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McDermott G, Walsh A, Crispie F, Frost S, Greally P, Cotter PD, O’Sullivan O, Renwick J. Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics. Int J Mol Sci 2024; 25:3893. [PMID: 38612702 PMCID: PMC11011389 DOI: 10.3390/ijms25073893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Cystic fibrosis (CF) is an inherited genetic disorder which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targeted 16S rDNA sequencing. Here, we employed whole-genome shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We carried out functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between microbial diversity measures and independent demographic and clinical variables were performed. Shotgun metagenomics detected a greater diversity of bacteria than culture-based methods. A large proportion of the top 25 most-dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity, while no CF pathogen was associated with reduced microbial diversity. There was a diverse resistome present in all samples in this study, with 57.8% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Stenotrophomonas maltophilia were observed to persist in young CF patients, while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF. Shotgun metagenomics could provide a very useful one-stop assay for detecting pathogens, emergence of resistance and conversion to persistent colonisation in early CF disease.
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Affiliation(s)
- Gillian McDermott
- Trinity Centre for Health Science, Clinical Microbiology Department, School of Medicine, Faculty of Health Science, Trinity College Dublin, Tallaght University Hospital, D24 NR0A Dublin, Ireland;
| | - Aaron Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Susanna Frost
- Tallaght University Hospital, Tallaght, D24 NR0 Dublin, Ireland (P.G.)
| | - Peter Greally
- Tallaght University Hospital, Tallaght, D24 NR0 Dublin, Ireland (P.G.)
- Hermitage Medical Clinic, Lucan, D20 W722 Dublin, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Orla O’Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Julie Renwick
- Trinity Centre for Health Science, Clinical Microbiology Department, School of Medicine, Faculty of Health Science, Trinity College Dublin, Tallaght University Hospital, D24 NR0A Dublin, Ireland;
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Shetty BD, Pandey PK, Mai K. Microbial diversity in dairy manure environment under liquid-solid separation systems. ENVIRONMENTAL TECHNOLOGY 2024:1-17. [PMID: 38310325 DOI: 10.1080/09593330.2024.2309481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
Abstract
In dairy manure, a wide array of microorganisms, including many pathogens, survive and grow under suitable conditions. This microbial community offers a tremendous opportunity for studying animal health, the transport of microbes into the soil, air, and water, and consequential impacts on public health. The aim of this study was to assess the impacts of manure management practices on the microbial community of manure. The key novelty of this work is to identify the impacts of various stages of manure management on microbes living in dairy manure. In general, the majority of dairy farms in California use a flush system to manage dairy manure, which involves liquid-solid separations. To separate liquid and solid in manure, Multi-stage Alternate Dairy Effluent Management Systems (ADEMS) that use mechanical separation systems (MSS) or weeping wall separation systems (WWSS) are used. Thus, this study was conducted to understand how these manure management systems affect the microbial community. We studied the microbial communities in the WWSS and MSS separation systems, as well as in the four stages of the ADEMS. The 16S rRNA gene from the extracted genomic DNA of dairy manure was amplified using the NovoSeq Illumina next-generation sequencing platform. The sequencing data were used to perform the analysis of similarity (ANOSIM) and multi-response permutation procedure (MRRP) statistical tests, and the results showed that microbial communities among WWSS and MSS were significantly different (p < 0.05). These findings have significant practical implications for the design and implementation of manure management practices in dairy farms.
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Affiliation(s)
- B Dharmaveer Shetty
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Pramod K Pandey
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Kelly Mai
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Mechanisms of Disease and Translational Research, School of Medical Science, University of New South Wales, Sydney, Australia
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3
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Abou Chacra L, Benatmane A, Iwaza R, Ly C, Alibar S, Armstrong N, Mediannikov O, Bretelle F, Fenollar F. Culturomics reveals a hidden world of vaginal microbiota with the isolation of 206 bacteria from a single vaginal sample. Arch Microbiol 2023; 206:20. [PMID: 38095693 PMCID: PMC10721685 DOI: 10.1007/s00203-023-03742-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/05/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023]
Abstract
The composition of the vaginal microbiota is known to be influenced by various factors and to be associated with several disorders affecting women's health. Although metagenomics is currently a widely used method for studying the human microbiota, it has certain limitations, such as a lack of information on bacterial viability. It is therefore important to use culture-based methods such as culturomics. Here, we used 35 different culture conditions to comprehensively characterize the vaginal bacterial diversity of a single woman's flora. A total of 206 bacterial species, belonging to six phyla (for a little more than half to Firmicutes, followed mainly by Actinobacteria, Bacteroidetes, and Proteobacteria) and 45 families, and 2 fungal species were cultivated. While several species of lactobacilli have been isolated, a wide variety of other bacteria were also separated, including 65 never reported before in vaginal flora, including a new bacterial species, Porphyromonas vaginalis sp. nov. Extensive culture-based methods are essential to establish a comprehensive, evidence-based repertoire of bacterial viability. If combined with molecular methods, they can provide a much more thorough understanding of the vaginal microbiota and fulfil the unknown part of metagenomic studies.
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Affiliation(s)
- Linda Abou Chacra
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Amel Benatmane
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Rim Iwaza
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Claudia Ly
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | | | | | - Oleg Mediannikov
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Florence Bretelle
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Department of Gynecology and Obstetrics, AP-HM, Gynépole, La Conception, Marseille, France
| | - Florence Fenollar
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.
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Farfour E, Roux A, Sage E, Revillet H, Vasse M, Vallée A. Rarely Encountered Gram-Negative Rods and Lung Transplant Recipients: A Narrative Review. Microorganisms 2023; 11:1468. [PMID: 37374970 DOI: 10.3390/microorganisms11061468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/18/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
The respiratory tract of lung transplant recipients (LTR) is likely to be colonized with non-fermentative Gram-negative rods. As a consequence of the improvements in molecular sequencing and taxonomy, an increasing number of bacterial species have been described. We performed a review of the literature of bacterial infections in LTR involving non-fermentative Gram-negative rods with exclusion of Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Achromobacter spp. and Burkholderia spp. Overall, non-fermenting GNR were recovered from 17 LTR involving the following genera: Acetobacter, Bordetella, Chryseobacterium, Elizabethkinga, Inquilinus, and Pandoraea. We then discuss the issues raised by these bacteria, including detection and identification, antimicrobial resistance, pathogenesis, and cross-transmission.
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Affiliation(s)
- Eric Farfour
- Service de Biologie Clinique, Hôpital Foch, 92150 Suresnes, France
| | - Antoine Roux
- Service de Pneumologie et Transplantation Pulmonaire, Hôpital Foch, 92150 Suresnes, France
| | - Edouard Sage
- Service de Chirurgie Thoracique et Transplantation Pulmonaire, Hôpital Foch, 92150 Suresnes, France
| | - Hélène Revillet
- Service de Bactériologie-Hygiène Hospitalière, CHU de Toulouse, 31300 Toulouse, France
- Observatoire National Burkholderia cepacia, 31403 Toulouse, France
| | - Marc Vasse
- Service de Biologie Clinique, Hôpital Foch, 92150 Suresnes, France
- INSERM Hémostase Inflammation Thrombose HITH U1176, Université Paris-Saclay, 94276 Le Kremlin-Bicêtre, France
| | - Alexandre Vallée
- Service d'Epidémiologie-Data-Biostatistiques, Délégation à la Recherche Clinique et à l'Innovation, Hôpital Foch, 92150 Suresnes, France
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5
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Milligan EG, Calarco J, Davis BC, Keenum IM, Liguori K, Pruden A, Harwood VJ. A Systematic Review of Culture-Based Methods for Monitoring Antibiotic-Resistant Acinetobacter, Aeromonas, and Pseudomonas as Environmentally Relevant Pathogens in Wastewater and Surface Water. Curr Environ Health Rep 2023:10.1007/s40572-023-00393-9. [PMID: 36821031 DOI: 10.1007/s40572-023-00393-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 02/24/2023]
Abstract
PURPOSE OF REVIEW Mounting evidence indicates that habitats such as wastewater and environmental waters are pathways for the spread of antibiotic-resistant bacteria (ARB) and mobile antibiotic resistance genes (ARGs). We identified antibiotic-resistant members of the genera Acinetobacter, Aeromonas, and Pseudomonas as key opportunistic pathogens that grow or persist in built (e.g., wastewater) or natural aquatic environments. Effective methods for monitoring these ARB in the environment are needed to understand their influence on dissemination of ARB and ARGs, but standard methods have not been developed. This systematic review considers peer-reviewed papers where the ARB above were cultured from wastewater or surface water, focusing on the accuracy of current methodologies. RECENT FINDINGS Recent studies suggest that many clinically important ARGs were originally acquired from environmental microorganisms. Acinetobacter, Aeromonas, and Pseudomonas species are of interest because their ability to persist and grow in the environment provides opportunities to engage in horizontal gene transfer with other environmental bacteria. Pathogenic strains of these organisms resistant to multiple, clinically relevant drug classes have been identified as an urgent threat. However, culture methods for these bacteria were generally developed for clinical samples and are not well-vetted for environmental samples. The search criteria yielded 60 peer-reviewed articles over the past 20 years, which reported a wide variety of methods for isolation, confirmation, and antibiotic resistance assays. Based on a systematic comparison of the reported methods, we suggest a path forward for standardizing methodologies for monitoring antibiotic resistant strains of these bacteria in water environments.
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Affiliation(s)
- Erin G Milligan
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.,Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Jeanette Calarco
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Benjamin C Davis
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ishi M Keenum
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Krista Liguori
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA. .,Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA.
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Dealing with Hidden Threats: The Antimicrobial Effect of the Embalming Process. Microorganisms 2022; 10:microorganisms10112180. [PMID: 36363772 PMCID: PMC9693414 DOI: 10.3390/microorganisms10112180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/01/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Individuals naturally carry bacteria and other microbes as part of their natural flora, with some being opportunistic pathogens. Approximately 30% of the population is known to carry Staphylococcus aureus in their nasal cavity, an organism that causes infections ranging from soft tissue abscesses to toxic shock syndrome. This problem is compounded by the presence of antibiotic-resistant strains such as Methicillin-Resistant Staphylococcus aureus (MRSA). Commensal bacteria present on cadavers pose a risk to those who handle the body. As a Medical School Anatomy laboratory that performs hands-on cadaveric dissection, we wanted to know whether the embalming process is sufficient to kill all commensal bacteria that pose a risk to staff and students. Even if these strains do not cause disease in these individuals, secondary transmission could occur to friends and family, who may be at higher risk of acquiring an infection. Embalming is assumed to eliminate all microbial contamination on the body. However, there are limited studies to confirm this. This study characterises the incidence of antibiotic sensitive and resistant bacteria in cadavers donated for medical teaching and research. We have screened for Methicillin-Resistant Organisms (MRO) and Extended-Spectrum Beta-Lactamase (ESBL) producing bacteria. In this study group of cadavers, approximately 46% (16/35) carry an MRO, while 51% (18/35) carry an ESBL positive organism prior to embalming. By determining the organisms’ presence pre- and post-embalming, we can evaluate the embalming procedure’s effectiveness. Our results show embalming eliminates detectable microbes in about 51% (18/35) of the cadavers. MRO dropped by 75% (16 to 4 positive cadavers), while ESBL organisms went down by almost 95% (from 18 to 1 positive cadaver). There was a further decrease in the number of positive cadavers after storage at 4 °C to 6% (2/32). Thus, although the embalming process does not immediately sterilise all the cadavers, prolonged storage at 4 °C can further reduce the number of viable bacteria.
