, Neisseria gonorrhoeae, Klebsiella pneumoniae and Helicobacter pylori. Most of the geographical locations in the city showed a similar landscape for AMR. Considering human mobility and anthropogenic activities, such an AMR landscape could be common across other regions too. The data indicates that pathogens are evolving and acquiring antibiotic resistance genes to evade antibiotics of multiple major drug classes in diverse hosts. The outcomes of the study are relevant not only in understanding the resistance landscape at a broader level but are also important for identifying the resistant drug classes, the mechanisms of gaining resistance and for developing new drugs that target specific pathways. This kind of surveillance protocol can be extended to regions in other developing countries to assess and combat the problem of antimicrobial resistance.
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Affiliation(s)
| | - Nirupama Singh
- Tata Institute for Genetics and Society, Bengaluru, 560065, India
| | - V Rajesh Iyer
- Tata Institute for Genetics and Society, Bengaluru, 560065, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Divya Tej Sowpati
- Centre for Cellular and Molecular Biology, Hyderabad, 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Karthik Bharadwaj Tallapaka
- Centre for Cellular and Molecular Biology, Hyderabad, 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rakesh Kumar Mishra
- Tata Institute for Genetics and Society, Bengaluru, 560065, India; Centre for Cellular and Molecular Biology, Hyderabad, 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Shivranjani Chandrashekhar Moharir
- Tata Institute for Genetics and Society, Bengaluru, 560065, India; Centre for Cellular and Molecular Biology, Hyderabad, 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Allegrini M, Iocoli GA, Zabaloy MC. Combined use of digestate and inorganic fertilizer alleviates the burden of class 1 integrons in perennial ryegrass rhizosphere without compromising aerial biomass production. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:47132-47143. [PMID: 38985425 DOI: 10.1007/s11356-024-34279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024]
Abstract
Antimicrobial resistance (AMR) is one of the main global health challenges. Anaerobic digestion (AD) can significantly reduce the burden of antibiotic resistance genes (ARGs) in animal manures. However, the reduction is often incomplete. The agronomic use of digestates requires assessments of their effects on soil ARGs. The objective of this study was to assess the effect of digestate on the abundance of ARGs and mobile genetic elements (MGEs) in the rhizosphere of ryegrass (Lolium perenne L.) and to determine whether half-dose replacement of digestate with urea (combined fertilizer) can be implemented as a safer approach while maintaining a similar biomass production. A greenhouse assay was conducted during 190 days under a completely randomized design with two experimental factors: fertilizer type (unfertilized control and fertilized treatments with equal N dose: digestate, urea and combined fertilizer) and sampling date (16 and 148 days after the last application). The results indicated that the digestate significantly increased the abundance of clinical class 1 integrons (intI1 gene) relative to the unfertilized control at both sampling dates (P < 0.05), while the combined fertilizer only increased them at the first sampling. Sixteen days after completing the fertilization scheme only the combined fertilizer and urea significantly increased the biomass production relative to the control (P < 0.05). Additionally, by the end of the assay, the combined fertilizer showed significantly lower levels of the macrolide-resistance gene ermB than digestate and a cumulative biomass similar to urea or digestate. Overall, the combined fertilizer can alleviate the burden of integrons and ermB while simultaneously improving biomass production.
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Affiliation(s)
- Marco Allegrini
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), Universidad Nacional de Rosario (UNR)-CONICET, Zavalla, Argentina
| | - Gastón Alejandro Iocoli
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - María Celina Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina.
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina.
