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Bodin J, Gallego-Hernanz MP, Plouzeau Jayle C, Michaud A, Broutin L, Cremniter J, Burucoa C, Pichon M. Bacteremia due to Lachnoanaerobaculum umeaense in a patient with acute myeloid leukemia during chemotherapy: A case report, and a review of the literature. J Infect Chemother 2024; 30:912-916. [PMID: 38336170 DOI: 10.1016/j.jiac.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/23/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
The present case reports a bacteremia due to Lachnoanaerobaculum umeaense (a Gram-positive, filamentous, rod-shaped, anaerobic, spore-forming bacillus present in the human oral microbiota) in a patient treated for acute myeloid leukemia. After failed identification by MALDI-TOF, identification was done by sequencing of 16s rRNA. The patient was successfully treated with Amoxicillin-clavulanic acid and ciprofloxacin for seven days. Comparison of V1-V3 regions of the bacterial 16S rRNA gene gene with published sequences failed to classify the strain as pathogenic or non-pathogenic based on this phylogenetic classification alone. Although Lachnoanaerobaculum gingivalis are known to be associated with bacteremia in patients with acute myeloid leukemia, this clinical case of infection by L. umeaense argues for further studies that will lead to more efficient classification of the infection by these microorganisms.
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Affiliation(s)
- Julie Bodin
- Université de Poitiers, Faculté de Médecine et Pharmacie, 86000, Poitiers, France
| | | | | | - Anthony Michaud
- CHU de Poitiers, Département des Agents Infectieux, 86021, Poitiers, France
| | - Lauranne Broutin
- CHU de Poitiers, Département des Agents Infectieux, 86021, Poitiers, France
| | - Julie Cremniter
- CHU de Poitiers, Département des Agents Infectieux, 86021, Poitiers, France; Université de Poitiers, INSERM U1070 Pharmacologie des Agents Antimicrobiens et Antibiorésistance, 86022, Poitiers, France
| | - Christophe Burucoa
- CHU de Poitiers, Département des Agents Infectieux, 86021, Poitiers, France; Université de Poitiers, INSERM U1070 Pharmacologie des Agents Antimicrobiens et Antibiorésistance, 86022, Poitiers, France
| | - Maxime Pichon
- CHU de Poitiers, Département des Agents Infectieux, 86021, Poitiers, France; Université de Poitiers, INSERM U1070 Pharmacologie des Agents Antimicrobiens et Antibiorésistance, 86022, Poitiers, France.
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Martineau M, Castagnet S, Kokabi E, Tricot A, Jaÿ M, Léon A, Tardy F. Detection of Mycoplasma spp. in horses with respiratory disorders. Equine Vet J 2023; 55:747-754. [PMID: 36572918 DOI: 10.1111/evj.13918] [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: 09/14/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Bacteria belonging to the genus Mycoplasma are small-sized, have no cell walls and small genomes. They commonly cause respiratory disorders in their animal hosts. Three species have been found in the respiratory tract of horses worldwide, that is., Mycoplasma (M.) equirhinis, M. pulmonis and M. felis, but their role in clinical cases remains unclear. OBJECTIVES The aim of this study was to i) develop and validate tools to detect, isolate and identify different Mycoplasma spp. strains in clinical equine respiratory-tract specimens and ii) subsequently define the prevalence of the three species in France depending on sample types and horse characteristics (age, breed, sex). STUDY DESIGN Validation of a workflow for mycoplasma diagnosis and subsequent prevalence study. METHODS Mycoplasma-free tracheal wash samples spiked with numerated strains and DNA dilutions were used to validate the culture methods and real-time PCR (rt-PCR) assay. Isolated strains were identified by 16S rRNA gene sequencing. Prevalences were determined on a population of 616 horses with respiratory disorders, sampled in France in 2020. RESULTS In total, 104 horses (16.9%) were found to be positive for Mycoplasma spp. by at least one method. M. equirhinis was the predominant circulating species, accounting for 85% of the rt-PCR-positive samples and 98% of the 40 cultured strains. MAIN LIMITATION The proposed pre-enrichment procedure improves the sensitivity of detection but hinders the quantification of the initial mycoplasma load in the clinical specimens. CONCLUSIONS Prevalence of mycoplasma varied with age, breed, and type of sample.
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Affiliation(s)
- Matthieu Martineau
- LABÉO, Research Department, St Contest, Caen, France
- NormandieUniversité, CAEN/ROUEN Universités, DYNAMICURE, INSERM U1311, France
- Université de Lyon, Anses, VetAgro Sup, UMR Mycoplasmoses Animales, Lyon, France
| | - Sophie Castagnet
- LABÉO, Research Department, St Contest, Caen, France
- NormandieUniversité, CAEN/ROUEN Universités, DYNAMICURE, INSERM U1311, France
| | - Elena Kokabi
- LABÉO, Research Department, St Contest, Caen, France
- NormandieUniversité, CAEN/ROUEN Universités, DYNAMICURE, INSERM U1311, France
| | - Agnès Tricot
- Université de Lyon, Anses, VetAgro Sup, UMR Mycoplasmoses Animales, Lyon, France
| | - Maryne Jaÿ
- Université de Lyon, Anses, VetAgro Sup, UMR Mycoplasmoses Animales, Lyon, France
| | - Albertine Léon
- LABÉO, Research Department, St Contest, Caen, France
- NormandieUniversité, CAEN/ROUEN Universités, DYNAMICURE, INSERM U1311, France
| | - Florence Tardy
- Université de Lyon, Anses, VetAgro Sup, UMR Mycoplasmoses Animales, Lyon, France
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Ma X, Gao Y, Li H, Wang D, Li J, Hu X, Huang X, Lin M, Tang Y, Liu Z. Identification and characterization of biocontrol agent Lysinibacillus boronitolerans P42 against Cerrena unicolor that causes root rot of arecanut palm. Arch Microbiol 2023; 205:157. [PMID: 37004578 DOI: 10.1007/s00203-023-03433-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 01/18/2023] [Accepted: 02/02/2023] [Indexed: 04/04/2023]
Abstract
The arecanut palm is one of the most important industrial crops in tropical area around the world. The root rot of arecanut palm, which is caused by Cerrena unicolor, has led to heavy economic losses and restricted greatly the development of arecanut industry, especially in Hainan province of China. The common use of chemical agents has worsened the problems of the emergence of resistant pathogens and the pollution of agricultural environment. This study aims to screen and identify a more effective and environment friendly biocontrol method for the prevention and treatment of root rot of arecanut palm. The mycelium growth rate is investigated to select antagonistic bacteria from tropical crop rotation fields which show improved resistance against soil-borne pathogens, and the strain P42 is revealed with the strongest antagonistic effects (82.18%). Based on 16 s rDNA sequence analysis, the strain P42 is identified as Lysinibacillus boronitolerans. In vitro antimicrobial activity shows that the strain P42 exhibits broad-spectrum antagonistic activity against a wide variety of tropical agricultural fungal pathogens, including Cerrena unicolor, Magnaporthe oryzea, Botryodiplodia theobromae, Neoscytalidium dimidiatum, Thanatephorus cucumeris, Fusarium oxysporum, and Botrytis cinerea Per.. The antagonistic activity of the culture of P42 is tolerant to common proteases, longer storage time, and temperature range of 40-121 °C; and is significantly influenced by alkaline (7-9) and acidic (1-2) pH, as well as by ultraviolet ray treatment for more than 30 min. The investigation on the antagonistic activity of the crude extract of fermentation filtrate indicates that the active compounds might be lipopeptides, polyketones, or proteins. To our knowledge, this is the first report of L. boronitolerans as potential bio-reagents for controlling root rot of arecanut palm caused by Cerrena unicolor.
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Affiliation(s)
- Xiang Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Yuxiao Gao
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Hong Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Dan Wang
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Juanjuan Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Xinwen Hu
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Xi Huang
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanqiong Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences, Hainan University, Haikou, 570228, China.
| | - Zhu Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences, Hainan University, Haikou, 570228, China.
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First Bacteremia Due to Corynebacterium gottingense in an Immunocompromised Child: A Case Report, 16S rDNA-Based Phylogenetic Analyses and Review of the Literature. Antibiotics (Basel) 2023; 12:antibiotics12030528. [PMID: 36978395 PMCID: PMC10044508 DOI: 10.3390/antibiotics12030528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Corynebacterium gottingense is a Gram-positive bacillus that has not been reported as pathogenic in pediatric patients. Herein, a case of catheter-associated bloodstream infection by C. gottingense in a 13-year-old immunocompromised child with febrile neutropenia induced for osteosarcoma is reported. The species was identified by Sanger sequencing of the 16s rRNA sequence of the bacterial strain and was compared phylogenetically with published sequences. As suggested in the literature, the presented strain was multi-susceptible, particularly to amoxicillin. The patient was treated with piperacillin/tazobactam for seven days in the context of a urinary co-infection, resulting in resolution of fever within 48 h and then relaunched with oral amoxicillin for 3 days (for a total of 10 days of antibiotic therapy). Phylogenetic analyses based on 16S rDNA demonstrated the complexity of the genus Corynebacterium spp. but failed to demonstrate a direct benefit in predicting clinical outcome based on this single information.
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Rodríguez RT, Solís Marquínez MN, Álvarez MDCC, Fernández Suárez J, Fernández Domínguez J, Rodríguez BI, Rodríguez Álvarez FJ. Clostridium paraputrificum bacteremia in a 64-year-old woman with colon carcinoma. Anaerobe 2023; 81:102716. [PMID: 36774980 DOI: 10.1016/j.anaerobe.2023.102716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 01/18/2023] [Accepted: 02/09/2023] [Indexed: 02/12/2023]
Abstract
Here we report a case of bacteremia caused by Clostridium paraputrificum in a 64-year-old woman with colon carcinoma and gastrointestinal disease. Using the new EUCAST 2022 clinical breakpoints [1] for Clostridium perfringens, the isolate was susceptible to metronidazole and vancomycin, but resistant to benzylpenicillin, meropenem, and clindamycin. Thus, treatment with metronidazole should be considered in all patients with Clostridium bacteremia until antibiotic susceptibility is determined to minimize the risk of treatment failure.