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7
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Itoh N, Akazawa N, Ishibana Y, Masuishi T, Nakata A, Murakami H. Clinical and microbiological features of obstructive cholangitis with bloodstream infection caused by Pandoraea apista identified by MALDI-TOF mass spectrometry and ribosomal RNA sequencing in a cancer patient. BMC Infect Dis 2022; 22:529. [PMID: 35672730 PMCID: PMC9171735 DOI: 10.1186/s12879-022-07514-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 06/01/2022] [Indexed: 11/12/2022] Open
Abstract
Background Pandoraea species are multidrug-resistant glucose-nonfermenting gram-negative bacilli that are usually isolated from patients with cystic fibrosis (CF) and from water and soil. Reports of diseases, including bloodstream infections, caused by Pandoraea spp. in non-CF patients are rare, and the clinical and microbiological characteristics are unclear. The identification of Pandorea spp. is limited by conventional microbiological methods and may be misidentified as other species owing to overlapping biochemical profiles. Here, we report the first case of obstructive cholangitis with bacteremia caused by Pandoraea apista in a patient with advanced colorectal cancer. A 61-year-old man with advanced colorectal cancer who underwent right nephrectomy for renal cell carcinoma 4 years earlier with well-controlled diabetes mellitus was admitted to our hospital with fever for 2 days. The last chemotherapy (regorafenib) was administered approximately 3 weeks ago, and an endoscopic ultrasound-guided hepaticogastrostomy was performed 2 weeks ago under hospitalization for obstructive jaundice. Two days prior, he presented with fever with chills. He was treated with piperacillin-tazobactam for obstructive cholangitis and showed improvement but subsequently presented with exacerbation. Bacterial isolates from the blood and bile samples were identified as P. apista using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S ribosomal RNA sequencing. Based on the susceptibility results of the isolates, he was successfully treated with oral trimethoprim-sulfamethoxazole 160 mg/800 mg/day for 14 days for P. apista infection. Conclusions Pandoraea species are often misidentified. Therefore, multiple approaches should be used to identify them, and decisions regarding antimicrobial treatment should be based on actual in vitro susceptibility. Only seven cases of Pandoraea spp. bloodstream infections have been reported, and we report the first case of cholangitis with bacteremia.
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Affiliation(s)
- Naoya Itoh
- Division of Infectious Diseases, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan. .,Collaborative Chairs Emerging and Reemerging Infectious Diseases, National Center for Global Health and Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
| | - Nana Akazawa
- Division of Infectious Diseases, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Yuichi Ishibana
- Division of Infectious Diseases, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Toshiki Masuishi
- Department of Clinical Oncology, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Akinobu Nakata
- Department of Clinical Oncology, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Hiromi Murakami
- Division of Infectious Diseases, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
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Accurate Identification of Diverse N-acyl Homoserine Lactones in Marine Vibrio fluvialis by UHPLC-MS/MS. Curr Microbiol 2022; 79:181. [PMID: 35508788 DOI: 10.1007/s00284-022-02879-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/12/2022] [Indexed: 11/03/2022]
Abstract
Vibrio fluvialis is a marine opportunistic pathogen that frequently causes diseases in aquatic animals and humans. V. fluvialis can produce quorum sensing signaling molecules to coordinate cell density-dependent behavioral changes, including N-acyl homoserine lactone (AHL), which acts as a vital mediator of virulence-associated gene expression. Currently, several AHL molecules in V. fluvialis have been detected via biological and physicochemical methods, although different detection approaches have generated diverse AHL profiles. Here, we describe the AHL-producing bacterium, V. fluvialis BJ-1, which was isolated from marine sediments from the East China Sea. V. fluvialis BJ-1 could stimulate AHL-mediated β-galactosidase synthesis of the biosensor Agrobacterium tumefaciens NTL4 (pZLR4) but could not induce violacein production in the AHL reporter strain, Chromobacterium violaceum CV026. This bacterial isolate exhibited strong AHL-producing activity at low cell density; however, the AHL activity declined when population density remained at high levels. Analysis of the AHLs by Ultra-High-Performance Liquid Chromatography tandem Mass Spectrometry demonstrated that V. fluvialis BJ-1 produced five different AHL signaling molecules, including two linear chain AHL products (C8- and C10-HSL), and three β-carbon-oxidative AHL products (3-O-C8-, 3-O-C10- and 3-O-C12-HSL). Significantly, the present study is the first to accurately define the AHL profile of marine V. fluvialis. In future, the coupling of UHPLC to ESI-MS/MS is expected to be utilized for the accurate determination of AHL profiles in marine Vibrio.
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A panoptic review of techniques for finfish disease diagnosis: The status quo and future perspectives. J Microbiol Methods 2022; 196:106477. [DOI: 10.1016/j.mimet.2022.106477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
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Kaboré B, Ouédraogo GA, Cissé H, Ouédraogo HS, Sampo E, Zongo KJ, Zeba B, Traoré Y, Gnankiné O, Sanou I, Savadogo A. (GTG) 5-PCR fingerprinting of multi-drug resistant Escherichia coli bacteria isolates from hospital in Ouagadougou, Burkina Faso. BMC Microbiol 2022; 22:118. [PMID: 35488211 PMCID: PMC9052641 DOI: 10.1186/s12866-022-02537-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Escherichia coli (E. coli) is the most common bacterial species implicated in various types of infections including septicemia, gastroenteritis, urinary tract infections, meningitis and others pathologies. These involve several bacterial clones with multidrug resistance making them difficult to treat. The aims of this study was to perform molecular typing of E. coli strains using universal primer (GTG)5. In this study, 53 E. coli strains were collected from inpatients and outpatients. The test of antimicrobial sensibility was realized using CA-SFM /EUCAST method and strains were identified by conventional microbiological tests. The carbapenemase-producing strains were demonstrated by phenotypic method. Bacterial DNA was extracted by boiling method. (GTG)5-PCR was used for strain subtyping. The DendroUPGMA software was used for grouping of strains from the genetic fingerprints obtained by (GTG)5-PCR. RESULTS Antibiotic susceptibility test revealed that all strains were multi-drug resistant (MDR). Its strains showed resistance to at least three different families of antibiotics. Of this MDR strains, only one was a metallo-β-lactamase producer. The dendrogram obtained using genetic fingerprinting allowed the E. coli strains to be grouped into 22 clusters (G1 to G22). CONCLUSION The (GTG) 5-PCR assay enabled rapid molecular typing of E. coli strains. The strains of E. coli typed in this study would belong to different clones.
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Affiliation(s)
- Boukaré Kaboré
- Department of Biochemistry and Microbiology, Laboratory of Applied Biochemistry and Immunology, University Joseph KI-ZERBO, BP 7021, Ouagadougou 03, Burkina Faso.
| | - Ganamé Abasse Ouédraogo
- Department of Biochemistry and Microbiology, Laboratory of Applied Biochemistry and Immunology, University Joseph KI-ZERBO, BP 7021, Ouagadougou 03, Burkina Faso
| | - Hama Cissé
- Department of Biochemistry and Microbiology, Laboratory of Applied Biochemistry and Immunology, University Joseph KI-ZERBO, BP 7021, Ouagadougou 03, Burkina Faso
| | - Henri S Ouédraogo
- Department of Biochemistry and Microbiology, Laboratory of Applied Biochemistry and Immunology, University Joseph KI-ZERBO, BP 7021, Ouagadougou 03, Burkina Faso
| | | | - Koudbi Jacob Zongo
- Department of Biochemistry and Microbiology, Faculty of Applied Science and Technology, University of Dedougou, BP 176, Dedougou, Burkina Faso
| | - Boukaré Zeba
- Department of Biochemistry and Microbiology, Laboratory of Applied Biochemistry and Immunology, University Joseph KI-ZERBO, BP 7021, Ouagadougou 03, Burkina Faso
| | - Yves Traoré
- Department of Biochemistry and Microbiology, Laboratory of Applied Biochemistry and Immunology, University Joseph KI-ZERBO, BP 7021, Ouagadougou 03, Burkina Faso
| | - Olivier Gnankiné
- Department of Biology and Physiology Aminale, University Joseph KI-ZERBO, BP 7021, Ouagadougou 03, Burkina Faso
| | - Idrissa Sanou
- UFR Health Sciences, University Joseph KI-ZERBO, BP 7021, Ouagadougou 03, Burkina Faso.,Laboratory of Bacteriology and Virology at, Tengadogo University Hospital, BP 104, Ouagadougou, Burkina Faso
| | - Aly Savadogo
- Department of Biochemistry and Microbiology, Laboratory of Applied Biochemistry and Immunology, University Joseph KI-ZERBO, BP 7021, Ouagadougou 03, Burkina Faso
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11
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A Variant Carbapenem Inactivation Method (CIM) for Acinetobacter baumannii Group with Shortened Time-to-Result: rCIM-A. Pathogens 2022; 11:pathogens11040482. [PMID: 35456157 PMCID: PMC9024794 DOI: 10.3390/pathogens11040482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/10/2022] [Accepted: 04/13/2022] [Indexed: 02/01/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii group organisms (CRAB) are challenging because the choice between targeted, new antibiotic drug options and hygiene measures should be guided by a timely identification of resistance mechanisms. In CRAB, acquired class-D carbapenemases (CHDLs) are active against meropenem and imipenem. If PCR methods are not the first choice, phenotypic methods have to be implemented. While promising, the carbapenemase inactivation method (CIM) using meropenem-hydrolysis is, however, hampered by poor performance or overly long time-to-result. We developed a rapid CIM (rCIM-A) with good performance using ertapenem, imipenem, and meropenem disks, 2-h permeabilization and incubation with the test strain in trypticase soy broth, and a read-out of residual carbapenem activity after 6 h, and optionally after 16–18 h. Using clinical isolates and type-strains of Acinetobacter (n = 67) not harboring carbapenemases (n = 28) or harboring acquired carbapenemases (n = 39), the sensitivity of detection was 97.4% with the imipenem disk after 6 h at a specificity of 92.9%. If the inhibition zone around the ertapenem disk at 6 h was 6 or ≤26 mm at 16–18 h, or ≤25.5 mm for meropenem, the specificity was 100%. Because of the high negative predictive value, the rCIM-A seems particularly appropriate in areas of lower CRAB-frequency.
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Ray T, Gaire TN, Dean CJ, Rowe S, Godden SM, Noyes NR. The microbiome of common bedding materials before and after use on commercial dairy farms. Anim Microbiome 2022; 4:18. [PMID: 35256016 PMCID: PMC8900318 DOI: 10.1186/s42523-022-00171-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/23/2022] [Indexed: 01/04/2023] Open
Abstract
Background Bovine mastitis is one of the most economically important diseases affecting dairy cows. The choice of bedding material has been identified as an important risk factor contributing to the development of mastitis. However, few reports examine both the culturable and nonculturable microbial composition of commonly used bedding materials, i.e., the microbiome. Given the prevalence of nonculturable microbes in most environments, this information could be an important step to understanding whether and how the bedding microbiome acts as a risk factor for mastitis. Therefore, our objective was to characterize the microbiome composition and diversity of bedding material microbiomes, before and after use.
Methods We collected 88 bedding samples from 44 dairy farms in the U.S. Unused (from storage pile) and used (out of stalls) bedding materials were collected from four bedding types: new sand (NSA), recycled manure solids (RMS), organic non-manure (ON) and recycled sand (RSA). Samples were analyzed using 16S rRNA sequencing of the V3–V4 region. Results The overall composition as well as the counts of several microbial taxa differed between bedding types, with Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes dominating across all types. Used bedding contained a significantly different microbial composition than unused bedding, but the magnitude of this difference varied by bedding type, with RMS bedding exhibiting the smallest difference. In addition, positive correlations were observed between 16S rRNA sequence counts of potential mastitis pathogens (bacterial genera) and corresponding bedding bacterial culture data. Conclusion Our results strengthen the role of bedding as a potential source of mastitis pathogens. The consistent shift in the microbiome of all bedding types that occurred during use by dairy cows deserves further investigation to understand whether this shift promotes pathogen colonization and/or persistence, or whether it can differentially impact udder health outcomes. Future studies of bedding and udder health may be strengthened by including a microbiome component to the study design. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00171-2.
