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Holger C Scholz - One of the best experts on this subject based on the ideXlab platform.
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application of whole genome sequencing and pan family multi locus sequence analysis to characterize relationships within the family brucellaceae
Frontiers in Microbiology, 2020Co-Authors: Roland Ashford, Mark S Koylass, Holger C Scholz, Jakub Muchowski, Adrian M WhatmoreAbstract:The bacterial family Brucellaceae is currently composed of seven genera, including species of the genus Brucella, a number of which are significant veterinary and zoonotic pathogens. The bacteriological identification of pathogenic Brucella spp. may be hindered by their close phenotypic similarity to other members of the Brucellaceae, particularly of the genus Ochrobactrum. Additionally, a number of novel atypical Brucella taxa have recently been identified, which exhibit greater genetic diversity than observed within the previously described species, and which share genomic features with organisms outside of the genus. Furthermore, previous work has indicated that the genus Ochrobactrum is polyphyletic, raising further questions regarding the relationship between the genus Brucella and wider Brucellaceae. We have applied whole genome sequencing (WGS) and pan-family multi-locus sequence analysis (MLSA) approaches to a comprehensive panel of Brucellaceae type strains, in order to characterize relationships within the family. Phylogenies based on WGS core genome alignments were able to resolve phylogenetic relationships of 31 non-Brucella spp. type strains from within the family, alongside type strains of twelve Brucella species. A phylogeny based on concatenated pan-family MLSA data was largely consistent with WGS based analyses. Notably, recently described atypical Brucella isolates were consistently placed in a single clade with existing species, clearly distinct from all members of the genus Ochrobactrum and wider family. Both WGS and MLSA methods closely grouped Brucella spp. with a sub-set of Ochrobactrum species. However, results also confirmed that the genus Ochrobactrum is polyphyletic, with seven species forming a separate grouping. The pan-family MLSA scheme was subsequently applied to a panel of 50 field strains of the family Brucellaceae, isolated from a wide variety of sources. This analysis confirmed the utility of the pan-Brucellaceae MLSA scheme in placing field isolates in relation to recognized type strains. However, a significant number of these isolates did not cluster with currently identified type strains, suggesting the existence of additional taxonomic diversity within some members of the Brucellaceae. The WGS and pan-family MLSA approaches applied here provide valuable tools for resolving the identity and phylogenetic relationships of isolates from an expanding bacterial family containing a number of important pathogens.
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genetic diversity and phylogenetic relationships of bacteria belonging to the Ochrobactrum brucella group by reca and 16s rrna gene based comparative sequence analysis
Systematic and Applied Microbiology, 2008Co-Authors: Holger C Scholz, Enevold Falsen, Peter Kampfer, Martin Pfeffer, Angela Witte, Heinrich Neubauer, Sascha Al Dahouk, Herbert Tomaso, Michael Schloter, Marion EngelAbstract:The genetic diversity and phylogenetic interrelationships among 106 Ochrobactrum strains (O. anthropi: 72, O. intermedium: 22, O. tritici: 5, O. oryzae: 2, O. grignonense: 2, O. gallinifaecis: 1, O. lupini: 2), the type strains of the eight Brucella species and other closely related taxa were studied by recA and rrs gene (16S rRNA) comparative sequence analysis. Both markers correctly delineated the various Ochrobactrum species; however, resolution at the subspecies level was considerably higher in the recA gene-based approach. Phylogenetic analyses using neighbor-joining, parsimony, and maximum likelihood algorithms generated trees with similar topologies but the overall branching order, and also the order of the subclades, were not stable in either assay, which could be explained by generally high recA and rrs sequence similarities. Ochrobactrum and PseudOchrobactrum formed separate clades distinct from other Alphaproteobacteria with Bartonella, Agrobacterium, and Rhizobium as the closest relatives. O. gallinifaecis was the most distinct member, when compared to the type species O. anthropi, with rrs and recA similarities of 96.2% and 81.4%. Brucella species were indistinguishable, exhibiting high rrs and recA gene similarities of 98.6% and 85.5% compared with Ochrobactrum intermedium. At the protein level, all RecA sequences among the various Ochrobactrum species and between Ochrobactrum and Brucella were highly similar with only a few amino acid substitutions. O. anthropi and O. tritici were indistinguishable by means of their RecA proteins. A set of initially biochemically classified strains did not cluster within their assigned species and they either grouped within other known species or grouped as potential novel Ochrobactrum species. In further investigations, these strains were reclassified and described as novel species. In summary, Ochrobactrum is a highly diverse genus comprising several novel species. We recommend recA- in addition to rrs gene-analysis for correct species allocation and subtyping of novel Ochrobactrum isolates.
