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Wang X, Wu Y, Fu C, Zhao W, Li L. Metabolic cross-feeding between the competent degrader Rhodococcus sp. strain p52 and an incompetent partner during catabolism of dibenzofuran: Understanding the leading and supporting roles. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134310. [PMID: 38640677 DOI: 10.1016/j.jhazmat.2024.134310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
Microbial interactions, particularly metabolic cross-feeding, play important roles in removing recalcitrant environmental pollutants; however, the underlying mechanisms involved in this process remain unclear. Thus, this study aimed to elucidate the mechanism by which metabolic cross-feeding occurs during synergistic dibenzofuran degradation between a highly efficient degrader, Rhodococcus sp. strain p52, and a partner incapable of utilizing dibenzofuran. A bottom-up approach combined with pairwise coculturing was used to examine metabolic cross-feeding between strain p52 and Arthrobacter sp. W06 or Achromobacter sp. D10. Pairwise coculture not only promoted bacterial pair growth but also facilitated dibenzofuran degradation. Specifically, strain p52, acting as a donor, released dibenzofuran metabolic intermediates, including salicylic acid and gentisic acid, for utilization and growth, respectively, by the partner strains W06 and D10. Both salicylic acid and gentisic acid exhibited biotoxicity, and their accumulation inhibited dibenzofuran degradation. The transcriptional activity of the genes responsible for the catabolism of dibenzofuran and its metabolic intermediates was coordinately regulated in strain p52 and its cocultivated partners, thus achieving synergistic dibenzofuran degradation. This study provides insights into microbial metabolic cross-feeding during recalcitrant environmental pollutant removal.
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Affiliation(s)
- Xudi Wang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Yanan Wu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Changai Fu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Wenhui Zhao
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Li Li
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China.
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Gu CH, Khatib LA, Fitzgerald AS, Graham-Wooten J, Ittner CA, Sherrill-Mix S, Chuang Y, Glaser LJ, Meyer NJ, Bushman FD, Collman RG. Tracking gut microbiome and bloodstream infection in critically ill adults. PLoS One 2023; 18:e0289923. [PMID: 37816004 PMCID: PMC10564172 DOI: 10.1371/journal.pone.0289923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/29/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The gut microbiome is believed to contribute to bloodstream infection (BSI) via translocation of dominant gut bacteria in vulnerable patient populations. However, conclusively linking gut and blood organisms requires stringent approaches to establish strain-level identity. METHODS We enrolled a convenience cohort of critically ill patients and investigated 86 bloodstream infection episodes that occurred in 57 patients. Shotgun metagenomic sequencing was used to define constituents of their gut microbiomes, and whole genome sequencing and assembly was done on 23 unique bloodstream isolates that were available from 21 patients. Whole genome sequences were downloaded from public databases and used to establish sequence-identity distribution and define thresholds for unrelated genomes of BSI species. Gut microbiome reads were then aligned to whole genome sequences of the cognate bloodstream isolate and unrelated database isolates to assess identity. RESULTS Gut microbiome constituents matching the bloodstream infection species were present in half of BSI episodes, and represented >30% relative abundance of gut sequences in 10% of episodes. Among the 23 unique bloodstream organisms that were available for whole genome sequencing, 14 were present in gut at the species level. Sequence alignment applying defined thresholds for identity revealed that 6 met criteria for identical strains in blood and gut, but 8 did not. Sequence identity between BSI isolates and gut microbiome reads was more likely when the species was present at higher relative abundance in gut. CONCLUSION In assessing potential gut source for BSI, stringent sequence-based approaches are essential to determine if organisms responsible for BSI are identical to those in gut: of 14 evaluable patients in which the same species was present in both sites, they were identical in 6/14, but were non-identical in 8/14 and thus inconsistent with gut source. This report demonstrates application of sequencing as a key tool to investigate infection tracking within patients.