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Sennaj R, Lemriss S, Souiri A, Kabbaj SEL, Chafik A, Essamadi AK, Benali T, Fassouane A, Dari K, Aassila H. Eco-friendly degradation of reactive red 195, reactive blue 214, and reactive yellow 145 by Klebsiella pneumoniae MW815592 isolated from textile waste. J Microbiol Methods 2023; 204:106659. [PMID: 36529157 DOI: 10.1016/j.mimet.2022.106659] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
The water is used in many textile manufacturing steps beyond cleaning. The quantity and the significant chemical load of the effluents generated constitute the primary challenge of the textile industry. In order to discover new sustainable methods to overcome this problem, the aim of this research was to study the potential for degradation of Reactive Blue 214, Reactive Red 195, and Reactive Yellow 145 using a dye degrading bacterium. Sequencing analysis reveals it to be Klebsiella pneumoniae MW815592. This strain completely decolorized artificial effluent (200 mg/L) after 42 h at pH 9 and 46 °C. The decolorization rate increased in the presence of glucose and yeast extract (2 g). In addition, our finding revealed that the decolorization is due to biodegradation rather than adsorption on the bacterial surface.
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Affiliation(s)
- Rajaa Sennaj
- Agrofood and Health Laboratory, Faculty of Science and Technology, Hassan First University, PO Box 577, Settat 26000, Morocco
| | - Sanaâ Lemriss
- Laboratory of Research and Medical Analysis of Gendarmerie Royale, Department of Biosafety PCL3, Rabat, Morocco
| | - Amal Souiri
- Laboratory of Research and Medical Analysis of Gendarmerie Royale, Department of Biosafety PCL3, Rabat, Morocco
| | - Saâd E L Kabbaj
- Laboratory of Research and Medical Analysis of Gendarmerie Royale, Department of Biosafety PCL3, Rabat, Morocco
| | - Abdelbasset Chafik
- Université Cadi Ayyad, Ecole Supérieure de Technologie d'El Kelâa des Sraghna, Route de Béni Mellal Km 8 BP 104, El Kelâa des Sraghna, Morocco
| | - Abdel Khalid Essamadi
- Laboratory of Biochemistry, Neurosciences, Natural Resources and Environment, Faculty of Sciences and Technologies, Hassan First University of Settat, Settat, PObox 577 Morocco
| | - Taoufiq Benali
- Environment and Health Team, Polydisciplinary Faculty of Safi, Cadi Ayyad University, Sidi Bouzid, B.P. 4162, Safi, Morocco.
| | | | - Khadija Dari
- Agrofood and Health Laboratory, Faculty of Science and Technology, Hassan First University, PO Box 577, Settat 26000, Morocco
| | - Hinde Aassila
- Agrofood and Health Laboratory, Faculty of Science and Technology, Hassan First University, PO Box 577, Settat 26000, Morocco
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Raible KM, Algazaq JN, Papanicolaou G, Babady NE. Acetobacter tropicalis bacteraemia in an immunocompromised patient: case report. Access Microbiol 2022; 4:acmi000374. [PMID: 36644433 PMCID: PMC9833420 DOI: 10.1099/acmi.0.000374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/20/2022] [Indexed: 11/27/2022] Open
Abstract
Introduction. The published literature characterizing the bacterial genus Acetobacter primarily explores the role of these organisms in the fermentation industry. Reports of human infections caused by Acetobacter species are rare and are primarily associated with immunocompromised patients. Case Presentation. A young patient with refractory acute myeloid leukaemia received a peripheral blood stem cell transplant at our institution. Both pre- and post-transplant courses were complicated by polymicrobial bloodstream infections. During this time a bacterium, later identified as Acetobacter tropicalis , was isolated from blood cultures. A. tropicalis was recovered in consecutive blood cultures for approximately 1 week; during this time the patient's condition deteriorated, ending in fatal cardiorespiratory failure. Conclusion. This case provides the first report of a human infection with A. tropicalis , although the significance of this finding in a complex patient is hard to establish. This illustrates how the routine implementation of molecular identification techniques by clinical microbiology laboratories will result in the reporting of more rare or novel micro-organisms involved in human infections.
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Affiliation(s)
- Kevin M. Raible
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jumanah N. Algazaq
- Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Genovefa Papanicolaou
- Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N. Esther Babady
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Screening and Characterization of Streptomyces spp. Isolated from Three Moroccan Ecosystems Producing a Potential Inhibitor of the Drug Efflux Pump AcrAB-TolC. BIOTECH (BASEL (SWITZERLAND)) 2022; 11:biotech11030022. [PMID: 35892927 PMCID: PMC9326602 DOI: 10.3390/biotech11030022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022]
Abstract
Traditional antimicrobial antibiotics are increasingly suffering from the emergence of multidrug resistance among pathogenic microorganisms. The antibiotic era is threatened by the ruthless rise of resistance in bacterial infections. A significant role in these resistance profiles is attributed to multidrug efflux pumps. Hence, much effort is being directed towards developing new compounds to overcome this problem. During our screening program of efflux pumps inhibitors (EPI) produced by bioactive Moroccan Actinobacteria, 210 isolates were screened for their antibacterial activities against Escherichia coli strains containing a system of efflux pump AcrAB-TolC, fully functional, and its mutant, inactivated due to the insertion of transposon Tn903 in AcrAB operon, using the method of agar disc diffusion. The results showed that 14 isolates were able to produce EPI as they were active against the wild type strain but not against the mutant in comparison with the synthetic inhibitor L-Phe-L-Arg-β-naphthylamide (PaβN). We focused on the highest EPI activity produced by four strains (Z332, Z35/G, Z385/b and 136). Taxonomic studies and the 16S rDNA sequence indicated that these strains belonged to the Streptomyces species. This work could contribute to the discovery of a new class of antibacterial agents that could expand the therapeutic arsenal.
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Streptomycetaceae and Promicromonosporaceae: Two Actinomycetes Families from Moroccan Oat Soils Enhancing Solubilization of Natural Phosphate. Microorganisms 2022; 10:microorganisms10061116. [PMID: 35744634 PMCID: PMC9230749 DOI: 10.3390/microorganisms10061116] [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: 04/09/2022] [Revised: 05/21/2022] [Accepted: 05/26/2022] [Indexed: 11/17/2022] Open
Abstract
Soil actinomycetes explorations appear to be an efficient alternative as biofertilizers to optimize the use of phosphorus (P) resources and enhance plant growth. This research aimed to explore the distribution of actinomycetes isolated from four different rhizospheric Moroccan oat soils and to investigate their potential for P solubilization. The distribution of actinomycetes was significantly more abundant in Settat (9.68%), Tangier (7.38%), and Beni Mellal (6.87%) than in the Merchouch-Rabat (4.90%) region. A total of 235 actinomycete strains were isolated from all sites and tested for their ability to grow on a synthetic minimum medium (SMM) containing insoluble natural rock phosphate (RP) or synthetic tricalcium phosphate (TCP) as the unique P source. One hundred forty-three isolates (60.8%) had the ability to grow in the SMM with RP whereas only twenty-five isolates (17%) had the most active growth using the SMM with TCP. Eight isolates with the most active growth in solid SMM were selected for their P solubilization abilities in liquid SMM cultures. The highest amount of P solubilized was 163.8 µg/mL for RP and 110.27 µg/mL for TCP after 5 days of culture. The biosolubilization process of AM2, the most efficient RP and TCP solubilizing strain, probably implied the highest excretion of siderophore substances. Eight of these strains were shown to belong to the Streptomyces genus and one to the Promicromonospora genus. These findings bolster the phosphate biosolubilization abilities of actinomycetes and may participate in increasing agricultural yields in an eco-efficient and environmentally friendly manner.
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Yarte ME, Gismondi MI, Llorente BE, Larraburu EE. Isolation of endophytic bacteria from the medicinal, forestal and ornamental tree Handroanthus impetiginosus. ENVIRONMENTAL TECHNOLOGY 2022; 43:1129-1139. [PMID: 32875965 DOI: 10.1080/09593330.2020.1818833] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/27/2020] [Indexed: 05/20/2023]
Abstract
Plant interactions with endophytic bacteria produce mutual benefits and contribute to environmental sustainability. Handroanthus impetiginosus (Mart. ex DC.) Mattos 'pink lapacho' (syn. Tabebuia impetiginosa, Bignoniaceae) is a medicinal, ornamental and forestal native tree from South and Mesoamerica. Plant growth promoting bacteria (PGPB) isolated from pink lapacho are scarcely described. The aim of this work was to isolate and characterize native endophytic bacteria from pink lapacho. Ten bacterial strains were isolated from leaves and six from roots of naturally growing trees in Luján (Central-Eastern region of Argentina). Endophytes were identified as Bacillus, Paenibacillus, Pseudomonas, Rhizobium, Rummeliibacillus and Methylobacterium genera, according to 16S rRNA gene sequencing and phylogenetic analysis. In the present study, a strain of the Rummelibacillus genus (L14) has been first ever reported as endophyte. This strain was capable of growing in Nfb medium and exhibited zinc solubilization ability. A high percentage of strains showed PGPB traits; namely 88% fixed nitrogen, 63% solubilized zinc, 69% solubilized phosphate and 63% produced indole compounds such as IAA. Most strains were salt tolerant that confer them a potential competitive advantage to survive in saline conditions. To the best of our knowledge, this is the first study reporting an approach to assess the diversity of cultivable endophytic bacteria of H. impetiginosus tree and its plant growth promoting capacity. The knowledge about this kind of associations could contribute to environmental sustainability by developing effective biofertilizers that minimize the use of chemical fertilizers and pesticides.
