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Castellana S, De Laurentiis V, Bianco A, Del Sambro L, Grassi M, De Leonardis F, Derobertis AM, De Carlo C, Sparapano E, Mosca A, Stolfa S, Ronga L, Santacroce L, Chironna M, Parisi M, Capozzi L, Parisi A. Pannonibacter anstelovis sp. nov. Isolated from Two Cases of Bloodstream Infections in Paediatric Patients. Microorganisms 2024; 12:799. [PMID: 38674743 PMCID: PMC11051880 DOI: 10.3390/microorganisms12040799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/05/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
This study describes two cases of bacteraemia sustained by a new putative Pannonibacter species isolated at the U.O.C. of Microbiology and Virology of the Policlinico of Bari (Bari, Italy) from the blood cultures of two patients admitted to the Paediatric Oncohaematology Unit. Pannonibacter spp. is an environmental Gram-negative bacterium not commonly associated with nosocomial infections. Species identification was performed using Sanger sequencing of the 16S rRNA gene and Whole-Genome Sequencing (WGS) for both strains. Genomic analyses for the two isolates, BLAST similarity search, and phylogeny for the 16S rDNA sequences lead to an assignment to the species Pannonibacter phragmitetus. However, by performing ANIb, ANIm, tetranucleotide correlation, and DNA-DNA digital hybridization, analyses of the two draft genomes showed that they were very different from those of the species P. phragmitetus. MALDI-TOF analysis, assessment of antimicrobial susceptibility by E-test method, and Analytical Profile Index (API) tests were also performed. This result highlights how environmental bacterial species can easily adapt to the human host and, especially in nosocomial environments, also gain pathogenic potential through antimicrobial resistance.
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Affiliation(s)
- Stefano Castellana
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
| | - Vittoriana De Laurentiis
- UOC Microbiology and Virology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (V.D.L.); (C.D.C.); (E.S.); (S.S.); (L.R.)
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
| | - Massimo Grassi
- Division of Paediatric Haematology and Oncology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (M.G.); (F.D.L.)
| | - Francesco De Leonardis
- Division of Paediatric Haematology and Oncology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (M.G.); (F.D.L.)
| | - Anna Maria Derobertis
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
| | - Carmen De Carlo
- UOC Microbiology and Virology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (V.D.L.); (C.D.C.); (E.S.); (S.S.); (L.R.)
| | - Eleonora Sparapano
- UOC Microbiology and Virology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (V.D.L.); (C.D.C.); (E.S.); (S.S.); (L.R.)
| | - Adriana Mosca
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.M.); (L.S.)
| | - Stefania Stolfa
- UOC Microbiology and Virology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (V.D.L.); (C.D.C.); (E.S.); (S.S.); (L.R.)
| | - Luigi Ronga
- UOC Microbiology and Virology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (V.D.L.); (C.D.C.); (E.S.); (S.S.); (L.R.)
| | - Luigi Santacroce
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.M.); (L.S.)
| | - Maria Chironna
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Michela Parisi
- University-Hospital Pediatric Department, Bambino Gesù Paediatric Hospital, 00165 Rome, Italy;
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
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2
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Wang R, Guragain M, Chitlapilly Dass S, Palanisamy V, Bosilevac JM. Impact of intense sanitization on environmental biofilm communities and the survival of Salmonella enterica at a beef processing plant. Front Microbiol 2024; 15:1338600. [PMID: 38435686 PMCID: PMC10906087 DOI: 10.3389/fmicb.2024.1338600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 03/05/2024] Open
Abstract
Salmonella enterica is a leading cause of foodborne illness in the U.S. In the meat industry, one action taken to address pathogen contamination incidence is an intense sanitization (IS) of the entire processing plant that many large processors perform annually or semiannually. However, this procedure's immediate and long-term impact on environment microbial community and pathogen colonization are unknown. Here we investigated the impact of IS procedure on environmental biofilms and the subsequent S. enterica colonization and stress tolerance. Environmental samples were collected from floor drains at various areas 1 week before, 1 week, and 4 weeks after the IS procedure at a beef plant with sporadic S. enterica prevalence. Biofilm formation by microorganisms in the drain samples without S. enterica presence was tested under processing temperature. The ability of the biofilms to recruit and/or protect a co-inoculated S. enterica strain from quaternary ammonium compound (QAC) treatment was determined. The community structure of each drain sample was elucidated through 16S rRNA amplicon community sequencing. Post-IS samples collected from 8 drains formed significantly stronger biofilms than the respective pre-IS samples. S. enterica colonization was not different between the pre- and post-IS biofilms at all drain locations. S. enterica survival in QAC-treated pre- and post-IS mixed biofilms varied depending upon the drain location but a higher survival was associated with a stronger biofilm matrix. The 16S rRNA amplicon gene community sequencing results exhibited a decrease in community diversity 1 week after IS treatment but followed by a significant increase 4 weeks after the treatment. The IS procedure also significantly altered the community composition and the higher presence of certain species in the post-IS community may be associated with the stronger mixed biofilm formation and Salmonella tolerance. Our study suggested that the IS procedure might disrupt the existing environmental microbial community and alter the natural population composition, which might lead to unintended consequences as a result of a lack of competition within the multispecies mixture. The survival and recruitment of species with high colonizing capability to the post-IS community may play crucial roles in shaping the ensuing ecological dynamics.