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specific detection and differentiation of Ochrobactrum anthropi Ochrobactrum intermedium and brucella spp by a multi primer pcr that targets the reca gene
Journal of Medical Microbiology, 2008Co-Authors: Holger C Scholz, Martin Pfeffer, Angela Witte, Heinrich Neubauer, Sascha Al Dahouk, Ulrich Wernery, Herbert TomasoAbstract:Ochrobactrum anthropi, Ochrobactrum intermedium and Brucella spp. are phenotypically and genetically closely related pathogens that may cause disease with similar clinical presentation. Consequently, difficulties in their identification and differentiation have been reported. In this study, a sensitive recA gene-based multi-primer single-target PCR (MP-ST-PCR) was developed that allowed the specific detection and differentiation of these clinically relevant pathogens. The specificity of the assay was evaluated using a representative panel of 50 O. anthropi and 16 O. intermedium strains and the type strains of all Brucella spp. Detection limits for purified DNA from O. anthropi, O. intermedium and Brucella melitensis were 100, 10 and 100 fg, respectively. Brucella DNA was also successfully detected in various clinical specimens from a human patient with culture-proven brucellosis and from a Brucella-infected sheep and its aborted fetuses. The sensitivity of the MP-ST-PCR was comparable to that of an evaluated in-house Brucella real-time PCR assay. The developed assay closes a diagnostic gap and provides a simple but robust tool for the sensitive detection and correct identification of O. anthropi, O. intermedium and Brucella spp.
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brucellosis of the common vole microtus arvalis
Vector-borne and Zoonotic Diseases, 2007Co-Authors: Zdeněk Hubalek, Holger C Scholz, Ivo Sedlacek, Falk Melzer, Yibairii Sanogo, J NesvadbovaAbstract:A systemic disease occurred in a wild population of the common vole Microtus arvalis in South Moravia. From the clinical samples, small Gram-negative coccobacilli were isolated and identified as Ochrobactrum intermedium, on the other hand the sequencing analysis identified both isolates as Brucella sp. This study demonstrates the limitations of commercial biochemical test systems in accurately differentiating among Ochrobactrum and Brucella.
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brucellosis of the common vole microtus arvalis
Vector-borne and Zoonotic Diseases, 2007Co-Authors: Zdeněk Hubalek, Holger C Scholz, Ivo Sedlacek, Falk Melzer, Yibairii Sanogo, J NesvadbovaAbstract:A systemic disease occurred in a wild population of the common vole Microtus arvalis in South Moravia (Czech Republic) during the years 1999-2003. Acute infections were characterized by edema of extremities, occasionally with colliquating abscesses, arthritis, lymphadenitis, perforations of the skin resulting from colliquated abscesses, orchitis, and peritoneal granulomas. From the clinical samples, small Gram-negative coccobacilli were isolated and identified as Ochrobactrum intermedium by API 20NE and colistin sensitivity profiles. However, subsequent rrs (16S rRNA) and recA (recombinase A) gene sequencing analysis of two isolates (CCM 4915=CAPM 6434; CCM 4916=CAPM 6435) identified them as Brucella sp. with sequence identities of 100% to other Brucella spp. Analysis of the omp2a/b genes confirmed the two isolates as Brucella. In AMOS polymerase chain reaction (PCR), a 2000-bp fragment was generated that was not seen in other brucellae. Experimental infection of outbred ICR mice with these isolates resulted in a mortality rate of 50%. Based on the results of the molecular investigations and the mortality observed in experimentally infected mice we conclude that the epizootic was caused by Brucella sp. and not by Ochrobactrum intermedium. The study demonstrates the limitations of commercial biochemical test systems in accurately differentiating among Ochrobactrum and Brucella.
J Nesvadbova - One of the best experts on this subject based on the ideXlab platform.
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brucellosis of the common vole microtus arvalis
Vector-borne and Zoonotic Diseases, 2007Co-Authors: Zdeněk Hubalek, Holger C Scholz, Ivo Sedlacek, Falk Melzer, Yibairii Sanogo, J NesvadbovaAbstract:A systemic disease occurred in a wild population of the common vole Microtus arvalis in South Moravia. From the clinical samples, small Gram-negative coccobacilli were isolated and identified as Ochrobactrum intermedium, on the other hand the sequencing analysis identified both isolates as Brucella sp. This study demonstrates the limitations of commercial biochemical test systems in accurately differentiating among Ochrobactrum and Brucella.