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Affiliation(s)
- Mauro Enrique Yarte
- Laboratorio de Cultivo de tejidos Vegetales, Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Inés Gismondi
- Laboratorio de Cultivo de tejidos Vegetales, Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Berta Elizabet Llorente
- Laboratorio de Cultivo de tejidos Vegetales, Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Ezequiel Enrique Larraburu
- Laboratorio de Cultivo de tejidos Vegetales, Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Roots of the xerophyte Panicum turgidum host a cohort of ionizing-radiation-resistant biotechnologically-valuable bacteria. Saudi J Biol Sci 2022; 29:1260-1268. [PMID: 35197792 PMCID: PMC8847929 DOI: 10.1016/j.sjbs.2021.09.020] [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: 10/08/2020] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 11/21/2022] Open
Abstract
Bacterial communities associated with roots of Panicum turgidum, exposed to arid conditions, were investigated with a combination of cultural and metataxonomic approaches. Traditional culture-based techniques were used and 32 isolates from the irradiated roots were identified as belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria phyla. Four actinobacterial strains were shown to be ionizing-radiation (IR)-resistant: Microbacterium sp. PT8 (4.8 kGy (kGy)), Micrococcus sp. PT11 (4.4 kGy), Kocuria rhizophila PT10 (2.9 kGy) and Promicromonospora panici PT9T (2.6 kGy), based on the D10 dose necessary for a 90% reduction in colony forming units (CFU). Concerning the investigation of microbial communities in situ, metataxonomic analyses of the diversity of IR-resistant microorganisms associated with irradiated roots revealed a marked dominance of Actinobacteria (46.6%) and Proteobacteria (31.5%) compared to Bacteroidetes (4.6%) and Firmicutes (3.2%). Gamma irradiation not only changed the structure of bacterial communities, but also affected their functional properties. Comparative analyses of metabolic profiles indicated the induction of several pathways related to adaptation to oxidative stress in irradiated roots, such as DNA repair, secondary metabolites synthesis, reactive oxygen species (ROS)-mitigating enzymes, etc. P. turgidum is emblematic of desert-adapted plants. Until now, there is no other work that has focused on the microbial profile of irradiated roots of this xerophyte.
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Kumaria A, Crusz SA, Lister M, Kirkman MA, Macarthur DC. Psychrobacter piechaudii shunt infection: first report of human infection. Childs Nerv Syst 2022; 38:1385-1388. [PMID: 34713345 PMCID: PMC8553102 DOI: 10.1007/s00381-021-05401-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/23/2021] [Indexed: 11/26/2022]
Abstract
Psychrobacter piechaudii is a recently described species of Gram-negative bacteria in the Moraxellaceae family. No cases of human infection due to this species have been described before. We report the case of an ex-premature infant girl with hydrocephalus secondary to intraventricular haemorrhage who underwent multiple cerebrospinal fluid (CSF) shunt operations. She ultimately developed Psychrobacter piechaudii meningitis, presenting as ventriculoperitoneal shunt dysfunction and wound leak, which necessitated removal of the shunt, a period of external ventricular drainage and antibiotics. We found this organism to be sensitive to intravenous ceftazidime (50 mg/kg) and ciprofloxacin, and a 7-10 day treatment course prior to shunt re-insertion (and 3 week total course) was sufficient. The patient is well post-operatively. To the best of our knowledge, this is the first reported case of Psychrobacter piechaudii infection in a human.
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Affiliation(s)
- Ashwin Kumaria
- Department of Paediatric Neurosurgery, Queen's Medical Centre, Derby Road, Nottingham, NG7 2UH, UK.
| | - Shanika A Crusz
- Department of Clinical Microbiology, Queen's Medical Centre, Nottingham, UK
| | - Michelle Lister
- Department of Clinical Microbiology, Queen's Medical Centre, Nottingham, UK
| | - Matthew A Kirkman
- Department of Paediatric Neurosurgery, Queen's Medical Centre, Derby Road, Nottingham, NG7 2UH, UK
| | - Donald C Macarthur
- Department of Clinical Microbiology, Queen's Medical Centre, Nottingham, UK
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Isolation and Characterization of Phosphate Solubilizing Streptomyces sp. Endemic from Sugar Beet Fields of the Beni-Mellal Region in Morocco. Microorganisms 2021; 9:microorganisms9050914. [PMID: 33923283 PMCID: PMC8146796 DOI: 10.3390/microorganisms9050914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 12/21/2022] Open
Abstract
In the course of our research, aimed at improving sugar beets phosphorus nutrition, we isolated and characterized Streptomyces sp. strains, endemic from sugar beet fields of the Beni-Mellal region, which are able to use natural rock phosphate (RP) and tricalcium phosphate (TCP) as sole phosphate sources. Ten Streptomyces sp. isolates yielded a comparable biomass in the presence of these two insoluble phosphate sources, indicating that they were able to extract similar amount of phosphorus (P) from the latter for their own growth. Interestingly, five strains released soluble P in large excess from TCP in their culture broth whereas only two strains, BP, related to Streptomyces bellus and BYC, related to Streptomyces enissocaesilis, released a higher or similar amount of soluble P from RP than from TCP, respectively. This indicated that the rate of P released from these insoluble phosphate sources exceeded its consumption rate for bacterial growth and that most strains solubilized TCP more efficiently than RP. Preliminary results suggested that the solubilization process of BYC, the most efficient RP and TCP solubilizing strain, involves both acidification of the medium and excretion of siderophores. Actinomycete strains possessing such interesting RP solubilizing abilities may constitute a novel kind of fertilizers beneficial for plant nutrition and more environmentally friendly than chemical fertilizers in current use.
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Ursenbach A, Schramm F, Séverac F, Hansmann Y, Lefebvre N, Ruch Y, Argemi X. Revised version (INFD-D-20-00242): impact of 16S rDNA sequencing on clinical treatment decisions: a single center retrospective study. BMC Infect Dis 2021; 21:190. [PMID: 33602178 PMCID: PMC7890971 DOI: 10.1186/s12879-021-05892-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/12/2021] [Indexed: 11/23/2022] Open
Abstract
Background PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger’s sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients’ treatments according to different sample types. Methods From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive. Results Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was rationalized in 31 patients (50%) and extended in 24 patients (39%), and an invasive procedure was chosen for 7 patients (11%) due to the 16S PCR sequencing results. Positive 16S PCR sequencing results on cerebrospinal fluid (CSF) had a greater impact on patients’ management than positive ones on cardiac valves (p = 0.044). The clinical impact of positive 16S PCR sequencing results were significantly higher when blood cultures were negative (p < 0.001), and this difference appeared larger when both blood and sample cultures were negative (p < 0.001). The diagnostic contribution of 16S PCR was higher in patients with previous antibiotic treatment (p < 0.001). Conclusion In all, 16S PCR analysis has a significant clinical impact on patient management, particularly for suspected CSF infections, for patients with culture-negative samples and for those with previous antibiotic treatments. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05892-4.
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Affiliation(s)
- Axel Ursenbach
- Laboratoire de bactériologie, Faculté de Médecine, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg, France.
| | - Frédéric Schramm
- Laboratoire de bactériologie, Faculté de Médecine, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg, France
| | - François Séverac
- Service de Santé Publique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yves Hansmann
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Nicolas Lefebvre
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yvon Ruch
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Xavier Argemi
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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Kargar F, Mortazavi M, Maleki M, Mahani MT, Ghasemi Y, Savardashtaki A. Isolation, Identification and In Silico Study of Native Cellulase Producing Bacteria. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164617666191127142035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
The purpose of this study was to screen the bacteria producing cellulase enzymes and
their bioinformatics studies.
Background:
Cellulose is a long-chain polymer of glucose that hydrolyzes by cellulases to glucose
molecules. In order to design the new biotechnological applications, some strategies have been used as
increasing the efficiency of enzyme production, generating cost-effective enzymes, producing stable
enzymes and identification of new strains.
Objective:
On the other hand, some bacteria special features have made them suitable candidates for the
identification of the new source of enzymes. In this regard, some native strains of bacteria were screened.
Methods:
These bacteria were grown on a culture containing the liquid M9 media containing CMC to
ensure the synthesis of cellulase. The formation of a clear area in the culture medium indicated decomposition
of cellulose. In the following, the DNA of these bacteria were extracted and their 16S rDNA
genes were amplified.
Result:
The results show that nine samples were able to synthesize cellulase. In following, these strains
were identified using 16S rDNA. The results show that these screened bacteria belonged to the Bacillus
sp., Alcaligenes sp., Alcaligenes sp., and Enterobacter sp.
Conclusion:
The enzyme activity analysis shows that the Bacillus toyonensis, Bacillus sp. strain
XA15-411 Bacillus cereus have produced the maximum yield of cellulases. However, these amounts
of enzyme production in these samples are not proportional to their growth rate. As the bacterial
growth chart within 4 consecutive days shows that the Alcaligenes sp. Bacillus cereus, Bacillus
toyonensis, Bacillus sp. strain XA15-411 have a maximum growth rate. The study of the phylogenetic
tree also shows that Bacillus species are more abundant in the production of cellulase enzyme. These
bioinformatics analyses show that the Bacillus species have different evolutionary relationships and
evolved in different evolutionary time. However, for maximum cellulase production by this bacteria,
some information as optimum temperature, optimum pH, carbon and nitrogen sources are needed for
the ideal formulation of media composition. The cellulase production is closely controlled in microorganisms
and the cellulase yields appear to depend on a variety of factors. However, the further studies
are needed for cloning, purification and application of these new microbial cellulases in the different
commercial fields as in food, detergent, and pharmaceutical, paper, textile industries and also various
chemical industries. However, these novel enzymes can be further engineered through rational design
or using random mutagenesis techniques.