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Yang Y, Hu H, Zhou C, Zhang W, Yu Y, Liu Q, Lu T, Zhang Q. Characteristics and accurate identification of Pantoea dispersa with a case of spontaneous rupture of hepatocellular carcinoma in China: A case report. Medicine (Baltimore) 2022; 101:e28541. [PMID: 35029210 PMCID: PMC8758028 DOI: 10.1097/md.0000000000028541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/21/2021] [Indexed: 01/05/2023] Open
Abstract
INTRODUCTION Pantoea dispersa belongs to the genus Pantoea, which is isolated from Enterobacteriaceae. It has been reported to cause some kinds of infections, but there are few detailed studies on it, especially its characteristics and identification methods, which has caused a lot of trouble in clinical work. PATIENT CONCERNS A 51-year-old Chinese man was admitted to our hospital with a 7-hour history of progressive abdominal pain. He was previously diagnosed with liver cirrhosis secondary to chronic hepatitis B infection and hepatocellular carcinoma. An emergency hepatic artery embolization for hemostasis was performed under local anesthesia. Forty-eight hours later, the patient presented sudden onset of high fever up to 39.0 °C and chill. DIAGNOSIS Morphological and phenotypic profiles were performed for preliminary identification for P dispersa. The biochemical features were obtained by VITEK 2 Test Kit. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis and 16S ribosomal RNA sequencing were performed to accurately identify P dispersa. INTERVENTION Antibiotic therapy of intravenous ceftazidime was started empirically. The antibiotic treatment was switched to intravenous cefepime at the same time because of suspected ceftazidime treatment failure and microbiological sensitivity. OUTCOMES The patient remained afebrile, and the second blood culture results were negative. Chest X-ray was normal as well. In order to control the progression of the hepatic lesion, transarterial chemoembolization was performed under local anesthesia. After completion of 14 days of antibiotic treatment, the patient was discharged with no signs of recurrence. CONCLUSION P dispersa, a gram-negative bacterium rod, were facultative anaerobic, which displayed yellow pigmentation, round, raised, smooth on culture plates. Conventional analysis was difficult to complete its identification. With biochemical tests, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis and 16S ribosomal RNA sequencing, P dispersa can be accurately identified. It will help physicians understand the related clinical manifestations and make timely and effective treatment for patients.
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El-Zamkan MA, Mohamed HMA. Antimicrobial resistance, virulence genes and biofilm formation in Enterococcus species isolated from milk of sheep and goat with subclinical mastitis. PLoS One 2021; 16:e0259584. [PMID: 34780540 PMCID: PMC8592430 DOI: 10.1371/journal.pone.0259584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/21/2021] [Indexed: 01/09/2023] Open
Abstract
This study is designed to discuss the antimicrobial resistance, virulence determinants and biofilm formation capacity of Enterococcus spp. isolated from milk of sheep and goat with subclinical mastitis in Qena, Egypt. The obtained isolates were identified by the VITEK2 system and 16S rDNA sequencing as E. faecalis, E. faecium, E. casseliflavus and E. hirae. Overall, E. faecalis and E. faecium were the dominant species recovered from mastitic milk samples. The antimicrobial susceptibility test evidenced multidrug resistance of the isolates against the following antimicrobials: oxacillin (89.2.%), followed by vancomycin (75.7%) and linezolid (70.3%). Also, most of these isolates (73%) could form biofilms. For example, 18.9% of Enterococcus strains formed strong biofilm, whereas 32.4% of isolates formed moderate biofilm and 21.6% of isolates formed weak biofilm. The most prevalent resistance genes found in our isolates were blaZ (54%), vanA (40%), ermB (51.4%), tetM (13.5%) and optrA (10.8%). Moreover, asa1 (37.8%), cylA (42.3%), gelE (78.4%), esp (32.4%), EF3314(48.6%) and ace (75.5%) were the most common virulence genes. A significant correlation was found between biofilm formation, multidrug resistance and virulence genes of the isolates. This study highlights several aspects of virulence and harmfulness of Enterococcus strains isolated from subclinical mastitic milk, which necessitates continuous inspection and monitoring of dairy animals.
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Affiliation(s)
- Mona A. El-Zamkan
- Faculty of Veterinary Medicine, Department of Food Hygiene and Control, South Valley University, Qena, Egypt
- * E-mail:
| | - Hams M. A. Mohamed
- Faculty of Veterinary Medicine, Department of Microbiology, South Valley University, Qena, Egypt
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Dubey S, Maiti B, Girisha SK, Das R, Lamkhannat M, Mutoloki S, Chen SC, Karunasagar I, Evensen Ø, Munang Andu HM. Aeromonas species obtained from different farmed aquatic species in India and Taiwan show high phenotypic relatedness despite species diversity. BMC Res Notes 2021; 14:313. [PMID: 34399833 PMCID: PMC8365956 DOI: 10.1186/s13104-021-05716-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/27/2021] [Indexed: 11/19/2022] Open
Abstract
Objectives Aeromonads cause severe diseases in farmed aquatic organisms. Herein, we examined 28 isolates causing disease in farmed aquatic organisms from India (n = 24) and Taiwan (n = 4) to gain insight of their genotypic and phenotypic properties. Results API 20NE biochemical phenotyping showed ≥ 90% similarity classifying all isolates as Aeromonas hydrophila. 16S rRNA genotyping showed ≥ 98% homology among all isolates with A. sobria (NR119044.1ATCC), A. veronii (MK990549.1), A. caviae (NR029252.1) and A. hydrophila (MG984625.1ATCC) and other reference strains. In contrast, gyrB showed a higher intraspecies diversity (≥ 96%) than 16S rRNA delineating the 28 isolates into three groups. Group-I consisted of seven Indian isolates clustered with A. sobria (MK484163.1ATCC), group-II comprised of five Indian and two Taiwanese isolates clustered with A. veronii AF417626.1ATCC while group-III had 11 Indian and three Taiwanese isolates grouped with A. hydrophila (AY987520.1 and DQ519366.1) reference strains. None of our isolates clustered with A. caviae (AJ868400.1ATCC) reference strain. These findings suggest that A. sobria, A. veronii and A. hydrophila could be the etiological agents of diseases observed in farmed fish and soft-shelled turtles (Pelodiscus sinensis) examined in this study. Overall, our findings accentuate the importance of combining phenotyping with genotyping for correct taxonomic classification of Aeromonas spp. in Aquaculture. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05716-3.
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Affiliation(s)
- Saurabh Dubey
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 369, 0102, Oslo, Norway
| | - Biswajit Maiti
- UNESCO MIRCEN for Medical and Marine Biotechnology, Nitte University Centre for Science Education and Research, NITTE (Deemed to be University), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Shivani Kallappa Girisha
- Department of Fisheries Microbiology, Karnataka Veterinary, Animal & Fisheries Sciences University, College of Fisheries, Mangalore, 575002, India
| | - Rakesh Das
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 369, 0102, Oslo, Norway.,ICAR-Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Odisha, 751002, India
| | - Mustapha Lamkhannat
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 369, 0102, Oslo, Norway
| | - Stephen Mutoloki
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 369, 0102, Oslo, Norway
| | - Shih-Chu Chen
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Indrani Karunasagar
- UNESCO MIRCEN for Medical and Marine Biotechnology, Nitte University Centre for Science Education and Research, NITTE (Deemed to be University), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Øystein Evensen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 369, 0102, Oslo, Norway
| | - Hetron M Munang Andu
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 369, 0102, Oslo, Norway.
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Population informative markers selected using Wright's fixation index and machine learning improves human identification using the skin microbiome. Appl Environ Microbiol 2021; 87:e0120821. [PMID: 34379455 DOI: 10.1128/aem.01208-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial DNA, shed from human skin, can be distinctive to its host and thus help individualize donors of forensic biological evidence. Previous studies have utilized single locus microbial DNA markers (e.g., 16S rRNA) to assess the presence/absence of personal microbiota to profile human hosts. However, since the taxonomic composition of the microbiome is in constant fluctuation, this approach may not be sufficiently robust for human identification (HID). Multi-marker approaches may be more powerful. Additionally, genetic differentiation, rather than taxonomic distinction, may be more individualizing. To this end, the non-dominant hands of 51 individuals were sampled in triplicate (n = 153). They were analyzed for markers in the hidSkinPlex, a multiplex panel comprising candidate markers for skin microbiome profiling. Single nucleotide polymorphisms (SNPs) with the highest Wright's fixation index (FST) estimates were then selected for predicting donor identity using a support vector machine (SVM) learning model. FST is an estimate of the genetic differences within and between populations. Three different SNP selection criteria were employed: SNPs with the highest-ranking FST estimates 1) common between any two samples regardless of markers present (termed overall); 2) each marker common between samples (termed per marker); and 3) common to all samples used to train the SVM algorithm for HID (termed selected). The SNPs chosen based on criteria for overall, per marker, and selected methods resulted in an accuracy of 92.00%, 94.77%, and 88.00%, respectively. The results support that estimates of FST, combined with SVM, can notably improve forensic HID via skin microbiome profiling. IMPORTANCE There is a need for additional genetic information to help identify the source of biological evidence found at a crime scene. The human skin microbiome is a potentially abundant source of DNA that can enable the identification of a donor of biological evidence. With microbial profiling for human identification, there will be an additional source of DNA to identify individuals as well as to exclude individuals wrongly associated with biological evidence, thereby improving the utility of forensic DNA profiling to support criminal investigations.
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Carrascosa C, Martínez R, Sanjuán E, Millán R, Del Rosario-Quintana C, Acosta F, García A, Jaber JR. Identification of the Pseudomonas fluorescens group as being responsible for blue pigment on fresh cheese. J Dairy Sci 2021; 104:6548-6558. [PMID: 33838893 DOI: 10.3168/jds.2020-19517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/10/2020] [Indexed: 11/19/2022]
Abstract
New cases of blue cheese discoloration has led to recent research to identify the causal agent and factors that favor blue pigment appearing. Nonetheless, very few reports have described the source of contamination and the measurements to eradicate the microbiological source on cheese farms by determining the relation between blue discoloration on fresh cheese and the Pseudomonas fluorescens group. Thus, 60 samples from a cheese farm (cheese, equipment surfaces, tap water, and raw and pasteurized milk) were analyzed by phenotypical, MALDI-TOF, 16S rRNA sequencing and pulsed-field gel electrophoresis tests to determine the causal agent. The results obtained by pulsed-field gel electrophoresis with restriction enzymes XbaI and SpeI confirmed tap water as the initial contaminated source. The above-mentioned result was essential to avoid Pseudomonas contamination due to the most residual microorganisms being inactivated through a new disinfection program.
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Affiliation(s)
- Conrado Carrascosa
- Food Hygiene Unit, Department of Animal Pathology, Animal Production, Bromatology, and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Arucas, 35413 Las Palmas, Spain.
| | - Remigio Martínez
- Red de Grupos de Investigación en Recursos Faunísticos, Instituto de Biotecnología Ganadera y Cinegética (INBIO), Facultad de Veterinaria, Universidad de Extremadura, 10003 Cáceres, Spain
| | - Esther Sanjuán
- Food Hygiene Unit, Department of Animal Pathology, Animal Production, Bromatology, and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Arucas, 35413 Las Palmas, Spain
| | - Rafael Millán
- Food Hygiene Unit, Department of Animal Pathology, Animal Production, Bromatology, and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Arucas, 35413 Las Palmas, Spain
| | - Cristóbal Del Rosario-Quintana
- Microbiology Service, Complejo Hospitalario Materno-Insular de Gran Canaria, Canary Health Service, 35016, Las Palmas de Gran Canaria, Spain
| | - Félix Acosta
- Grupo de Investigación de Acuicultura (GIA), Instituto EcoAqua, Universidad de Las Palmas de Gran Canaria, Spain
| | - Alfredo García
- Department of Animal Production, CICYTEX-La Orden, 06187 Junta de Extremadura, Spain
| | - José R Jaber
- Department of Morphology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Arucas, 35413 Las Palmas, Spain
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Nousias O, Montesanto F. Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea with MetaPhlAn3. Mar Genomics 2021; 59:100866. [PMID: 33812777 DOI: 10.1016/j.margen.2021.100866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022]
Abstract
Microbial communities play fundamental roles in association with marine algae; in fact, they are recognized to be actively involved in growth and morphogenesis of the algae. Porphyra purpurea is a red alga commonly found in the intertidal zone with a high economic value, however little is known about the bacterial species associated with this genus. Here we report the bacterial-associated diversity of P. purpurea in four different localities (Ireland, Italy United Kingdom and the USA) from analyzing eight publicly available metagenomic datasets. These were analyzed with Methaplan3 to identify the putative bacterial taxonomies and their relative abundances. Furthermore, we compared these results to the 16S rRNA metagenomic analysis pipeline of the MGnify database to evaluate both methods. Kraken2 was used to verify and support the results, as a complementary classification method to Metaphlan3. This approach highlighted the different taxonomic resolution of a 16S rRNA OTU-based method compared to the pan-genome approach deployed by Metaphlan3 and complemented by Kraken2. The results presented here provide valuable preliminary data on the putative host-associated bacterial species of P. purpurea.