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Affiliation(s)
- Rong Wang
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Manita Guragain
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, PA, United States
| | | | - Vignesh Palanisamy
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, United States
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3
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Ferreira WT, Hong HA, Adams JRG, Hess M, Kotowicz NK, Tan S, Ferrari E, Brisson A, Zentek J, Soloviev M, Cutting SM. Environmentally Acquired Bacillus and Their Role in C. difficile Colonization Resistance. Biomedicines 2022; 10:930. [PMID: 35625667 PMCID: PMC9138776 DOI: 10.3390/biomedicines10050930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 01/27/2023] Open
Abstract
Clostridioides difficile is an environmentally acquired, anaerobic, spore-forming bacterium which ordinarily causes disease following antibiotic-mediated dysbiosis of the intestinal microbiota. Although much is understood regarding the life cycle of C. difficile, the fate of C. difficile spores upon ingestion remains unclear, and the underlying factors that predispose an individual to colonization and subsequent development of C. difficile infection (CDI) are not fully understood. Here, we show that Bacillus, a ubiquitous and environmentally acquired, spore-forming bacterium is associated with colonization resistance to C. difficile. Using animal models, we first provide evidence that animals housed under conditions that mimic reduced environmental exposure have an increased susceptibility to CDI, correlating with a loss in Bacillus. Lipopeptide micelles (~10 nm) produced by some Bacilli isolated from the gastro-intestinal (GI)-tract and shown to have potent inhibitory activity to C. difficile have recently been reported. We show here that these micelles, that we refer to as heterogenous lipopeptide lytic micelles (HELMs), act synergistically with components present in the small intestine to augment inhibitory activity against C. difficile. Finally, we show that provision of HELM-producing Bacillus to microbiota-depleted animals suppresses C. difficile colonization thereby demonstrating the significant role played by Bacillus in colonization resistance. In the wider context, our study further demonstrates the importance of environmental microbes on susceptibility to pathogen colonization.
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Affiliation(s)
- William T. Ferreira
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Huynh A. Hong
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - James R. G. Adams
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Mateusz Hess
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Natalia K. Kotowicz
- SporeGen Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK;
| | - Sisareuth Tan
- Laboratoire d’Imagerie Moléculaire et Nano-Bio-Technologie, UMR-CBMN CNRS-Université de Bordeaux-IPB, 33607 Pessac, France; (S.T.); (A.B.)
| | - Enrico Ferrari
- School of Life Sciences, University of Lincoln, Lincoln LN6 7TS, UK;
| | - Alain Brisson
- Laboratoire d’Imagerie Moléculaire et Nano-Bio-Technologie, UMR-CBMN CNRS-Université de Bordeaux-IPB, 33607 Pessac, France; (S.T.); (A.B.)
| | - Jurgen Zentek
- Institute for Animal Health, Freie University of Berlin, Berlin 14195, Germany;
| | - Mikhail Soloviev
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Simon M. Cutting
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
- SporeGen Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK;
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4
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Zhao Z, Anderson AN, Kannapell CC, Kwok WW, Gaskin F, Fu SM. HLA-DR3 restricted environmental epitopes from the bacterium Clostridium tetani have T cell cross-reactivity to the SLE-related autoantigen SmD. Front Immunol 2022; 13:928374. [PMID: 36389825 PMCID: PMC9659850 DOI: 10.3389/fimmu.2022.928374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
HLA-DR3 (DR3) is one of the dominant HLA-DR alleles associated with systemic lupus erythematosus (SLE) susceptibility. Our previous studies showed multiple intramolecular DR3 restricted T cell epitopes in the Smith D (SmD) protein, from which we generated a non-homologous, bacterial epitope mimics library. From this library we identified ABC247-261 Mimic as one new DR3 restricted bacterial T cell epitope from the ABC transporter ATP-binding protein in Clostridium tetani. It activated and induced autoreactive SmD66-80-specific T cells and induced autoantibodies to lupus-related autoantigens in vivo. Compared to healthy donors, SLE patients have a greater percentage of cross-reactive T cells to ABC247-261 Mimic and SmD66-80. In addition, we analyzed the ability of single DR3 restricted Tetanus toxoid (TT) T cell epitopes to induce autoimmune T cells. We found that the immunodominant TT epitope TT826-845 stimulated SmD66-80 reactive T cells but failed to induce persistent anti-SmD autoantibodies compared to the ABC247-261 Mimic. Thus, exposure to the ABC247-261 Mimic epitope may contribute to autoimmunity in susceptible DR3 individuals.
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Affiliation(s)
- Zhenhuan Zhao
- Division of Rheumatology, Department of Medicine, University of Virginia, Charlottesville, VA, United States.,Center for Immunity, Inflammation and Regenerative Medicine, Division of Nephrology, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Ashley N Anderson
- Center for Immunity, Inflammation and Regenerative Medicine, Division of Nephrology, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Carol C Kannapell
- Division of Rheumatology, Department of Medicine, University of Virginia, Charlottesville, VA, United States.,Center for Immunity, Inflammation and Regenerative Medicine, Division of Nephrology, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - William W Kwok
- Benaroya Research Institute, Virginia Mason, Seattle, WA, United States
| | - Felicia Gaskin
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA, United States
| | - Shu Man Fu
- Division of Rheumatology, Department of Medicine, University of Virginia, Charlottesville, VA, United States.,Center for Immunity, Inflammation and Regenerative Medicine, Division of Nephrology, Department of Medicine, University of Virginia, Charlottesville, VA, United States
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5
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Vilela FP, Falcão JP. Analysis of the antimicrobial resistance gene frequency in whole-genome sequenced Vibrio from Latin American countries. J Med Microbiol 2021; 70. [PMID: 34586052 DOI: 10.1099/jmm.0.001428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vibrio species are important environmental-related bacteria responsible for diverse infections in humans due to consumption of contaminated water and seafood in underdeveloped areas of the world. This study aimed to investigate the frequency of antimicrobial resistance genes in 577 sequenced Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus strains isolated in Latin American countries available at the NCBI Pathogen Detection database and to determine the sequence type (ST) of the strains. Almost all strains studied (99.8%) carried at least one antimicrobial resistance gene, while 54.2 % presented a multidrug-resistance profile. The Vibrio strains exhibited genotypic resistance to 11 antimicrobial classes and almG, varG, and catB9, which confer resistance to antibiotic peptides, β-lactams and amphenicols, respectively, were the most detected genes. Vibrio parahaemolyticus and V. vulnificus showed a broad diversity of STs. Vibrio cholerae strains isolated in Haiti after 2010's earthquake presented the highest diversity and amount of resistance genes in the set of strains analysed and mostly belonged to ST69. In conclusion, the detection of resistance genes from 11 antimicrobial classes and the high number of multidrug-resistant Vibrio species strains emphasize that Latin American public health authorities should employ more efficient control measures and that special attention should be given for the rational use of antimicrobials in human therapy and aquaculture, since the consumption of contaminated water and seafood with resistant Vibrio may result in human infections difficult to be treated.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Av. do Café, s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | - Juliana Pfrimer Falcão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Av. do Café, s/n, 14040-903, Ribeirão Preto, SP, Brazil
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Sanz-García F, Gil-Gil T, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat. Int J Mol Sci 2021; 22:8080. [PMID: 34360847 PMCID: PMC8347278 DOI: 10.3390/ijms22158080] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/24/2022] Open
Abstract
The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.