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Affiliation(s)
- Farzane Kargar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Tabriz University of Medical Sciences Tabriz, Iran
| | - Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mahmood Maleki
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Masoud Torkzadeh Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Younes Ghasemi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies Shiraz University of Medical Sciences, Shiraz, Iran
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Guesmi S, Pujic P, Nouioui I, Dubost A, Najjari A, Ghedira K, Igual JM, Miotello G, Cherif A, Armengaud J, Klenk HP, Normand P, Sghaier H. Ionizing-radiation-resistant Kocuria rhizophila PT10 isolated from the Tunisian Sahara xerophyte Panicum turgidum: Polyphasic characterization and proteogenomic arsenal. Genomics 2020; 113:317-330. [PMID: 33279651 DOI: 10.1016/j.ygeno.2020.11.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/17/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
A new strain belonging to the genus Kocuria, designed PT10, was isolated from irradiated roots of the xerophyte Panicum turgidum. Isolate PT10 is a Gram-positive, coccoid, aerobic and ionizing-radiation (IR)-resistant actinobacterium. PT10 has shown an ability to survive under extreme conditions, such as gamma irradiation, desiccation and high concentration of hydrogen peroxide. Phenotypic, chemotaxonomic and comparative genome analyses support the assignment of strain PT10 (LMG 31102 = DSM 108617) as Kocuria rhizophila. The complete genome sequence of PT10 consists of one chromosome (2,656,287 bps), with a 70.7% G + C content and comprises 2481 protein-coding sequences. A total of 1487 proteins were identified by LC-MS/MS profiling. In silico analyses revealed that the proteome of the oxidation-tolerant PT10 possesses several features explaining its IR-resistant phenotype and many adaptive pathways implicated in response to environmental pressures - desiccation, cold, reactive oxygen species and other stressors.
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Affiliation(s)
- Sihem Guesmi
- National Agronomy Institute of Tunisia, 43, Avenue Charles Nicolle, 1082 Tunis, Mahrajène, Tunisia; Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Tunisia.
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon, France; CNRS, UMR 5557, Ecologie Microbienne, 69622 Villeurbanne, Cedex, INRA, UMR1418, Villeurbanne, France
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne NE1 7RU, UK; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Afef Najjari
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR03ES03 Microorganismes et Biomolécules Actives, 2092 Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, 13, Place Pasteur, Tunis 1002, Tunisia
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Guylaine Miotello
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne NE1 7RU, UK
| | | | - Haïtham Sghaier
- Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Tunisia; Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia.
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17
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Guesmi S, Nouioui I, Pujic P, Dubost A, Najjari A, Ghedira K, Igual JM, Cherif A, Klenk HP, Sghaier H, Normand P. Draft genome sequence of Promicromonospora panici sp. nov., a novel ionizing-radiation-resistant actinobacterium isolated from roots of the desert plant Panicum turgidum. Extremophiles 2020; 25:25-38. [PMID: 33104875 DOI: 10.1007/s00792-020-01207-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/07/2020] [Indexed: 11/26/2022]
Abstract
A novel strain of the genus Promicromonospora, designated PT9T, was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9T is aerobic, non-spore-forming, Gram- positive actinomycete that produces branched hyphae and forms white to yellowish-white colonies. Chemotaxonomic features, including fatty acids, whole cell sugars and polar lipid profiles, support the assignment of PT9T to the genus Promicromonospora. The genomic relatedness indexes based on DNA-DNA hybridization and average nucleotide identity values revealed a significant genomic divergence between strain PT9T and all sequenced type strains of the taxon. Phylogenomic analysis showed that isolate PT9T was most closely related to Promicromonospora soli CGMCC 4.7398T. Phenotypic and phylogenomic analyses suggest that isolate PT9T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora panici sp. nov. is proposed. The type strain is PT9T (LMG 31103T = DSM 108613T).The isolate PT9T is an ionizing-radiation-resistant actinobacterium (D10 value = 2.6 kGy), with resistance to desiccation and hydrogen peroxide. The complete genome sequence of PT9T consists of 6,582,650 bps with 71.2% G+C content and 6291 protein-coding sequences. This genome will help to decipher the microbial genetic bases for ionizing-radiation resistance mechanisms including the response to oxidative stress.
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Affiliation(s)
- Sihem Guesmi
- National Agronomy Institute of Tunisia, Avenue Charles Nicolle, 1082, Tunis, Mahrajène, Tunisia
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Sidi Thabet, Tunisia
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon, France
- CNRS, UMR 5557, Écologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, Université Lyon 1, Lyon, France
- CNRS, UMR 5557, Écologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Afef Najjari
- Université de Tunis el Manar, Faculté des Sciences de Tunis, LR03ES03 Microorganismes et Biomolécules Actives, 2092, Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, Université de Tunis El Manar, 1002, Tunis, Tunisia
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - Ameur Cherif
- University Manouba, ISBST, BVBGR-LR11ES31,, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Haïtham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Sidi Thabet, Tunisia
- University Manouba, ISBST, BVBGR-LR11ES31,, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, Lyon, France.
- CNRS, UMR 5557, Écologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France.
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18
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Leyer C, Sassi M, Gourmelen F, Burel A, Beyrouthy R, Kayal S, Bonnet R, Cattoir V. Avrilella dinanensis gen. nov., sp. nov., a novel bacterium of the family Flavobacteriaceae isolated from human blood. Syst Appl Microbiol 2020; 43:126124. [PMID: 32847790 DOI: 10.1016/j.syapm.2020.126124] [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: 05/07/2020] [Revised: 07/10/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
Abstract
Polyphasic taxonomic analysis was performed on a novel bacterium, designated UR159T, isolated in 2016 from human blood of a septic patient hospitalized in France. Preliminary 16S rRNA gene sequence-based phylogenetic analysis indicated that strain UR159T belonged to the family Flavobacteriaceae, forming a distinct phyletic line distantly related (<94% sequence similarity) to known species of the family. Further phenotypic, chemotaxonomic and genomic analyses were performed. Cells were non-motile, oxidase-negative, catalase-positive Gram-negative rods. It was strictly aerobic yielding yellow-pigmented colonies, and was metabolically rather inert. Major fatty acids were iso-branched fatty acids, predominantly iso-C15:0 (55.5%) and iso-C17:1ω9c (8.8%). Whole genome sequencing revealed a 2.3-Mbp genome encoding a total of 2262 putative genes with a genomic DNA G+C content at 37.6mol%. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between strain UR159T and the most closely related members of the Flavobacteriaceae family were <75% and <39%, respectively, much below the established cut-offs for ANI (<95-96%) and isDDH (<70%) for species and genus delineation. Average Amino Acid Identity (AAI) percentages were also estimated and were lower than 65% (cut-off proposed for genus delineation for uncultivated prokaryotes) in all cases, except for F. marinum that was just at the limit (65.1%). Based on these findings, we propose it as a new genus and species, Avrilella dinanensis gen. nov., sp. nov. (type strain UR159T=CIP 111616T=DSM 105483T).
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Affiliation(s)
- Caroline Leyer
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
| | - Mohamed Sassi
- Université de Rennes 1, Unité Inserm U1230, Rennes, France
| | | | - Agnès Burel
- Univ Rennes, MRic TEM, CNRS, Inserm, BIOSIT - UMS 3480, US_S 018, Rennes, France
| | - Racha Beyrouthy
- CHU Clermont-Ferrand, Laboratoire de Bactériologie & CNR de la Résistance aux Antibiotiques, Clermont-Ferrand, France; CNR de la Résistance aux Antibiotiques (laboratoire associé «Entérobactéries: résistance aux C3G et colistine»), Clermont-Ferrand, France; Université Clermont Auvergne, UMR INSERM 1071 USC INRA2018, Clermont-Ferrand, France
| | - Samer Kayal
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
| | - Richard Bonnet
- CHU Clermont-Ferrand, Laboratoire de Bactériologie & CNR de la Résistance aux Antibiotiques, Clermont-Ferrand, France; CNR de la Résistance aux Antibiotiques (laboratoire associé «Entérobactéries: résistance aux C3G et colistine»), Clermont-Ferrand, France; Université Clermont Auvergne, UMR INSERM 1071 USC INRA2018, Clermont-Ferrand, France
| | - Vincent Cattoir
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France; Université de Rennes 1, Unité Inserm U1230, Rennes, France; CNR de la Résistance aux Antibiotiques (laboratoire associé «Entérocoques»), Rennes, France.
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Broutin L, Deroche L, Michaud A, Le Moal G, Burucoa C, Gayet LE, Plouzeau C, Pichon M. First description of bacteremia caused by Oscillibacter valericigenes in a patient hospitalized for leg amputation. Anaerobe 2020; 64:102244. [PMID: 32712374 DOI: 10.1016/j.anaerobe.2020.102244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 07/07/2020] [Accepted: 07/15/2020] [Indexed: 01/08/2023]
Abstract
Initially isolated from the alimentary canal of a Japanese corbicula clam, Oscillibacter valericigenes is a Gram-negative rod, of which culture remains very difficult. Herein we present the first case of bacteremia due to Oscillibacter valericigenes, in humans. A 55-year-old man was hospitalized for clinical management of multiple neglected leg wounds (colonized with maggots) that had occurred during a motorcycle accident. Following radiological confirmation of the bone infection, a transfemoral amputation was performed to limit the risk of extended infection. During hospitalization, before the amputation, the patient experienced fever, biological inflammation justifying the sampling of multiple blood cultures. Anaerobic blood culture was positive after 34 hours, without identification by routine procedure (MALDI-TOF), justifying identification by 16S DNA sequencing. In the absence of possible subculture, antibiotic sensitivity testing could not be performed. A pre-emptive treatment by piperacillin-tazobactam was introduced for 14 days. The evolution was good, except for a local disunion. Complete phylogenic analysis of the clinical strain showed that it significantly differed from the reference strain, which is distantly related to the Clostridia cluster IV. Due to the culture conditions and specialized identification method by sequencing, prevalence of O. valericigenes may be underestimated. Optimization of blood culture procedures and utilization of 16S rRNA gene sequencing are tools needed for identification of rare pathogens that could help to optimize clinical management of infected patients.
