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Chibwe K, Sundararaju S, Zhang L, Tsui C, Tang P, Ling F. Intra-hospital microbiome variability is driven by accessibility and clinical activities. Microbiol Spectr 2024:e0029624. [PMID: 38940596 DOI: 10.1128/spectrum.00296-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/30/2024] [Indexed: 06/29/2024] Open
Abstract
The hospital environmental microbiome, which can affect patients' and healthcare workers' health, is highly variable and the drivers of this variability are not well understood. In this study, we collected 37 surface samples from the neonatal intensive care unit (NICU) in an inpatient hospital before and after the operation began. Additionally, healthcare workers collected 160 surface samples from five additional areas of the hospital. All samples were analyzed using 16S rRNA gene amplicon sequencing, and the samples collected by healthcare workers were cultured. The NICU samples exhibited similar alpha and beta diversities before and after opening, which indicated that the microbiome there was stable over time. Conversely, the diversities of samples taken after opening varied widely by area. Principal coordinate analysis (PCoA) showed the samples clustered into two distinct groups: high alpha diversity [the pediatric intensive care unit (PICU), pathology lab, and microbiology lab] and low alpha diversity [the NICU, pediatric surgery ward, and infection prevention and control (IPAC) office]. Least absolute shrinkage and selection operator (LASSO) classification models identified 156 informative amplicon sequence variants (ASVs) for predicting the sample's area of origin. The testing accuracy ranged from 86.37% to 100%, which outperformed linear and radial support vector machine (SVM) and random forest models. ASVs of genera that contain emerging pathogens were identified in these models. Culture experiments had identified viable species among the samples, including potential antibiotic-resistant bacteria. Though area type differences were not noted in the culture data, the prevalences and relative abundances of genera detected positively correlated with 16S sequencing data. This study brings to light the microbial community temporal and spatial variation within the hospital and the importance of pathogenic and commensal bacteria to understanding dispersal patterns for infection control. IMPORTANCE We sampled surface samples from a newly built inpatient hospital in multiple areas, including areas accessed by only healthcare workers. Our analysis of the neonatal intensive care unit (NICU) showed that the microbiome was stable before and after the operation began, possibly due to access restrictions. Of the high-touch samples taken after opening, areas with high diversity had more potential external seeds (long-term patients and clinical samples), and areas with low diversity and had fewer (short-term or newborn patients). Classification models performed at high accuracy and identified biomarkers that could be used for more targeted surveillance and infection control. Though culturing data yielded viability and antibiotic-resistance information, it disproportionately detected the presence of genera relative to 16S data. This difference reinforces the utility of 16S sequencing in profiling hospital microbiomes. By examining the microbiome over time and in multiple areas, we identified potential drivers of the microbial variation within a hospital.
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Affiliation(s)
- Kaseba Chibwe
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Lin Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Clement Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, Singapore
| | - Patrick Tang
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Fangqiong Ling
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Division of Biological and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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2
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Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021. J Clin Microbiol 2023; 61:e0028222. [PMID: 36533910 PMCID: PMC9879126 DOI: 10.1128/jcm.00282-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.
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Rabe A, Gesell Salazar M, Michalik S, Kocher T, Below H, Völker U, Welk A. Impact of different oral treatments on the composition of the supragingival plaque microbiome. J Oral Microbiol 2022; 14:2138251. [PMID: 36338832 PMCID: PMC9629129 DOI: 10.1080/20002297.2022.2138251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background Dental plaque consists of a diverse microbial community embedded in a complex structure of exopolysaccharides. Dental biofilms form a natural barrier against pathogens but lead to oral diseases in a dysbiotic state. Objective Using a metaproteome approach combined with a standard plaque-regrowth study, this pilot study examined the impact of different concentrations of lactoperoxidase (LPO) on early plaque formation, and active biological processes. Design Sixteen orally healthy subjects received four local treatments as a randomized single-blind study based on a cross-over design. Two lozenges containing components of the LPO-system in different concentrations were compared to a placebo and Listerine®. The newly formed dental plaque was analyzed by mass spectrometry (nLC-MS/MS). Results On average 1,916 metaproteins per sample were identified, which could be assigned to 116 genera and 1,316 protein functions. Listerine® reduced the number of metaproteins and their relative abundance, confirming the plaque inhibiting effect. The LPO-lozenges triggered mainly higher metaprotein abundances of early and secondary colonizers as well as bacteria associated with dental health but also periodontitis. Functional information indicated plaque biofilm growth. Conclusion In conclusion, the mechanisms on plaque biofilm formation of Listerine® and the LPO-system containing lozenges are different. In contrast to Listerine®, the lozenges led to a higher bacterial diversity.
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Affiliation(s)
- Alexander Rabe
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany,CONTACT Alexander Rabe University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, Felix-Hausdorff-Str. 8, 17489Greifswald, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany
| | - Thomas Kocher
- Center for Dentistry, Oral and Maxillofacial Medicine, Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, Dental School of University Medicine Greifswald, Fleischmannstraße 42-44, 17489
| | - Harald Below
- Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, Walter-Rathenau-Straße 49 A17475Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany
| | - Alexander Welk
- Center for Dentistry, Oral and Maxillofacial Medicine, Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, Dental School of University Medicine Greifswald, Fleischmannstraße 42-44, 17489
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Gołębiewski M, Łoś-Rycharska E, Sikora M, Grzybowski T, Gorzkiewicz M, Krogulska A. Mother's Milk Microbiome Shaping Fecal and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Analysis. Nutrients 2021; 13:nu13103600. [PMID: 34684601 PMCID: PMC8537811 DOI: 10.3390/nu13103600] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 01/04/2023] Open
Abstract
The child microbiome, including gut and skin communities, is shaped by a multitude of factors, and breastfeeding is one of the most essential. Food allergy (FA) and atopic dermatitis (AD) are among the most common diseases in pediatrics, with the prevalence of each up to 6% and 20%, respectively. Therefore, we aimed at finding differences between the fecal and skin microbiomes of FA and AD patients in the context of breastfeeding, by means of the Illumina sequencing of 16S rRNA gene fragment libraries amplified from the total DNA isolated from samples collected from allergic and healthy infants. We also analyzed milk samples from the mothers of the examined children and searched for patterns of incidence suggesting milk influence on an infant's allergy status. Here we show that a mother's milk influences her child's fecal and skin microbiomes and identify Acinetobacter as the taxon whose abundance is correlated with milk and child-derived samples. We demonstrate that breastfeeding makes allergic children's fecal and skin communities more similar to those of healthy infants than in the case of formula-feeding. We also identify signature taxa that might be important in maintaining health or allergy development.
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Affiliation(s)
- Marcin Gołębiewski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, 87-100 Torun, Poland
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland;
- Correspondence: (M.G.); (E.Ł.-R.); Tel.: +48-56-611-2512 (M.G.); +48-52-585-4850 (E.Ł.-R.); Fax: +48-56-611-4559 (M.G.); +48-52-585-4086 (E.Ł.-R.)
| | - Ewa Łoś-Rycharska
- Department of Pediatrics, Allergology and Gastroenterology, Collegium Medicum Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland;
- Correspondence: (M.G.); (E.Ł.-R.); Tel.: +48-56-611-2512 (M.G.); +48-52-585-4850 (E.Ł.-R.); Fax: +48-56-611-4559 (M.G.); +48-52-585-4086 (E.Ł.-R.)
| | - Marcin Sikora
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland;
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Collegium Medicum Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland; (T.G.); (M.G.)
| | - Marta Gorzkiewicz
- Department of Forensic Medicine, Collegium Medicum Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland; (T.G.); (M.G.)
| | - Aneta Krogulska
- Department of Pediatrics, Allergology and Gastroenterology, Collegium Medicum Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland;
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İnal N, Hazırolan G. A case of bacteremia caused by Leptotrichia trevisanii in pediatric patient with febrile neutropenia and review of literature. Acta Microbiol Immunol Hung 2021. [PMID: 34051072 DOI: 10.1556/030.2021.01358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/28/2021] [Indexed: 11/19/2022]
Abstract
Leptotrichia species are fastidious anaerobic, fusiform, pencil-shaped Gram-negative bacilli that reside in microbiota of humans. Leptotrichia species have increasingly been recognized as an opportunistic pathogen in humans, mainly in the immunocompromised patient. Anaerobic organisms have rarely been isolated from blood cultures of pediatric patients. In our study, we isolated Leptotrichia trevisanii from central venous catheter culture of a five-year-old male patient. It was identified with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry and confirmed via 16S rRNA gene sequencing. The early recognition of anaerobic bacteremia and administration of appropriate antimicrobial and play an important role preventing mortality and morbidity in children. In our study we report a rarely diagnosed case of L. trevisanii bacteremia in a pediatric patient.