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Affiliation(s)
- Orestis Nousias
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Crete, Greece; Department of Biology, University of Crete, Greece.
| | - Federica Montesanto
- Department of Biology, University of Bari Aldo Moro, Via Orabona 4, 70125, Bari, Italy; CoNISMa, Piazzale Flaminio 9, 00197 Roma, Italy.
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Jahan NA, Godden SM, Royster E, Schoenfuss TC, Gebhart C, Timmerman J, Fink RC. Evaluation of the matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) system in the detection of mastitis pathogens from bovine milk samples. J Microbiol Methods 2021; 182:106168. [PMID: 33600875 DOI: 10.1016/j.mimet.2021.106168] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 12/08/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
MALDI-TOF is a chemistry analytical tool that has recently been deployed in the identification of microorganisms isolated from nosocomial environments. Its use in diagnostics has been extremely advantageous in terms of cost effectiveness, sample preparation easiness, turn-around time and result analysis accessibility. In the dairy industry, where mastitis causes great financial losses, a rapid diagnostic method such as MALDI-TOF could assist in the control and prevention program of mastitis, in addition to the sanitation and safety level of the dairy farms and processing facility. However, the diagnostic strengths and limitations of this test method require further understanding. In the present study, we prospectively compared MALDI-TOF MS to conventional 16S rDNA sequencing method for the identification of pathogens recovered from milk associated with clinical and subclinical bovine mastitis cases. Initially, 810 bacterial isolates were collected from raw milk samples over a period of three months. However, only the isolates (481) having both 16S rDNA sequencing and MALDI-TOF identification were included in the final phase of the study. Among the 481 milk isolates, a total of 26 genera (12 g-postive and 14 g-negative), including 71 different species, were taxonomically charecterized by 16S rDNA at the species level. Comparatively, MALDI-TOF identified 17 genera (9 g-positive and 8 g-negative) and 33 differernt species. Overall, 445 (93%) were putatively identified to the genus level by MALDI-TOF MS and 355 (74%) were identified to the species level, but no reliable identification was obtained for 16 (3.3%), and 20 (4.2%) discordant results were identified. Future studies may help to overcome the limitations of the MALDI database and additional sample preparation steps might help to reduce the number of discordances in identification. In conclusion, our results show that MALDI-TOF MS is a fast and reliable technique which has the potential to replace conventional identification methods for common mastitis pathogens, routinely isolated from raw milk. Thus it's adoption will strengthen the capacity, quality, and possibly the scope of diagnostic services to support the dairy industry.
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Affiliation(s)
- Nusrat A Jahan
- Department of Biology, St. Cloud State University, Saint Cloud, MN, USA
| | - Sandra M Godden
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Erin Royster
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Tonya C Schoenfuss
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
| | - Connie Gebhart
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Jennifer Timmerman
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Ryan C Fink
- Department of Biology, St. Cloud State University, Saint Cloud, MN, USA,.
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Górny RL, Frączek K, Ropek DR. Size distribution of microbial aerosols in overground and subterranean treatment chambers at health resorts. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2020; 18:1437-1450. [PMID: 33312653 PMCID: PMC7721825 DOI: 10.1007/s40201-020-00559-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/04/2020] [Indexed: 06/12/2023]
Abstract
PURPOSE to perform comparative analyzes of the size distributions of bacteria and fungi in the air of overground therapy chambers in Szczawnica sanatorium and subterranean inhalation chambers in Bochnia Salt Mine health resort taking into account influence of the season and presence of pathogenic species. METHODS bioaerosol samples were collected using 6-stage Andersen impactor. Bacterial and fungal aerosol concentrations and size distributions were calculated and isolated microorganisms were taxonomically identified based on their morphological, biochemical, and molecular features. Results: in both treatment rooms and atmospheric (outdoor) air, the acceptable microbial pollution levels were periodically exceeded. The size distribution analyzes revealed that in the case of bacteria - emission from the patients and in the case of fungi - transport with atmospheric (outdoor) air were the major processes responsible for microbiological contamination of indoor premises. The majority of microbial particulates were present in the air of studied premises as single bacterial vegetative cells, spores and fungal conidia or (most commonly) formed small microbial or microbial-dust aggregates. This phenomenon may have a significant effect on patients' actual exposure (especially on those treated for respiratory diseases) in terms of the dose of inhaled particles. CONCLUSIONS the microbiological quality of the air in sanatoriums and health resorts is a key factor for their therapeutic and prophylactic functions. When microbial pollution crossed the acceptable level, the measures that enable reducing undesirable contamination should be introduced, especially if large groups of patients undergo such therapy.
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Affiliation(s)
- Rafał L. Górny
- Laboratory of Biohazards, Department of Chemical, Aerosol and Biological Hazards, Central Institute for Labour Protection–National Research Institute, Czerniakowska 16 Street, 00-701 Warsaw, Poland
| | - Krzysztof Frączek
- Department of Microbiology and Biomonitoring, University of Agriculture, Cracow, Poland
| | - Dariusz R. Ropek
- Department of Microbiology and Biomonitoring, University of Agriculture, Cracow, Poland
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Bagudo AI, Obande GA, Harun A, Singh KKB. Advances in automated techniques to identify Acinetobacter calcoaceticus-Acinetobacter baumannii complex. ASIAN BIOMED 2020; 14:177-186. [PMID: 37551265 PMCID: PMC10373397 DOI: 10.1515/abm-2020-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Acinetobacter species, particularly those within Acinetobacter calcoaceticus-A. baumannii complex (ACB complex), have emerged as clinically relevant pathogens in hospital environments worldwide. Early and quick detection and identification of Acinetobacter infections is challenging, and traditional culture and biochemical methods may not achieve adequate levels of speciation. Moreover, currently available techniques to identify and differentiate closely related Acinetobacter species are insufficient. The objective of this review is to recapitulate the current evolution in phenotypic and automated techniques used to identify the ACB complex. Compared with other automated or semiautomated systems of bacterial identification, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) demonstrates a high level of Acinetobacter species identification and discrimination, including newly discovered species A. seifertii and A. dijkshoorniae.
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Affiliation(s)
- Ahmad Ibrahim Bagudo
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Godwin Attah Obande
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
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Boutin CA, Cornut G, Bilik Pinto V, Grandjean Lapierre S. Pandoraea sp infection in a lung transplant patient and the critical role of MALDI-TOF in accurate bacterial identification. JOURNAL OF THE ASSOCIATION OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASE CANADA = JOURNAL OFFICIEL DE L'ASSOCIATION POUR LA MICROBIOLOGIE MEDICALE ET L'INFECTIOLOGIE CANADA 2020; 5:177-181. [PMID: 36341313 PMCID: PMC9608733 DOI: 10.3138/jammi-2020-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/03/2020] [Indexed: 06/16/2023]
Abstract
Diagnosis and clinical management of pulmonary infections in lung transplant patients are challenging. The increased diversity of bacterial species identified from clinical samples with novel proteomics-based systems can further complicate clinical decision making in this highly vulnerable population. Whether newly recognized organisms are colonizers or true pathogens often remains controversial since symptoms causality and impact on lung function is often unknown. We present the case of a 48-year-old female lung transplant patient with Pandoraea sp infection. We review and discuss the role of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for accurate bacterial identification. We report on therapeutic management and clinical outcome.
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Affiliation(s)
| | - Gilbert Cornut
- Université de Montréal, Montréal, Quebec, Canada
- Fleury Hospital, Montréal, Quebec, Canada
| | | | - Simon Grandjean Lapierre
- Université de Montréal, Montréal, Quebec, Canada
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
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Obesity Worsens Gulf War Illness Symptom Persistence Pathology by Linking Altered Gut Microbiome Species to Long-Term Gastrointestinal, Hepatic, and Neuronal Inflammation in a Mouse Model. Nutrients 2020; 12:nu12092764. [PMID: 32927823 PMCID: PMC7551189 DOI: 10.3390/nu12092764] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/30/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
Persistence of Gulf War illness (GWI) pathology among deployed veterans is a clinical challenge even after almost three decades. Recent studies show a higher prevalence of obesity and metabolic disturbances among Gulf War veterans primarily due to the existence of post-traumatic stress disorder (PTSD), chronic fatigue, sedentary lifestyle, and consumption of a high-carbohydrate/high-fat diet. We test the hypothesis that obesity from a Western-style diet alters host gut microbial species and worsens gastrointestinal and neuroinflammatory symptom persistence. We used a 5 month Western diet feeding in mice that received prior Gulf War (GW) chemical exposure to mimic the home phase obese phenotype of the deployed GW veterans. The host microbial profile in the Western diet-fed GWI mice showed a significant decrease in butyrogenic and immune health-restoring bacteria. The altered microbiome was associated with increased levels of IL6 in the serum, Claudin-2, IL6, and IL1β in the distal intestine with concurrent inflammatory lesions in the liver and hyperinsulinemia. Microbial dysbiosis was also associated with frontal cortex levels of increased IL6 and IL1β, activated microglia, decreased levels of brain derived neurotrophic factor (BDNF), and higher accumulation of phosphorylated Tau, an indicator of neuroinflammation-led increased risk of cognitive deficiencies. Mechanistically, serum from Western diet-fed mice with GWI significantly increased microglial activation in transformed microglial cells, increased tyrosyl radicals, and secreted IL6. Collectively, the results suggest that an existing obese phenotype in GWI worsens persistent gastrointestinal and neuronal inflammation, which may contribute to poor outcomes in restoring cognitive function and resolving fatigue, leading to the deterioration of quality of life.
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Zhang L, Jiang C, Chen X, Gu J, Song Q, Zhong H, Xiong S, Dong Q, Yu J, Deng N. Large-scale production, purification, and function of a tumor multi-epitope vaccine: Peptibody with bFGF/VEGFA. Eng Life Sci 2020; 20:422-436. [PMID: 32944017 PMCID: PMC7481771 DOI: 10.1002/elsc.202000020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/24/2020] [Accepted: 07/02/2020] [Indexed: 12/23/2022] Open
Abstract
In tumor tissue, basic fibroblast growth factor (bFGF) and vascular endothelial growth factor A (VEGFA) promote tumorigenesis by activating angiogenesis, but targeting single factor may produce drug resistance and compensatory angiogenesis. The Peptibody with bFGF/VEGFA was designed to simultaneously blockade these two factors. We were aiming to produce this Fc fusion protein in a large scale. The biological characterizations of Peptibody strains were identified as Escherichia coli and the fermentation mode was optimized in the shake flasks and 10-L bioreactor. The fermentation was scaled up to 100 L, with wet cell weight (WCW) 126 g/L, production 1.41 g/L, and productivity 0.35 g/(L·h) of IPTG induction. The target protein was isolated by cation-exchange, hydrophobic and Protein A chromatography, with total recovery of 60.28% and HPLC purity of 86.71%. The host cells protein, DNA, and endotoxin residues were within the threshold. In mouse model, immunization of Peptibody vaccine could significantly suppressed the tumor growth and angiogenesis, with inhibition rate of 57.73 and 39.34%. The Peptibody vaccine could elicit high-titer anti-bFGF and anti-VEGFA antibodies, which inhibited the proliferation and migration of Lewis lung cancer cell cells by decreasing the Akt/MAPK signal pathways. Therefore, the Peptibody with bFGF/VEGFA might be used as a therapeutic tumor vaccine. The large-scale process we developed could support its industrial production and pre-clinical study in the future.