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Singh S, Singh S, Trivedi M, Dwivedi M. An insight into MDR Acinetobacter baumannii infection and its pathogenesis: Potential therapeutic targets and challenges. Microb Pathog 2024; 192:106674. [PMID: 38714263 DOI: 10.1016/j.micpath.2024.106674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/22/2024] [Accepted: 05/01/2024] [Indexed: 05/09/2024]
Abstract
Acinetobacter baumannii is observed as a common species of Gram-negative bacteria that exist in soil and water. Despite being accepted as a typical component of human skin flora, it has become an important opportunistic pathogen, especially in healthcare settings. The pathogenicity of A. baumannii is attributed to its virulence factors, which include adhesins, pili, lipopolysaccharides, outer membrane proteins, iron uptake systems, autotransporter, secretion systems, phospholipases etc. These elements provide the bacterium the ability to cling to and penetrate host cells, get past the host immune system, and destroy tissue. Its infection is a major contributor to human pathophysiological conditions including pneumonia, bloodstream infections, urinary tract infections, and surgical site infections. It is challenging to treat infections brought on by this pathogen since this bacterium has evolved to withstand numerous drugs and further emergence of drug-resistant A. baumannii results in higher rates of morbidity and mortality. The long-term survival of this bacterium on surfaces of medical supplies and hospital furniture facilitates its frequent spread in humans from one habitat to another. There is a need for urgent investigations to find effective drug targets for A. baumannii as well as designing novel drugs to reduce the survival and spread of infection. In the current review, we represent the specific features, pathogenesis, and molecular intricacies of crucial drug targets of A. baumannii. This would also assist in proposing strategies and alternative therapies for the prevention and treatment of A. baumannii infections and their spread.
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Affiliation(s)
- Sukriti Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Sushmita Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Mala Trivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India; Research Cell, Amity University Uttar Pradesh, Lucknow, 226028, India.
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González-Gómez JP, Rodríguez-Arellano SN, Gomez-Gil B, Vergara-Jiménez MDJ, Chaidez C. Genomic and biological characterization of bacteriophages against Enterobacter cloacae, a high-priority pathogen. Virology 2024; 595:110100. [PMID: 38714025 DOI: 10.1016/j.virol.2024.110100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
Enterobacter cloacae is a clinically significant pathogen due to its multi-resistance to antibiotics, presenting a challenge in the treatment of infections. As concerns over antibiotic resistance escalate, novel therapeutic approaches have been explored. Bacteriophages, characterized by their remarkable specificity and ability to self-replicate within target bacteria, are emerging as a promising alternative therapy. In this study, we isolated and partially characterized nine lytic bacteriophages targeting E. cloacae, with two selected for comprehensive genomic analysis based on their host range and bacteriolytic activity. All identified phages exhibited a narrow host range, demonstrated stability within a temperature range of 30-60 °C, displayed pH tolerance from 3 to 10, and showed an excellent bacteriolytic capacity for up to 18 h. Notably, the fully characterized phage genomes revealed an absence of lysogenic, virulence, or antibiotic-resistance genes, positioning them as promising candidates for therapeutic intervention against E. cloacae-related diseases. Nonetheless, translating this knowledge into practical therapeutic applications mandates a deeper understanding of bacteriophage interactions within complex biological environments.
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Affiliation(s)
- Jean Pierre González-Gómez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico
| | | | - Bruno Gomez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Unidad Mazatlán en Acuicultura y Manejo Ambiental, AP 711, Mazatlan, Sinaloa, Mexico
| | | | - Cristobal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico.
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Thant EP, Surachat K, Chusri S, Romyasamit C, Pomwised R, Wonglapsuwan M, Yaikhan T, Suwannasin S, Singkhamanan K. Exploring Weissella confusa W1 and W2 Strains Isolated from Khao-Mahk as Probiotic Candidates: From Phenotypic Traits to Genomic Insights. Antibiotics (Basel) 2024; 13:604. [PMID: 39061286 PMCID: PMC11273482 DOI: 10.3390/antibiotics13070604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Growing interest in probiotics has spurred research into their health benefits for hosts. This study aimed to evaluate the probiotic properties, especially antibacterial activities and the safety of two Weissella confusa strains, W1 and W2, isolated from Khao-Mahk by describing their phenotypes and genotypes through phenotypic assays and whole genome sequencing. In vitro experiments demonstrated that both strains exhibited robust survival under gastric and intestinal conditions, such as in the presence of low pH, bile salt, pepsin, and pancreatin, indicating their favorable gut colonization traits. Additionally, both strains showed auto-aggregation and strong adherence to Caco2 cells, with adhesion rates of 86.86 ± 1.94% for W1 and 94.74 ± 2.29% for W2. These high adherence rates may be attributed to the significant exopolysaccharide (EPS) production observed in both strains. Moreover, they exerted remarkable antimicrobial activities against Stenotrophomonas maltophilia, Salmonella enterica serotype Typhi, Vibrio cholerae, and Acinetobacter baumannii, along with an absence of hemolytic activities and antibiotic resistance, underscoring their safety for probiotic application. Genomic analysis corroborated these findings, revealing genes related to probiotic traits, including EPS clusters, stress responses, adaptive immunity, and antimicrobial activity. Importantly, no transferable antibiotic-resistance genes or virulence genes were detected. This comprehensive characterization supports the candidacy of W1 and W2 as probiotics, offering substantial potential for promoting health and combating bacterial infections.