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Affiliation(s)
| | | | | | | | - José L. Martínez
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain; (F.S.-G.); (T.G.-G.); (P.L.); (L.E.O.-S.); (S.H.-A.)
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Miloud SB, Dziri O, Ferjani S, Ali MM, Mysara M, Boutiba I, Houdt RVAN, Chouchani C. First Description of Various Bacteria Resistant to Heavy Metals and Antibiotics Isolated from Polluted Sites in Tunisia. Pol J Microbiol 2021; 70:161-174. [PMID: 34335797 PMCID: PMC8318066 DOI: 10.33073/pjm-2021-012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 01/11/2023] Open
Abstract
Environmental bacteria belonging to various families were isolated from polluted water collected from ten different sites in Tunisia. Sites were chosen near industrial and urban areas known for their high degree of pollution. The aim of this study was to investigate cross-resistance between heavy metals (HM), i.e., silver, mercury and copper (Ag, Hg, and Cu), and antibiotics. In an initial screening, 80 isolates were selected on ampicillin, and 39 isolates, retained for further analysis, could grow on a Tris-buffered mineral medium with gluconate as carbon source. Isolates were identified based on their 16S rRNA gene sequence. Results showed the prevalence of antibiotic resistance genes, especially all isolates harbored the blaTEM gene. Some of them (15.38%) harbored blaSHV. Moreover, several were even ESBLs and MBLs-producers, which can threaten the human health. On the other hand, 92.30%, 56.41%, and 51.28% of the isolates harbored the heavy metals resistance genes silE, cusA, and merA, respectively. These genes confer resistance to silver, copper, and mercury. A cross-resistance between antibiotics and heavy metals was detected in 97.43% of our isolates.
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Affiliation(s)
- Samar Ben Miloud
- Research Laboratory of Environmental Sciences and Technologies, Higher Institute of Environmental Sciences and Technologies of Borj-Cedria, University of Carthage, Hammam-Lif, Tunisia.,Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis El-Manar, Tunisia.,Research Laboratory Antibiotic Resistance, Faculty of Medicine of Tunis, Tunisia
| | - Olfa Dziri
- Research Laboratory of Environmental Sciences and Technologies, Higher Institute of Environmental Sciences and Technologies of Borj-Cedria, University of Carthage, Hammam-Lif, Tunisia.,Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis El-Manar, Tunisia
| | - Sana Ferjani
- Research Laboratory Antibiotic Resistance, Faculty of Medicine of Tunis, Tunisia
| | - Muntasir Md Ali
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Ilhem Boutiba
- Research Laboratory Antibiotic Resistance, Faculty of Medicine of Tunis, Tunisia
| | - Rob VAN Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Chedly Chouchani
- Research Laboratory of Environmental Sciences and Technologies, Higher Institute of Environmental Sciences and Technologies of Borj-Cedria, University of Carthage, Hammam-Lif, Tunisia.,Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis El-Manar, Tunisia
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8
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Bjerketorp J, Levenfors JJ, Nord C, Guss B, Öberg B, Broberg A. Selective Isolation of Multidrug-Resistant Pedobacter spp., Producers of Novel Antibacterial Peptides. Front Microbiol 2021; 12:642829. [PMID: 33717041 PMCID: PMC7947920 DOI: 10.3389/fmicb.2021.642829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Abstract
Twenty-eight multidrug-resistant bacterial strains closely related or identical to Pedobacter cryoconitis, Pedobacter lusitanus and Pedobacter steynii were isolated from soil samples by selection for multidrug-resistance. Approximately 3-30% of the selected isolates were identified as Pedobacter, whereas isolation without antibiotics did not yield any isolates of this genus. Next generation sequencing data showed Pedobacter to be on 69th place among the bacterial genera (0.32% of bacterial sequences). The Pedobacter isolates produced a wide array of novel compounds when screened by UHPLC-MS/MSMS, and hierarchical cluster analysis resulted in several distinct clusters of compounds produced by specific isolates of Pedobacter, and most of these compounds were found to be peptides. The Pedobacter strain UP508 produced isopedopeptins, whereas another set of strains produced pedopeptins, which both are known cyclic lipodepsipeptides produced by Pedobacter sp. Other Pedobacter strains produced analogous peptides with a sequence variation. Further strains of Pedobacter produced additional novel antibacterial cyclic lipopeptides (ca 800 or 1400 Da in size) and/or linear lipopeptides (ca 700-960 Da in size). A 16S rRNA phylogenetic tree for the Pedobacter isolates revealed several distinct clades and subclades of isolates. One of the subclades comprised isolates producing isopedopeptin analogs, but the isopedopeptin producing isolate UP508 was clearly placed on a separate branch. We suggest that the non-ribosomal peptide synthases producing pedopeptins, isopedopeptins, and the analogous peptides, may derive from a common ancestral non-ribosomal peptide synthase gene cluster, which may have been subjected to a mutation leading to changed specificity in one of the modules and then to a modular rearrangement leading to the changed sequence found in the isopedopeptins produced by isolate UP508.