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Affiliation(s)
- Ligang Zhang
- Guangdong Province Engineering Research Center for Antibody Drug and ImmunoassayDepartment of BiologyJinan UniversityGuangzhouP. R. China
| | - Chengcheng Jiang
- Guangdong Province Engineering Research Center for Antibody Drug and ImmunoassayDepartment of BiologyJinan UniversityGuangzhouP. R. China
| | - Xi Chen
- Guangdong Province Engineering Research Center for Antibody Drug and ImmunoassayDepartment of BiologyJinan UniversityGuangzhouP. R. China
| | - Jiangtao Gu
- Guangdong Province Engineering Research Center for Antibody Drug and ImmunoassayDepartment of BiologyJinan UniversityGuangzhouP. R. China
| | - Qifang Song
- Guangdong Province Engineering Research Center for Antibody Drug and ImmunoassayDepartment of BiologyJinan UniversityGuangzhouP. R. China
| | - Hui Zhong
- The Biomedicine Translational Institute in Jinan UniversityGuangzhouP. R. China
| | - Sheng Xiong
- Guangdong Jida Genetic Medicine Engineering Research Center Co. LtdGuangzhouP. R. China
| | | | - Jin‐Chen Yu
- Bio‐Thera Solution Co. LtdGuangzhouP. R. China
| | - Ning Deng
- Guangdong Province Engineering Research Center for Antibody Drug and ImmunoassayDepartment of BiologyJinan UniversityGuangzhouP. R. China
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Laczeski ME, Onetto AL, Cortese IJ, Mallozzi GY, Castrillo ML, Bich GÁ, Gortari F, Zapata PD, Otegui MÓB. Isolation and selection of endophytic spore-forming bacteria with plant growth promoting properties isolated from Ilex paraguariensis St. Hil. (yerba mate). AN ACAD BRAS CIENC 2020; 92 Suppl 1:e20181381. [PMID: 32638866 DOI: 10.1590/0001-3765202020181381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/17/2019] [Indexed: 01/05/2023] Open
Abstract
Yerba mate (Ilex paraguariensis St. Hil.) is a species native to the subtropical regions of South America. Despite being an important crop for the region, there are few studies on the use of microorganisms to improve the growth of seedlings in the nursery stage. The objective of this study was to isolate spore-forming endophytic bacteria with plant growth promoting properties associated with yerba mate seedlings and determine their phytobeneficial effect under controlled laboratory conditions. Isolates were selected based on their sporulation capacity and evaluated for in vitro plant growth promoting properties (nitrogen fixation, phosphate solubilization, production of siderophores and synthesis of indolic compounds). Yerba mate seedlings were inoculated with the most promising isolates, which were identified via analyses of the sequence of their 16S rDNA gene as Bacillus circulans (12RS3) and Bacillus altitudinis (19RS3, T5S-T4). After 120 days plants showed higher root dry weight when inoculated with isolate 19RS3 and higher shoot dry weight with 19RS3 and T5S-T4. In conclusion, further studies to determine the ability of these isolates to adapt to the climatic conditions and to survive amidst the native soil microflora in yerba mate cultivated native soils, will be crucial for developing such strains as biofertilizer.
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Affiliation(s)
- Margarita E Laczeski
- Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (InBioMis), Universidad Nacional de Misiones/UNaM, Argentina
| | - Andrea L Onetto
- Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (InBioMis), Universidad Nacional de Misiones/UNaM, Argentina
| | - Iliana J Cortese
- Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (InBioMis), Universidad Nacional de Misiones/UNaM, Argentina
| | - Gisela Y Mallozzi
- Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (InBioMis), Universidad Nacional de Misiones/UNaM, Argentina
| | - MarÍa Lorena Castrillo
- Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (InBioMis), Universidad Nacional de Misiones/UNaM, Argentina
| | - Gustavo Á Bich
- Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (InBioMis), Universidad Nacional de Misiones/UNaM, Argentina
| | - FermÍn Gortari
- Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (InBioMis), Universidad Nacional de Misiones/UNaM, Argentina
| | - Pedro D Zapata
- Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (InBioMis), Universidad Nacional de Misiones/UNaM, Argentina
| | - MÓnica B Otegui
- Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (InBioMis), Universidad Nacional de Misiones/UNaM, Argentina
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26
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Price EP, Soler Arango V, Kidd TJ, Fraser TA, Nguyen TK, Bell SC, Sarovich DS. Duplex real-time PCR assay for the simultaneous detection of Achromobacter xylosoxidans and Achromobacter spp. Microb Genom 2020; 6:mgen000406. [PMID: 32667877 PMCID: PMC7478622 DOI: 10.1099/mgen.0.000406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/26/2020] [Indexed: 01/10/2023] Open
Abstract
Several members of the Gram-negative environmental bacterial genus Achromobacter are associated with serious infections, with Achromobacter xylosoxidans being the most common. Despite their pathogenic potential, little is understood about these intrinsically drug-resistant bacteria and their role in disease, leading to suboptimal diagnosis and management. Here, we performed comparative genomics for 158 Achromobacter spp. genomes to robustly identify species boundaries, reassign several incorrectly speciated taxa and identify genetic sequences specific for the genus Achromobacter and for A. xylosoxidans. Next, we developed a Black Hole Quencher probe-based duplex real-time PCR assay, Ac-Ax, for the rapid and simultaneous detection of Achromobacter spp. and A. xylosoxidans from both purified colonies and polymicrobial clinical specimens. Ac-Ax was tested on 119 isolates identified as Achromobacter spp. using phenotypic or genotypic methods. In comparison to these routine diagnostic methods, the duplex assay showed superior identification of Achromobacter spp. and A. xylosoxidans, with five Achromobacter isolates failing to amplify with Ac-Ax confirmed to be different genera according to 16S rRNA gene sequencing. Ac-Ax quantified both Achromobacter spp. and A. xylosoxidans down to ~110 genome equivalents and detected down to ~12 and ~1 genome equivalent(s), respectively. Extensive in silico analysis, and laboratory testing of 34 non-Achromobacter isolates and 38 adult cystic fibrosis sputa, confirmed duplex assay specificity and sensitivity. We demonstrate that the Ac-Ax duplex assay provides a robust, sensitive and cost-effective method for the simultaneous detection of all Achromobacter spp. and A. xylosoxidans and will facilitate the rapid and accurate diagnosis of this important group of pathogens.
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Affiliation(s)
- Erin P. Price
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Valentina Soler Arango
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Timothy J. Kidd
- School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, St Lucia, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Tamieka A. Fraser
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Thuy-Khanh Nguyen
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Scott C. Bell
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - Derek S. Sarovich
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
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Shanmugam S, PradeepKumar AR, Abbott PV, Periasamy R, Velayutham G, Krishnamoorthy S, Mahalakshmi K. Coronal Bacterial Penetration after 7 days in class II endodontic access cavities restored with two temporary restorations: A Randomised Clinical Trial. AUST ENDOD J 2020; 46:358-364. [PMID: 32568470 DOI: 10.1111/aej.12415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/12/2020] [Accepted: 05/20/2020] [Indexed: 11/26/2022]
Abstract
The aim of this in vivo randomised clinical trial was to assess coronal bacterial penetration after placement of Cavit G and IRM temporary restorations in Class II endodontic access cavities. After completion of endodontic treatment, placement of an orifice seal and disinfection of the operating field, sterile cotton pellets were placed in the pulp chamber and the cavities were restored with Cavit G or IRM. After 7 days, coronal and proximal restoration thickness was measured by digital radiographs. Cotton pellet was evaluated by culture methods and polymerase chain reaction assay and bacterial species identified. Bacterial growth was observed in 5 of the 27 (18%) Cavit G samples and in 11 of the 27 (40%) IRM samples which was not significant. Coronal restoration thickness of 4-5 mm and proximal restoration thickness of more than 2.15 mm for Cavit G and 2.35 mm for IRM are recommended to prevent bacterial penetration over 7 days. Adequate restoration thickness is critical to prevent bacterial penetration.
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Affiliation(s)
- Sandhya Shanmugam
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr M.G.R. Educational and Research Institute, Chennai, Tamil Nadu, India
| | - Angambakkam Rajasekaran PradeepKumar
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr M.G.R. Educational and Research Institute, Chennai, Tamil Nadu, India
| | - Paul Vincent Abbott
- UWA Dental School, The University of Western Australia, Nedlands, WA, Australia
| | - Ravishankar Periasamy
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr M.G.R. Educational and Research Institute, Chennai, Tamil Nadu, India
| | - Gopikrishna Velayutham
- Dept of Conservative Dentistry & Endodontics, Sri Ramachandra Institute of Higher Education & Reasearch, Chennai, Tamil Nadu, India
| | - Sridevi Krishnamoorthy
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr M.G.R. Educational and Research Institute, Chennai, Tamil Nadu, India
| | - Krishnan Mahalakshmi
- Department of Microbiology, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai, Tamil Nadu, India
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28
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Fermentation, purification and immunogenicity of a recombinant tumor multi-epitope vaccine, VBP3. Protein Expr Purif 2020; 174:105658. [PMID: 32360598 DOI: 10.1016/j.pep.2020.105658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 11/21/2022]
Abstract
The recombinant multi-epitope vaccine called VBP3 is designed to suppress tumor growth and angiogenesis through targeting both basic fibroblast growth factor (bFGF) and vascular endothelial growth factor A (VEGFA). We are aiming to produce VBP3 vaccine in a large scale and provide sufficient protein for pre-clinical study. High cost and potential toxicity are severe limitations of IPTG and we investigated whether lactose can mediate VBP3 induction. Firstly, we identified the biological characteristics and established a culture bank of VBP3 strains. The best-performing strains were selected and the fermentation mode of medium, bacterial growth and protein expression were optimized in shake flasks. We scaled up the VBP3 production in 10 L bioreactor using lactose as inducer and the protein yield was comparable with IPTG induction. Next, the target protein was purified by nickel-nitrilotriacetic acid (Ni-NTA) affinity chromatography, with a SDS-PAGE purity over 90%. Further, the purified VBP3 vaccine was subcutaneously injected in BALB/c mice and elicited high-titer anti-bFGF (1:32,000) and anti-VEGFA (1:4000) antibodies. Take together, lactose was an applicable inducer for VBP3 production and the eligible product of VBP3 was harvested in the large-scale fermentation, supporting the industrial production and pre-clinical study in the future. The VBP3 vaccine with superior immunogenicity might be used as a potential therapeutic vaccine for tumor treatment.
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29
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Loraine J, Heinz E, Soontarach R, Blackwell GA, Stabler RA, Voravuthikunchai SP, Srimanote P, Kiratisin P, Thomson NR, Taylor PW. Genomic and Phenotypic Analyses of Acinetobacter baumannii Isolates From Three Tertiary Care Hospitals in Thailand. Front Microbiol 2020; 11:548. [PMID: 32328045 PMCID: PMC7153491 DOI: 10.3389/fmicb.2020.00548] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/13/2020] [Indexed: 12/24/2022] Open
Abstract
Antibiotic resistant strains of Acinetobacter baumannii are responsible for a large and increasing burden of nosocomial infections in Thailand and other countries of Southeast Asia. New approaches to their control and treatment are urgently needed and an attractive strategy is to remove the bacterial polysaccharide capsule, and thus the protection from the host's immune system. To examine phylogenetic relationships, distribution of capsule chemotypes, acquired antibiotic resistance determinants, susceptibility to complement and other traits associated with systemic infection, we sequenced 191 isolates from three tertiary referral hospitals in Thailand and used phenotypic assays to characterize key aspects of infectivity. Several distinct lineages were circulating in three hospitals and the majority belonged to global clonal group 2 (GC2). Very high levels of resistance to carbapenems and other front-line antibiotics were found, as were a number of widespread plasmid replicons. A high diversity of capsule genotypes was encountered, with only three of these (KL6, KL10, and KL47) showing more than 10% frequency. Almost 90% of GC2 isolates belonged to the most common capsule genotypes and were fully resistant to the bactericidal action of human serum complement, most likely protected by their polysaccharide capsule, which represents a key determinant of virulence for systemic infection. Our study further highlights the importance to develop therapeutic strategies to remove the polysaccharide capsule from extensively drug-resistant A. baumanii during the course of systemic infection.