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Affiliation(s)
- Christopher H. Gu
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
| | - Layla A. Khatib
- Department of Medicine, Pulmonary and Critical Care Division and the Center for Translational Lung Biology / Lung Biology Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
| | - Ayannah S. Fitzgerald
- Department of Medicine, Pulmonary and Critical Care Division and the Center for Translational Lung Biology / Lung Biology Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
| | - Jevon Graham-Wooten
- Department of Medicine, Pulmonary and Critical Care Division and the Center for Translational Lung Biology / Lung Biology Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
| | - Caroline A. Ittner
- Department of Medicine, Pulmonary and Critical Care Division and the Center for Translational Lung Biology / Lung Biology Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
| | - YuChung Chuang
- Department of Medicine, Pulmonary and Critical Care Division and the Center for Translational Lung Biology / Lung Biology Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
| | - Laurel J. Glaser
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
| | - Nuala J. Meyer
- Department of Medicine, Pulmonary and Critical Care Division and the Center for Translational Lung Biology / Lung Biology Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
| | - Ronald G. Collman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
- Department of Medicine, Pulmonary and Critical Care Division and the Center for Translational Lung Biology / Lung Biology Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America
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3
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Xiong Z, Hong Z, Li X, Gao D, Wang L, Liu S, Zhao J, Li X, Qian P. The multidrug-resistant Pseudomonas fluorescens strain: a hidden threat in boar semen preservation. Front Microbiol 2023; 14:1279630. [PMID: 37869660 PMCID: PMC10588451 DOI: 10.3389/fmicb.2023.1279630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Although the bacterial composition of boar ejaculate has been extensively studied, the bacterial composition of extended boar semen is often overlooked, despite the potential risks these microorganisms may pose to the long-term preservation of extended boar semen at 15-17°C. In this study, we characterized the bacterial community composition of extended semen and discovered that Pseudomonas spp. was the dominant flora. The dominant strains were further isolated and identified as a potential new species in the Pseudomonas fluorescens group and named GXZC strain, which had adverse effects on sperm quality and was better adapted to growth at 17°C. Antimicrobial susceptibility testing showed that the GXZC strain was resistant to all commonly used veterinary antibiotics. Whole-genome sequencing (WGS) and genome annotation revealed the large genetic structure and function [7,253,751 base pairs and 6,790 coding sequences (CDSs)]. Comparative genomic analysis with the closest type strains showed that the GXZC strain predicted more diversity of intrinsic and acquired resistance genes to multi-antimicrobial agents. Taken together, our study highlights a problem associated with the long-term storage of extended boar semen caused by a P. fluorescens group strain with unique biological characteristics. It is essential to develop a new antibacterial solution for the long-term preservation of boar semen.
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Affiliation(s)
- Zhixuan Xiong
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Ziqiang Hong
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Xinxin Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Dongyang Gao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Linkang Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Shudan Liu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Junna Zhao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Xiangmin Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Ping Qian
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
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4
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Achromobacter spp. prevalence and adaptation in cystic fibrosis lung infection. Microbiol Res 2022; 263:127140. [DOI: 10.1016/j.micres.2022.127140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/11/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022]
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Houlihan E, Lucey M, Pandian A, Hanahoe B, Higgins F, DeLappe N, Krawczyk J, Keady D. Case of recurrent Achromobacter xylosoxidans bacteraemia and PICC (peripherally-inserted central catheter) line infection in an immunocompromised patient. Infect Prev Pract 2022; 4:100202. [PMID: 35198965 PMCID: PMC8844297 DOI: 10.1016/j.infpip.2022.100202] [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: 11/16/2021] [Accepted: 01/13/2022] [Indexed: 11/02/2022] Open
Abstract
Background Presentation of Case Discussion Conclusion
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Arjun R, John KE, Niyas VKM, Nair SR, Mohan V, Ratheesh RS. Achromobacter spp. bacteremia outbreak related to contaminated furosemide ampoules. LE INFEZIONI IN MEDICINA 2021; 29:427-433. [PMID: 35146348 PMCID: PMC8805504 DOI: 10.53854/liim-2903-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/27/2021] [Indexed: 06/14/2023]
Abstract
Nosocomial outbreaks related to medication contamination are reported world-wide. A sudden increase in cases of Achromobacter spp. bacteremia led to an outbreak investigation in our setting. Line listing and environmental sampling led to identification of contaminated furosemide ampoules as the source. Molecular identification helped in species identification and in this outbreak more than one species was identified. Prompt withdrawal of the contaminated batch of ampoules curtailed the outbreak.