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Affiliation(s)
- Joakim Bjerketorp
- Department of Molecular Sciences, Uppsala BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Ultupharma AB, Uppsala, Sweden
| | - Jolanta J Levenfors
- Department of Molecular Sciences, Uppsala BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Ultupharma AB, Uppsala, Sweden
| | - Christina Nord
- Department of Molecular Sciences, Uppsala BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bengt Guss
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bo Öberg
- Ultupharma AB, Uppsala, Sweden.,Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Uppsala BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden
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9
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Abstract
Ochrobactrum species are non-enteric, Gram-negative organisms that are closely related to the genus Brucella. Since the designation of the genus in 1988, several distinct species have now been characterised and implicated as opportunistic pathogens in multiple outbreaks. Here, we examine the genus, its members, diagnostic tools used for identification, data from recent Ochrobactrum whole genome sequencing and the pathogenicity associated with reported Ochrobactrum infections. This review identified 128 instances of Ochrobactrum spp. infections that have been discussed in the literature. These findings indicate that infection review programs should consider investigation of possible Ochrobactrum spp. outbreaks if these bacteria are clinically isolated in more than one patient and that Ochrobactrum spp. are more important pathogens than previously thought.
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Affiliation(s)
- Michael P. Ryan
- Department of Applied Sciences, Limerick Institute of Technology, Moylish V94 EC5T, Limerick, Ireland;
- Molecular Biochemistry Laboratory, Department of Chemical Sciences, School of Natural Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX2, Ireland
| | - J. Tony Pembroke
- Molecular Biochemistry Laboratory, Department of Chemical Sciences, School of Natural Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX2, Ireland
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10
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Böttger S, Zechel-Gran S, Streckbein P, Knitschke M, Hain T, Weigel M, Wilbrand JF, Domann E, Howaldt HP, Attia S. A New Type of Chronic Wound Infection after Wisdom Tooth Extraction: A Diagnostic Approach with 16S-rRNA Gene Analysis, Next-Generation Sequencing, and Bioinformatics. Pathogens 2020; 9:E798. [PMID: 32998201 DOI: 10.3390/pathogens9100798] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 11/29/2022] Open
Abstract
Delayed-onset infections are rare postoperative complications of lower third molar extractions. This article presents a case of a chronic combined hard and soft tissue infection after the extraction of a third molar, where the causative organisms could only be elucidated by molecular methods. Experimental 16S-rRNA gene analysis with next-generation sequencing and bioinformatics was used to identify the bacterial spectrum of the infection. 16S-rRNA gene analysis delivered the microbiome of the abscessing inflammation while standard culture and laboratory examinations were all sterile. The microbiome showed a mixed bacterial infection with a dominance of Delftia and Alcanivorax (spp.) besides other bacteria of the normal oral flora. Using 16S-rRNA-gene analysis, next-generation sequencing, and bioinformatics, a new type of chronic wound infection after wisdom tooth extraction was found. The property of Delftia and Alcanivorax (spp.) as water-affine environmental bacteria raises suspicion of infection from contaminated water from a dental unit. Thus, osteotomies of teeth should only be done with sterile cooling water. The 16S-rRNA gene analysis should become a part of the routine diagnostics in medical microbiology.
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11
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Kolokotsa A, Leotsinidis M, Kalavrouziotis I, Sazakli E. Effects of tourist flows on antibiotic resistance in wastewater of a Greek island. J Appl Microbiol 2020; 130:516-527. [PMID: 32743833 DOI: 10.1111/jam.14808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/09/2020] [Accepted: 07/24/2020] [Indexed: 12/01/2022]
Abstract
AIM Antibiotic resistance in wastewaters reflects the clinical resistome. This study aimed at investigating whether changes in the population size and composition in the popular tourist destination of Zakynthos island are associated with differentiation in the antibiotic resistance of environmental micro-organisms isolated from wastewater. METHODS AND RESULTS The resistance profiles of four species (Escherichia coli, Staphylococcus sp., Pseudomonas sp. and Enterococcus sp.) were studied in 124 raw and treated municipal wastewaters from November 2015 to August 2016. Isolates were tested against their susceptibility to several antibiotics of different antimicrobial categories. Data concerning the alteration in the population size and composition, due to the tourist mobility, were collected and logistic regression models were used to examine the relationships between antimicrobial resistance and population changes. The decrease in resistance of E. coli to amoxicillin-clavulanate, of enterococci to norfloxacin and ampicillin, and of pseudomonads to almost all antibiotics tested was associated with population increase due to tourist flows. In contrast, the presence of tourists was linked to an increase in quinupristin-dalfopristin resistant enterococci. Resistance of staphylococci did not change during the tourist period. CONCLUSION Changes in population composition in touristic areas are reflected in antibiotic resistance of environmental bacteria in wastewater. SIGNIFICANCE AND IMPACT OF THE STUDY In touristic areas, where people carrying different resistomes are merged, medication should be adapted accordingly.