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Affiliation(s)
- Lauranne Broutin
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France
| | - Luc Deroche
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France
| | - Anthony Michaud
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France
| | - Gwenaël Le Moal
- University Hospital of Poitiers, Department of Infectious Diseases, CHU, Poitiers, France
| | - Christophe Burucoa
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France
| | - Louis-Etienne Gayet
- University Hospital of Poitiers, Department of Orthopedic Surgery and Traumatology, CHU, Poitiers, France
| | - Chloé Plouzeau
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France
| | - Maxime Pichon
- University Hospital of Poitiers, Bacteriology and Infection Control Laboratory, Infectious Agents Department, Poitiers, France.
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20
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Neuenschwander SM, Terrazos Miani MA, Amlang H, Perroulaz C, Bittel P, Casanova C, Droz S, Flandrois JP, Leib SL, Suter-Riniker F, Ramette A. A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing. J Clin Microbiol 2020; 58:e00060-20. [PMID: 32229603 PMCID: PMC7269405 DOI: 10.1128/jcm.00060-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/25/2020] [Indexed: 12/20/2022] Open
Abstract
Amplicon sequencing of the 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations, with the most significant being the inability to resolve mixed amplicons when closely related species are coamplified from a mixed culture. This often leads to either increased turnaround time or absence of usable sequence data. Short-read next-generation sequencing (NGS) technologies could solve the mixed amplicon issue but would lack both cost efficiency at low throughput and fast turnaround times. Nanopore sequencing developed by Oxford Nanopore Technologies (ONT) could solve those issues by enabling a flexible number of samples per run and an adjustable sequencing time. Here, we report on the development of a standardized laboratory workflow combined with a fully automated analysis pipeline LORCAN (long read consensus analysis), which together provide a sample-to-report solution for amplicon sequencing and taxonomic identification of the resulting consensus sequences. Validation of the approach was conducted on a panel of reference strains and on clinical samples consisting of single or mixed rRNA amplicons associated with various bacterial genera by direct comparison to the corresponding Sanger sequences. Additionally, simulated read and amplicon mixtures were used to assess LORCAN's behavior when dealing with samples with known cross-contamination levels. We demonstrate that by combining ONT amplicon sequencing results with LORCAN, the accuracy of Sanger sequencing can be closely matched (>99.6% sequence identity) and that mixed samples can be resolved at the single-base resolution level. The presented approach has the potential to significantly improve the flexibility, reliability, and availability of amplicon sequencing in diagnostic settings.
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Affiliation(s)
| | | | - Heiko Amlang
- University of Bern, Institute for Infectious Diseases, Bern, Switzerland
| | - Carmen Perroulaz
- University of Bern, Institute for Infectious Diseases, Bern, Switzerland
| | - Pascal Bittel
- University of Bern, Institute for Infectious Diseases, Bern, Switzerland
| | - Carlo Casanova
- University of Bern, Institute for Infectious Diseases, Bern, Switzerland
| | - Sara Droz
- University of Bern, Institute for Infectious Diseases, Bern, Switzerland
| | - Jean-Pierre Flandrois
- University of Lyon, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Stephen L Leib
- University of Bern, Institute for Infectious Diseases, Bern, Switzerland
| | | | - Alban Ramette
- University of Bern, Institute for Infectious Diseases, Bern, Switzerland
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21
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Unusual subdural empyema in a homeless patient diagnosed by molecular approach: a case report. BMC Infect Dis 2020; 20:357. [PMID: 32429864 PMCID: PMC7236200 DOI: 10.1186/s12879-020-05088-2] [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: 01/19/2020] [Accepted: 05/13/2020] [Indexed: 01/06/2023] Open
Abstract
Background We report a case of subdural empyema in a homeless patient caused by Bartonella quintana. B. quintana is a facultative intracellular bacteria for which bacterial growth is fastidious. The molecular biology approach has been a real help in establishing the diagnosis. Case report A 59-years old homeless patient, with a history of chronic alcohol abuse, was brought to the emergency department with a massive subdural empyema. Extensive microbiological evaluation didn’t reveal any pathogen in the pus collected before antibiotic treatment. B. quintana was detected in the pus from the empyema using a 16S rRNA-based PCR. Histology of intraoperative samples was consistent with the diagnosis and a serological assay was positive. The patient responded well to a treatment that included craniectomy with drainage of the loculated pus, total removal of the infected capsule and a combination of antibiotics. Conclusion This unique case of B. quintana-related empyema illustrates the risk of secondary infection of subdural hematoma with B. quintana since such infections have recently reemerged, predominantly among the homeless populations. Patients with subdural empyema in at-risk populations should be systematically evaluated for B. quintana with an appropriate diagnostic approach involving molecular biology.
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Boyer PH, Koetsveld J, Zilliox L, Sprong H, Talagrand-Reboul É, Hansmann Y, de Martino SJ, Boulanger N, Hovius JW, Jaulhac B. Assessment of Borrelia miyamotoi in febrile patients and ticks in Alsace, an endemic area for Lyme borreliosis in France. Parasit Vectors 2020; 13:199. [PMID: 32303256 PMCID: PMC7165395 DOI: 10.1186/s13071-020-04071-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Background Borrelia miyamotoi is a relapsing fever Borrelia species transmitted by ticks of the Ixodes ricinus complex. Human disease caused by B. miyamotoi was first described in Russia and later in the USA and Japan. Additionally, five cases of meningoencephalitis in immunocompromised patients and one case in an apparently immunocompetent patient were described. Methods We investigated the presence of B. miyamotoi in I. ricinus nymphs and in patients suspected of human granulocytic anaplasmosis, in Alsace (France), an endemic area for I. ricinus ticks and Lyme borreliosis, using direct (PCR) and indirect diagnosis (glycerophosphoryldiester-phosphodiesterase (GlpQ) serology). Results Borrelia miyamotoi was found in 2.2% of 4354 ticks collected between 2013 and 2016. None of the 575 blood samples, collected from the patients suspected of HGA, was found positive for B. miyamotoi by PCR. Acute and late sera from 138 of these 575 patients were available. These paired sera were tested for IgM and IgG antibodies against the B. miyamotoi GlpQ antigen. A total of 14 out of 138 patients had at least one positive parameter (i.e. anti-GlpQ IgG and/or IgM). One patient seroconverted for IgG, and three had isolated IgM in the acute serum. These three patients were treated with doxycycline which could have prevented seroconversion. After reviewing clinical data and other biological tests performed, co-exposure among different microorganisms vectored by ticks or serological cross-reactivity could not be ruled out in these different cases. One patient had persistent IgG, which strongly suggests previous exposure to B. miyamotoi. Conclusions Humans can be exposed to B. miyamotoi through tick bites in Alsace. We present serological data for possible B. miyamotoi exposure or infection of patients with fever after tick bite. Future studies should determine the incidence, clinical course and burden of this emerging tick-borne disease in other parts of Western Europe.![]()
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Affiliation(s)
- Pierre H Boyer
- University of Strasbourg, Virulence bactérienne précoce UR7290-Lyme borreliosis group, FMTS - CHRU Strasbourg, Institut de Bactériologie, Strasbourg, France
| | - Joris Koetsveld
- Center for Experimental and Molecular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Laurence Zilliox
- French National Reference Center for Borrelia, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Hein Sprong
- Centre for Zoonoses & Environmental Microbiology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Émilie Talagrand-Reboul
- University of Strasbourg, Virulence bactérienne précoce UR7290-Lyme borreliosis group, FMTS - CHRU Strasbourg, Institut de Bactériologie, Strasbourg, France
| | - Yves Hansmann
- University of Strasbourg, Virulence bactérienne précoce UR7290-Lyme borreliosis group, FMTS - CHRU Strasbourg, Institut de Bactériologie, Strasbourg, France.,Department of Infectious and Tropical Diseases, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Sylvie Josiane de Martino
- University of Strasbourg, Virulence bactérienne précoce UR7290-Lyme borreliosis group, FMTS - CHRU Strasbourg, Institut de Bactériologie, Strasbourg, France.,French National Reference Center for Borrelia, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Nathalie Boulanger
- University of Strasbourg, Virulence bactérienne précoce UR7290-Lyme borreliosis group, FMTS - CHRU Strasbourg, Institut de Bactériologie, Strasbourg, France.,French National Reference Center for Borrelia, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Joppe W Hovius
- Center for Experimental and Molecular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Benoît Jaulhac
- University of Strasbourg, Virulence bactérienne précoce UR7290-Lyme borreliosis group, FMTS - CHRU Strasbourg, Institut de Bactériologie, Strasbourg, France. .,French National Reference Center for Borrelia, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
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23
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Piepenbrock E, Higgins PG, Wille J, Xanthopoulou K, Zweigner J, Jahn P, Reuter S, Skov R, Eichhorn J, Seifert H. Klebsiella variicola causing nosocomial transmission among neonates - an emerging pathogen? J Med Microbiol 2020; 69:396-401. [PMID: 32125266 DOI: 10.1099/jmm.0.001143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Introduction. Transmission of Enterobacterales in neonatal intensive care units (NICU) can cause outbreaks of colonization and invasive infections among neonates. Two clusters of nosocomial transmission of Klebsiella pneumoniae identified by MALDI-ToF mass-spectrometry were suspected at two NICUs in July and August 2016.Aim. To assess the potential transmission of K. pneumoniae among neonates.Methodology. Whole-genome sequencing (WGS) was performed of K. pneumoniae isolates obtained through targeted surveillance of patients and environmental sampling.Results. WGS data revealed that patient and environmental isolates represented two species, K. pneumoniae and K. variicola. Core-genome multi-locus sequence typing (cgMLST) of the isolates identified three separate transmission clusters, in Hospital A a cluster of K. pneumoniae isolates in 12 children and two environmental samples and a second cluster of K. variicola isolates in five children. In Hospital B a cluster of K. pneumoniae isolates from three children and five unrelated isolates of K. pneumoniae and two unrelated isolates of K. variicola were found.Conclusion. K. variicola can cause hospital outbreaks of colonization and infection similar to other Klebsiella spp.Preliminary results from this study were presented at the 27th European Congress of Clinical Microbiology and Infectious Diseases, April 22-25, 2018, Vienna, Austria.