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Affiliation(s)
- Rajalakshmi Arjun
- Department of Infectious Diseases, KIMSHEALTH, Thiruvananthapuram, Kerala, India
| | - Kalpana E John
- Department of Microbiology, KIMSHEALTH, Thiruvananthapuram, Kerala, India
| | | | - Sreerekha R Nair
- Department of Hospital Infection Control, KIMSHEALTH, Thiruvananthapuram, Kerala, India
| | - Viji Mohan
- Department of Microbiology, KIMSHEALTH, Thiruvananthapuram, Kerala, India
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7
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Characterization of Novel Lytic Bacteriophages of Achromobacter marplantensis Isolated from a Pneumonia Patient. Viruses 2020; 12:v12101138. [PMID: 33049935 PMCID: PMC7600146 DOI: 10.3390/v12101138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 01/21/2023] Open
Abstract
Achromobacter spp. are becoming increasingly associated with lung infections in patients suffering from cystic fibrosis (CF). A. marplatensis, which is closely related to A. xylosoxidans, has been isolated from the lungs of CF patients and other human infections. This article describes the isolation, morphology and characterization of two lytic bacteriophages specific for an A. marplatensis strain isolated from a pneumonia patient. This host strain was the causal agent of hospital acquired pneumonia–the first clinical report of such an occurrence. Full genome sequencing revealed bacteriophage genomes ranging in size from 45901 to 46,328 bp. Transmission electron microscopy revealed that the two bacteriophages AMA1 and AMA2 belonged to the Siphoviridae family. Host range analysis showed that their host range did not extend to A. xylosoxidans. The possibility exists for future testing of such bacteriophages in the control of Achromobacter infections such as those seen in CF and other infections of the lungs. The incidence of antibiotic resistance in this genus highlights the importance of seeking adjuncts and alternatives in CF and other lung infections.
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8
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Shah DH, Board MM, Crespo R, Guard J, Paul NC, Faux C. The occurrence of Salmonella, extended-spectrum β-lactamase producing Escherichia coli and carbapenem resistant non-fermenting Gram-negative bacteria in a backyard poultry flock environment. Zoonoses Public Health 2020; 67:742-753. [PMID: 32710700 DOI: 10.1111/zph.12756] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/30/2020] [Accepted: 06/15/2020] [Indexed: 12/15/2022]
Abstract
Increase in the number of small-scale backyard poultry flocks in the USA has substantially increased human-to-live poultry contact, leading to increased public health risks of the transmission of multi-drug resistant (MDR) zoonotic and food-borne bacteria. The objective of this study was to detect the occurrence of Salmonella and MDR Gram-negative bacteria (GNB) in the backyard poultry flock environment. A total of 34 backyard poultry flocks in Washington State (WA) were sampled. From each flock, one composite coop sample and three drag swabs from nest floor, waterer-feeder, and a random site with visible faecal smearing, respectively, were collected. The samples were processed for isolation of Salmonella and other fermenting and non-fermenting GNB under ceftiofur selection. Each isolate was identified to species level using MALDI-TOFF and tested for resistance against 16 antibiotics belonging to eight antibiotic classes. Salmonella serovar 1,4,[5],12:i:- was isolated from one (3%) out of 34 flocks. Additionally, a total of 133 ceftiofur resistant (CefR ) GNB including Escherichia coli (53), Acinetobacter spp. (45), Pseudomonas spp. (22), Achromobacter spp. (8), Bordetella trematum (1), Hafnia alvei (1), Ochrobactrum intermedium (1), Raoultella ornithinolytica (1), and Stenotrophomonas maltophilia (1) were isolated. Of these, 110 (82%) isolates displayed MDR. Each flock was found positive for the presence of one or more CefR GNB. Several MDR E. coli (n = 15) were identified as extended-spectrum β-lactamase (ESBL) positive. Carbapenem resistance was detected in non-fermenting GNB including Acinetobacter spp. (n = 20), Pseudomonas spp. (n = 11) and Stenotrophomonas maltophila (n = 1). ESBL positive E. coli and carbapenem resistant non-fermenting GNB are widespread in the backyard poultry flock environment in WA State. These GNB are known to cause opportunistic infections, especially in immunocompromised hosts. Better understanding of the ecology and epidemiology of these GNB in the backyard poultry flock settings is needed to identify potential risks of transmission to people in proximity.
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Affiliation(s)
- Devendra H Shah
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Melissa M Board
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Rocio Crespo
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Jean Guard
- US National Poultry Research Center, United States Department of Agriculture, Athens, GA, USA
| | - Narayan C Paul
- Texas A & M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - Cynthia Faux
- Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, USA
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9
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Jaing C, Thissen J, Morrison M, Dillon MB, Waters SM, Graham GT, Be NA, Nicoll P, Verma S, Caro T, Smith DJ. Sierra Nevada sweep: metagenomic measurements of bioaerosols vertically distributed across the troposphere. Sci Rep 2020; 10:12399. [PMID: 32709938 PMCID: PMC7382458 DOI: 10.1038/s41598-020-69188-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/08/2020] [Indexed: 12/14/2022] Open
Abstract
To explore how airborne microbial patterns change with height above the Earth’s surface, we flew NASA’s C-20A aircraft on two consecutive days in June 2018 along identical flight paths over the US Sierra Nevada mountain range at four different altitudes ranging from 10,000 ft to 40,000 ft. Bioaerosols were analyzed by metagenomic DNA sequencing and traditional culturing methods to characterize the composition and diversity of atmospheric samples compared to experimental controls. The relative abundance of taxa changed significantly at each altitude sampled, and the diversity profile shifted across the two sampling days, revealing a regional atmospheric microbiome that is dynamically changing. The most proportionally abundant microbial genera were Mycobacterium and Achromobacter at 10,000 ft; Stenotrophomonas and Achromobacter at 20,000 ft; Delftia and Pseudoperonospora at 30,000 ft; and Alcaligenes and Penicillium at 40,000 ft. Culture-based detections also identified viable Bacillus zhangzhouensis, Bacillus pumilus, and Bacillus spp. in the upper troposphere. To estimate bioaerosol dispersal, we developed a human exposure likelihood model (7-day forecast) using general aerosol characteristics and measured meteorological conditions. By coupling metagenomics to a predictive atmospheric model, we aim to set the stage for field campaigns that monitor global bioaerosol emissions and impacts.