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Affiliation(s)
- A Kolokotsa
- School of Science and Technology, Hellenic Open University, Patras, Greece
| | - M Leotsinidis
- Laboratory of Public Health, School of Medicine, University of Patras, Patras, Greece
| | - I Kalavrouziotis
- School of Science and Technology, Hellenic Open University, Patras, Greece
| | - E Sazakli
- School of Science and Technology, Hellenic Open University, Patras, Greece.,Laboratory of Public Health, School of Medicine, University of Patras, Patras, Greece
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12
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Déjean G, Tauzin AS, Bennett SW, Creagh AL, Brumer H. Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity. Appl Environ Microbiol 2019; 85:e01491-19. [PMID: 31420336 PMCID: PMC6805095 DOI: 10.1128/aem.01491-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/08/2019] [Indexed: 12/16/2022] Open
Abstract
Genome sequencing has revealed substantial variation in the predicted abilities of individual species within animal gut microbiota to metabolize the complex carbohydrates comprising dietary fiber. At the same time, a currently limited body of functional studies precludes a richer understanding of how dietary glycan structures affect the gut microbiota composition and community dynamics. Here, using biochemical and biophysical techniques, we identified and characterized differences among recombinant proteins from syntenic xyloglucan utilization loci (XyGUL) of three Bacteroides and one Dysgonomonas species from the human gut, which drive substrate specificity and access to distinct polysaccharide side chains. Enzymology of four syntenic glycoside hydrolase family 5 subfamily 4 (GH5_4) endo-xyloglucanases revealed surprising differences in xyloglucan (XyG) backbone cleavage specificity, including the ability of some homologs to hydrolyze congested branched positions. Further, differences in the complement of GH43 alpha-l-arabinofuranosidases and GH95 alpha-l-fucosidases among syntenic XyGUL confer distinct abilities to fully saccharify plant species-specific arabinogalactoxyloglucan and/or fucogalactoxyloglucan. Finally, characterization of highly sequence-divergent cell surface glycan-binding proteins (SGBPs) across syntenic XyGUL revealed a novel group of XyG oligosaccharide-specific SGBPs encoded within select BacteroidesIMPORTANCE The catabolism of complex carbohydrates that otherwise escape the endogenous digestive enzymes of humans and other animals drives the composition and function of the gut microbiota. Thus, detailed molecular characterization of dietary glycan utilization systems is essential both to understand the ecology of these complex communities and to manipulate their compositions, e.g., to benefit human health. Our research reveals new insight into how ubiquitous members of the human gut microbiota have evolved a set of microheterogeneous gene clusters to efficiently respond to the structural variations of plant xyloglucans. The data here will enable refined functional prediction of xyloglucan utilization among diverse environmental taxa in animal guts and beyond.
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Affiliation(s)
- Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexandra S Tauzin
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stuart W Bennett
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - A Louise Creagh
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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13
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Ullmann IF, Tunsjø HS, Andreassen M, Nielsen KM, Lund V, Charnock C. Detection of Aminoglycoside Resistant Bacteria in Sludge Samples From Norwegian Drinking Water Treatment Plants. Front Microbiol 2019; 10:487. [PMID: 30918503 PMCID: PMC6424899 DOI: 10.3389/fmicb.2019.00487] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/25/2019] [Indexed: 02/01/2023] Open
Abstract
Through a culture-based approach using sludge from drinking water treatment plants, this study reports on the presence of aminoglycoside resistant bacteria at 23 different geographical locations in Norway. Sludge samples are derived from a large environmental area including drinking water sources and their surrounding catchment areas. Aminoglycoside resistant bacteria were detected at 18 of the sample sites. Only five samples did not show any growth of isolates resistant to the selected aminoglycosides, kanamycin and gentamycin. There was a statistically significant correlation between the numbers of kanamycin and gentamycin resistant bacteria isolated from the 23 samples, perhaps suggesting common determinants of resistance. Based on 16S rRNA sequencing of 223 aminoglycoside resistant isolates, three different genera of Bacteroidetes were found to dominate across samples. These were Flavobacterium, Mucilaginibacter and Pedobacter. Further phenotypic and genotypic analyses showed that efflux pumps, reduced membrane permeability and four assayed genes coding for aminoglycoside modifying enzymes AAC(6′)-Ib, AAC(3′)-II, APH(3′)-II, APH(3′)-III, could only explain the resistance of a few of the isolates selected for testing. aph(3′)-II was detected in 1.6% of total isolates, aac(6′)-Ib and aph(3′)-III in 0.8%, while aac(3′)-II was not detected in any of the isolates. The isolates, for which potential resistance mechanisms were found, represented 13 different genera suggesting that aminoglycoside resistance is widespread in bacterial genera indigenous to sludge. The present study suggests that aminoglycoside resistant bacteria are present in Norwegian environments with limited anthropogenic exposures. However, the resistance mechanisms remain largely unknown, and further analyses, including culture-independent methods, could be performed to investigate other potential resistance mechanisms. This is, to our knowledge, the first large scale nationwide investigation of aminoglycoside resistance in the Norwegian environment.