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Affiliation(s)
- Jessica Loraine
- School of Pharmacy, University College London, London, United Kingdom
| | - Eva Heinz
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | - Grace A Blackwell
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom.,European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, Cambridge, United Kingdom
| | - Richard A Stabler
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Potjanee Srimanote
- Faculty of Allied Health Sciences, Thammasat University, Pathumtanee, Thailand
| | | | - Nicholas R Thomson
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom.,London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Peter W Taylor
- School of Pharmacy, University College London, London, United Kingdom
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30
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Rohowetz LJ, Yannuzzi NA, Gupta S, Patel NA, Miller D, Flynn HW. Endophthalmitis Caused by Agrobacterium radiobacter following Intravitreal Aflibercept for Diabetic Retinopathy. Case Rep Ophthalmol 2020; 11:22-27. [PMID: 32231556 PMCID: PMC7098332 DOI: 10.1159/000505227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/03/2019] [Indexed: 11/19/2022] Open
Abstract
Agrobacterium (Rhizobium) radiobacter is a gram-negative bacillus rarely implicated in ocular disease. A 79-year-old male who performed extensive yardwork following intravitreal injection with aflibercept for diabetic macular edema developed endophthalmitis caused by Agrobacterium radiobacter on post-injection day 7. The patient was treated with vitreous tap and intravitreal injection of vancomycin and ceftazidime with clearance of the infection and restoration of his baseline visual acuity at 20/80.
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Affiliation(s)
- Landon J Rohowetz
- University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Nicolas A Yannuzzi
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, Florida, USA
| | - Sunil Gupta
- Retina Specialty Institute, Pensacola, Florida, USA
| | - Nimesh A Patel
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, Florida, USA
| | - Darlene Miller
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, Florida, USA
| | - Harry W Flynn
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, Florida, USA
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Górny RL, Gołofit-Szymczak M, Cyprowski M, Stobnicka-Kupiec A. Nasal lavage as analytical tool in assessment of exposure to particulate and microbial aerosols in wood pellet production facilities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134018. [PMID: 31479905 DOI: 10.1016/j.scitotenv.2019.134018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
Occupational exposure to wood dust and bioaerosols may lead to numerous respiratory tract diseases. We aimed to assess a degree of workplace contamination with dust, bacteria, fungi, endotoxins, and (1 → 3)-β-D-glucans released into the air during wood processing in pellet production facilities and to check against this background the usefulness of nasal lavage (NAL) as analytical tool for assessment of combined workers' exposure to airborne dust and microbiological contaminants. In 10 pellet plants, the particulate (wood dust) aerosol concentrations were determined by using Grimm aerosol spectrometer and CIS filter sampler. The collected CIS samples were subsequently used to evaluate endotoxin and (1 → 3)-β-D-glucan concentrations. Simultaneously with particulate aerosol, bioaerosol samples were collected by using 6-stage Andersen and single-stage MAS impactors. Bacterial and fungal aerosol concentrations were calculated and all isolated microorganisms were taxonomically identified. NAL fluid samples were collected from workers exposed to studied aerosols and the concentrations of proinflammatory mediators (IL-1β, IL-6, IL-8, and TNFα) and cytological image of nasal mucosa (expressed as cell counts) were established. The dynamics of production activities resulted in wide range of observed wood dust, microorganism, endotoxin and (1 → 3)-β-D-glucan concentrations reaching periodically extremely high values up to 65 mg m-3, 19,320 CFU m-3, 215 ng m-3 and 1525 ng m-3, respectively. Environmental stress caused by exposure to particulate and microbial aerosols stimulated immune response among workers of pellet production facilities. Correlation analysis revealed that interleukin levels and the number of cells in NAL were significantly affected by both wood dust and bioaerosol concentrations. As nasal mucosa serves as the primary barrier against inhaled pollutants, NAL seems a reliable analytical material to assess work-related adverse respiratory health outcomes derived from such exposure.
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Affiliation(s)
- Rafał L Górny
- Laboratory of Biohazards, Department of Chemical, Aerosol and Biological Hazards, Central Institute for Labour Protection - National Research Institute, Warsaw, Poland.
| | - Małgorzata Gołofit-Szymczak
- Laboratory of Biohazards, Department of Chemical, Aerosol and Biological Hazards, Central Institute for Labour Protection - National Research Institute, Warsaw, Poland
| | - Marcin Cyprowski
- Laboratory of Biohazards, Department of Chemical, Aerosol and Biological Hazards, Central Institute for Labour Protection - National Research Institute, Warsaw, Poland
| | - Agata Stobnicka-Kupiec
- Laboratory of Biohazards, Department of Chemical, Aerosol and Biological Hazards, Central Institute for Labour Protection - National Research Institute, Warsaw, Poland
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Sant' Anna D, Sampaio JLM, Sommaggio LRD, Mazzeo DEC, Marin-Morales MA, Marson FAL, Levy CE. The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates. Antonie van Leeuwenhoek 2019; 113:233-252. [PMID: 31560092 DOI: 10.1007/s10482-019-01333-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/13/2019] [Indexed: 11/26/2022]
Abstract
Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.
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Affiliation(s)
- Débora Sant' Anna
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, Barretos, São Paulo, Brazil.
| | - Jorge Luiz Mello Sampaio
- Microbiology Section, Fleury-Centers for Diagnostic Medicine, Av. General Waldomiro de Lima 508, São Paulo, 04344-070, Brazil
- Clinical Analysis and Toxicology Department, School of Pharmacy, University of São Paulo, Av. Professor Lineu Prestes, 580, Butantã, São Paulo, 05508-000, Brazil
| | - Lais Roberta Deroldo Sommaggio
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Dânia Elisa Christofoletti Mazzeo
- Department of Analytical Chemistry, Institute of Chemistry, São Paulo State University - Araraquara, Rua Professor Francisco Degni, 55, Araraquara, São Paulo, 14800-060, Brazil
| | - Maria Aparecida Marin-Morales
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Fernando Augusto Lima Marson
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Laboratory of Pulmonary Physiology, Center for Pediatrics Investigation, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Post-Graduate Program in Health Science, São Francisco University, Avenida São Francisco de Assis, 218, Cidade Universitária, Bragança Paulista, São Paulo, 12916-400, Brazil.
| | - Carlos Emílio Levy
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
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Hemdan BA, El-Liethy MA, ElMahdy MEI, El-Taweel GE. Metagenomics analysis of bacterial structure communities within natural biofilm. Heliyon 2019; 5:e02271. [PMID: 31485510 PMCID: PMC6716113 DOI: 10.1016/j.heliyon.2019.e02271] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/11/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022] Open
Abstract
The bacterial profiles of natural household biofilm have not been widely investigated. The majorities of these bacterial lineages are not cultivable. Thus, this study aims (i) to enumerate some potential bacterial lineages using culture based method within biofilm samples and confirmed using Biolog GEN III and polymerase chain reaction (PCR). (ii) To investigate the bacterial profiles of communities in two biofilm samples using next generation sequencing (NGS). Forty biofilm samples were cultured and colonies of each selected prevailing potential lineages (E. coli, Salmonella entrica, Pseudomonas aeruginosa, Staphylococcus aureus and Listeria monocytogenes) were selected for confirmation. From obtained results, the counts of the tested bacterial lineages in kitchen biofilm samples were greater than those in bathroom samples. Precision of PCR was higher than Biolog GEN III to confirm the bacterial isolates. Using NGS analysis, the results revealed that a total of 110,554 operational taxonomic units (OTUs) were obtained for two biofilm samples, representing kitchen and bathroom biofilm samples. The numbers of phyla in the kitchen biofilm sample (35 OTUs) was higher than that in bathroom sample (18 OTUs). A total of 435 genera were observed in the bathroom biofilm sample compared to only 256 in the kitchen sample. Evidences have shown that the empirical gadgets for biofilm investigation are becoming convenient and affordable. Many distinct bacterial lineages observed in biofilm are one of the most significant issues that threaten human health and lead to disease outbreaks.
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Affiliation(s)
- Bahaa A Hemdan
- Environmental Microbiology Lab., Water Pollution Research Department, National Research Centre, Dokki, 12622, Giza, Egypt
| | - Mohamed Azab El-Liethy
- Environmental Microbiology Lab., Water Pollution Research Department, National Research Centre, Dokki, 12622, Giza, Egypt
| | - M E I ElMahdy
- Environmental Virology Lab., Water Pollution Research Department, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Gamila E El-Taweel
- Environmental Microbiology Lab., Water Pollution Research Department, National Research Centre, Dokki, 12622, Giza, Egypt
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Benga L, Knorr JI, Engelhardt E, Gougoula C, Benten PM, Christensen H, Sager M. Current Distribution of Rodentibacter Species Among the Mice and Rats of an Experimental Facility. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE 2019; 58:475-478. [PMID: 31239009 DOI: 10.30802/aalas-jaalas-19-000001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The uncertain taxonomy of [Pasteurella] pneumotropica and other rodent Pasteurellaceae has hindered the acquisition of knowledge on the biology and disease for this group of bacteria. Recently, these organisms have been reclassified within the new genus Rodentibacter. In this study, we documented which of the new described Rodentibacter spp. are present in the mouse and rat microbiologic units of an experimental facility. Screening all of the microbiologic units populated with mice and rats yielded 51 Rodentibacter isolates. Molecular and phenotypic diagnosis indicated the colonization of mice by R. pneumotropicus and R. heylii, whereas R. ratti and R. heylii were found in rats. Overall, we document the association of laboratory rodents with 3 of the newly described Rodentibacter. Diagnostics of the Rodentibacter spp. at the species level can decisively contribute to the progress of knowledge on these bacteria.
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Affiliation(s)
- Laurentiu Benga
- Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich-Heine University, Dusseldorf, Germany;,
| | - Jeanette I Knorr
- Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich-Heine University, Dusseldorf, Germany
| | - Eva Engelhardt
- Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich-Heine University, Dusseldorf, Germany
| | - Christina Gougoula
- Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich-Heine University, Dusseldorf, Germany
| | - Peter M Benten
- Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich-Heine University, Dusseldorf, Germany
| | - Henrik Christensen
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Sager
- Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich-Heine University, Dusseldorf, Germany
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Dubey S, Maiti B, Kim SH, Sivadasan SM, Kannimuthu D, Pandey PK, Girisha SK, Mutoloki S, Chen SC, Evensen Ø, Karunasagar I, Munang'andu HM. Genotypic and phenotypic characterization of Edwardsiella isolates from different fish species and geographical areas in Asia: Implications for vaccine development. JOURNAL OF FISH DISEASES 2019; 42:835-850. [PMID: 30851008 DOI: 10.1111/jfd.12984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/06/2019] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
The genus Edwardsiella is one of the major causes of fish diseases globally. Herein, we examined 37 isolates from ten different fish species from India, South Korea and Taiwan to gain insight into their phenotypic and genotypic properties, of which 30 were characterized as E. tarda with phenotypic homology estimated at 85.71% based on API-20E biochemical tests. Genotyping using 16S rRNA put all isolates together with E. anguillarum, E. hoshinae, E. tarda, E. piscicida and E. ictaluri reference strains in a monophyletic group. In contrast, the gyrB phylogenetic tree clearly separated E. ictaluri, E. tarda and E. hoshinae reference strains from our isolates and put our isolates into two groups with group I being homologous with the E. anguillarum reference strain while group II was homologous with the E. piscicida reference strain. Hence, our findings point to E. piscicida and E. anguillarum as species infecting different fish species in Asia. Homology of the ompW protein suggested that strains with broad protective coverage could be identified as vaccine candidates. This study underscores the importance of combining genotyping with phenotyping for valid species classification. In addition, it accentuates the importance of phylogenetic comparison of bacterial antigens for identification of potential vaccine candidates.