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Affiliation(s)
- Neşe İnal
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Gülşen Hazırolan
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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6
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Amin N, Schwarzkopf S, Kinoshita A, Tröscher-Mußotter J, Dänicke S, Camarinha-Silva A, Huber K, Frahm J, Seifert J. Evolution of rumen and oral microbiota in calves is influenced by age and time of weaning. Anim Microbiome 2021; 3:31. [PMID: 33883031 PMCID: PMC8059317 DOI: 10.1186/s42523-021-00095-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/04/2021] [Indexed: 01/04/2023] Open
Abstract
Background The rumen bacterial communities are changing dynamically throughout the first year of calf’s life including the weaning period as a critical event. Rumen microbiome analysis is often limited to invasive rumen sampling procedures but the oral cavity of ruminants is expected to harbour rumen microbes due to regurgitation activity. The present study used buccal swab samples to define the rumen core microbiome and characterize the shifts in rumen and oral microbial communities occurring as result of calf’s age as well as time of weaning. Results Buccal swab samples of 59 calves were collected along the first 140 days of life and compared to stomach tubing sample of the rumen at day 140. Animals were randomly divided into two weaning groups. Microbiota of saliva and rumen content was analysed by 16S rRNA gene amplicon sequencing. Our study showed that most rumen-specific bacterial taxa were equally observed in rumen samples as well as in the buccal swabs, though relative abundance varied. The occurrence of rumen-specific OTUs in buccal swab samples increased approximately 1.7 times from day 70 to day 140, indicating the gradual development of rumen as calf aged. The rumen-specific bacterial taxa diversity increased, and inter-animal variations decreased with age. Early weaning (7 weeks of age) rapidly increased the rumen microbial diversity from pre- to post-weaned state. Rumen microbiota of early-weaned calves seemed to have a suppressed growth of starch- and carbohydrate-utilizing bacteria and increased fibre degraders. Whereas, in late-weaned calves (17 weeks of age) no impact of dietary modifications on rumen microbiota composition was observed after weaning. Oral-specific bacterial community composition was significantly affected by calf’s age and time of weaning. Conclusions The present study showed the significant impact of calf’s age and weaning on the establishment of rumen- and oral-specific bacterial communities utilizing buccal swab samples. The results emphasize the possibility of using buccal swab samples as a replacement of complex stomach tube method for large-scale predictive studies on ruminants. For in-depth rumen microbiome studies, the time of sampling should be carefully considered using an active phase of regurgitation. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00095-3.
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Affiliation(s)
- Nida Amin
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Sarah Schwarzkopf
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Asako Kinoshita
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany.,Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Bundesallee 37, 38116, Braunschweig, Germany
| | - Johanna Tröscher-Mußotter
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Sven Dänicke
- Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Bundesallee 37, 38116, Braunschweig, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Korinna Huber
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Jana Frahm
- Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Bundesallee 37, 38116, Braunschweig, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany.
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Theis KR, Florova V, Romero R, Borisov AB, Winters AD, Galaz J, Gomez-Lopez N. Sneathia: an emerging pathogen in female reproductive disease and adverse perinatal outcomes. Crit Rev Microbiol 2021; 47:517-542. [PMID: 33823747 DOI: 10.1080/1040841x.2021.1905606] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sneathia is an emerging pathogen implicated in adverse reproductive and perinatal outcomes. Although scarce, recent data suggest that vaginally residing Sneathia becomes pathogenic following its ascension into the upper urogenital tract, amniotic fluid, placenta, and foetal membranes. The role of Sneathia in women's health and disease is generally underappreciated because the cultivation of these bacteria is limited by their complex nutritional requirements, slow growth patterns, and anaerobic nature. For this reason, molecular methods are typically required for the detection and differential diagnosis of Sneathia infections. Here, we review the laboratory methods used for the diagnosis of Sneathia infections, the molecular mechanisms underlying its virulence, and its sensitivity to antibiotics. We further review the evidence of Sneathia's contributions to the pathogenesis of bacterial vaginosis, chorioamnionitis, preterm prelabour rupture of membranes, spontaneous preterm labour, stillbirth, maternal and neonatal sepsis, HIV infection, and cervical cancer. Collectively, growing evidence indicates that Sneathia represents an important yet underappreciated pathogen affecting the development and progression of several adverse clinical conditions diagnosed in pregnant women and their neonates, as well as in non-pregnant women.
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Affiliation(s)
- Kevin R Theis
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Violetta Florova
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA.,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.,Detroit Medical Center, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Florida International University, Miami, FL, USA
| | - Andrei B Borisov
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Andrew D Winters
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jose Galaz
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
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8
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Eisenberg T, Gronow S, Falgenhauer J, Imirzalioglu C, Mühldorfer K, Rau J, Blom J, Fawzy A, Glaeser SP, Kämpfer P. Sneathia vaginalis sp. nov. ( Fusobacteriales, Leptotrichiaceae) as a replacement of the species ' Sneathia amnii' Harwich et al. 2012 and ' Leptotrichia amnionii' Shukla et al. 2002, and emended description of Sneathia Collins et al. 2001. Int J Syst Evol Microbiol 2021; 71. [PMID: 33616512 DOI: 10.1099/ijsem.0.004663] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Members of the genus Sneathia are fastidious bacteria that predominantly colonise the female genital tract and are significantly associated with reproductive disorders and genital and neonatal disease. From a taxonomical perspective, the genus only comprises the species Sneathia sanguinegens. Numerous reports on a second species, 'Sneathia amnii', have been published, but the name has never been validated. The same is the case for 'Leptotrichia amnionii', which was previously shown to belong to the same species as 'Sneathia amnii'. We studied strains DSM 16631T and DSM 16630, which have been identified and deposited as 'Leptotrichia amnionii' previously. At the time of isolation, these strains were found to be most closely related to, but clearly different from, Sneathia sanguinegens based on 16S rRNA gene sequence similarities. Both strains proved to be almost indistinguishable from 'Sneathia amnii' based on molecular, morphological and physiological traits. The 16S rRNA gene sequence analysis revealed that strain DSM 16631T was assigned to the genus Sneathia with a sequence similarity of 95.47 % to Sneathia sanguinegens CCUG 41628T, followed by type strains of Caviibacter abscessus (93.03 %), Oceanivirga salmonicida (92.68 %) and Oceanivirga miroungae (91.97 %) as the next closely related members of the Leptotrichiaceae. The novel species was also clearly differentiated from other related taxa by core genome phylogeny, average nucleotide and amino acid identities, in silico DNA-DNA hybridization and MALDI-TOF MS. With respect to chemotaxonomic and physiological patterns, strains DSM 16631T and DSM 16630 were again highly similar to Sneathia sanguinegens. On the basis of these data, we propose the novel species Sneathia vaginalis sp. nov. with the type strain DSM 16631T (=CCUG 52977T=CCUG 52889AT) and a second strain DSM 16630 (=CCUG 52976=CCUG 52888) that were both isolated from bloodstream infections in women with puerperal fever in France. The G+C content of the DNA of the type strain is 28.4 mol% and the genome size is 1.28 Mbp. Based on the observed extremely high similarities of genotypic and phenotypic traits of the novel proposed species to those reported for 'Sneathia amnii', we recommend using this new name in all further publications on this taxon.
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Affiliation(s)
- Tobias Eisenberg
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, 35392 Giessen, Germany.,Hessian State Laboratory (LHL), 35392 Giessen, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Culture GmbH, 38124 Braunschweig, Germany
| | - Jane Falgenhauer
- Institute for Medical Microbiology, Justus Liebig University Giessen, 35392 Giessen, Germany and German Center of Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Germany
| | - Can Imirzalioglu
- Institute for Medical Microbiology, Justus Liebig University Giessen, 35392 Giessen, Germany and German Center of Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Germany
| | - Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
| | - Jörg Rau
- Chemical and Veterinary Analysis Agency Stuttgart, 70736 Fellbach, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ahmad Fawzy
- Cairo University, Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Giza Square 12211, Egypt.,Hessian State Laboratory (LHL), 35392 Giessen, Germany
| | - Stefanie P Glaeser
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Peter Kämpfer
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
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9
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Identification of Leptotrichia goodfellowii infective endocarditis by next-generation sequencing of 16S rDNA amplicons. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005876. [PMID: 33288524 PMCID: PMC7903886 DOI: 10.1101/mcs.a005876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/23/2020] [Indexed: 12/02/2022] Open
Abstract
The oral aerotolerant anaerobe Leptotrichia goodfellowii is an unusual cause of endocarditis and is amenable to treatment with β-lactam antibiotics. Because this organism is difficult to identify by conventional methods, molecular detection is a key diagnostic modality. Broad-range 16S rDNA PCR followed by Sanger sequencing constitute the first-line molecular approach, yet poor DNA quality, contaminating DNA, or low template quantity make identification challenging. Here we report a case of culture-negative, aortic and mitral valve endocarditis in a 66-yr-old woman with a history of cardiomyopathy, atrial fibrillation with intracardiac pacer, poor dentition, and recent tooth infection. In this case, 16S rDNA amplicon Sanger sequencing was not sufficient for pathogen identification because of interfering DNA, but deconvolution of the clinical sample using reflexive next-generation amplicon sequencing enabled confident identification of a single pathogenic organism, L. goodfellowii. The patient developed a sigmoid colon perforation and died despite additional surgical treatment. Most Leptotrichia endocarditis cases have been subacute and have been successfully treated with antibiotics, with or without valve replacement. This case highlights both an unusual etiologic agent of endocarditis, as well as the rational utilization of advanced molecular diagnostics tools for characterizing serious infections.