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Affiliation(s)
- Ei Phway Thant
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand (K.S.); (T.Y.); (S.S.)
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand (K.S.); (T.Y.); (S.S.)
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Sarunyou Chusri
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand;
| | - Chonticha Romyasamit
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhonsithammarat 80161, Thailand;
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand; (R.P.); (M.W.)
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand; (R.P.); (M.W.)
| | - Thunchanok Yaikhan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand (K.S.); (T.Y.); (S.S.)
| | - Sirikan Suwannasin
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand (K.S.); (T.Y.); (S.S.)
| | - Kamonnut Singkhamanan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand (K.S.); (T.Y.); (S.S.)
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Machado RAR, Malan AP, Boss A, Claasen NJ, Bhat AH, Abolafia J. Photorhabdus africana sp. nov. isolated from Heterorhabditis entomopathogenic nematodes. Curr Microbiol 2024; 81:240. [PMID: 38910178 PMCID: PMC11194217 DOI: 10.1007/s00284-024-03744-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/20/2024] [Indexed: 06/25/2024]
Abstract
One Gram-negative, rod-shaped bacterial strain, isolated from an undescribed Heterorhabditis entomopathogenic nematode species was characterized to determine its taxonomic position. The 16S rRNA gene sequences indicate that it belongs to the class Gammaproteobacteria, to the family Morganellaceae, to the genus Photorhabdus, and likely represents a novel bacterial species. This strain, designated here as CRI-LCT, was therefore molecularly, biochemically, and morphologically characterized to describe the novel bacterial species. Phylogenetic reconstructions using 16S rRNA gene sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. The 16rRNA gene sequences between CRI-LCT and P. laumondii subsp. laumondii TT01T are 99.1% identical, and between CRI-LCT and P. laumondii subsp. clarkei BOJ-47T are 99.2% identical. Phylogenetic reconstructions using whole genome sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. Moreover, digital DNA-DNA hybridization (dDDH) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 65% and 63%, respectively. In addition, we observed that average nucleotide identity (ANI) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 95.8% and 95.5%, respectively. These values are below the 70% dDDH and the 95-96% ANI divergence thresholds that delimits prokaryotic species. Based on these genomic divergence values, and the phylogenomic separation, we conclude that CRI-LCT represents a novel bacterial species, for which we propose the name Photorhabdus africana sp. nov. with CRI-LCT (= CCM 9390T = CCOS 2112T) as the type strain. The following biochemical tests allow to differentiate P. africana sp. nov. CRI-LCT from other species of the genus, including its more closely related taxa: β-Galactosidase, citrate utilization, urease and tryptophan deaminase activities, indole and acetoin production, and glucose and inositol oxidation. Our study contributes to a better understanding of the taxonomy and biodiversity of this important bacterial group with great biotechnological and agricultural potential.