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Affiliation(s)
- Saurabh Dubey
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Biswajit Maiti
- UNESCO MIRCEN for Medical and Marine Biotechnology, Nitte University Centre for Science Education and Research, NITTE (Deemed to be University), Mangalore, India
| | | | - Sangeetha Madambithara Sivadasan
- Department of Fisheries Microbiology, College of Fisheries, Karnataka Veterinary Animal & Fisheries Sciences University, Mangalore, India
| | | | | | - Shivani Kallappa Girisha
- Department of Fisheries Microbiology, College of Fisheries, Karnataka Veterinary Animal & Fisheries Sciences University, Mangalore, India
| | - Stephen Mutoloki
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Shih-Chu Chen
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Øystein Evensen
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Indrani Karunasagar
- UNESCO MIRCEN for Medical and Marine Biotechnology, Nitte University Centre for Science Education and Research, NITTE (Deemed to be University), Mangalore, India
| | - Hetron Mweemba Munang'andu
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
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Hanaka A, Ozimek E, Majewska M, Rysiak A, Jaroszuk-Ściseł J. Physiological Diversity of Spitsbergen Soil Microbial Communities Suggests Their Potential as Plant Growth-Promoting Bacteria. Int J Mol Sci 2019; 20:E1207. [PMID: 30857335 PMCID: PMC6429280 DOI: 10.3390/ijms20051207] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 11/16/2022] Open
Abstract
The objective of the study was to assess the physiological diversity and metabolic activity of the soil bacterial communities inhabiting Spitsbergen soils in search of bacterial abilities facilitating plant growth promotion. In the soil, the total number of culturable microorganisms, the number of their individual physiological groups (including Siderophore Synthesizing; SSB and Phosphate Solubilizing Bacteria; PSB), the dehydrogenase (DH) activity, and the ability to utilize sources of C, N, P (EcoPlate) were analysed. In bacterial isolates, siderophores production, ACC (1-aminocyclopropane-1-carboxylate) deaminase (ACCD) activity, IAA (indole-3-acetic acid) synthesis were examined. The isolates were applied to the seeds of Phaseolus coccineus regarding their germination and root length. The results showed differences between copio- and oligotrophic bacteria. A usually high number of SSB was accompanied by the raised number of PSB. A bigger number of SSB was connected with low values of Fe in the soil. High DH activity was assisted by greater number of copio- and oligotrophic bacteria, raised average well color development value, and N and C contents in the soil. Germination index was more alike relative seed germination than relative root growth. IAA concentration and ACCD activity were conversely related. Synthesis of siderophores was matched with ACCD activity and its high level was combined with elevated germination index. In spite of different localization of soil samples, some isolates proved similar traits of activity. Distinct affiliation of isolates and their various localizations were displayed. Among all isolates tested, some possessed one main trait of activity, but most of them had two or more significant features for potential plant growth stimulation. These isolates could be an important source of useful bacteria.
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Affiliation(s)
- Agnieszka Hanaka
- Department of Plant Physiology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
| | - Ewa Ozimek
- Department of Environmental Microbiology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
| | - Małgorzata Majewska
- Department of Environmental Microbiology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
| | - Anna Rysiak
- Department of Ecology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
| | - Jolanta Jaroszuk-Ściseł
- Department of Environmental Microbiology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
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Tohya M, Watanabe S, Teramoto K, Uechi K, Tada T, Kuwahara-Arai K, Kinjo T, Maeda S, Nakasone I, Zaw NN, Mya S, Zan KN, Tin HH, Fujita J, Kirikae T. Pseudomonas asiatica sp. nov., isolated from hospitalized patients in Japan and Myanmar. Int J Syst Evol Microbiol 2019; 69:1361-1368. [PMID: 30810522 DOI: 10.1099/ijsem.0.003316] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative, aerobic, rod-shaped, non-spore-forming bacterial strain, RYU5T, was isolated from a stool sample of an inpatient at a hospital in Okinawa, Japan. The optimal growth temperature of RYU5T was 30 °C. Phylogenetic analysis based on the sequences of housekeeping genes, including the 16S rRNA, rpoB, rpoD and gyrB genes, showed that RYU5T was a member of the Pseudomonas putida group and was located close to Pseudomonas monteilii and P. putida. Whole-genome comparisons, using average nucleotide identity and digital DNA-DNA hybridization, confirmed that strain RYU5T should be classified as a novel species of Pseudomonas. Phenotypic characterization tests showed that utilization of d-mannose, d-serine, l-arabinose and d-fructose could distinguish this strain from other related species of the genus Pseudomonas. Based on genetic and phenotypic evidence, strain RYU5T should be classified as a novel species, for which the name Pseudomonas asiatica sp. nov. is proposed. The type strain is RYU5T (=DSM 107182T, =JCM 32716T), with a DNA G+C content of 62.25 mol%.
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Affiliation(s)
- Mari Tohya
- 1Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Shin Watanabe
- 2Department of Microbiome Research, Juntendo University School of Medicine, Tokyo, Japan
| | - Kanae Teramoto
- 3Koichi Tanaka Mass Spectrometry Research Laboratory, Kyoto, Japan
| | - Kohei Uechi
- 4Department of Infectious Diseases, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Tatsuya Tada
- 1Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Kyoko Kuwahara-Arai
- 1Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Takeshi Kinjo
- 4Department of Infectious Diseases, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Shiro Maeda
- 5Division of Clinical Laboratory and Blood Transfusion, University Hospital of the Ryukyus, Okinawa, Japan
| | - Isamu Nakasone
- 4Department of Infectious Diseases, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Ni Ni Zaw
- 6Clinical Pathology Section, Mandalay General Hospital, Mandalay, Myanmar
| | - San Mya
- 7National Health Laboratory, Yangon, Myanmar
| | | | | | - Jiro Fujita
- 4Department of Infectious Diseases, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Teruo Kirikae
- 1Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
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Furlan JPR, Pitondo-Silva A, Braz VS, Gallo IFL, Stehling EG. Evaluation of different molecular and phenotypic methods for identification of environmental Burkholderia cepacia complex. World J Microbiol Biotechnol 2019; 35:39. [PMID: 30739255 DOI: 10.1007/s11274-019-2614-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/05/2019] [Indexed: 12/01/2022]
Abstract
The correct identification of different genera and bacterial species is essential, especially when these bacteria cause infections and appropriate therapies need to be chosen. Bacteria belonging to the Burkholderia cepacia complex are considered important opportunistic pathogens, causing different types of infections in immunocompromised, principally in patients with cystic fibrosis. Twenty-one isolates were obtained from different soil samples and identified by sequencing of 16S rRNA, 23S rRNA, recA gene, MLST and by VITEK 2 and MALDI-TOF MS systems. Then, statistical analyses were performed. VITEK 2 and MALDI-TOF MS systems showed different bacterial genera. Sequencing of the 16S rRNA, 23S rRNA gene and amplification of recA gene showed that all the isolates belong to the B. cepacia complex. Sequencing of the recA gene showed a predominance of B. cenocepacia. The PCR of the recA gene showed a high specificity when it is necessary to identify the bacteria belonging to the B. cepacia complex in comparison with 16S and 23S rRNA genes sequencing. MLST analyzes showed a diversity of STs, which have not yet been correlated to the species. Phenotypic identification was not suitable for the identification of these pathogens since in many cases different genera have been reported, including identification by using MALDI-TOF MS.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - André Pitondo-Silva
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.,School of Dentistry, University of Ribeirao Preto (UNAERP), Ribeirão Preto, Brazil
| | - Vânia Santos Braz
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Inara Fernanda Lage Gallo
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Eliana Guedes Stehling
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.
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Jung-Schroers V, Jung A, Ryll M, Bauer J, Teitge F, Steinhagen D. Diagnostic methods for identifying different Aeromonas species and examining their pathogenicity factors, their correlation to cytotoxicity and adherence to fish mucus. JOURNAL OF FISH DISEASES 2019; 42:189-219. [PMID: 30521094 DOI: 10.1111/jfd.12917] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/28/2018] [Accepted: 09/28/2018] [Indexed: 06/09/2023]
Abstract
Aeromonas spp. are ubiquitous in the aquatic environment, acting as facultative or obligate pathogens for fish. Identifying Aeromonas spp. is important for pathogenesis and prognosis in diagnostic cases but can be difficult because of their close relationship. Forty-four already characterized isolates of Aeromonas spp. were analysed by 16S rRNA gene sequencing, by gyrase B sequencing, by analysing their fatty acid profiles, by biochemical reactions and by MALDI-TOF MS. To determine their pathogenicity, cytotoxicity, adhesion to mucus and the expression of 12 virulence factors were tested. The susceptibility of the isolates towards 13 different antibiotics was determined. MALDI-TOF MS was found to be an acceptable identification method for Aeromonas spp. Although the method does not detect all species correctly, it is time-effective and entails relatively low costs and no other methods achieved better results. A high prevalence of virulence-related gene fragments was detected in almost all examined Aeromonas spp., especially in A. hydrophila and A. salmonicida, and most isolates exhibited a cytotoxic effect. Single isolates of A. hydrophila and A. salmonicida showed multiple resistance to antibiotics. These results might indicate the potentially pathogenic capacity of Aeromonas spp., suggesting a risk for aquatic animals and even humans, given their ubiquitous nature.
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Affiliation(s)
- Verena Jung-Schroers
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - Arne Jung
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany
| | - Martin Ryll
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany
| | - Julia Bauer
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - Felix Teitge
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - Dieter Steinhagen
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
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Zhang H, Zheng L, Zhao J, Ding S, Xia Y. Investigation of fluoroquinolone resistance mechanism in Mycoplasma hominis isolated from urogenital samples in a Chinese hospital. J Med Microbiol 2019; 68:206-210. [PMID: 30632961 DOI: 10.1099/jmm.0.000913] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
PURPOSE Mycoplasma hominis is considered among the causes of urogenital infections and shows increasing resistance to fluoroquinolones. However, data regarding the fluoroquinolone resistance mechanism of M. hominis in Southwest China are limited. This study aimed to investigate gene mutations of quinolone resistance-determining regions (QRDRs) of M. hominis isolated from clinical urogenital samples in a Chinese hospital. METHODOLOGY Strains of M. hominis were identified by 16S rRNA gene sequencing. The minimal inhibitory concentrations (MICs) of fluoroquinolones were determined by the broth microdilution method, following CLSI guidelines. PCR was used to amplify the QRDRs of the genes gyrA, gyrB, parC and parE. Positive products were sequenced, and gene mutations and amino acid substitutions were analysed by DNAMAN software and BLAST. RESULTS The resistance rates of M. hominis to ciprofloxacin (CIP), levofloxacin (LVX), moxifloxacin (MXF) and gatifloxacin (GAT) were 90.5, 85.7, 73.8 and 71.4 %, respectively. A total of 57 isolates of M. hominis were screened, among which 52 strains demonstrated different resistant phenotypes to fluoroquinolones, 41 harboured amino acid substitutions of GyrA S153L, 51 harboured ParC S91I and 22 harboured ParC K144R. ParE A463S and ParC A154T were recorded for the first time and no amino acid change was detected in GyrB. CONCLUSION The resistance of M. hominis to fluoroquinolones in Southwest China is mainly related to mutations in QRDRs of either gyrA or parC. High-level resistance is associated with mutations in both DNA gyrase and topoisomerase IV.