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Affiliation(s)
- Crystal Jaing
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - James Thissen
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Michael Morrison
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Michael B Dillon
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Samantha M Waters
- Universities Space Research Association, Maryland, USA.,NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA, USA
| | | | - Nicholas A Be
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | - Sonali Verma
- Blue Marble Space Institute of Science, Space Bioscences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Tristan Caro
- Department of Geological Sciences, University of Colorado, Boulder, CO, USA
| | - David J Smith
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA, USA
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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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Garrigos T, Neuwirth C, Chapuis A, Bador J, Amoureux L. Development of a database for the rapid and accurate routine identification of Achromobacter species by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Clin Microbiol Infect 2020; 27:126.e1-126.e5. [PMID: 32283265 DOI: 10.1016/j.cmi.2020.03.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 02/17/2020] [Accepted: 03/26/2020] [Indexed: 10/24/2022]
Abstract
OBJECTIVES Achromobacter spp. are emerging pathogens in respiratory samples from cystic fibrosis patients. The current reference methods (nrdA-sequencing or multilocus sequence typing) can identify 18 species which are often misidentified by conventional techniques as A. xylosoxidans. A few studies have suggested that matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) provides accurate identification of the genus but not of species. The aims of this study were (a) to generate a database for MALDI-TOF/MS Bruker including the 18 species, (b) to evaluate the suitability of the database for routine laboratory identification, and (c) to compare its performance with that of the currently available Bruker default database. METHODS A total of 205 isolates belonging to the 18 species identified by nrdA sequencing were used to build a local database. Main spectra profiles (MSPs) were created according to Bruker's recommendations for each isolate with the Biotyper software. Performance of the default Bruker database and ours for routine use were compared by testing 167 strains (including 38 isolates used from MSP creation) belonging to the 18 species identified by nrdA sequencing directly from colonies cultivated on various media. RESULTS Our new database accurately identified 99.4% (166/167) of the isolates from the 18 species (score ≥2.0) versus only 50.9% (85/167) with the Bruker database. In the Bruker database 17.3% of the isolates (29/167) were incorrectly identified as another species despite a score of ≥2.0. CONCLUSIONS The use of MALDI-TOF/MS in combination with a database developed with samples from 18 Achromobacter species provides rapid and accurate identification. This tool could be used to help future clinical studies.
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Affiliation(s)
- T Garrigos
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France
| | - C Neuwirth
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France; UMR/CNRS 6249 Chrono-environnement, University of Bourgogne- Franche-Comté, Besançon, France
| | - A Chapuis
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France
| | - J Bador
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France; UMR/CNRS 6249 Chrono-environnement, University of Bourgogne- Franche-Comté, Besançon, France
| | - L Amoureux
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France; UMR/CNRS 6249 Chrono-environnement, University of Bourgogne- Franche-Comté, Besançon, France.