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Affiliation(s)
- Ellen Piepenbrock
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Germany
| | - Paul G Higgins
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Germany
| | - Julia Wille
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Germany
| | - Kyriaki Xanthopoulou
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Germany
| | - Janine Zweigner
- Department of Infection Control and Hygiene, University of Cologne, Cologne, Germany
| | - Peter Jahn
- Children's Hospital, Klinikum Leverkusen, Leverkusen, Germany
| | - Stefan Reuter
- Department of Infectious Diseases and General Internal Medicine, Klinikum Leverkusen, Leverkusen, Germany
| | | | | | - Harald Seifert
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Germany
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24
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Howard JC, Chen K, Anderson T, Dalton SC. Elizabethkingia miricola bacteraemia in a haemodialysis patient. Access Microbiol 2020; 2:acmi000098. [PMID: 34568756 PMCID: PMC8459099 DOI: 10.1099/acmi.0.000098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/20/2019] [Indexed: 11/18/2022] Open
Abstract
We report a case of catheter-associated Elizabethkingia miricola bacteraemia in a haemodialysis patient. The patient was a 73-year-old home haemodialysis patient who presented with a history of recurrent falls and fevers. Blood cultures grew Gram-negative bacilli identified by MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry 6903 MSP Library) and 16S rRNA gene sequencing as E. miricola. E. miricola is an emerging human pathogen and is multidrug-resistant, making the choice of antimicrobial therapy challenging. There are only a small number of case reports of human infection worldwide and this is the second reported case of catheter-related bacteraemia. It has also been found in the hospital environment in South Korea and is pathogenic in black-spotted frogs.
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Affiliation(s)
- Julia C Howard
- Microbiology Department, Canterbury Health Laboratories, Christchurch, New Zealand.,Present address: Microbiology Department, Waikato Hospital, Hamilton, New Zealand
| | - Kevin Chen
- Department of Infectious Diseases, Christchurch Hospital, New Zealand.,Present address: Department of Medicine, Tauranga Hospital, Tauranga, New Zealand
| | - Trevor Anderson
- Microbiology Department, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Simon C Dalton
- Department of Infectious Diseases, Christchurch Hospital, New Zealand
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25
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Sune D, Rydberg H, Augustinsson ÅN, Serrander L, Jungeström MB. Optimization of 16S rRNA gene analysis for use in the diagnostic clinical microbiology service. J Microbiol Methods 2020; 170:105854. [PMID: 31982454 DOI: 10.1016/j.mimet.2020.105854] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 12/01/2022]
Abstract
Broad-range amplification and sequencing of the 16S rRNA gene, directly from clinical samples, is a method that potentially allows detection of any cultivable or non-cultivable bacteria. However, the method is prone to false positive results due to PCR contamination. Another concern is the human DNA abundance compared to bacterial DNA in samples from sterile sites. Those factors may decrease the sensitivity and specificity of the assay and can complicate the analysis and interpretation of the results. The objective of this prospective study was to try to avoid the most common pitfalls, mentioned above, and develop a molecular 16S assay with a high clinical sensitivity and specificity. Fifty-six consecutive tissue samples from patients with suspected deep infections were extracted by 3 different DNA-extraction methods; two based on a principle of bacterial DNA enrichment, and one conventional DNA extraction method. We compared three primer pairs, including both conventional and DPO principle, targeting different variable regions of the 16S rRNA gene. Results from routine tissue culture were used as reference. Clinical data was recorded from patient charts and analyzed in parallel. Of a total of 56 samples, collected from 39 patients, 70% (39 samples) were assessed as true infections by analysis of clinical data. Bacterial enrichment extraction increased sensitivity from 54% to 72%. The 2 sets of primer pairs defining region V1-V3 and V3-V4, showed similar sensitivity, but DPO-primers resulted in better specificity, i.e. less contaminations. The primer pairs covering V1-V8 show significantly lower sensitivity (p < .001) than V1-V3 and V3-V4. Optimizing extraction protocols and choice of primers can increase the sensitivity and specificity of a molecular 16S-analysis, rendering a valuable complement to tissue culture.
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Affiliation(s)
- Dan Sune
- Division of Infectious Diseases, Department of Clinical and Experimental Medicine, Linköping University, Sweden.
| | - Helene Rydberg
- Division of Clinical Microbiology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
| | - Åsa Nilsdotter Augustinsson
- Division of Infectious Diseases, Department of Clinical and Experimental Medicine, Linköping University, Sweden.
| | - Lena Serrander
- Division of Clinical Microbiology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
| | - Malin Bergman Jungeström
- Division of Clinical Microbiology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
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26
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Jacquier H, Fihman V, Amarsy R, Vicaut E, Bousson V, Cambau E, Crémieux AC, Delcey V, Hannouche D, Kaci R, Laredo JD, Meunier F, Nizard R, Ottaviani S, Parlier C, Richette P, Sellier P, Zadegan F, Lioté F, Berçot B. Benefits of Polymerase Chain Reaction Combined With Culture for the Diagnosis of Bone and Joint Infections: A Prospective Test Performance Study. Open Forum Infect Dis 2019; 6:ofz511. [PMID: 31909081 PMCID: PMC6935679 DOI: 10.1093/ofid/ofz511] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 11/30/2019] [Indexed: 12/28/2022] Open
Abstract
Background The microbiological diagnosis of bone and joint infections (BJI) currently relies on cultures, and the relevance of molecular methods is still debated. The aim of this study was to determine whether polymerase chain reaction (PCR) could improve the etiological diagnosis of BJI. Methods A prospective study was conducted during a 4-year period at Lariboisiere University Hospital (Paris, France), including patients with suspicion of infectious spondylodiscitis, septic arthritis, prosthetic joint infections, and respective noninfected groups. Clinical and radiological data were collected at inclusion and during follow-up. All samples were analyzed by conventional cultures and 16S ribosomal deoxyribonucleic acid (rDNA) gene (16S-PCR). Specific cultures and PCR targeting Mycobacterium tuberculosis were also performed for spondylodiscitis samples. Case records were subsequently analyzed by an independent expert committee to confirm or invalidate the suspicion of infection and definitively classify the patients in a case or control group. The sensitivity of the combination of culture and PCR was compared with culture alone. Results After expert committee analysis, 105 cases of BJI cases and 111 control patients were analyzed. The most common pathogens of BJI were staphylococci (30%), M tuberculosis (19%), and streptococci (14%). Adding PCR enhanced the sensitivity compared with culture alone (1) for the diagnosis of M tuberculosis spondylodiscitis (64.4% vs 42.2%; P < .01) and (2) for nonstaphylococci BJI (81.6% vs 71.3%; P < .01). It is interesting to note that 16S-PCR could detect BJI due to uncommon bacteria such as Mycoplasma and fastidious bacteria. Conclusions Our study showed the benefit of 16S-PCR and PCR targeting M tuberculosis as add-on tests in cases of suspected BJI.
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Affiliation(s)
- Hervé Jacquier
- Laboratory of Bacteriology, Infectious Agents Department, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France.,IAME UMR 1137, INSERM and Université de Paris, Paris, France
| | - Vincent Fihman
- Bacteriology and Infection Control Unit, Department of Microbiology, University Hospital Henri Mondor, APHP, Creteil, France.,EA Dynamyc, Université Paris Est Créteil-Ecole Vétérinaire de Maison Alfort, Créteil, France
| | - Rishma Amarsy
- Infection Control Department, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Eric Vicaut
- Unit of Clinical Research, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Valérie Bousson
- Unit of Radiology, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Emmanuelle Cambau
- Laboratory of Bacteriology, Infectious Agents Department, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France.,IAME UMR 1137, INSERM and Université de Paris, Paris, France
| | - Anne-Claude Crémieux
- Department of Infectious Diseases, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Véronique Delcey
- Department of Medecine, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Didier Hannouche
- Department of Orthopaedic Surgery, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Rachid Kaci
- Department of Pathological Anatomy and Cytology, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Jean-Denis Laredo
- Unit of Radiology, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Fabienne Meunier
- Laboratory of Bacteriology, Infectious Agents Department, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Rémy Nizard
- Department of Orthopaedic Surgery, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Sébastien Ottaviani
- Federation of Rheumatology, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Caroline Parlier
- Unit of Clinical Research, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Pascal Richette
- Department of Pathological Anatomy and Cytology, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Pierre Sellier
- Department of Medecine, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Fréderic Zadegan
- Department of Orthopaedic Surgery, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Fréderic Lioté
- Federation of Rheumatology, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, APHP, Paris, France
| | - Béatrice Berçot
- Laboratory of Bacteriology, Infectious Agents Department, Saint Louis-Lariboisiere-Fernand Widal Hospital Group, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France.,IAME UMR 1137, INSERM and Université de Paris, Paris, France
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Guesmi S, Chouchane H, Neifar M, Hosni F, Cherif A, Sghaier H. Radiation-inducible radioprotective exopolysaccharides of Bacillus siamensis CV5 from irradiated roots of Cistanche violacea to decrease free radical damage produced by ionizing radiation. Int J Radiat Biol 2019; 95:1552-1563. [DOI: 10.1080/09553002.2019.1649501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sihem Guesmi
- National Agronomy Institute (INAT), Avenue Charles Nicolle, Mahrajène, Tunisia
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, Sidi Thabet, Tunisia
| | - Habib Chouchane
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Mohamed Neifar
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Faouzi Hosni
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, Sidi Thabet, Tunisia
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Haïtham Sghaier
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, Sidi Thabet, Tunisia
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
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28
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Flandrois JP, Brochier-Armanet C, Briolay J, Abrouk D, Schwob G, Normand P, Fernandez MP. Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon. Res Microbiol 2019; 170:280-287. [PMID: 31279085 DOI: 10.1016/j.resmic.2019.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 05/02/2019] [Accepted: 06/25/2019] [Indexed: 11/28/2022]
Abstract
The taxonomic assignment of uncultured prokaryotes to known taxa is a major challenge in microbial systematics. This relies usually on the phylogenetic analysis of the ribosomal small subunit RNA or a few housekeeping genes. Recent works have disclosed ribosomal proteins as valuable markers for systematics and, due to the boom in complete genome sequencing, their use has become widespread. Yet, in the case of uncultured strains, for which complete genome sequences cannot be easily obtained, sequencing many markers is complicated and time consuming. Taking the advantage of the organization of ribosomal protein coding genes in large gene clusters, we amplified a 32 kb conserved region encompassing the spectinomycin (spc) operon using long range PCR from isolated and from uncultured nodular endophytic Frankia strains. The phylogenetic analysis of the 27 ribosomal protein genes contained in this region provided a robust phylogenetic tree consistent with phylogenies based on larger set of markers, indicating that this subset of ribosomal proteins contains enough phylogenetic signal to address systematic issues. This work shows that using long range PCR could break down the barrier preventing the use of ribosomal proteins as phylogenetic markers when complete genome sequences cannot be easily obtained.