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Affiliation(s)
- Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
| | - Antoinette P Malan
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Anja Boss
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Nicholle J Claasen
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Aashaq Hussain Bhat
- Department of Biosciences and University Center for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600077, India
| | - Joaquín Abolafia
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Campus 'Las Lagunillas', Jaén, Spain
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Sreekumaran S, V K P, Premnath M, P R P, M N A, Mathew J, K J, E K R. Novel in-genome based analysis demonstrates the evolution of OmpK37, antimicrobial resistance gene from a potentially pathogenic pandrug resistant Klebsiella pneumoniae MS1 isolated from healthy broiler feces. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172713. [PMID: 38657814 DOI: 10.1016/j.scitotenv.2024.172713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/19/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Antimicrobial resistance transmission from farm animals to humans is a critical health concern and hence a detailed molecular surveillance is essential for tracking the spread and consequent evolution of antimicrobial resistance. In this study, a pan-drug resistant Klebsiella pneumoniae MS1 strain was isolated from a healthy broiler farm and studied. From the results of the study, MS1 was found to be is resistant to 18 tested antibiotics and has a high-risk to be pathogenic to humans with a probability of 0.80. The whole genome sequencing data of MS1 was used to predict the presence of antimicrobial resistance genes and pathogenicity. The genome analysis has revealed MS1 to have 34 AMR genes. Out of these, the AMR gene OmpK37 codes for an important protein involved in cell permeability and hence in antibiotic resistance. Further analysis was carried out by using an in-genome analysis method to understand the evolution of OmpK37 and the underlying reason for the emergence of resistance. From the detailed analysis, the current study could demonstrate for the first time the evolution of OmpK37 from OmpC. Though structurally OmpK37 was very similar to other porins present in MS1, it was found to have higher mutability as a distinguishing feature which makes it an important protein in monitoring the evolving resistances in microorganisms.
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Affiliation(s)
- Sreejith Sreekumaran
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Priya V K
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Manjusha Premnath
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Prathiush P R
- State Institute of Animal Diseases, Thiruvananthapuram, Kerala 695563, India
| | - Anisha M N
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Jyothis Mathew
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Jayachandran K
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Radhakrishnan E K
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India.
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Gillieatt BF, Coleman NV. Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria. FEMS Microbiol Rev 2024; 48:fuae017. [PMID: 38897736 PMCID: PMC11253441 DOI: 10.1093/femsre/fuae017] [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: 11/27/2023] [Revised: 06/09/2024] [Accepted: 06/18/2024] [Indexed: 06/21/2024] Open
Abstract
The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.
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Affiliation(s)
- Brodie F Gillieatt
- School of Life and Environmental Sciences, The University of Sydney, F22 - LEES Building, NSW 2006, Australia
| | - Nicholas V Coleman
- School of Natural Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, 6 Wally’s Walk, Macquarie Park, NSW 2109, Australia
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47
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Qu T, Wang P, Zhao X, Liang L, Ji Q, Ge Y, Chen Y. Metagenomic profiles of the antimicrobial resistance in traditional Chinese fermented meat products: Core resistome and co-occurrence patterns. Int J Food Microbiol 2024; 418:110740. [PMID: 38754174 DOI: 10.1016/j.ijfoodmicro.2024.110740] [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: 01/11/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Antimicrobial resistance (AMR) poses a significant challenge to global health, and the presence of antibiotic resistance genes (ARGs) in food poses a potential threat to public health. Traditional Chinese fermented meat products (FMPs) are highly favored because of their unique flavors and cultural value. However, microbial safety and the potential distribution and composition of AMR in these products remain unclear. In this study, a comprehensive analysis of bacterial composition and antibiotic-resistant populations in 216 samples of traditional fermented meat products from different regions of China was conducted using a metagenomic approach. Staphylococcus was the most abundant genus in the samples, accounting for an average abundance of 29.9 %, followed by Tetragenococcus (17.1 %), and Latilactobacillus (3.6 %). A core resistome of FMP samples was constructed for the first time using co-occurrence network analysis, which revealed the distribution and interrelationships of ARGs and bio/metal-resistant genes (BMRGs). Random forest analysis identified the lincosamide nucleotidyltransferase lnuA and the multidrug and toxic compound extrusion (MATE) transporter abeM as potential indicators for assessing the overall abundance of the core resistome. Additionally, Staphylococcus, Acinetobacter, and Pseudomonas were identified as hosts constituting the core resistome. Despite their low abundance, the latter two still serve as major reservoirs of antibiotic resistance genes. Notably, Lactococcus cremoris was identified as the key host for tetracycline resistance genes in the samples, highlighting the need for enhanced resistance monitoring in lactic acid bacteria. Based on our findings, in the microbial safety assessment of fermented meat products, beyond common foodborne pathogens, attention should be focused on detecting and controlling coagulase-negative Staphylococcus, Acinetobacter, and Pseudomonas, and addressing bacterial resistance. The quantitative detection of lnuA and abeM could provide a convenient and rapid method for assessing the overall abundance of the core resistome. Our findings have important implications for the control of bacterial resistance and prevention of pathogenic bacteria in fermented meat products.