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10
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Dental plaque microbiota profiles of children with caries-free and caries-active dentition. J Dent 2020; 104:103539. [PMID: 33248211 DOI: 10.1016/j.jdent.2020.103539] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Microbiota comparisons between healthy and diseased dental tissues have accentuated the importance of cultivating and identifying bacterial species that play a role in the initiation and progression of dental caries. The objective of this study was to evaluate the bacterial community composition in caries-active and caries-free children. METHODS Supragingival plaque samples were collected from 64 caries-active and 64 caries-free Middle Eastern children. The hypervariable V3-V4 of the bacterial 16S rRNA gene was sequenced with Human Oral Microbe Identification using Next Generation Sequencing. Microbial community structure and composition analyses were performed by processing operational taxonomic units. Bioinformatic analyses, including analysis of similarity, alpha and beta diversities, and principal coordinate analysis, were carried out. RESULTS Diversity indices did not find differences between the caries-active and caries-free groups (p > 0.05). Similarity analysis demonstrated that the microbiota composition did not differ between the two groups. Comparative analysis at the species level revealed a significantly higher relative abundance of Leptotrichia shahii, Prevotella melaninogenica, Veillonella dispar, Leptotrichia HOT 498, and Streptococcus mutans in caries-active children (p < 0.05). Corynebacterium matruchotii, Lautropia mirabilis, Neisseria elongata, and Corynebacterium durum were relatively more abundant in the caries-free group (p < 0.05). Species belonging to the Leptotrichia, Prevotella, and Veillonella genera were significantly predominant in the caries-active subjects. CONCLUSION In view of the lack of a clear association between Corynebacterium spp. and dental caries status in the literature, the predominance of these species in caries-free children warrants further research to understand their possible role in a health-associated microbial community. CLINICAL SIGNIFICANCE Understanding the relationship between specific bacteria present in dental biofilms and health and disease is essential for preventing and combating dental caries. Using advanced next generation sequencing techniques, the present study demonstrated the complexity of the caries microbiome and identified species/genera whose virulence or protective properties should be further explored.
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11
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Longhi G, van Sinderen D, Ventura M, Turroni F. Microbiota and Cancer: The Emerging Beneficial Role of Bifidobacteria in Cancer Immunotherapy. Front Microbiol 2020; 11:575072. [PMID: 33013813 PMCID: PMC7507897 DOI: 10.3389/fmicb.2020.575072] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022] Open
Abstract
Many intestinal bacteria are believed to be involved in various inflammatory and immune processes that influence tumor etiology because of their metabolic properties and their ability to alter the microbiota homeostasis. Although many functions of the microbiota are still unclear, there is compelling experimental evidence showing that the intestinal microbiota is able to modulate carcinogenesis and the response to anticancer therapies, both in the intestinal tract and other body sites. Among the wide variety of gut-colonizing microorganisms, various species belonging to the Bifidobacterium genus are believed to elicit beneficial effects on human physiology and on the host-immune system. Recent findings, based on preclinical mouse models and on human clinical trials, have demonstrated the impact of gut commensals including bifidobacteria on the efficacy of tumor-targeting immunotherapy. Although the underlying molecular mechanisms remain obscure, bifidobacteria and other microorganisms have become a promising aid to immunotherapeutic procedures that are currently applied to treat cancer. The present review focuses on strategies to recruit the microbiome in order to enhance anticancer responses and develop therapies aimed at fighting the onset and progression of malignancies.
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Affiliation(s)
- Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- Alimentary Pharmabotic Centre (APC) Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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12
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Murugkar PP, Collins AJ, Chen T, Dewhirst FE. Isolation and cultivation of candidate phyla radiation Saccharibacteria (TM7) bacteria in coculture with bacterial hosts. J Oral Microbiol 2020; 12:1814666. [PMID: 33209205 PMCID: PMC7651992 DOI: 10.1080/20002297.2020.1814666] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background The vast majority of bacteria on earth have not yet been cultivated. There are many bacterial phyla with no cultivated examples including most members of the Candidate Phylum Radiation with the exception of human oral isolates from the phylum Saccharibacteria. Aims The aims of this research were to develop reproducible methods and validate approaches for the cultivation of human oral Saccharibacteria and to identify the conceptual pitfalls that delayed isolation of these bacteria for 20 years after their discovery. Methods Oral samples were dispersed and passed through 0.2 µm membrane filters. The ultrasmall saccharibacterial cells in the filtrate were pelleted, inoculated into broth cultures of potential bacterial host cells and passaged into fresh medium every 2–3 days. Results Thirty-two isolates representing four species of Saccharibacteria were isolated in stable coculture with three species of host bacteria from the phylum Actinobacteria. Complete genome sequences were obtained for 16 isolates. Conclusions Human oral Saccharibacteria are obligate bacterial parasites that can be stably passaged in coculture with specific species of host bacteria. Isolating these important members of the human oral microbiome, and many natural environments, requires abandoning many of Koch’s concepts and methods and embracing novel microbiological approaches.
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Affiliation(s)
- Pallavi P Murugkar
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Andrew J Collins
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Tsute Chen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Floyd E Dewhirst
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
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13
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Proposal to reclassify Leptotrichia goodfellowii into a novel genus as Pseudoleptotrichia goodfellowii gen. nov., comb. nov. Int J Syst Evol Microbiol 2020; 70:2084-2088. [DOI: 10.1099/ijsem.0.004024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reclassification of
Leptotrichia goodfellowii
as Pseudoleptotrichia goodfellowii gen. nov., comb. nov. is proposed because of the separate phylogenetic position on the basis of the results of 16S rRNA gene sequence analysis, the genomic differences from all other
Leptotrichia
species and phenotypic differences from
Leptotrichia
species. The species Pseudoleptotrichia goodfellowii is the type species of the genus. The type strain is LB 57T, CCUG 32286 T, DSM 19756T.
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14
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Watanabe S, Cui B, Kiga K, Aiba Y, Tan XE, Sato'o Y, Kawauchi M, Boonsiri T, Thitiananpakorn K, Taki Y, Li FY, Azam AH, Nakada Y, Sasahara T, Cui L. Composition and Diversity of CRISPR-Cas13a Systems in the Genus Leptotrichia. Front Microbiol 2019; 10:2838. [PMID: 31921024 PMCID: PMC6914741 DOI: 10.3389/fmicb.2019.02838] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13a, previously known as CRISPR-C2c2, is the most recently identified RNA-guided RNA-targeting CRISPR-Cas system that has the unique characteristics of both targeted and collateral single-stranded RNA (ssRNA) cleavage activities. This system was first identified in Leptotrichia shahii. Here, the complete whole genome sequences of 11 Leptotrichia strains were determined and compared with 18 publicly available Leptotrichia genomes in regard to the composition, occurrence and diversity of the CRISPR-Cas13a, and other CRISPR-Cas systems. Various types of CRISPR-Cas systems were found to be unevenly distributed among the Leptotrichia genomes, including types I-B (10/29, 34.4%), II-C (1/29, 2.6%), III-A (6/29, 15.4%), III-D (6/29, 15.4%), III-like (3/29, 7.7%), and VI-A (11/29, 37.9%), while 8 strains (20.5%) had no CRISPR-Cas system at all. The Cas13a effectors were found to be highly divergent with amino acid sequence similarities ranging from 61% to 90% to that of L. shahii, but their collateral ssRNA cleavage activities leading to impediment of bacterial growth were conserved. CRISPR-Cas spacers represent a sequential achievement of former intruder encounters, and the retained spacers reflect the evolutionary phylogeny or relatedness of strains. Analysis of spacer contents and numbers among Leptotrichia species showed considerable diversity with only 4.4% of spacers (40/889) were shared by two strains. The organization and distribution of CRISPR-Cas systems (type I-VI) encoded by all registered Leptotrichia species revealed that effector or spacer sequences of the CRISPR-Cas systems were very divergent, and the prevalence of types I, III, and VI was almost equal. There was only one strain carrying type II, while none carried type IV or V. These results provide new insights into the characteristics and divergences of CRISPR-Cas systems among Leptotrichia species.