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Affiliation(s)
- Jean-Pierre Flandrois
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France.
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France.
| | - Jérôme Briolay
- Université de Lyon, Université Lyon 1, DTAMB, Villeurbanne, France.
| | - Danis Abrouk
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, INRA, UMR1418, Laboratoire d'Écologie Microbienne, Villeurbanne, France.
| | - Guillaume Schwob
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, INRA, UMR1418, Laboratoire d'Écologie Microbienne, Villeurbanne, France.
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, INRA, UMR1418, Laboratoire d'Écologie Microbienne, Villeurbanne, France.
| | - Maria P Fernandez
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, INRA, UMR1418, Laboratoire d'Écologie Microbienne, Villeurbanne, France.
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Gras E, Bailly E, Le Brun C, Lemaignen A, Lanotte P. Borrelia crocidurae tick-borne relapsing fever upon return from Senegal. Med Mal Infect 2019; 49:624-625. [PMID: 31202618 DOI: 10.1016/j.medmal.2019.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 12/22/2018] [Accepted: 05/21/2019] [Indexed: 11/16/2022]
Affiliation(s)
- E Gras
- Service de bactériologie-virologie-hygiène hospitalière, hôpital Bretonneau, CHRU de Tours, 2 boulevard Tonnellé, 37044 Tours, France
| | - E Bailly
- Service de parasitologie-mycologie, hôpital Bretonneau, CHRU de Tours, 2 boulevard Tonnellé, 37044 Tours, France
| | - C Le Brun
- Service de bactériologie-virologie-hygiène hospitalière, hôpital Bretonneau, CHRU de Tours, 2 boulevard Tonnellé, 37044 Tours, France
| | - A Lemaignen
- Service de médecine interne et maladies infectieuses, Hôpital Bretonneau, CHRU de Tours, 2 boulevard Tonnellé, 37044 Tours, France
| | - P Lanotte
- Service de bactériologie-virologie-hygiène hospitalière, hôpital Bretonneau, CHRU de Tours, 2 boulevard Tonnellé, 37044 Tours, France; Infectiologie et santé publique, INRA, université de Tours, UMR1282, 37380 Nouzilly, France.
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30
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Duprey A, Taib N, Leonard S, Garin T, Flandrois JP, Nasser W, Brochier-Armanet C, Reverchon S. The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity. Environ Microbiol 2019; 21:2809-2835. [PMID: 30969462 DOI: 10.1111/1462-2920.14627] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022]
Abstract
Dickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep-branching species among Dickeya genus, its precise phylogenetic position remained elusive. Here, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquatica strain 174/2 for acidic fruits such as tomato and cucumber and show that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes, we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothesize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflect adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.
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Affiliation(s)
- Alexandre Duprey
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Najwa Taib
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Simon Leonard
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Tiffany Garin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Jean-Pierre Flandrois
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - William Nasser
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Sylvie Reverchon
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 Rue Raphaël Dubois, 69622, Villeurbanne, France
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LANDRIEL SOLEDADCAMINATA, CASTILLO JULIETAD, TABOGA OSCARA, FERRAROTTI SUSANAA, GOTTLIEB ALEXANDRAM, COSTA HERNÁN. Molecular identification of a cyclodextrin glycosyltransferase-producing microorganism and phylogenetic assessment of enzymatic activities. AN ACAD BRAS CIENC 2019; 91:e20180568. [DOI: 10.1590/0001-3765201920180568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 01/10/2019] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | - OSCAR A. TABOGA
- Instituto Nacional de Tecnología Agropecuaria (IABIMO-INTA-CONICET), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, Argentina
| | | | - ALEXANDRA M. GOTTLIEB
- Universidad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, Argentina
| | - HERNÁN COSTA
- Universidad Nacional de Luján, Argentina; Universidad Nacional de Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, Argentina
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Tkadlec J, Krutova M, Matejkova J, Nyc O, Drevinek P. Bloodstream infection caused by Bacteroides denticanum, a close relative of Bacteroides pyogenes, misidentified by MALDI TOF- mass spectrometry. Anaerobe 2018; 54:23-25. [DOI: 10.1016/j.anaerobe.2018.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
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Colombo FM, Cattaneo P, Bernardi C. Selected results of DNA-based species identification on animal foods. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:2437-2439. [PMID: 28981165 DOI: 10.1002/jsfa.8713] [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: 08/11/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Animal food species identification by DNA sequencing has been increasing in recent years. During the last 10 years our species identification laboratory (LIS) produced nearly 1500 sequences from DNA of food species by means of polymerase chain reaction product sequencing. In this paper we desire to make public the LIS output of the last 10 years; that is, summarizing food species authentication projects that yielded good-quality (i.e. provided by Genbank accession number) DNA sequences. RESULTS Thirteen project clusters yielded n = 705 sequences with accession number. CONCLUSION The most relevant characteristics from the aforementioned project clusters were summarized. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Fabio M Colombo
- Università Degli Studi di Milano, Department of Health, Animal Science and Food Safety, Milan, Italy
| | - Patrizia Cattaneo
- Università Degli Studi di Milano, Department of Health, Animal Science and Food Safety, Milan, Italy
| | - Cristian Bernardi
- Università Degli Studi di Milano, Department of Health, Animal Science and Food Safety, Milan, Italy
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Gasc C, Peyret P. Hybridization capture reveals microbial diversity missed using current profiling methods. MICROBIOME 2018; 6:61. [PMID: 29587880 PMCID: PMC5870382 DOI: 10.1186/s40168-018-0442-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 03/13/2018] [Indexed: 06/07/2023]
Abstract
BACKGROUND Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method has resulted in the discovery of many unexpected evolutionary lineages. However, amplicon sequencing is subject to numerous biases, with some taxa being missed, and is limited by the read length of second-generation sequencing platforms, which drastically reduces the phylogenetic resolution. RESULTS Here, we describe a hybridization capture strategy that allows the enrichment of 16S rRNA genes from metagenomic samples and enables an exhaustive identification and a complete reconstruction of the biomarker. Applying this approach to a microbial mock community and a soil sample, we demonstrated that hybridization capture is able to reveal greater microbial diversity than 16S rDNA amplicon sequencing and shotgun sequencing. The reconstruction of full-length 16S rRNA genes facilitated the improvement of phylogenetic resolution and the discovery of novel prokaryotic taxa. CONCLUSIONS Our results demonstrate that hybridization capture can lead to major breakthroughs in our understanding of microbial diversity, overcoming the limitations of conventional 16S rRNA gene studies. If applied to a broad range of environmental samples, this innovative approach could reveal the undescribed diversity of the still underexplored microbial communities and could provide a better understanding of ecosystem function.
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Affiliation(s)
- Cyrielle Gasc
- Université Clermont Auvergne, INRA, UMR 454 MEDIS, 28, place Henri Dunant, F-63000 Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRA, UMR 454 MEDIS, 28, place Henri Dunant, F-63000 Clermont-Ferrand, France
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Vicente-Martins S, Oleastro M, Domingues FC, Ferreira S. Arcobacter spp. at retail food from Portugal: Prevalence, genotyping and antibiotics resistance. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.09.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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CTX-M-15-Producing Shewanella Species Clinical Isolate Expressing OXA-535, a Chromosome-Encoded OXA-48 Variant, Putative Progenitor of the Plasmid-Encoded OXA-436. Antimicrob Agents Chemother 2017; 62:AAC.01879-17. [PMID: 29038283 DOI: 10.1128/aac.01879-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 10/11/2017] [Indexed: 11/20/2022] Open
Abstract
Shewanella spp. constitute a reservoir of antibiotic resistance determinants. In a bile sample, we identified three extended-spectrum-β-lactamase (ESBL)-producing bacteria (Escherichia coli, Klebsiella pneumoniae, and Shewanella sp. strain JAB-1) isolated from a child suffering from cholangitis. Our objectives were to characterize the genome and the resistome of the first ESBL-producing isolate of the genus Shewanella and determine whether plasmidic exchange occurred between the three bacterial species. Bacterial isolates were characterized using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), standard biochemical tools, and antimicrobial susceptibility testing. Shewanella sp. JAB-1 and ESBL gene-encoding plasmids were characterized using PacBio and Illumina whole-genome sequencing, respectively. The Shewanella sp. JAB-1 chromosome-encoded OXA-48 variant was cloned and functionally characterized. Whole-genome sequencing (WGS) of the Shewanella sp. clinical isolate JAB-1 revealed the presence of a 193-kb plasmid belonging to the IncA/C incompatibility group and harboring two ESBL genes, blaCTX-M-15 and blaSHV-2ablaCTX-M-15 gene-carrying plasmids belonging to the IncY and IncR incompatibility groups were also found in the E. coli and K. pneumoniae isolates from the same patient, respectively. A comparison of the blaCTX-M-15 genetic environment indicated the independent origin of these plasmids and dismissed in vivo transfers. Furthermore, characterization of the resistome of Shewanella sp. JAB-1 revealed the presence of a chromosome-carried blaOXA-535 gene, likely the progenitor of the plasmid-carried blaOXA-436 gene, a novel blaOXA-48-like gene. The expression of blaOXA-535 in E. coli showed the carbapenem-hydrolyzing activity of OXA-535. The production of OXA-535 in Shewanella sp. JAB-1 could be evidenced using molecular and immunoenzymatic tests, but not with biochemical tests that monitor carbapenem hydrolysis. In this study, we have identified a CTX-M-15-producing Shewanella species that was responsible for a hepatobiliary infection and that is likely the progenitor of OXA-436, a novel plasmid-encoded OXA-48-like class D carbapenemase.