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Affiliation(s)
- Tianming Qu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China; College of Food Science and Engineering, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Ping Wang
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xiaomei Zhao
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Lijiao Liang
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China; College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Qinglong Ji
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Yiqiang Ge
- China Rural Technology Development Center, Beijing 100045, China; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ying Chen
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China.
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48
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Zeng X, Liang S, Dong J, Gao G, Hu Y, Sun Y. The trade-off of Vibrio parahaemolyticus between bacteriophage resistance and growth competitiveness. Front Microbiol 2024; 15:1346251. [PMID: 38919495 PMCID: PMC11196418 DOI: 10.3389/fmicb.2024.1346251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/10/2024] [Indexed: 06/27/2024] Open
Abstract
Vibrio parahaemolyticus is a food-borne pathogen, which is often isolated from various seafood products. In this study, two kinds of bacteriophages was isolated from the offshore sediments samples. The anti-phage mutant strain were obtained after seventeen rounds of co-culture of Vibrio parahaemolyticus and mixed bacteriophage, multigroup sequencing was carried out on spontaneous the anti-phage mutant strain and the wild-type strain. We used the Sanger sequencing to verify the accuracy of the mutation sites. Biolog GEN III MicroPlates were used to evaluate the metabolic capacity of wild-type strains and the anti-phage mutant strain. In this study, we found that with flaG gene (slight homology to N terminus of multiple flagellins) mutated, making the bacteriophage unable to absorb to the cell surface of the host. And, the growth competitiveness of the anti-phage mutant strain is lower than the wild-type strain. These results indicated that the fitness cost, including loss of the growth competitiveness, constitutes a barrier to the prevalence of these defense mechanisms. And the selection pressure on different anti-phage strategies depends on the trade-off between mortality imposed by bacteriophages and fitness cost of the defense strategy under the given environmental conditions. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in Vibrio parahaemolyticus. Our study provided knowledge for the evolutionary adaption of bacteria against the bacteriophage, which could add more information to understand the phage resistance mechanism before applying in the industry.
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Affiliation(s)
- Xiuxiu Zeng
- Ningbo No.2 Hospital, Ningbo, Zhejiang, China
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, Zhejiang, China
| | | | - Jiayi Dong
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, Zhejiang, China
| | | | - Yaoren Hu
- Ningbo No.2 Hospital, Ningbo, Zhejiang, China
| | - Yuechao Sun
- Ningbo No.2 Hospital, Ningbo, Zhejiang, China
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, Zhejiang, China
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Sung K, Nawaz M, Park M, Chon J, Khan SA, Alotaibi K, Revollo J, Miranda JA, Khan AA. Whole-Genome Sequence Analysis of Antibiotic Resistance, Virulence, and Plasmid Dynamics in Multidrug-Resistant E. coli Isolates from Imported Shrimp. Foods 2024; 13:1766. [PMID: 38890994 PMCID: PMC11171581 DOI: 10.3390/foods13111766] [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: 04/23/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
We analyzed antimicrobial resistance and virulence traits in multidrug-resistant (MDR) E. coli isolates obtained from imported shrimp using whole-genome sequences (WGSs). Antibiotic resistance profiles were determined phenotypically. WGSs identified key characteristics, including their multilocus sequence type (MLST), serotype, virulence factors, antibiotic resistance genes, and mobile elements. Most of the isolates exhibited resistance to gentamicin, streptomycin, ampicillin, chloramphenicol, nalidixic acid, ciprofloxacin, tetracycline, and trimethoprim/sulfamethoxazole. Multilocus sequence type (MLST), serotype, average nucleotide identity (ANI), and pangenome analysis showed high genomic similarity among isolates, except for EC15 and ECV01. The EC119 plasmid contained a variety of efflux pump genes, including those encoding the acid resistance transcriptional activators (gadE, gadW, and gadX), resistance-nodulation-division-type efflux pumps (mdtE and mdtF), and a metabolite, H1 symporter (MHS) family major facilitator superfamily transporter (MNZ41_23075). Virulence genes displayed diversity, particularly EC15, whose plasmids carried genes for adherence (faeA and faeC-I), invasion (ipaH and virB), and capsule (caf1A and caf1M). This comprehensive analysis illuminates antimicrobial resistance, virulence, and plasmid dynamics in E. coli from imported shrimp and has profound implications for public health, emphasizing the need for continued surveillance and research into the evolution of these important bacterial pathogens.