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Affiliation(s)
- Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Bintao Cui
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Kotaro Kiga
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yoshifumi Aiba
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yusuke Sato'o
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Moriyuki Kawauchi
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Tanit Boonsiri
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Kanate Thitiananpakorn
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yusuke Taki
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Fen-Yu Li
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Aa Haeruman Azam
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yumi Nakada
- Division of Clinical Laboratory, Tottori University Hospital, Tottori, Japan
| | - Teppei Sasahara
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
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15
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Hou H, Chen Z, Tian L, Sun Z. Leptotrichia trevisanii bacteremia in a woman with systemic lupus erythematosus receiving high-dose chemotherapy. BMC Infect Dis 2018; 18:661. [PMID: 30547754 PMCID: PMC6295021 DOI: 10.1186/s12879-018-3495-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/01/2018] [Indexed: 12/31/2022] Open
Abstract
Background Leptotrichia species are aerotolerant, Gram-negative fusiform bacteria. Cases of bacteremia caused by Leptotrichia trevisanii in immunocompromised patients have been rarely reported. Case presentation A 33-year-old female with systemic lupus erythematosus (SLE) was admitted to the department of rheumatology with bleeding from a mucosal ulcer. One month previously, she had visited our hospital and begun to receive methotrexate therapy, but mis-dosed for nearly 1 month at home. Methotrexate toxicity resulted in a severe oral ulcer and bone marrow suppression. On day-7 of hospital admission, she developed a fever, and Gram-negative rods (Leptotrichia trevisanii) were detected in blood cultures. She was diagnosed with methotrexate poisoning followed by L. trevisanii bacteremia. After antibiotic and detoxification therapy, she recovered from bacteremia, and the oral ulcer and bone-marrow suppression improved obviously. Conclusions This is the first reported case of Leptotrichia trevisanii bacteremia in a SLE patient who took mis-dosed an immunosuppressant and had an oral mucosal lesion.
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Affiliation(s)
- Hongyan Hou
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1095#, Wuhan, 430030, China
| | - Zhongju Chen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1095#, Wuhan, 430030, China
| | - Lei Tian
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1095#, Wuhan, 430030, China
| | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1095#, Wuhan, 430030, China.
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16
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Emergent genital infection by Leptotrichia trevisanii. Infection 2018; 47:111-114. [PMID: 29980937 DOI: 10.1007/s15010-018-1175-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
Abstract
We report the first case of an association between Leptotrichia trevisanii and an episode of pelvic inflammatory disease (PID) and the second case of the isolation of this infection in the cervical canal. A 45-yr-old woman was admitted to our emergency department with clinical and radiological signs and symptoms compatible with an episode of PID. She was hospitalized for intravenous antibiotic control and treatment and the subsequent surgical drainage of abscesses. Cultures were taken throughout the process, but only cultures from cervical canal exudate were positive, with the growth of L. trevisanii species. It appears important to carry out a complete microbiological screening, not limited to conventional agents, on adequate clinical samples to detect possible infectious agents that may be missed in these cases.
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17
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Eribe ERK, Olsen I. Leptotrichia species in human infections II. J Oral Microbiol 2017; 9:1368848. [PMID: 29081911 PMCID: PMC5646626 DOI: 10.1080/20002297.2017.1368848] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 08/15/2017] [Indexed: 12/19/2022] Open
Abstract
Leptotrichia species are non-motile facultative anaerobic/anaerobic bacteria that are found mostly in the oral cavity and some other parts of the human body, in animals, and even in ocean sediments. Valid species include L. buccalis, L. goodfellowii, L. hofstadii, L. honkongensis, L. shahii, L. trevisanii, and L. wadei. Some species require serum or blood for growth. All species ferment carbohydrates and produce lactic acid that may be involved with tooth decay. Acting as opportunistic pathogens, they are involved in a variety of diseases, and have been isolated from immunocompromised but also immunocompetent individuals. Mucositis, oral lesions, wounds, and abscesses may predispose to Leptotrichia septicemia. Because identification of Leptotrichia species by phenotypic features occasionally lead to misidentification, genetic techniques such as 16S rRNA gene sequencing is recommended. Early diagnosis and treatment of leptotrichia infections is important for positive outcomes. Over the last years, Leptotrichia species have been associated with several changes in taxonomy and new associations with clinical diseases. Such changes are reported in this updated review.
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Affiliation(s)
- Emenike R K Eribe
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Ingar Olsen
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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18
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He Y, Gong D, Shi C, Shao F, Shi J, Fei J. Dysbiosis of oral buccal mucosa microbiota in patients with oral lichen planus. Oral Dis 2017; 23:674-682. [PMID: 28199766 DOI: 10.1111/odi.12657] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/15/2016] [Accepted: 01/25/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Y He
- Department of Oral Medicine, School & Hospital of Stomatology, Tongji University; Shanghai Engineering Research Center of Tooth Restoration and Regeneration; Shanghai China
| | - D Gong
- Department of Oral Medicine, School & Hospital of Stomatology, Tongji University; Shanghai Engineering Research Center of Tooth Restoration and Regeneration; Shanghai China
| | - C Shi
- Department of Oral Medicine, School & Hospital of Stomatology, Tongji University; Shanghai Engineering Research Center of Tooth Restoration and Regeneration; Shanghai China
| | - F Shao
- Department of Oral Medicine, School & Hospital of Stomatology, Tongji University; Shanghai Engineering Research Center of Tooth Restoration and Regeneration; Shanghai China
| | - J Shi
- School of Life Science and Technology; Tongji University; Shanghai China
| | - J Fei
- School of Life Science and Technology; Tongji University; Shanghai China
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19
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Subacute Bacterial Endocarditis with Leptotrichia goodfellowii in a Patient with a Valvular Allograft: A Case Report and Review of the Literature. Case Rep Infect Dis 2016; 2016:3051212. [PMID: 27895947 PMCID: PMC5118523 DOI: 10.1155/2016/3051212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/16/2016] [Indexed: 11/17/2022] Open
Abstract
Leptotrichia species are normal constituents of the oral cavity and the genitourinary tract microbiota that are known to provoke disease in immunocompromised patients and rarely in immunocompetent individuals. Following the description of Leptotrichia goodfellowii sp. nov., two cases of endocarditis by this species have been reported. Here, we report a case of Leptotrichia goodfellowii endocarditis in an immunocompetent patient with a valvular allograft. The isolation and identification of Leptotrichia can be challenging, and it is likely that infection with this pathogen is significantly underdiagnosed. A definitive identification, as in this case, most often requires 16S rRNA gene sequencing, highlighting the increasingly important role of this diagnostic modality among immunocompetent patients with undetermined anaerobic bacteremia.
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20
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Eisenberg T, Fawzy A, Nicklas W, Semmler T, Ewers C. Phylogenetic and comparative genomics of the family Leptotrichiaceae and introduction of a novel fingerprinting MLVA for Streptobacillus moniliformis. BMC Genomics 2016; 17:864. [PMID: 27809782 PMCID: PMC5093955 DOI: 10.1186/s12864-016-3206-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/25/2016] [Indexed: 11/30/2022] Open
Abstract
Background The Leptotrichiaceae are a family of fairly unnoticed bacteria containing both microbiota on mucous membranes as well as significant pathogens such as Streptobacillus moniliformis, the causative organism of streptobacillary rat bite fever. Comprehensive genomic studies in members of this family have so far not been carried out. We aimed to analyze 47 genomes from 20 different member species to illuminate phylogenetic aspects, as well as genomic and discriminatory properties. Results Our data provide a novel and reliable basis of support for previously established phylogeny from this group and give a deeper insight into characteristics of genome structure and gene functions. Full genome analyses revealed that most S. moniliformis strains under study form a heterogeneous population without any significant clustering. Analysis of infra-species variability for this highly pathogenic rat bite fever organism led to the detection of three specific variable number tandem analysis loci with high discriminatory power. Conclusions This highly useful and economical tool can be directly employed in clinical samples without laborious prior cultivation. Our and prospective case-specific data can now easily be compared by using a newly established MLVA database in order to gain a better insight into the epidemiology of this presumably under-reported zoonosis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3206-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Eisenberg
- Abteilung Veterinärmedizin, Landesbetrieb Hessisches Landeslabor (LHL), Schubertstr. 60/H13, D-35392, Giessen, Germany.