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Affiliation(s)
- Ingvild F Ullmann
- Department of Life Sciences and Health, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Hege S Tunsjø
- Department of Life Sciences and Health, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Monica Andreassen
- Department of Zoonotic, Food- and Waterborne Infections, Norwegian Institute of Public Health, Oslo, Norway
| | - Kaare Magne Nielsen
- Department of Life Sciences and Health, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Vidar Lund
- Department of Zoonotic, Food- and Waterborne Infections, Norwegian Institute of Public Health, Oslo, Norway
| | - Colin Charnock
- Department of Life Sciences and Health, OsloMet - Oslo Metropolitan University, Oslo, Norway
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14
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 PMCID: PMC6283892 DOI: 10.3389/fmicb.2018.02928] [Citation(s) in RCA: 412] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 11/13/2022] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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15
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Bruno A, Sandionigi A, Bernasconi M, Panio A, Labra M, Casiraghi M. Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy). Front Microbiol 2018; 9:2557. [PMID: 30429832 PMCID: PMC6220058 DOI: 10.3389/fmicb.2018.02557] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/08/2018] [Indexed: 11/13/2022] Open
Abstract
While safe and of high quality, drinking water can host an astounding biodiversity of microorganisms, dismantling the belief of its "biological simplicity." During the very few years, we are witnessing an exponential growth in scientific publications, exploring the ecology hidden in drinking water treatment plants (DWTPs) and drinking water distribution system (DWDS). We focused on what happens to the microbial communities from source water (groundwater) throughout the main steps of the potabilization process of a DWTP, located in an urbanized area in Northern Italy. Samples were processed by a stringent water filtration to retain even the smallest environmental bacteria and then analyzed with High-Throughput DNA Sequencing (HTS) techniques. We showed that carbon filters harbored a microbial community seeding and shaping water microbiota downstream, introducing a significant variation on incoming (groundwater) microbial community. Chlorination did not instantly affect the altered microbiota. We were also able to correctly predict (through machine learning analysis) samples belonging to groundwater (overall accuracy was 0.71), but the assignation was not reliable with carbon filter samples, which were incorrectly predicted as chlorination samples. The presence and abundance of specific microorganisms allowed us to hypothesize their role as indicators. In particular, Candidatus Adlerbacteria (Parcubacteria), together with microorganisms belonging to Alphaproteobacteria and Gammaproteobacteria, characterized treated water, but not raw water. An exception, confirming our hypothesis, is given by the samples downstream the filters renewal, which had a composition resembling groundwater. Volatility analysis illustrated how carbon filters represented an ecosystem that is stable over time, probably bearing the environmental conditions that promote the survival and growth of this peculiar microbial community.
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Affiliation(s)
- Antonia Bruno
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Anna Sandionigi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | | | - Antonella Panio
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Massimo Labra
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Bicocca cEnter of Science and Technology for FOOD, University of Milano-Bicocca, Milan, Italy
| | - Maurizio Casiraghi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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16
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Abstract
Non-fermenting Gram-negative bacteria are problematic in clinical locations, being one of the most prevalent causes of nosocomial infections. Many of these non-fermenting Gram-negative bacteria are opportunistic pathogens that affect patients that are suffering with underlying medical conditions and diseases. Brevundimonas spp., in particular Brevundimonas diminuta and Brevundimonas vesicularis, are a genus of non-fermenting Gram-negative bacteria considered of minor clinical importance. Forty-nine separate instances of infection relating to Brevundimonas spp were found in the scientific literature along with two pseudo-infections. The majority of these instances were infection with Brevundimonas vesicularis (thirty-five cases – 71%). The major condition associated with Brevundimonas spp infection was bacteraemia with seventeen individual cases/outbreaks (35%). This review identified forty-nine examples of Brevundimonas spp. infections have been discussed in the literature. These findings indicate that infection review programs should consider investigation of possible Brevundimonas spp outbreaks if these bacteria are clinically isolated in more than one patient.
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Affiliation(s)
- Michael P Ryan
- a Industrial Biochemistry Programme, Department of Chemical Sciences , School of Natural Sciences, University of Limerick , Limerick , Ireland
| | - J Tony Pembroke
- b Molecular Biochemistry Laboratory, Department of Chemical Sciences , School of Natural Sciences, University of Limerick , Limerick , Ireland.,c Bernal Institute, University of Limerick , Limerick , Ireland
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17
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Figueroa M, Fernandez V, Arenas-Salinas M, Ahumada D, Muñoz-Villagrán C, Cornejo F, Vargas E, Latorre M, Morales E, Vásquez C, Arenas F. Synthesis and Antibacterial Activity of Metal(loid) Nanostructures by Environmental Multi-Metal(loid) Resistant Bacteria and Metal(loid)-Reducing Flavoproteins. Front Microbiol 2018; 9:959. [PMID: 29869640 PMCID: PMC5962736 DOI: 10.3389/fmicb.2018.00959] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/24/2018] [Indexed: 12/13/2022] Open
Abstract
Microbes are suitable candidates to recover and decontaminate different environments from soluble metal ions, either via reduction or precipitation to generate insoluble, non-toxic derivatives. In general, microorganisms reduce toxic metal ions generating nanostructures (NS), which display great applicability in biotechnological processes. Since the molecular bases of bacterial reduction are still unknown, the search for new -environmentally safe and less expensive- methods to synthesize NS have made biological systems attractive candidates. Here, 47 microorganisms isolated from a number of environmental samples were analyzed for their tolerance or sensitivity to 19 metal(loid)s. Ten of them were highly tolerant to some of them and were assessed for their ability to reduce these toxicants in vitro. All isolates were analyzed by 16S rRNA gene sequencing, fatty acids composition, biochemical tests and electron microscopy. Results showed that they belong to the Enterobacter, Staphylococcus, Acinetobacter, and Exiguobacterium genera. Most strains displayed metal(loid)-reducing activity using either NADH or NADPH as cofactor. While Acinetobacter schindleri showed the highest tellurite ( TeO32- ) and tetrachloro aurate ( AuCl4- ) reducing activity, Staphylococcus sciuri and Exiguobacterium acetylicum exhibited selenite ( SeO32- ) and silver (Ag+) reducing activity, respectively. Based on these results, we used these bacteria to synthetize, in vivo and in vitro Te, Se, Au, and Ag-containing nanostructures. On the other hand, we also used purified E. cloacae glutathione reductase to synthesize in vitro Te-, Ag-, and Se-containing NS, whose morphology, size, composition, and chemical composition were evaluated. Finally, we assessed the putative anti-bacterial activity exhibited by the in vitro synthesized NS: Te-containing NS were more effective than Au-NS in inhibiting Escherichia coli and Listeria monocytogenes growth. Aerobically synthesized TeNS using MF09 crude extracts showed MICs of 45- and 66- μg/ml for E. coli and L. monocytogenes, respectively. Similar MIC values (40 and 82 μg/ml, respectively) were observed for TeNS generated using crude extracts from gorA-overexpressing E. coli. In turn, AuNS MICs for E. coli and L. monocytogenes were 64- and 68- μg/ml, respectively.