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Mohapatra B, Kazy SK, Sar P. Comparative genome analysis of arsenic reducing, hydrocarbon metabolizing groundwater bacterium Achromobacter sp. KAs 3-5T explains its competitive edge for survival in aquifer environment. Genomics 2019; 111:1604-1619. [DOI: 10.1016/j.ygeno.2018.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/25/2018] [Accepted: 11/05/2018] [Indexed: 11/24/2022]
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13
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Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN. Salt-responsive gut commensal modulates T H17 axis and disease. Nature 2017; 551:585-589. [PMID: 29143823 PMCID: PMC6070150 DOI: 10.1038/nature24628] [Citation(s) in RCA: 806] [Impact Index Per Article: 115.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/10/2017] [Indexed: 12/12/2022]
Abstract
A Western lifestyle with high salt consumption can lead to hypertension and cardiovascular disease. High salt may additionally drive autoimmunity by inducing T helper 17 (TH17) cells, which can also contribute to hypertension. Induction of TH17 cells depends on gut microbiota; however, the effect of salt on the gut microbiome is unknown. Here we show that high salt intake affects the gut microbiome in mice, particularly by depleting Lactobacillus murinus. Consequently, treatment of mice with L. murinus prevented salt-induced aggravation of actively induced experimental autoimmune encephalomyelitis and salt-sensitive hypertension by modulating TH17 cells. In line with these findings, a moderate high-salt challenge in a pilot study in humans reduced intestinal survival of Lactobacillus spp., increased TH17 cells and increased blood pressure. Our results connect high salt intake to the gut-immune axis and highlight the gut microbiome as a potential therapeutic target to counteract salt-sensitive conditions.
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Affiliation(s)
- Nicola Wilck
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Mariana G Matus
- Center for Microbiome Informatics and Therapeutics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sean M Kearney
- Center for Microbiome Informatics and Therapeutics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Scott W Olesen
- Center for Microbiome Informatics and Therapeutics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Kristoffer Forslund
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Hendrik Bartolomaeus
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Stefanie Haase
- Department of Neurology, Friedrich-Alexander-University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Anja Mähler
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - András Balogh
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Lajos Markó
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Olga Vvedenskaya
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Integrative Proteomics and Metabolomics Platform, Berlin Institute for Medical Systems Biology BIMSB, 13125 Berlin, Germany
- Berlin School of Integrative Oncology, Charité University Medicine Berlin, Berlin, Germany
| | - Friedrich H Kleiner
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
| | - Dmitry Tsvetkov
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Lars Klug
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Paul I Costea
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Shinichi Sunagawa
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
- Institute of Microbiology, ETH Zurich, 8092 Zurich, Switzerland
| | - Lisa Maier
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Natalia Rakova
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Department of Neurology, Friedrich-Alexander-University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Valentin Schatz
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Patrick Neubert
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | | | | | - Maik Gollasch
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Diana A Grohme
- Translational Immunology, Department of Clinical Pathobiochemistry, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Beatriz F Côrte-Real
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, Campus Diepenbeek, 3590 Diepenbeek, Belgium
| | - Roman G Gerlach
- Project Group 5, Robert Koch Institute, 38855 Wernigerode, Germany
| | - Marijana Basic
- Hannover Medical School, Institute for Laboratory Animal Science and Central Animal Facility, 30625 Hannover, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Jens M Titze
- Division of Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jonathan Jantsch
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Michael Boschmann
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Ralf Dechend
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Markus Kleinewietfeld
- Translational Immunology, Department of Clinical Pathobiochemistry, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, Campus Diepenbeek, 3590 Diepenbeek, Belgium
- Center for Regenerative Therapies Dresden (CRTD), 01307 Dresden, Germany
| | - Stefan Kempa
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Integrative Proteomics and Metabolomics Platform, Berlin Institute for Medical Systems Biology BIMSB, 13125 Berlin, Germany
| | - Peer Bork
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Ralf A Linker
- Department of Neurology, Friedrich-Alexander-University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Dominik N Müller
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
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Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
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Moremi N, Claus H, Hingi M, Vogel U, Mshana SE. Multidrug-resistant Achromobacter animicus causing wound infection in a street child in Mwanza, Tanzania. Diagn Microbiol Infect Dis 2017; 88:58-61. [DOI: 10.1016/j.diagmicrobio.2017.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/03/2017] [Accepted: 02/04/2017] [Indexed: 01/24/2023]