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Affiliation(s)
- Hongyan Zhang
- 1Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, PR China.,2Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, PR China
| | - Liangjian Zheng
- 3Radiotherapy Center of Oncology, The Third People's Hospital of Chengdu, Chengdu, PR China
| | - Juan Zhao
- 2Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, PR China
| | - Shaochuan Ding
- 2Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, PR China
| | - Yun Xia
- 1Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
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Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures. INFECTION GENETICS AND EVOLUTION 2018; 66:130-151. [DOI: 10.1016/j.meegid.2018.09.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/12/2018] [Accepted: 09/19/2018] [Indexed: 11/21/2022]
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Berg JA, Merrill BD, Breakwell DP, Hope S, Grose JH. A PCR-Based Method for Distinguishing between Two Common Beehive Bacteria, Paenibacillus larvae and Brevibacillus laterosporus. Appl Environ Microbiol 2018; 84:e01886-18. [PMID: 30217838 PMCID: PMC6210111 DOI: 10.1128/aem.01886-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/01/2018] [Indexed: 12/18/2022] Open
Abstract
Paenibacillus larvae and Brevibacillus laterosporus are two bacteria that are members of the Paenibacillaceae family. Both are commonly found in beehives and have historically been difficult to distinguish from each other due to related genetic and phenotypic characteristics and a shared ecological niche. Here, we discuss the likely mischaracterization of three 16S rRNA sequences previously published as P. larvae and provide the phylogenetic evidence that supported the GenBank reassignment of the sequences as B. laterosporus We explore the issues that arise by using only 16S rRNA or other single-gene analyses to distinguish between these bacteria. We also present three sets of molecular markers, two sets that distinguish P. larvae from B. laterosporus and other closely related species within the Paenibacillus genus and a third set that distinguishes B. laterosporus from P. larvae and other closely related species within the Brevibacillus genus. These molecular markers provide a tool for proper identification of these oft-mistaken species.IMPORTANCE 16S rRNA gene sequencing in bacteria has long been held as the gold standard for typing bacteria and, for the most part, is an excellent method of taxonomically identifying different bacterial species. However, the high level of 16S rRNA sequence similarity of some published strains of P. larvae and B. laterosporus, as well as possible horizontal gene transfer events within their shared ecological niche, complicates the use of 16S rRNA sequence as an effective molecular marker for differentiating these two species. Additionally, shared characteristics of these bacteria limit the effectiveness of using traditional phenotypic identification assays, such as the catalase test. The results from this study provide PCR methods to quickly differentiate between these two genera and will be useful when studying Brevibacillus, Paenibacillus, and other disease-relevant bacteria commonly found in beehives.
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Affiliation(s)
- Jordan A Berg
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Bryan D Merrill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Donald P Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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Gołofit-Szymczak M, Górny RL. Microbiological air quality in office buildings equipped with dventilation systems. INDOOR AIR 2018; 28:792-805. [PMID: 30059607 DOI: 10.1111/ina.12495] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 05/27/2023]
Abstract
Proper hygienic conditions in office buildings are of a high importance for both health and well-being of the employees. The aim of this study was the direct comparison of different ventilation systems on microbiological environments in 15 office buildings. The results showed that both bacterial and fungal concentrations in the naturally ventilated office buildings were between 70 and 1600 cfu/m3 , while in the offices equipped with air-conditioning and mechanical ventilation systems, concentrations were lower, that is, between 10 and 530 cfu/m3 and 20 and 410 cfu/m3 , respectively. The size distribution analysis revealed that microorganisms were present in the air mainly as single cells (1.1-3.3 μm) and large aggregates (4.7->7 μm). If deposited in the human respiratory tract, they may be responsible for nose and eyes irritations, asthmatic reactions, and allergic inflammations. The most prevalent bacterial species indoors were Gram-positive cocci (mainly from Staphylococcus and Micrococcus/Kocuria genera) and endospore-forming Gram-positive rods (from Bacillus genus). Among the most common fungal species were those from genera Penicillium, Aspergillus, and Cladosporium. Effectively working and regularly maintained mechanical ventilation or air-conditioning systems ensure a better hygienic quality in the office buildings than natural/gravitational ventilation.
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Affiliation(s)
| | - Rafał L Górny
- Central Institute for Labour Protection, National Research Institute, Warsaw, Poland
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44
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Mishra A, Nam GH, Gim JA, Lee HE, Jo A, Kim HS. Current Challenges of Streptococcus Infection and Effective Molecular, Cellular, and Environmental Control Methods in Aquaculture. Mol Cells 2018; 41:495-505. [PMID: 29754470 PMCID: PMC6030242 DOI: 10.14348/molcells.2018.2154] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 03/15/2018] [Accepted: 04/02/2018] [Indexed: 12/02/2022] Open
Abstract
Several bacterial etiological agents of streptococcal disease have been associated with fish mortality and serious global economic loss. Bacterial identification based on biochemical, molecular, and phenotypic methods has been routinely used, along with assessment of morphological analyses. Among these, the molecular method of 16S rRNA sequencing is reliable, but presently, advanced genomics are preferred over other traditional identification methodologies. This review highlights the geographical variation in strains, their relatedness, as well as the complexity of diagnosis, pathogenesis, and various control methods of streptococcal infections. Several limitations, from diagnosis to control, have been reported, which make prevention and containment of streptococcal disease difficult. In this review, we discuss the challenges in diagnosis, pathogenesis, and control methods and suggest appropriate molecular (comparative genomics), cellular, and environmental solutions from among the best available possibilities.
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Affiliation(s)
- Anshuman Mishra
- Institute of Systems Biology, Pusan National University, Busan 46241,
Korea
| | - Gyu-Hwi Nam
- Institute of Systems Biology, Pusan National University, Busan 46241,
Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241,
Korea
| | - Jeong-An Gim
- Institute of Systems Biology, Pusan National University, Busan 46241,
Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241,
Korea
- The Genomics Institute, Life Sciences Department, UNIST, Ulsan 44919,
Korea
| | - Hee-Eun Lee
- Institute of Systems Biology, Pusan National University, Busan 46241,
Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241,
Korea
| | - Ara Jo
- Institute of Systems Biology, Pusan National University, Busan 46241,
Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241,
Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241,
Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241,
Korea
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45
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Zhou W, Bian Y. Thanatomicrobiome composition profiling as a tool for forensic investigation. Forensic Sci Res 2018; 3:105-110. [PMID: 30483658 PMCID: PMC6197100 DOI: 10.1080/20961790.2018.1466430] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/29/2018] [Indexed: 12/22/2022] Open
Abstract
Thanatomicrobiome, or the postmortem microbiome, has been recognized as a useful microbial marker of the time and location of host death. In this mini-review, we compare the experimental methods commonly applied to thanatomicrobiome studies to the state-of-the-art methodologies in the microbiome field. Then, we review present findings in thanatomicrobiome studies, focusing on the diversity of the thanatomicrobiome composition and prediction models that have been proposed. Finally, we discuss potential improvements and future directions of the field.
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Affiliation(s)
- Wei Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai, China
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46
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Seuylemezian A, Aronson HS, Tan J, Lin M, Schubert W, Vaishampayan P. Development of a Custom MALDI-TOF MS Database for Species-Level Identification of Bacterial Isolates Collected From Spacecraft and Associated Surfaces. Front Microbiol 2018; 9:780. [PMID: 29867782 PMCID: PMC5968301 DOI: 10.3389/fmicb.2018.00780] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/06/2018] [Indexed: 11/13/2022] Open
Abstract
Since the 1970s, the Planetary Protection Group at the Jet Propulsion Laboratory (JPL) has maintained an archive of spacecraft-associated bacterial isolates. Identification of these isolates was routinely performed by sequencing the 16S rRNA gene. Although this technique is an industry standard, it is time consuming and has poor resolving power for some closely related taxa. Matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry is widely used in clinical diagnostics and is a promising method to substitute standard 16S rRNA sequencing. However, manufacturer-provided databases lack the bacterial diversity found in spacecraft-assembly cleanrooms. This study reports the development of the first custom database of MALDI-TOF MS profiles of bacterial isolates obtained from spacecraft and associated cleanroom environments. With the use of this in-house database, 454 bacterial isolates were successfully identified in concurrence with their 16S rRNA sequence-based classifications. Additionally, MALDI-TOF MS resolved strain-level variations, identified potential novel species and distinguished between members of taxonomic groups, which is not possible using conventional 16S rRNA sequencing. MALDI-TOF MS has proved to be an accurate, high-throughput approach for real-time identification of bacterial isolates during the spacecraft assembly process.
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Affiliation(s)
- Arman Seuylemezian
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Heidi S Aronson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - James Tan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Mandy Lin
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Wayne Schubert
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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47
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Schreiber PW, Kuster SP, Hasse B, Bayard C, Rüegg C, Kohler P, Keller PM, Bloemberg GV, Maisano F, Bettex D, Halbe M, Sommerstein R, Sax H. Reemergence of Mycobacterium chimaera in Heater-Cooler Units despite Intensified Cleaning and Disinfection Protocol. Emerg Infect Dis 2018; 22:1830-3. [PMID: 27649345 PMCID: PMC5038437 DOI: 10.3201/eid2210.160925] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Invasive Mycobacterium chimaera infections after open-heart surgery have been reported internationally. These devastating infections result from aerosols generated by contaminated heater–cooler units used with extracorporeal circulation during surgery. Despite intensified cleaning and disinfection, surveillance samples from factory-new units acquired during 2014 grew nontuberculous mycobacteria after a median of 174 days.
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48
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Beye M, Fahsi N, Raoult D, Fournier PE. Careful use of 16S rRNA gene sequence similarity values for the identification of Mycobacterium species. New Microbes New Infect 2017; 22:24-29. [PMID: 29556405 PMCID: PMC5857167 DOI: 10.1016/j.nmni.2017.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/20/2017] [Indexed: 11/03/2022] Open
Abstract
In order to evaluate the suitability of 16S rRNA nucleotide sequence similarity for the classification of new Mycobacterium isolates at the species level, we systematically studied the pairwise identity values of this gene for 131 Mycobacterium species with standing in nomenclature. Only one of the studied species, M. poriferae (0.76%), strictly respected the 95% and 98.65% threshold values currently recommended to determine the affiliation of bacterial isolates to an existing or new genus or species, respectively. All other species exhibited at least an identity value >98.65% and/or <95% with another Mycobacterium species. Therefore, we suggest that interpretation of interspecies 16S rRNA identity values should be made cautiously when classifying a new mycobacterial isolate at the species level.
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Affiliation(s)
- M Beye
- URMITE, UM63, CNRS7278, IRD198, Inserm1095, Institut Hospitalo-Universitaire Méditerranée-infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - N Fahsi
- URMITE, UM63, CNRS7278, IRD198, Inserm1095, Institut Hospitalo-Universitaire Méditerranée-infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - D Raoult
- URMITE, UM63, CNRS7278, IRD198, Inserm1095, Institut Hospitalo-Universitaire Méditerranée-infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- URMITE, UM63, CNRS7278, IRD198, Inserm1095, Institut Hospitalo-Universitaire Méditerranée-infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
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Diversity of Aerobic Bacteria Isolated from Oral and Cloacal Cavities from Free-Living Snakes Species in Costa Rica Rainforest. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2017; 2017:8934285. [PMID: 28913414 PMCID: PMC5585637 DOI: 10.1155/2017/8934285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/28/2017] [Accepted: 07/06/2017] [Indexed: 11/18/2022]
Abstract
Costa Rica has a significant number of snakebites per year and bacterial infections are often complications in these animal bites. Hereby, this study aims to identify, characterize, and report the diversity of the bacterial community in the oral and cloacal cavities of venomous and nonvenomous snakes found in wildlife in Costa Rica. The snakes where captured by casual encounter search between August and November of 2014 in the Quebrada González sector, in Braulio Carrillo National Park. A total of 120 swabs, oral and cloacal, were taken from 16 individuals of the Viperidae and Colubridae families. Samples were cultured on four different media at room temperature. Once isolated in pure culture, colonies were identified with the VITEK® 2C platform (bioMérieux). In order to test the identification provided on environmental isolates, molecular analyses were conducted on 27 isolates of different bacterial species. Specific 16S rDNA PCR-mediated amplification for bacterial taxonomy was performed, then sequenced, and compared with sequences of Ribosomal Database Project (RDP). From 90 bacterial isolates, 40 different bacterial species were identified from both oral and cloacal swabs. These results indicate the diversity of opportunistic pathogens present and their potential to generate infections and zoonosis in humans.
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50
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Comparative evaluation of 16S rRNA gene in world-wide strains of Streptococcus iniae and Streptococcus parauberis for early diagnostic marker. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0542-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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