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Affiliation(s)
- Maximiliano Figueroa
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Valentina Fernandez
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | | | - Diego Ahumada
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Claudia Muñoz-Villagrán
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Departamento de Ciencias Básicas, Facultad de Ciencia, Universidad Santo Tomas, Sede Santiago, Chile
| | - Fabián Cornejo
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Esteban Vargas
- Center for the Development of Nanoscience and Nanotechnology, Santiago, Chile
| | - Mauricio Latorre
- Mathomics, Centro de Modelamiento Matemático, Universidad de Chile, Beauchef, Santiago, Chile.,Fondap-Center of Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | | | - Claudio Vásquez
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe Arenas
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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18
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 DOI: 10.3389/fmicb.2018.02928/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 05/20/2023] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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19
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Indrelid S, Kleiveland C, Holst R, Jacobsen M, Lea T. The Soil Bacterium Methylococcus capsulatus Bath Interacts with Human Dendritic Cells to Modulate Immune Function. Front Microbiol 2017; 8:320. [PMID: 28293233 PMCID: PMC5329024 DOI: 10.3389/fmicb.2017.00320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/15/2017] [Indexed: 01/09/2023] Open
Abstract
The prevalence of inflammatory bowel disease (IBD) has increased in Western countries during the course of the twentieth century, and is evolving to be a global disease. Recently we showed that a bacterial meal of a non-commensal, non-pathogenic methanotrophic soil bacterium, Methylococcus capsulatus Bath prevents experimentally induced colitis in a murine model of IBD. The mechanism behind the effect has this far not been identified. Here, for the first time we show that M. capsulatus, a soil bacterium adheres specifically to human dendritic cells, influencing DC maturation, cytokine production, and subsequent T cell activation, proliferation and differentiation. We characterize the immune modulatory properties of M. capsulatus and compare its immunological properties to those of another Gram-negative gammaproteobacterium, the commensal Escherichia coli K12, and the immune modulatory Gram-positive probiotic bacterium, Lactobacillus rhamnosus GG in vitro. M. capsulatus induces intermediate phenotypic and functional DC maturation. In a mixed lymphocyte reaction M. capsulatus-primed monocyte-derived dendritic cells (MoDCs) enhance T cell expression of CD25, the γ-chain of the high affinity IL-2 receptor, supports cell proliferation, and induce a T cell cytokine profile different from both E. coli K12 and Lactobacillus rhamnosus GG. M. capsulatus Bath thus interacts specifically with MoDC, affecting MoDC maturation, cytokine profile, and subsequent MoDC directed T cell polarization.
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Affiliation(s)
- Stine Indrelid
- Research and Innovation, Østfold Hospital TrustKalnes, Norway; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life SciencesAas, Norway
| | - Charlotte Kleiveland
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences Aas, Norway
| | - René Holst
- Research and Innovation, Østfold Hospital Trust Kalnes, Norway
| | - Morten Jacobsen
- Research and Innovation, Østfold Hospital TrustKalnes, Norway; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life SciencesAas, Norway
| | - Tor Lea
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences Aas, Norway
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20
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Bruno A, Sandionigi A, Galimberti A, Siani E, Labra M, Cocuzza C, Ferri E, Casiraghi M. One step forwards for the routine use of high-throughput DNA sequencing in environmental monitoring. An efficient and standardizable method to maximize the detection of environmental bacteria. Microbiologyopen 2016; 6. [PMID: 27790854 PMCID: PMC5300880 DOI: 10.1002/mbo3.421] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/21/2016] [Accepted: 09/28/2016] [Indexed: 11/21/2022] Open
Abstract
We propose an innovative, repeatable, and reliable experimental workflow to concentrate and detect environmental bacteria in drinking water using molecular techniques. We first concentrated bacteria in water samples using tangential flow filtration and then we evaluated two methods of environmental DNA extraction. We performed tests on both artificially contaminated water samples and real drinking water samples. The efficiency of the experimental workflow was measured through qPCR. The successful applicability of the high‐throughput DNA sequencing (HTS) approach was demonstrated on drinking water samples. Our results demonstrate the feasibility of our approach in high‐throughput‐based studies, and we suggest incorporating it in monitoring strategies to have a better representation of the microbial community. In the recent years, HTS techniques have become key tools in the study of microbial communities. To make the leap from academic laboratories to the routine monitoring (e.g., water treatment plants laboratories), we here propose an experimental workflow suitable for the introduction of HTS as a standard method for detecting environmental bacteria.