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16
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Multilocus Sequence Analysis of Phylogroup 1 and 2 Oral Treponeme Strains. Appl Environ Microbiol 2017; 83:AEM.02499-16. [PMID: 27864174 DOI: 10.1128/aem.02499-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/14/2016] [Indexed: 02/08/2023] Open
Abstract
More than 75 "species-level" phylotypes of spirochete bacteria belonging to the genus Treponema reside within the human oral cavity. The majority of these oral treponeme phylotypes correspond to as-yet-uncultivated taxa or strains of uncertain standing in taxonomy. Here, we analyze phylogenetic and taxonomic relationships between oral treponeme strains using a multilocus sequence analysis (MLSA) scheme based on the highly conserved 16S rRNA, pyrH, recA, and flaA genes. We utilized this MLSA scheme to analyze genetic data from a curated collection of oral treponeme strains (n = 71) of diverse geographical origins. This comprises phylogroup 1 (n = 23) and phylogroup 2 (n = 48) treponeme strains, including all relevant American Type Culture Collection reference strains. The taxonomy of all strains was confirmed or inferred via the analysis of ca. 1,450-bp 16S rRNA gene sequences using a combination of bioinformatic and phylogenetic approaches. Taxonomic and phylogenetic relationships between the respective treponeme strains were further investigated by analyzing individual and concatenated flaA (1,074-nucleotide [nt]), recA (1,377-nt), and pyrH (696-nt) gene sequence data sets. Our data confirmed the species differentiation between Treponema denticola (n = 41) and Treponema putidum (n = 7) strains. Notably, our results clearly supported the differentiation of the 23 phylogroup 1 treponeme strains into five distinct "species-level" phylotypes. These respectively corresponded to "Treponema vincentii" (n = 11), Treponema medium (n = 1), "Treponema sinensis" (Treponema sp. IA; n = 4), Treponema sp. IB (n = 3), and Treponema sp. IC (n = 4). In conclusion, our MLSA-based approach can be used to effectively discriminate oral treponeme taxa, confirm taxonomic assignment, and enable the delineation of species boundaries with high confidence. IMPORTANCE Periodontal diseases are caused by persistent polymicrobial biofilm infections of the gums and underlying tooth-supporting structures and have a complex and variable etiology. Although Treponema denticola is strongly associated with periodontal diseases, the etiological roles of other treponeme species/phylotypes are less well defined. This is due to a paucity of formal species descriptions and a poor understanding of genetic relationships between oral treponeme taxa. Our study directly addresses these issues. It represents one of the most comprehensive analyses of oral treponeme strains performed to date, including isolates from North America, Europe, and Asia. We envisage that our results will greatly facilitate future metagenomic efforts aimed at characterizing the clinical distributions of oral treponeme species/phylotypes, helping investigators to establish a more detailed understanding of their etiological roles in periodontal diseases and other infectious diseases. Our results are also directly relevant to various polymicrobial tissue infections in animals, which also involve treponeme populations.
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17
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Takei T, Konuma T, Takahashi S, Miharu Y, Suzuki M, Shibata H, Ishii H, Kato S, Takahashi S, Tojo A. Multi-locus sequence analysis for identification of Achromobacter xylosoxidans from blood culture. Infect Dis (Lond) 2016; 48:864-6. [DOI: 10.1080/23744235.2016.1203987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Tomomi Takei
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takaaki Konuma
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Yuta Miharu
- Department of Laboratory Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masato Suzuki
- Department of Laboratory Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroko Shibata
- Department of Laboratory Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroto Ishii
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seiko Kato
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoshi Takahashi
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Arinobu Tojo
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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18
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Fagerquist CK. Unlocking the proteomic information encoded in MALDI-TOF-MS data used for microbial identification and characterization. Expert Rev Proteomics 2016; 14:97-107. [DOI: 10.1080/14789450.2017.1260451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clifton K. Fagerquist
- United States Department of Agriculture (USDA), Agricultural Research Service, Albany, CA, USA
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19
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Characterization of Achromobacter Species in Cystic Fibrosis Patients: Comparison of bla(OXA-114) PCR Amplification, Multilocus Sequence Typing, and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2016; 53:3894-6. [PMID: 26400790 DOI: 10.1128/jcm.02197-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Molecular methodologies were used to identify 28 Achromobacter spp. from patients with cystic fibrosis (CF). Multilocus sequence typing (MLST) identified 17 Achromobacter xylosoxidans isolates (all bla(OXA-114) positive), nine Achromobacter ruhlandii isolates (all bla(OXA-114) positive), one Achromobacter dolens isolate, and one Achromobacter insuavis isolate. All less common species were misidentified as A. xylosoxidans by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Chronic colonization by clonally related A. ruhlandii isolates was demonstrated.