| | - Ahmad Fawzy
- Abteilung Veterinärmedizin, Landesbetrieb Hessisches Landeslabor (LHL), Schubertstr. 60/H13, D-35392, Giessen, Germany.,Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza Square, 12211, Egypt.,Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Giessen, D-35392, Giessen, Germany
| | - Werner Nicklas
- Deutsches Krebsforschungszentrum, D-69120, Heidelberg, Germany
| | | | - Christa Ewers
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Giessen, D-35392, Giessen, Germany
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21
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Jang JY, Song IS, Baek KJ, Choi Y, Ji S. Immunologic characteristics of human gingival fibroblasts in response to oral bacteria. J Periodontal Res 2016; 52:447-457. [DOI: 10.1111/jre.12410] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2016] [Indexed: 01/12/2023]
Affiliation(s)
- J. Y. Jang
- Department of Periodontology; Institute of Oral Health Science; Ajou University School of Medicine; Suwon Korea
| | - I.-S. Song
- Department of Oral and Maxillofacial Surgery; Korea University Anam Hospital; Seoul Korea
| | - K. J. Baek
- Department of Oromaxillofacial Infection & Immunity; BK21 CLS; School of Dentistry and Dental Research Institute; Seoul National University; Seoul Korea
| | - Y. Choi
- Department of Oromaxillofacial Infection & Immunity; BK21 CLS; School of Dentistry and Dental Research Institute; Seoul National University; Seoul Korea
| | - S. Ji
- Department of Periodontology; Institute of Oral Health Science; Ajou University School of Medicine; Suwon Korea
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22
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Eisenberg T, Kämpfer P, Ewers C, Semmler T, Glaeser SP, Collins E, Ruttledge M, Palmer R. Oceanivirga salmonicida gen. nov., sp. nov., a member of the Leptotrichiaceae isolated from Atlantic salmon (Salmo salar). Int J Syst Evol Microbiol 2016; 66:2429-2437. [PMID: 27031261 DOI: 10.1099/ijsem.0.001050] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pleomorphic, Gram-negative, rod-shaped, indole-, oxidase- and catalase- negative, non-spore-forming, non-motile bacterium was originally isolated in 1992 from moribund, seawater farmed Atlantic salmon with multifocal tissue necrosis. Strain AVG 2115T displayed considerable similarities with Streptobacillus moniliformis, one of the two etiological agents of rat bite fever, and has been stored as Streptobacillus sp. NCIMB 703044T. On the basis of 16S rRNA gene sequence analyses, this strain displayed >99 % sequence similarities with uncultured bacterial clones from the digestive tracts of marine mammals, followed by Sneathia sanguinegens CCUG 41628T (92.7 %), 'Sneathia amnii' Sn35 (92.5 %), Caviibacter abscessus CCUG 39713T (92.2 %), Streptobacillus ratti OGS16T (91.3 %), Streptobacillus notomytis AHL 370-1T (91.2 %), S. moniliformis DSM 12112T (91.0 %), Streptobacillus felis 131000547T (90.9 %) and Streptobacillus hongkongensis DSM 26322T (89.7 %). Sequence similarities to all other taxa were below 89 %. Phylogenetic analysis for strain NCIMB 703044T revealed highly similar results for gyrB, groEL and recA nucleotide and deduced amino acid sequence analyses independent of the employed treeing method. Average nucleotide identities (ANI) for complete genomes ranged from 66.00 % to 72.08 % between strain NCIMB 703044T and the type strains of Sebaldella termitidis, Leptotrichiabuccalis, Streptobacillus moniliformis, Sneathia sanguinegens and Caviibacter abscessus. Chemotaxonomic and physiological data of strain NCIMB 703044t were in congruence with closely related members of the family Leptotrichiaceae, represented by highly similar enzyme profiles and fatty acid patterns. MALDI-TOF MS analysis was capable to clearly discriminate strain NCIMB 703044T from all currently described taxa of the family Leptotrichiaceae. On the basis of these data we propose the novel taxon Oceanivirga salmonicida gen. nov. sp. nov. with the type strain AVG 2115T (=NCIMB 703044T) (=DSM 101867T). The G+C content is 25.4 %, genome size is 1.77 Mbp.
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Affiliation(s)
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Christa Ewers
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | | | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Evelyn Collins
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
| | | | - Roy Palmer
- Maribio Consultants, Moycullen, Co. Galway, Ireland
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23
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Clinical Significance and Characterization of Streptococcus tigurinus Isolates in an Adult Population. J Clin Microbiol 2015; 53:3574-9. [PMID: 26354809 DOI: 10.1128/jcm.01551-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/30/2015] [Indexed: 11/20/2022] Open
Abstract
Streptococcus tigurinus is a newly described member of the Streptococcus mitis group. Due to the difficulty in distinguishing viridans group streptococci (VGS) by phenotype, analysis of 16S rRNA sequences is necessary for the accurate identification of most species. Through a laboratory policy of analyzing all clinically significant isolates from the VGS group by16S rRNA gene sequencing, we identified 14 S. tigurinus isolates from 11 patients. The Vitek 2 system most commonly gave an excellent rating to an incorrect identification (e.g., Streptococcus mitis), as did matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (e.g., Streptococcus oralis). S. tigurinus strains were recovered from numerous body sites, including the blood, peritoneal fluid, bone, synovial fluid, a perianal abscess, and an arm wound. Retrospective chart review indicated that most isolates were clinically significant, with bacteremia (n = 5), soft tissue infections (n = 3) osteomyelitis (n = 2), infected joint prosthesis (n = 2), and peritonitis (n = 2) being the most common, thus expanding the spectrum of disease associated with S. tigurinus.
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Martín-Gutiérrez G, Rodríguez N, Lepe JA, Parody R, Torres MJ, Aznar J. Rapid identification of a Leptotrichia trevisanii catheter-related bloodstream infection using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. JMM Case Rep 2015. [DOI: 10.1099/jmmcr.0.000036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guillermo Martín-Gutiérrez
- Infectious Diseases, Clinical Microbiology and Preventive Medicine Unit, Virgen del Rocío University Hospital, Seville, Spain
| | - Nancy Rodríguez
- Division of Clinical Hematology, Hospital Universitario Virgen del Rocío, Seville, Spain
| | - José Antonio Lepe
- Infectious Diseases, Clinical Microbiology and Preventive Medicine Unit, Virgen del Rocío University Hospital, Seville, Spain
| | - Rocío Parody
- Division of Clinical Hematology, Hospital Universitario Virgen del Rocío, Seville, Spain
| | - María José Torres
- Molecular Microbiology Division, Microbiology Department, University of Seville, Spain
| | - Javier Aznar
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Spain
- Molecular Microbiology Division, Microbiology Department, University of Seville, Spain
- Infectious Diseases, Clinical Microbiology and Preventive Medicine Unit, Virgen del Rocío University Hospital, Seville, Spain
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Devi U, Bora R, Das JK, Malik V, Mahanta J. Sneathia species in a case of neonatal meningitis from Northeast India. Oxf Med Case Reports 2014; 2014:112-4. [PMID: 25988049 PMCID: PMC4369986 DOI: 10.1093/omcr/omu044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/15/2014] [Accepted: 08/21/2014] [Indexed: 12/02/2022] Open
Abstract
Here we report the detection of Sneathia species most closely related to Sneathia sanguinegens, an infrequently reported bacterium, in the cerebrospinal fluid of a neonate by a culture independent method. Even though on rare occasions, this bacterium was isolated previously from the blood of neonatal bacteraemia cases. To the best of our knowledge there exists no previous report of detection of S. sanguinegens in the cerebrospinal fluid even though recently there has been a report of isolation of closely related species, Leptotrichia amnionii. The neonate recovered following antimicrobial therapy for 21 days. We conclude that uncultivable or difficult- to-cultivate bacteria like Sneathia could be an emerging pathogen for neonatal infection.
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Affiliation(s)
- Utpala Devi
- Regional Medical Research Centre , North East Region (ICMR) , Dibrugarh , India
| | - Reeta Bora
- Neonatology Unit , Assam Medical College & Hospital , Dibrugarh , India
| | - Jayanta Kumar Das
- Department of Microbiology , Assam Medical College & Hospital , Dibrugarh , India
| | - Vinita Malik
- Regional Medical Research Centre , North East Region (ICMR) , Dibrugarh , India
| | - Jagadish Mahanta
- Regional Medical Research Centre , North East Region (ICMR) , Dibrugarh , India
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Bacterial vaginosis-associated bacteria in men: association of Leptotrichia/Sneathia spp. with nongonococcal urethritis. Sex Transm Dis 2014; 40:944-9. [PMID: 24220356 DOI: 10.1097/olq.0000000000000054] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Approximately 45% of nongonococcal urethritis cases have no identified etiology. Novel bacteria recently associated with bacterial vaginosis (BV) in women may be involved. We evaluated the association of idiopathic nongonococcal urethritis and 5 newly described BV-associated bacteria (BVAB). METHODS Heterosexual men 16 years or older attending a sexually transmitted disease clinic in Seattle, Washington, from May 2007 to July 2011 and negative for Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Mycoplasma genitalium, and Ureaplasma urealyticum-biovar2 were eligible. Cases had urethral discharge or 5 or more polymorphonuclear leukocytes per high-power field in urethral exudates. Controls had no urethral discharge and less than 5 polymorphonuclear leukocytes per high-power field. Urine was tested for Atopobium spp., BVAB-2, BVAB-3, Megasphaera spp., and Leptotrichia/Sneathia spp. using quantitative taxon-directed polymerase chain reaction. RESULTS Cases (n = 157) and controls (n = 102) were of similar age, education, and income, and most were white. Leptotrichia/Sneathia spp. was significantly associated with urethritis (24/157 [15.3%] vs. 6/102 [5.9%], P = 0.03). BVAB-2 was more common in cases than in controls (7/157 [4.5%] vs. 1/102 [1.0%], P = 0.15), and BVAB-3 (n = 2) and Megasphaera spp. (n = 1) were only detected in men with urethritis, but these bacteria were found only in men who also had Leptotrichia/Sneathia spp. Atopobium spp. was not associated with urethritis. The quantity of bacteria did not differ between cases and controls. Among treated cases, doxycycline was more effective than azithromycin for clinical cure of men with Leptotrichia/Sneathia spp. (9/10 vs. 7/12, P = 0.16) and BVAB-2 (3/3 vs. 0/3, P = 0.10). CONCLUSIONS Leptotrichia/Sneathia spp. may be urethral pathogens or contribute to a pathogenic microbiota that can also include BVAB-2, BVAB-3, and Megasphaera spp. Doxycycline may be more effective than azithromycin against these newly identified bacteria.