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Affiliation(s)
- Antonia Bruno
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
| | - Anna Sandionigi
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
| | - Andrea Galimberti
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
| | - Eleonora Siani
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
| | - Massimo Labra
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
| | - Clementina Cocuzza
- Medicine and Surgery Department, University of Milano-Bicocca, Monza, Italy
| | - Emanuele Ferri
- FEM2-Ambiente, University of Milano-Bicocca, Milan, Italy
| | - Maurizio Casiraghi
- ZooPlantLab, Biotechnologies and Bioscience Department, University of Milano-Bicocca, Milan, Italy
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Li H, Li T, Yao M, Li J, Zhang S, Wirth S, Cao W, Lin Q, Li X. Pika Gut May Select for Rare but Diverse Environmental Bacteria. Front Microbiol 2016; 7:1269. [PMID: 27582734 PMCID: PMC4987353 DOI: 10.3389/fmicb.2016.01269] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/02/2016] [Indexed: 02/01/2023] Open
Abstract
The composition of the mammalian gut bacterial communities can be influenced by the introduction of environmental bacteria in their respective habitats. However, there are no extensive studies examining the interactions between environmental bacteriome and gut bacteriome in wild mammals. Here, we explored the relationship between the gut bacterial communities of pika (Ochotona spp.) and the related environmental bacteria across host species and altitudinal sites using 16S rRNA gene sequencing. Plateau pikas (O. curzoniae) and Daurian pikas (O. daurica) were sampled at five different sites, and plant and soil samples were collected at each site as well. Our data indicated that Plateau pikas and Daurian pikas had distinct bacterial communities. The pika, plant and soil bacterial communities were also distinct. Very little overlap occurred in the pika core bacteria and the most abundant environmental bacteria. The shared OTUs between pikas and environments were present in the environment at relatively low abundance, whereas they were affiliated with diverse bacterial taxa. These results suggested that the pika gut may mainly select for low-abundance but diverse environmental bacteria in a host species-specific manner.
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Affiliation(s)
- Huan Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of SciencesSichuan, China; University of Chinese Academy of SciencesBeijing, China
| | - Tongtong Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
| | - Minjie Yao
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
| | - Shiheng Zhang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
| | - Stephan Wirth
- Leibniz-Center for Agricultural Landscape Research (ZALF), Institute of Landscape Biogeochemistry Müncheberg, Germany
| | - Weidong Cao
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural SciencesBeijing, China; Soil and Fertilizer Institute, Qinghai Academy of Agriculture and Forestry Sciences, Qinghai UniversityXining, China
| | - Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Sichuan, China
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Römling U, Galperin MY. Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. Trends Microbiol 2015; 23:545-57. [PMID: 26077867 DOI: 10.1016/j.tim.2015.05.005] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/05/2015] [Accepted: 05/18/2015] [Indexed: 12/30/2022]
Abstract
Recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. In most studied bacteria, just two subunits, BcsA and BcsB, are necessary and sufficient for the formation of the polysaccharide chain in vitro. Other subunits - which differ among various taxa - affect the enzymatic activity and product yield in vivo by modulating (i) the expression of the biosynthesis apparatus, (ii) the export of the nascent β-D-glucan polymer to the cell surface, and (iii) the organization of cellulose fibers into a higher-order structure. These auxiliary subunits play key roles in determining the quantity and structure of resulting biofilms, which is particularly important for the interactions of bacteria with higher organisms - leading to rhizosphere colonization and modulating the virulence of cellulose-producing bacterial pathogens inside and outside of host cells. We review the organization of four principal types of cellulose synthase operon found in various bacterial genomes, identify additional bcs genes that encode components of the cellulose biosynthesis and secretion machinery, and propose a unified nomenclature for these genes and subunits. We also discuss the role of cellulose as a key component of biofilms and in the choice between acute infection and persistence in the host.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Farmer JT, Shimkevitch AV, Reilly PS, Mlynek KD, Jensen KS, Callahan MT, Bushaw-Newton KL, Kaplan JB. Environmental bacteria produce abundant and diverse antibiofilm compounds. J Appl Microbiol 2014; 117:1663-73. [PMID: 25179003 DOI: 10.1111/jam.12639] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/23/2014] [Accepted: 08/22/2014] [Indexed: 11/26/2022]
Abstract
AIMS The aim of this study was to isolate novel antibiofilm compounds produced by environmental bacteria. METHODS AND RESULTS Cell-free extracts were prepared from lawns of bacteria cultured on agar. A total of 126 bacteria isolated from soil, cave and river habitats were employed. Extracts were tested for their ability to inhibit Staphylococcus aureus biofilm in a 96-well microtitre plate assay. A total of 55/126 extracts (44%) significantly inhibited Staph. aureus biofilm. Seven extracts were selected for further analysis. The antibiofilm activities in all seven extracts exhibited unique patterns of molecular mass, chemical polarity, heat stability and spectrum of activity against Staph. aureus, Staphylococcus epidermidis and Pseudomonas fluorescens, suggesting that these seven antibiofilm activities were mediated by unique chemical compounds with different mechanisms of action. CONCLUSIONS Environmental bacteria produce abundant and diverse antibiofilm compounds. SIGNIFICANCE AND IMPACT OF THE STUDY Screening cell-free extracts is a useful method for identifying secreted compounds that regulate biofilm formation. Such compounds may represent a novel source of antibiofilm agents for technological development.
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Affiliation(s)
- J T Farmer
- Department of Biology, American University, Washington, DC, USA
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Abstract
Bacteria can become resistant to antibiotics by mutation, transformation, and/or acquisition of new genes which are normally associated with mobile elements (plasmids, transposons, and integrons). Mobile elements are the main driving force in horizontal gene transfer between strains, species, and genera and are responsible for the rapid spread of particular elements throughout a bacterial community and between ecosystems. Today, antibiotic resistant bacteria are widely distributed throughout the world and have even been isolated from environments that are relatively untouched by human civilization. In this review macrolides, lincosamides, streptogramins, and tetracycline resistance genes and bacteria will be discussed with an emphasis on the resistance genes which are unique to environmental bacteria which are defined for this review as species and genera that are primarily found outside of humans and animals.
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Affiliation(s)
- Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington Seattle, WA, USA
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