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Cools P, Ho E, Vranckx K, Schelstraete P, Wurth B, Franckx H, Ieven G, Van Simaey L, Van Daele S, Verhulst S, De Baets F, Vaneechoutte M. Epidemic Achromobacter xylosoxidans strain among Belgian cystic fibrosis patients and review of literature. BMC Microbiol 2016; 16:122. [PMID: 27342812 PMCID: PMC4919866 DOI: 10.1186/s12866-016-0736-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 06/08/2016] [Indexed: 12/11/2022] Open
Abstract
Background Achromobacter xylosoxidans is increasingly being recognized as an emerging pathogen in cystic fibrosis. Recent severe infections with A. xylosoxidans in some of our cystic fibrosis (CF) patients led to a re-evaluation of the epidemiology of CF-associated A. xylosoxidans infections in two Belgian reference centres (Antwerp and Ghent). Several of these patients also stayed at the Rehabilitation Centre De Haan (RHC). In total, 59 A. xylosoxidans isolates from 31 patients (including 26 CF patients), collected between 2001 and 2014, were studied. We evaluated Matrix Assisted Laser Desorption Ionisation -Time of Flight mass spectrometry (MALDI-TOF) as an alternative for McRAPD typing. Results Both typing approaches established the presence of a major cluster, comprising isolates, all from 21 CF patients, including from two patients sampled when staying at the RHC a decade ago. This major cluster was the same as the cluster established already a decade ago at the RHC. A minor cluster consisted of 13 isolates from miscellaneous origin. A further seven isolates, including one from a non-CF patient who had stayed recently at the RHC, were singletons. Conclusions Typing results of both methods were similar, indicating transmission of a single clone of A. xylosoxidans among several CF patients from at least two reference centres. Isolates of the same clone were already observed at the RHC, a decade ago. It is difficult to establish to what extent the RHC is the source of transmission, because the epidemic strain was already present when the first epidemiological study in the RHC was carried out. This study also documents the applicability of MALDI-TOF for typing of strains within the species A. xylosoxidans and the need to use the dynamic cutoff algorithm of the BioNumerics® software for correct clustering of the fingerprints. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0736-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Piet Cools
- Laboratory Bacteriology Research (LBR), Department of Microbiology, Immunology, and Clinical Chemistry, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Erwin Ho
- Cystic Fibrosis Centre, Antwerp University Hospital (AUH), Antwerp, Belgium
| | | | | | - Bettina Wurth
- Zeepreventorium (Rehabilitation Centre, RHC), De Haan, Belgium
| | - Hilde Franckx
- Zeepreventorium (Rehabilitation Centre, RHC), De Haan, Belgium
| | - Greet Ieven
- Department of Microbiology, Antwerp University Hospital, Antwerp, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research (LBR), Department of Microbiology, Immunology, and Clinical Chemistry, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Sabine Van Daele
- Cystic Fibrosis Centre, Ghent University Hospital (GUH), Ghent, Belgium
| | - Stijn Verhulst
- Cystic Fibrosis Centre, Antwerp University Hospital (AUH), Antwerp, Belgium
| | - Frans De Baets
- Cystic Fibrosis Centre, Ghent University Hospital (GUH), Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research (LBR), Department of Microbiology, Immunology, and Clinical Chemistry, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.
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Firmida MC, Pereira RHV, Silva EASR, Marques EA, Lopes AJ. Clinical impact of Achromobacter xylosoxidans colonization/infection in patients with cystic fibrosis. Braz J Med Biol Res 2016; 49:e5097. [PMID: 26909788 PMCID: PMC4792508 DOI: 10.1590/1414-431x20155097] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/17/2015] [Indexed: 12/20/2022] Open
Abstract
The rate of diagnosis of colonization/infection of the airways with
Achromobacter xylosoxidans has increased in cystic fibrosis
patients, but its clinical significance is still controversial. This retrospective,
case-control study aimed to evaluate the clinical impact of A.
xylosoxidans colonization/infection in cystic fibrosis patients.
Individuals who were chronically colonized/infected (n=10), intermittently
colonized/infected (n=15), and never colonized/infected with A.
xylosoxidans (n=18) were retrospectively evaluated during two
periods that were 2 years apart. Demographic characteristics, clinical data, lung
function, and chronic bacterial co-colonization data were evaluated. Of the total
study population, 87% were pediatric patients and 65.1% were female. Individuals
chronically colonized/infected with A. xylosoxidans had decreased
forced expiratory volume in 1 s (51.7% in the chronic colonization/infection group
vs 82.7% in the intermittent colonization/infection group
vs 76% in the never colonized/infected group). Compared with the
other two groups, the rate of co-colonization with methicillin-resistant
Staphylococcus aureus was higher in individuals chronically
colonized/infected with A. xylosoxidans (P=0.002).
Changes in lung function over 2 years in the three groups were not significant,
although a trend toward a greater decrease in lung function was observed in the
chronically colonized/infected group. Compared with the other two groups, there was a
greater number of annual hospitalizations in patients chronically colonized/infected
with A. xylosoxidans (P=0.033). In cystic fibrosis patients, there
was an increased frequency of A. xylosoxidans colonization/infection
in children, and lung function was reduced in patients who were chronically
colonized/infected with A. xylosoxidans. Additionally, there were no
differences in clinical outcomes during the 2-year period, except for an increased
number of hospitalizations in patients with A. xylosoxidans.