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Shakir SM, Powers-Fletcher MV, Slechta ES, Fisher MA. Helicobacter canis bacteraemia and cellulitis in a patient with end-stage renal disease. JMM Case Rep 2017; 4:e005126. [PMID: 29255610 PMCID: PMC5729898 DOI: 10.1099/jmmcr.0.005126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/16/2017] [Indexed: 12/14/2022] Open
Abstract
Introduction. Invasive infections by Helicobacter canis are uncommon and occur primarily in immunocompromised patients. Here, we describe a case of H. canis bacteraemia and cellulitis in a patient with end-stage renal disease (ESRD). Case presentation. A 49-year-old male with ESRD on haemodialysis presented to an emergency department with cellulitis overlying his left upper extremity arteriovenous fistula for 3 days without constitutional symptoms. Mild leucocytosis and thrombocytopenia was noted on initial laboratory work up. The patient received a dose of vancomycin initially, and then transitioned to oral doxycycline prior to discharge 3 days later. Blood cultures drawn on admission were positive with curved Gram-negative rods at day 5. Routine sub-cultures initially failed to isolate the organism; however, small, tan colonies were observed on sheep blood agar incubated under microaerobic conditions. H. canis was identified by 16S rRNA sequencing. Antimicrobial-susceptibility testing was not performed due to poor growth and lack of interpretive guidelines. The patient was ultimately treated successfully with amoxicillin/clavulanic acid. Conclusion. This case illustrates the importance of recognizing H. canis infections in immunocompromised patients, especially in those with recent pet exposure. In addition, this case highlights the need for improved laboratory diagnostics for H. canis as isolation and identification of this fastidious organism is challenging.
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Affiliation(s)
- Salika M. Shakir
- Department of Pathology, University of Utah School of Medicine/ARUP Laboratories, Salt Lake City, UT, USA
- *Correspondence: Salika M. Shakir,
| | | | - E. Susan Slechta
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Mark A. Fisher
- Department of Pathology, University of Utah School of Medicine/ARUP Laboratories, Salt Lake City, UT, USA
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
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Hoza AS, Mfinanga SG, Moser I, König B. Isolation, biochemical and molecular identification of Nocardia species among TB suspects in northeastern, Tanzania; a forgotten or neglected threat? BMC Infect Dis 2017; 17:407. [PMID: 28595598 PMCID: PMC5463502 DOI: 10.1186/s12879-017-2520-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/01/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Pulmonary nocardiosis mimic pulmonary tuberculosis in most clinical and radiological manifestations. In Tanzania, where tuberculosis is one of the major public health threat clinical impact of nocardiosis as the cause of the human disease remains unknown. The objective of the present study was to isolate and identify Nocardia isolates recovered from TB suspects in Northeastern, Tanzania by using biochemical and molecular methods. METHODS The study involved 744 sputum samples collected from 372 TB suspects from four periphery diagnostic centers in Northeastern, Tanzania. Twenty patients were diagnosed as having presumptively Nocardia infections based on microscopic, cultural characteristics and biomèrieux ID 32C Yeast Identification system and confirmed using 16S rRNA and hsp65 gene specific primers for Nocardia species and sequencing. RESULTS Biochemically, the majority of the isolates were N. asteroides (n = 8/20, 40%), N. brasiliensis (n = 4/20, 20%), N. farcinica (n = 3/20, 15%), N. nova (n = 1/20, 5%). Other aerobic actinomycetales included Streptomyces cyanescens (n = 2/20, 10%), Streptomyces griseus, Actinomadura madurae each (n = 1/20, 5%). Results of 16S rRNA and hsp65 sequencing were concordant in 15/17 (88. 2%) isolates and discordant in 2/17 (11.8%) isolates. Majority of the isolates belonged to N. cyriacigeorgica and N. farcinica, four (23.5%) each. CONCLUSIONS Our findings suggest that Nocardia species may be an important cause of pulmonary nocardiosis that is underdiagnosed or ignored. This underscores needs to consider pulmonary nocardiosis as a differential diagnosis when there is a failure of anti-TB therapy and as a possible cause of human infections.
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Affiliation(s)
- Abubakar S. Hoza
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Faculty of Medicine, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany
- Department of Microbiology, Parasitology and Immunology, College of Veterinary and Medical Sciences, Sokoine University of Agriculture, P. O. Box, 3019 Morogoro, Tanzania
| | - Sayoki G.S. Mfinanga
- National Institute for Medical Research, Muhimbili Medical Research Centre, P. O. Box, 3436 Dar es Salaam, Tanzania
| | - Irmgard Moser
- Friedrich Loeffler Institut, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany
| | - Brigitte König
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Faculty of Medicine, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany
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Ambroset C, Pau-Roblot C, Game Y, Gaurivaud P, Tardy F. Identification and Characterization of Mycoplasma feriruminatoris sp. nov. Strains Isolated from Alpine Ibex: A 4th Species in the Mycoplasma mycoides Cluster Hosted by Non-domesticated Ruminants? Front Microbiol 2017; 8:939. [PMID: 28611743 PMCID: PMC5447728 DOI: 10.3389/fmicb.2017.00939] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/10/2017] [Indexed: 12/15/2022] Open
Abstract
The genus Mycoplasma, a group of free-living, wall-less prokaryotes includes more than 100 species of which dozens are primary pathogens of humans and domesticated animals. Mycoplasma species isolated from wildlife are rarely investigated but could provide a fuller picture of the evolutionary history and diversity of this genus. In 2013 several isolates from wild Caprinae were tentatively assigned to a new species, Mycoplasma (M.) feriruminatoris sp. nov., characterized by an unusually rapid growth in vitro and close genetic proximity to ruminant pathogenic species. We suspected that atypical isolates recently collected from Alpine ibex in France belonged to this new species. The present study was undertaken to verify this hypothesis and to further characterize the French ibex isolates. Phylogenetic analyses were performed to identify the isolates and position them in trees containing several other mycoplasma species pathogenic to domesticated ruminants. Population diversity was characterized by genomic macrorestriction and by examining the capacity of different strains to produce capsular polysaccharides, a feature now known to vary amongst mycoplasma species pathogenic to ruminants. This is the first report of M. feriruminatoris isolation from Alpine ibex in France. Phylogenetic analyses further suggested that M. feriruminatoris might constitute a 4th species in a genetic cluster that so far contains only important ruminant pathogens, the so-called Mycoplasma mycoides cluster. A PCR assay for specific identification is proposed. These French isolates were not clonal, despite being collected in a restricted region of the Alps, which signifies a considerable diversity of the new species. Strains were able to concomitantly produce two types of capsular polysaccharides, β-(1→6)-galactan and β-(1→6)-glucan, with variation in their respective ratio, a feature never before described in mycoplasmas.
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Affiliation(s)
- Chloé Ambroset
- Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des RuminantsMarcy-l'Étoile, France.,Anses, Laboratoire de Lyon, UMR Mycoplasmoses des RuminantsLyon, France
| | - Corinne Pau-Roblot
- Unité de Biologie des Plantes et Innovation, EA 3900, Université de Picardie Jules VerneAmiens, France
| | - Yvette Game
- Laboratoire Départemental d'Analyses Vétérinaires de SavoieChambéry, France
| | - Patrice Gaurivaud
- Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des RuminantsMarcy-l'Étoile, France.,Anses, Laboratoire de Lyon, UMR Mycoplasmoses des RuminantsLyon, France
| | - Florence Tardy
- Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des RuminantsMarcy-l'Étoile, France.,Anses, Laboratoire de Lyon, UMR Mycoplasmoses des RuminantsLyon, France
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Comparison of Saramis 4.12 and IVD 3.0 Vitek MS Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacteria from Solid and Liquid Culture Media. J Clin Microbiol 2017; 55:2045-2054. [PMID: 28424252 DOI: 10.1128/jcm.00006-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/04/2017] [Indexed: 01/25/2023] Open
Abstract
During the last decade, many investigators have studied matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for identification of mycobacteria. Diverse and contradictory results indicated that optimal level for routine testing has not been reached yet. This work aimed to assess Vitek MS through two distinct versions, Saramis v4.12 RUO and the IVD v3.0, under conditions close to routine laboratory practice. Overall, 111 mycobacterial isolates were subjected to protein extraction and same spectra were matched against both databases. The IVD v3.0 database proved to be superior to Saramis v4.12 and its identification rates remarkably increased, from 67% to 94% for isolates grown on Middlebrook 7H10 solid medium and from 62% to 91% for isolates grown on mycobacterial growth indicator tube (MGIT) liquid medium. With this new version, IVD v3.0, MALDI-TOF MS might be integrated into routine clinical diagnostics, although molecular techniques remain mandatory in some cases.
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Meseguer AS, Manzano-Marín A, Coeur d'Acier A, Clamens AL, Godefroid M, Jousselin E. Buchnerahas changed flatmate but the repeated replacement of co-obligate symbionts is not associated with the ecological expansions of their aphid hosts. Mol Ecol 2016; 26:2363-2378. [DOI: 10.1111/mec.13910] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 09/30/2016] [Accepted: 10/27/2016] [Indexed: 02/02/2023]
Affiliation(s)
- A. S. Meseguer
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
| | - A. Manzano-Marín
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
| | - A. Coeur d'Acier
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
| | - A.-L. Clamens
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
| | - M. Godefroid
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
| | - E. Jousselin
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
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