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Two cases of bacteremia caused by Leptotrichia trevisanii in patients with febrile neutropenia. J Infect Chemother 2013; 19:1181-4. [PMID: 23584842 DOI: 10.1007/s10156-013-0596-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 03/26/2013] [Indexed: 10/27/2022]
Abstract
We present two cases of bacteremia caused by Leptotrichia trevisanii: a 12-year-old girl with recurrent myeloid leukemia of the mandible and a 66-year-old man with esophageal carcinoma. As this filamentous bacillus showed indefinite Gram staining and the identification based on biochemical enzymatic reactions was not definitive, identification required 16s rRNA analysis. For this organism, drug sensitivity testing showed susceptiblity to each β-lactam antibiotics and clindamycin, but resistance to fluoroquinolone and erythromycin. This filamentous bacillus needs careful identification and appropriate antibiotic treatment.
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Donahoo RS, Jones JB, Lacy GH, Stromberg VK, Norman DJ. Genetic analyses of Xanthomonas axonopodis pv. dieffenbachiae strains reveal distinct phylogenetic groups. PHYTOPATHOLOGY 2013; 103:237-244. [PMID: 23134337 DOI: 10.1094/phyto-08-12-0191-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A comprehensive analysis of 175 Xanthomonas axonopodis pv. dieffenbachiae strains isolated from 10 Araceae hosts was done to identify pathogen variation. The strains were subjected to repetitive extragenic palindromic sequence polymerase chain reaction and four major phylogenetic clusters were generated. A subset of 40 strains isolated from Anthurium, Dieffenbachia, and Syngonium was further defined by amplified fragment length polymorphism and fatty acid methyl ester analysis and the same four phylogenetic clusters were observed. Comparison of representative strains in the first three clusters using DNA-DNA hybridization and multilocus sequence analysis supports the previous reclassification of strains in cluster I, including the X. axonopodis pv. dieffenbachiae pathovar reference strain (LMG695), to X. citri. Our research findings indicate that strains in cluster I, isolated primarily from anthurium, probably represent an undescribed pathovar. Other phylogenetic subclusters consisting primarily of strains isolated from xanthosoma and philodendron in clusters III and IV, respectively, may yet represent other undescribed species or pathovars of Xanthomonas.
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Scher JU, Ubeda C, Equinda M, Khanin R, Buischi Y, Viale A, Lipuma L, Attur M, Pillinger MH, Weissmann G, Littman DR, Pamer EG, Bretz WA, Abramson SB. Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis. ACTA ACUST UNITED AC 2013; 64:3083-94. [PMID: 22576262 DOI: 10.1002/art.34539] [Citation(s) in RCA: 335] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To profile the abundance and diversity of subgingival oral microbiota in patients with never-treated, new-onset rheumatoid arthritis (RA). METHODS Periodontal disease (PD) status, clinical activity, and sociodemographic factors were determined in patients with new-onset RA, patients with chronic RA, and healthy subjects. Multiplexed-454 pyrosequencing was used to compare the composition of subgingival microbiota and establish correlations between the presence/abundance of bacteria and disease phenotypes. Anti-Porphyromonas gingivalis antibody testing was performed to assess prior exposure to the bacterial pathogen P gingivalis. RESULTS The more advanced forms of periodontitis were already present at disease onset in patients with new-onset RA. The subgingival microbiota observed in patients with new-onset RA was distinct from that found in healthy controls. In most cases, however, these microbial differences could be attributed to the severity of PD and were not inherent to RA. The presence and abundance of P gingivalis were also directly associated with the severity of PD and were not unique to RA. The presence of P gingivalis was not correlated with anti-citrullinated protein antibody (ACPA) titers. Overall exposure to P gingivalis was similar between patients with new-onset RA and controls, observed in 78% of patients and 83% of controls. The presence and abundance of Anaeroglobus geminatus correlated with the presence of ACPAs/rheumatoid factor. Prevotella and Leptotrichia species were the only characteristic taxa observed in patients with new-onset RA irrespective of PD status. CONCLUSION Patients with new-onset RA exhibited a high prevalence of PD at disease onset, despite their young age and paucity of smoking history. The subgingival microbiota profile in patients with new-onset RA was similar to that in patients with chronic RA and healthy subjects whose PD was of comparable severity. Although colonization with P gingivalis correlated with the severity of PD, overall exposure to P gingivalis was similar among the groups. The role of A geminatus and Prevotella/Leptotrichia species in this process merits further study.
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Affiliation(s)
- Jose U Scher
- Division of Rheumatology, New York University and New York University Hospital for Joint Diseases, New York, New York 10003, USA.
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Harwich MD, Serrano MG, Fettweis JM, Alves JMP, Reimers MA, Buck GA, Jefferson KK. Genomic sequence analysis and characterization of Sneathia amnii sp. nov. BMC Genomics 2012; 13 Suppl 8:S4. [PMID: 23281612 PMCID: PMC3535699 DOI: 10.1186/1471-2164-13-s8-s4] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteria of the genus Sneathia are emerging as potential pathogens of the female reproductive tract. Species of Sneathia, which were formerly grouped with Leptotrichia, can be part of the normal microbiota of the genitourinary tracts of men and women, but they are also associated with a variety of clinical conditions including bacterial vaginosis, preeclampsia, preterm labor, spontaneous abortion, post-partum bacteremia and other invasive infections. Sneathia species also exhibit a significant correlation with sexually transmitted diseases and cervical cancer. Because Sneathia species are fastidious and rarely cultured successfully in vitro; and the genomes of members of the genus had until now not been characterized, very little is known about the physiology or the virulence of these organisms. RESULTS Here, we describe a novel species, Sneathia amnii sp. nov, which closely resembles bacteria previously designated "Leptotrichia amnionii". As part of the Vaginal Human Microbiome Project at VCU, a vaginal isolate of S. amnii sp. nov. was identified, successfully cultured and bacteriologically cloned. The biochemical characteristics and virulence properties of the organism were examined in vitro, and the genome of the organism was sequenced, annotated and analyzed. The analysis revealed a reduced circular genome of ~1.34 Mbp, containing ~1,282 protein-coding genes. Metabolic reconstruction of the bacterium reflected its biochemical phenotype, and several genes potentially associated with pathogenicity were identified. CONCLUSIONS Bacteria with complex growth requirements frequently remain poorly characterized and, as a consequence, their roles in health and disease are unclear. Elucidation of the physiology and identification of genes putatively involved in the metabolism and virulence of S. amnii may lead to a better understanding of the role of this potential pathogen in bacterial vaginosis, preterm birth, and other issues associated with vaginal and reproductive health.
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Affiliation(s)
- Michael D Harwich
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, 1101 E. Marshall Street - PO Box 980678, Richmond, VA 23298-0678, USA
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Bouvet P, Grégory A, Bellon L, Marmouset C. [Fetal Leptotrichia goodfellowii bacteremia]. Med Mal Infect 2012; 42:174-5. [PMID: 22465058 DOI: 10.1016/j.medmal.2012.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/01/2012] [Accepted: 02/09/2012] [Indexed: 11/29/2022]
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Luo AH, Yang DQ, Xin BC, Paster BJ, Qin J. Microbial profiles in saliva from children with and without caries in mixed dentition. Oral Dis 2012; 18:595-601. [PMID: 22458262 DOI: 10.1111/j.1601-0825.2012.01915.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The purpose of this study was to determine the bacterial profiles in saliva of the isolated children for studying caries etiology. MATERIALS AND METHODS Samples were collected from isolated children from 6 to 8years old including 20 caries-free (dmfs=0) (healthy) and 30 caries-active individuals (dmfs>8) (patients). 16S rRNA genes were amplified by PCR from bacterial DNA of saliva sample and labeled via incorporation of Cy3-dCTP in second nested PCR. After hybridization of labeled amplicons on HOMIM, the microarray slides were scanned and original data acquired from professional software. RESULTS Collectively, 94 bacterial species or clusters representing six bacterial phyla and 30 genera were detected. A higher bacterial diversity was observed in patients than in healthy samples. Statistical analyses revealed eight species or clusters were detected more frequently in diseased patients than in healthy samples, while six different species were detected more frequently in healthy as compared to diseased patients. CONCLUSION The diversity of microbe within saliva derived from isolated population increased in caries-active status, and there are some bacteria in salivary flora can be as candidate biomarkers for caries prognosis in mixed dentition. The imbalances in the resident microflora may be the ultimate mechanism of dental caries.