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Affiliation(s)
- M C Firmida
- Programa de Pós-Graduação em Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - R H V Pereira
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - E A S R Silva
- Laboratório de Bacteriologia, Hospital Universitário Pedro Ernesto, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - E A Marques
- Programa de Pós-Graduação em Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - A J Lopes
- Programa de Pós-Graduação em Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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22
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Amoureux L, Bador J, Bounoua Zouak F, Chapuis A, de Curraize C, Neuwirth C. Distribution of the species of Achromobacter in a French Cystic Fibrosis Centre and multilocus sequence typing analysis reveal the predominance of A. xylosoxidans and clonal relationships between some clinical and environmental isolates. J Cyst Fibros 2016; 15:486-94. [PMID: 26778615 DOI: 10.1016/j.jcf.2015.12.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/01/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Achromobacter spp. are emerging pathogens in Cystic Fibrosis (CF) patients. Recent studies proposed Multilocus Sequence Typing (MLST) scheme and a species-level identification method by nrdA sequencing for this genus. Epidemiological data are needed to assess the species and/or the sequence types (STs) involved and their potential role in CF patients lung function degradation. The aims of this study were i) to describe the distribution of the different species of Achromobacter in our CF centre ii) to detect potential STs more involved in chronic colonisations iii) to detect a potential local or worldwide predominance of some STs among clinical and environmental isolates. METHODS All the isolates (477) collected in our CF centre from 2007 to 2014 among the 177 patients attending the centre were identified using nrdA sequencing. MLST analysis was performed for 37 clinical and 14 environmental isolates. RESULTS A total of 47 out of 177 patients presented positive culture(s) with Achromobacter spp., representing 12.7% of the patients of the centre each year. Eleven species were detected, A. xylosoxidans being the most prevalent species (27 patients). Only A. xylosoxidans (>80%) and A. insuavis were involved in chronic colonisation (6.7%). MLST analysis revealed a wide diversity among the isolates (36 STs for 51 isolates). Nevertheless, one third of the isolates belonged to STs previously detected in clinical isolates from other countries. CONCLUSIONS This study is a first approach in understanding the global epidemiology of Achromobacter species in CF. These results confirm the high prevalence of the species A. xylosoxidans among CF patients, reveal the worldwide distribution of some STs and point out the potential role of environmental sources of contamination. More studies are needed to search for relationships between species and/or ST and pathogenicity.
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Affiliation(s)
- Lucie Amoureux
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France.
| | - Julien Bador
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France
| | - Fatma Bounoua Zouak
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France
| | - Angélique Chapuis
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France
| | - Claire de Curraize
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France
| | - Catherine Neuwirth
- Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070 DIJON CEDEX, France
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Vandamme PA, Peeters C, Cnockaert M, Gomila M, Moore ERB, Spilker T, LiPuma JJ. Reclassification of Achromobacter spiritinus Vandamme et al. 2013 as a later heterotypic synonym of Achromobacter marplatensis Gomila et al. 2011. Int J Syst Evol Microbiol 2016; 66:1641-1644. [PMID: 26738485 DOI: 10.1099/ijsem.0.000872] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A repeat multi-locus sequence analysis (MLSA) of concatenated nusA, eno, rpoB, gltB, lepA, nuoL and nrdA sequences of strains classified as Achromobacter marplatensis was performed. The results revealed that earlier reported sequence data of the proposed type strain were erroneous, and that the corrected concatenated sequence divergence between the A. marplatensis LMG 26219T (=CCUG 56371T) sequence type and that of strains of Achromobacter spiritinus was well below the 2.1% threshold value that delineates species of the genus Achromobacter. These results therefore demonstrated that strains which were classified as A. spiritinus should be reclassified as A. marplatensis and that the name Achromobacter spiritinus should no longer be used. An emendation of the description of Achromobacter marplatensis is warranted.
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Affiliation(s)
- Peter A Vandamme
- Laboratorium voor Microbiologie, Vakgroep Biochemie en microbiologie, Faculteit Wetenschappen, Universiteit Gent, Gent, Belgium
| | - Charlotte Peeters
- Laboratorium voor Microbiologie, Vakgroep Biochemie en microbiologie, Faculteit Wetenschappen, Universiteit Gent, Gent, Belgium
| | - Margo Cnockaert
- Laboratorium voor Microbiologie, Vakgroep Biochemie en microbiologie, Faculteit Wetenschappen, Universiteit Gent, Gent, Belgium
| | - Margarita Gomila
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Islas Baleares, Spain
| | - Edward R B Moore
- Culture Collection University of Gothenburg (CCUG), Department of Infectious Diseases, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Theodore Spilker
- Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John J LiPuma
- Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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