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Affiliation(s)
- Kidon Sung
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (M.N.); (M.P.); (S.A.K.); (A.A.K.)
| | - Mohamed Nawaz
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (M.N.); (M.P.); (S.A.K.); (A.A.K.)
| | - Miseon Park
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (M.N.); (M.P.); (S.A.K.); (A.A.K.)
| | - Jungwhan Chon
- Department of Companion Animal Health, Inje University, Gimhae 50834, Republic of Korea;
| | - Saeed A. Khan
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (M.N.); (M.P.); (S.A.K.); (A.A.K.)
| | - Khulud Alotaibi
- Saudi Food and Drug Authority (SFDA), Riyadh 13513, Saudi Arabia;
| | - Javier Revollo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (J.R.); (J.A.M.)
| | - Jaime A. Miranda
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (J.R.); (J.A.M.)
| | - Ashraf A. Khan
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (M.N.); (M.P.); (S.A.K.); (A.A.K.)
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50
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Gomes CN, Frazão MR, Seribelli AA, Barker DOR, Che EV, Nogueira MCL, Taboada EN, Falcão JP. Insights on the genomic diversity, virulence and resistance profile of a Campylobacter jejuni strain isolated from a hospitalized patient in Brazil. Braz J Microbiol 2024; 55:1381-1391. [PMID: 38546951 PMCID: PMC11153483 DOI: 10.1007/s42770-024-01314-0] [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: 10/09/2023] [Accepted: 03/21/2024] [Indexed: 06/07/2024] Open
Abstract
Campylobacteriosis is currently recognized as one of the major causes of foodborne bacterial diseases worldwide. In Brazil, there is insufficient data to estimate the impact of Campylobacter in public health. The aim of this present study was to characterize a C. jejuni CJ-HBSJRP strain isolated from a hospitalized patient in Brazil by its ability to invade human Caco-2 epithelial cells, to survive in U937 human macrophages, and to assess its phenotypic antimicrobial resistance profile. In addition, prophages, virulence and antimicrobial resistance genes were search using whole-genome sequencing data. The genetic relatedness was evaluated by MLST and cgMLST analysis by comparison with 29 other C. jejuni genomes isolated from several countries. The CJ-HBSJRP strain showed an invasion percentage of 50% in Caco-2 polarized cells, 37.5% of survivability in U937 cells and was phenotypically resistant to ampicillin, ciprofloxacin and nalidixic acid. A total of 94 virulence genes related to adherence, biofilm, chemotaxis, immune modulation, invasion process, metabolism, motility and toxin were detected. The resistance genes blaOXA-605 (blaOXA-61), cmeB and mutations in the QRDR region of gyrA were also found and none prophages were detected. The MLST analysis showed 23 different STs among the strains studied. Regarding cgMLST analysis, the CJ-HBSJRP strain was genetically distinct and did not group closely to any other isolate. The results obtained reinforce the pathogenic potential of the CJHBSJRP strain and highlighted the need for more careful attention to Campylobacter spp. infections in Brazil since this pathogen has been the most commonly reported zoonosis in several countries worldwide.
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Affiliation(s)
- Carolina Nogueira Gomes
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto- Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Miliane Rodrigues Frazão
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto- Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Amanda Aparecida Seribelli
- Laboratório de Patogenicidade Microbiana E Imunidade Inata, Faculdade de Medicina de Ribeirão Preto- Universidade de São Paulo, São Paulo, Brazil
| | | | - Emily Victoria Che
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Mara Corrêa Lelles Nogueira
- Centro de Investigação de Microrganismos, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias- Faculdade de Medicina de São José Do Rio Preto, São José Do Rio Preto, São Paulo, Brazil
| | | | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto- Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil.
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