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Affiliation(s)
- A H Luo
- The Affiliated Stomatological Hospital of Zunyi Medical College, Zunyi, Guizhou, PR China
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Thompson J, Pikis A. Metabolism of sugars by genetically diverse species of oral Leptotrichia. Mol Oral Microbiol 2011; 27:34-44. [PMID: 22230464 DOI: 10.1111/j.2041-1014.2011.00627.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Leptotrichia buccalis ATCC 14201 is a gram-negative, anaerobic rod-shaped bacterium resident in oral biofilm at the tooth surface. The sequenced genome of this organism reveals three contiguous genes at loci: Lebu_1525, Lebu_1526 and Lebu_1527. The translation products of these genes exhibit significant homology with phospho-α-glucosidase (Pagl), a regulatory protein (GntR) and a phosphoenol pyruvate-dependent sugar transport protein (EIICB), respectively. In non-oral bacterial species, these genes comprise the sim operon that facilitates sucrose isomer metabolism. Growth studies showed that L. buccalis fermented a wide variety of carbohydrates, including four of the five isomers of sucrose. Growth on the isomeric disaccharides elicited expression of a 50-kDa polypeptide comparable in size to that encoded by Lebu_1525. The latter gene was cloned, and the expressed protein was purified to homogeneity from Escherichia coli TOP10 cells. In the presence of two cofactors, NAD(+) and Mn(2+) ions, the enzyme readily hydrolyzed p-nitrophenyl-α-glucopyranoside 6-phosphate (pNPαG6P), a chromogenic analogue of the phosphorylated isomers of sucrose. By comparative sequence alignment, immunoreactivity and signature motifs, the enzyme can be assigned to the phospho-α-glucosidase (Pagl) clade of Family 4 of the glycosyl hydrolase super family. We suggest that the products of Lebu_1527 and Lebu_1525, catalyze the phosphorylative translocation and hydrolysis of sucrose isomers in L. buccalis, respectively. Four genetically diverse, but 16S rDNA-related, species of Leptotrichia have recently been described: L. goodfellowii, L. hofstadii, L. shahii and L. wadei. The phenotypic traits of these new species, with respect to carbohydrate utilization, have also been determined.
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Affiliation(s)
- J Thompson
- Microbial Biochemistry and Genetics Unit, Oral Infection and Immunity Branch, NIDCR, National Institutes of Health, Bethesda, MD 20892, USA.
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Abstract
Severe early childhood caries (ECC), while strongly associated with Streptococcus mutans using selective detection (culture, PCR), has also been associated with a widely diverse microbiota using molecular cloning approaches. The aim of this study was to evaluate the microbiota of severe ECC using anaerobic culture. The microbial composition of dental plaque from 42 severe ECC children was compared with that of 40 caries-free children. Bacterial samples were cultured anaerobically on blood and acid (pH 5) agars. Isolates were purified, and partial sequences for the 16S rRNA gene were obtained from 5,608 isolates. Sequence-based analysis of the 16S rRNA isolate libraries from blood and acid agars of severe ECC and caries-free children had >90% population coverage, with greater diversity occurring in the blood isolate library. Isolate sequences were compared with taxon sequences in the Human Oral Microbiome Database (HOMD), and 198 HOMD taxa were identified, including 45 previously uncultivated taxa, 29 extended HOMD taxa, and 45 potential novel groups. The major species associated with severe ECC included Streptococcus mutans, Scardovia wiggsiae, Veillonella parvula, Streptococcus cristatus, and Actinomyces gerensceriae. S. wiggsiae was significantly associated with severe ECC children in the presence and absence of S. mutans detection. We conclude that anaerobic culture detected as wide a diversity of species in ECC as that observed using cloning approaches. Culture coupled with 16S rRNA identification identified over 74 isolates for human oral taxa without previously cultivated representatives. The major caries-associated species were S. mutans and S. wiggsiae, the latter of which is a candidate as a newly recognized caries pathogen.
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Cooreman S, Schuermans C, Van Schaeren J, Olive N, Wauters G, Verhaegen J, Jeurissen A. Bacteraemia caused by Leptotrichia trevisanii in a neutropenic patient. Anaerobe 2010; 17:1-3. [PMID: 21184838 DOI: 10.1016/j.anaerobe.2010.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 12/07/2010] [Indexed: 11/25/2022]
Abstract
We describe an episode of Leptotrichia trevisanii bacteraemia in a neutropenic hemato-oncology patient receiving chemotherapy for Refractory Anemia with Excess Blasts-2 (RAEB-2). Although Leptotrichia spp. colonize the oral cavity and genitourinary tract, serious episodes of bacteraemia might occur in immunocompromised patients, particularly in those with severe neutropenia. Therefore, microbiologists should consider the possibility of Leptotrichia spp. septicemia in patients with blood cultures positive for gram negative bacilli, when routine microbiology tests fail to reveal a correct identification of the organism.
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Affiliation(s)
- S Cooreman
- Department of Microbiology, GZA Sint-Augustinus, Wilrijk, Belgium.
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Woo PCY, Wong SSY, Teng JLL, Leung KW, Ngan AHY, Zhao DQ, Tse H, Lau SKP, Yuen KY. Leptotrichia hongkongensis sp. nov., a novel Leptotrichia species with the oral cavity as its natural reservoir. J Zhejiang Univ Sci B 2010; 11:391-401. [PMID: 20506569 DOI: 10.1631/jzus.b1000056] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A straight, non-sporulating, Gram-variable bacillus (HKU24(T)) was recovered from the blood culture of a patient with metastatic breast carcinoma. After repeated subculturing in BACTEC Plus Anaerobic/F blood culture broth, HKU24(T) grew on brucella agar as non-hemolytic, pinpoint colonies after 96 h of incubation at 37 degrees C in an anaerobic environment and aerobic environment with 5% CO2. Growth was enhanced with a streak of Staphylococcus aureus. HKU24(T) was non-motile and catalase-negative, but positive for alkaline phosphatase, beta-glucosidase, and alpha-glucosidase. It hydrolyzed phenylphosphonate and reduced resazurin. 16S rRNA, groEL, gyrB, recA, and rpoB sequencing showed that HKU24(T) occupies a distinct phylogenetic position among the Leptotrichia species, being most closely related to Leptotrichia trevisanii. Using HKU24(T) groEL, gyrB, recA, and rpoB gene-specific primers, fragments of these genes were amplified from one of 20 oral specimens. Based on phenotypic and genotypic characteristics, we propose a new species, Leptotrichia hongkongensis sp. nov., to describe this bacterium.
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Affiliation(s)
- Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.
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Leuckfeld I, Paster BJ, Kristoffersen AK, Olsen I. Diversity of Veillonella spp. from subgingival plaque by polyphasic approach. APMIS 2010; 118:230-42. [PMID: 20132189 DOI: 10.1111/j.1600-0463.2009.02584.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In a biofilm such as the subgingival microflora, strain-specific properties or factors induced by the host may impart a survival advantage to some bacterial strains. Periodontal disease has been associated with chronic obstructive pulmonary disease (COPD) and we previously found high amounts of Veillonella in the subgingival microflora of COPD subjects. Differentiation of Veillonella is difficult. The aims of this study were to identify subgingival Veillonella isolates by phenotypic, genetic typing and molecular genetic methods, and further, to assess if Veillonella strain properties or identity correlated with periodontal disease or COPD. From 22 subjects, 26 subgingival Veillonella isolates and one pulmonary isolate were analysed. The majority of the subgingival Veillonella isolates were identified as Veillonella parvula. Genotyping showed heterogeneity within strains of the same species. A subgingival and pulmonary isolate in one COPD subject was found to be genetically identical strains of V. parvula. Scanning electron microscopy of the lung biopsy confirmed single small cocci adhering or coaggregating with larger cocci on the airway epithelium. Apart from a variation in cellular fatty acid composition of six subgingival isolates from periodontitis subjects, no correlation between the subgingival Veillonella strains or genotypes and the presence of either periodontitis or COPD was found. In conclusion, V. parvula was the predominant subgingival Veillonella species with high genetic variability within strains of the same species. Subgingival V. parvula can translocate to the lungs; however, Veillonella identity or genotype did not correlate with periodontal disease or COPD.
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Affiliation(s)
- Inga Leuckfeld
- Faculty of Dentistry, Institute of Oral Biology, University of Oslo, Oslo, Norway.
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Patel M, Chettiar TP, Wadee AA. Isolation of Staphylococcus aureus and black-pigmented bacteroides indicate a high risk for the development of Ludwig's angina. ACTA ACUST UNITED AC 2009; 108:667-72. [DOI: 10.1016/j.tripleo.2009.06.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 06/11/2009] [Accepted: 06/30/2009] [Indexed: 10/20/2022]
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Ivanova N, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Bruce D, Goodwin L, Brettin T, Detter JC, Han C, Pitluck S, Mikhailova N, Pati A, Mavrommatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde C, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b). Stand Genomic Sci 2009; 1:126-32. [PMID: 21304648 PMCID: PMC3035221 DOI: 10.4056/sigs.1854] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leptotrichia buccalis (Robin 1853) Trevisan 1879 is the type species of the genus, and is of phylogenetic interest because of its isolated location in the sparsely populated and neither taxonomically nor genomically adequately accessed family 'Leptotrichiaceae' within the phylum 'Fusobacteria'. Species of Leptotrichia are large, fusiform, non-motile, non-sporulating rods, which often populate the human oral flora. L. buccalis is anaerobic to aerotolerant, and saccharolytic. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the order 'Fusobacteriales' and no more than the second sequence from the phylum 'Fusobacteria'. The 2,465,610 bp long single replicon genome with its 2306 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Shah HN, Olsen I, Bernard K, Finegold SM, Gharbia S, Gupta RS. Approaches to the study of the systematics of anaerobic, gram-negative, non-sporeforming rods: current status and perspectives. Anaerobe 2009; 15:179-94. [PMID: 19695337 DOI: 10.1016/j.anaerobe.2009.08.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 08/11/2009] [Indexed: 11/29/2022]
Abstract
The present article gives an overview of recent taxonomic changes among the Gram-negative, anaerobic rods, briefly highlighting areas where the biology and ecology have a bearing on recent nomenclatorial changes. The focus is among the genera Bacteroides, Prevotella, Porphyromonas, Leptotrichia, Dysgonomonas, Fusobacterium and the Synergistes group and additionally demonstrates the value of conserved indels and group-specific proteins for identifying and circumscribing many of these taxa and the Bacteroidetes-Chlorobi species in general.
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Affiliation(s)
- Haroun N Shah
- Molecular Identification Services Unit, Department for Bioanalysis and Horizon Technologies, Centre for Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5EQ, UK
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García-Sánchez JE, José Fresnadillo M, García-Sánchez E. [New anaerobic bacterial species in human infections]. Enferm Infecc Microbiol Clin 2009; 28:173-84. [PMID: 19477040 DOI: 10.1016/j.eimc.2008.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 09/18/2008] [Accepted: 09/19/2008] [Indexed: 10/20/2022]
Abstract
This review offers succinct, precise, and complete information based on the available data concerning new anaerobic bacterial species involved in infectious diseases in humans. All hitherto undescribed species, those not previously implicated in clinical conditions, those with confirmed implication in human disease that have not been characterized, and those that have undergone taxonomic changes are considered to be "new".
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42
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Zahner V, Lucarotti CJ, McIntosh D. Application of 16S rDNA-DGGE and Plate Culture to Characterization of Bacterial Communities Associated with the Sawfly, Acantholyda erythrocephala (Hymenoptera, Pamphiliidae). Curr Microbiol 2008; 57:564-9. [PMID: 18769850 DOI: 10.1007/s00284-008-9243-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Revised: 08/01/2008] [Accepted: 08/05/2008] [Indexed: 11/29/2022]
Affiliation(s)
- Viviane Zahner
- Laboratory of Systematic Biochemistry, Instituto Oswaldo Cruz, FIOCRUZ, Manguinhos, Avenida Brasil 4365, Rio de Janeiro CEP 21045-900, Brazil.
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43
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Eribe ERK, Olsen I. Leptotrichia species in human infections. Anaerobe 2008; 14:131-7. [PMID: 18539056 DOI: 10.1016/j.anaerobe.2008.04.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 04/29/2008] [Indexed: 11/28/2022]
Abstract
Leptotrichia species typically colonize the oral cavity and genitourinary tract. These anaerobic bacteria belong to the normal flora of humans and are seldom found in clinically significant specimens. However, on rare occasions, Leptotrichia has been isolated from blood cultures of patients with lesions in the oral mucosa, in particular from patients with neutropenia. These organisms should be considered potential pathogens in neutropenic patients, especially when breaks in the mucosal barriers are present through which they frequently spread to the bloodstream. Leptotrichia has also been recovered from immunocompetent persons, e.g. patients with endocarditis. Although their role in infections remains elusive and not much is known, they have been suggested as emerging pathogens. The present review deals with taxonomy, diagnosis, clinical importance, pathogenesis, host defence, infection control, and spectrum of Leptotrichia infections, and ends with a few typical case reports. Currently, six species have been validly published, but a number of yet uncultivable species exist. Molecular methods recovering uncultivable species should be used to get a real idea of their role as pathogens.
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Leptotrichia endocarditis: Report of two cases from the International Collaboration on Endocarditis (ICE) database and review of previous cases. Eur J Clin Microbiol Infect Dis 2007; 27:139-43. [DOI: 10.1007/s10096-007-0406-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 09/29/2007] [Indexed: 10/22/2022]
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45
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Bhally HS, Lema C, Romagnoli M, Borek A, Wakefield T, Carroll KC. Leptotrichia buccalis bacteremia in two patients with acute myelogenous leukemia. Anaerobe 2007; 11:350-3. [PMID: 16701598 DOI: 10.1016/j.anaerobe.2005.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Revised: 03/30/2005] [Accepted: 04/01/2005] [Indexed: 10/25/2022]
Abstract
Leptotrichia buccalis is rarely implicated in systemic disease. We report two patients with clinically significant L. buccalis bacteremia which developed during the neutropenia secondary to chemotherapy. Based upon our experience, L. buccalis bacteremia should be considered in certain high-risk immunocompromised patients with mucositis and/or gingivitis.
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Affiliation(s)
- Hasan S Bhally
- Division of Medical Microbiology, The Johns Hopkins Medical Institutions, Meyer B1-193, 600 N. Wolfe St., Baltimore, MD 21287, USA
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Thilesen CM, Nicolaidis M, Lökebö JE, Falsen E, Jorde AT, Müller F. Leptotrichia amnionii, an emerging pathogen of the female urogenital tract. J Clin Microbiol 2007; 45:2344-7. [PMID: 17522272 PMCID: PMC1933011 DOI: 10.1128/jcm.00167-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leptotrichia amnionii, a recently described, very fastidious, gram-negative anaerobic bacterium, is an opportunistic pathogen of the female urogenital tract. We report a case of second-trimester abortion in a patient with chorioamnionitis and L. amnionii bacteremia and a case of renal abscess in a female 5 weeks postpartum.
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Affiliation(s)
- Carina M Thilesen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsö, Norway.
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47
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Finegold SM. Changes in taxonomy, anaerobes associated with humans, 2001-2004. Anaerobe 2006; 10:309-12. [PMID: 16701532 DOI: 10.1016/j.anaerobe.2004.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Accepted: 09/09/2004] [Indexed: 11/24/2022]
Affiliation(s)
- Sydney M Finegold
- Infectious Diseases Section (111 F), VA Medical Center West Los Angeles, 11301 Wilshire Boulevard, Los Angeles, CA 90073, USA.
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Jones JB, Lacy GH, Bouzar H, Stall RE, Schaad NW. Reclassification of the xanthomonads associated with bacterial spot disease of tomato and pepper. Syst Appl Microbiol 2005; 27:755-62. [PMID: 15612634 DOI: 10.1078/0723202042369884] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Four phenotypic xanthomonad groups have been identified that are pathogenic to pepper, tomato, or both hosts. These include groups A and C which are found in Xanthomonas axonopodis pv. vesicatoria, group B found in X. vesicatoria, and group D found in 'X. gardneri'. We present DNA:DNA hybridization data in which X. axonopodis pv. vesicatoria group A and C strains have less than 70% DNA relatedness with each other, with the type strain of X. axonopodis, and with the currently classified species within Xanthomonas and, therefore, should be removed from this species and given species status. We present information that the A strains most closely resemble the strains originally isolated by Doidge in 1921. In an attempt to avoid confusion in nomenclature as stated in Principle 1 of the Bacteriological Code, we propose that the A strains of X. axonopodis pv. vesicatoria be renamed as X. euvesicatoria (ATCC11633T= NCPPB2968T = ICMP 109T = ICMP 98T). Use of the euvesicatoria epithet should be reserved for strains originally identified by Doidge, which she designated Bacterium vesicatorium (Ann. Appl. Biol. 7: 407-430, 1921) in the original description when she referred to those strains as being feebly amylolytic. The name X. perforans sp. nov. is proposed for the C group of strains previously designated as X. axonopodis pv. vesicatoria (ATCC BAA-983T = NCPPB 4321T). We also propose that 'X. gardneri', which has less than 70% DNA relatedness with any of the Xanthomonas species and which has never had taxonomic status, be named X. gardneri (ATCC 19865T = NCPPB 881T) to reflect the specific epithet proposed by Sutic in 1957.
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Affiliation(s)
- Jeffrey B Jones
- University of Florida, Plant Pathology Department, Gainesville 32611, USA.
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