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brucellosis of the common vole microtus arvalis
Vector-borne and Zoonotic Diseases, 2007Co-Authors: Zdeněk Hubalek, Holger C Scholz, Ivo Sedlacek, Falk Melzer, Yibairii Sanogo, J NesvadbovaAbstract:A systemic disease occurred in a wild population of the common vole Microtus arvalis in South Moravia (Czech Republic) during the years 1999-2003. Acute infections were characterized by edema of extremities, occasionally with colliquating abscesses, arthritis, lymphadenitis, perforations of the skin resulting from colliquated abscesses, orchitis, and peritoneal granulomas. From the clinical samples, small Gram-negative coccobacilli were isolated and identified as Ochrobactrum intermedium by API 20NE and colistin sensitivity profiles. However, subsequent rrs (16S rRNA) and recA (recombinase A) gene sequencing analysis of two isolates (CCM 4915=CAPM 6434; CCM 4916=CAPM 6435) identified them as Brucella sp. with sequence identities of 100% to other Brucella spp. Analysis of the omp2a/b genes confirmed the two isolates as Brucella. In AMOS polymerase chain reaction (PCR), a 2000-bp fragment was generated that was not seen in other brucellae. Experimental infection of outbred ICR mice with these isolates resulted in a mortality rate of 50%. Based on the results of the molecular investigations and the mortality observed in experimentally infected mice we conclude that the epizootic was caused by Brucella sp. and not by Ochrobactrum intermedium. The study demonstrates the limitations of commercial biochemical test systems in accurately differentiating among Ochrobactrum and Brucella.
Sivagnanam Silambarasan - One of the best experts on this subject based on the ideXlab platform.
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biodegradation of chlorpyrifos and its hydrolysis product 3 5 6 trichloro 2 pyridinol using a novel bacterium Ochrobactrum sp jas2 a proposal of its metabolic pathway
Pesticide Biochemistry and Physiology, 2016Co-Authors: Jayanthi Abraham, Sivagnanam SilambarasanAbstract:Abstract Biodegradation of chlorpyrifos and its major metabolite 3,5,6-trichloro-2-pyridinol (TCP) were studied with a novel bacterial strain JAS2 isolated from paddy rhizosphere soil. The molecular characterization based on 16S rRNA gene sequence homology confirmed its identity as Ochrobactrum sp. JAS2. The JAS2 strain degraded 300 mg l − 1 of chlorpyrifos within 12 h of incubation in the aqueous medium and it produced the TCP metabolite. However, after 72 h of incubation TCP was also completely degraded by the JAS2 strain. A tentative degradation pathway of chlorpyrifos by Ochrobactrum sp. JAS2 has been proposed on basis of GC–MS analysis. The complete degradation of chlorpyrifos occurred within 24 h in the soil spiked with and without addition of nutrients inoculated with Ochrobactrum sp. JAS2. TCP was obtained in both the studies which was degraded completely by 96 h in the soil spiked with nutrients and whereas 120 h in absence of nutrients in the soil. The mpd gene which is responsible for organophosphorus hydrolase production was identified. The isolates Ochrobactrum sp. JAS2 also exhibited a time dependent increase in the amount of tricalcium phosphate solubilization in Pikovskaya's medium. Further screening of the strain JAS2 for auxiliary plant growth promoting activities revealed its remarkable capability of producing the indole acetic acid (IAA), hydrogen cyanide (HCN) and ammonia.
Tao Sha - One of the best experts on this subject based on the ideXlab platform.
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isolation and characterization of a cr vi reduction Ochrobactrum sp strain cscr 3 from chromium landfill
Journal of Hazardous Materials, 2009Co-Authors: Fengling Gao, Tao ShaAbstract:A strain CSCr-3 with high Cr(VI)-reducing ability under alkaline conditions was isolated from a chromium landfill and identified as Ochrobactrum sp. on the basis of 16S rRNA gene sequence analysis. The cells were rod shaped, Gram-negative and motile. The physiological characteristics and Cr(VI)-reduction of the strain were also studied. The results showed that the Ochrobactrum sp. strain CSCr-3 was tolerant to very high concentration of Cr(VI) (800 mg/L) and capable of reducing different forms of Cr(VI) (chromate and dichromate), under a wide range of temperatures (25–40 °C) and pH (7–11) with optimum at 35 °C and initial pH 10. Higher rates of Cr(VI)-reduction were observed with higher initial cell and Cr(VI) concentrations. Strain CSCr-3 could reduce Cr(VI) very efficiently over a wide range of Cr(VI) concentrations (100–800 mg/L). The addition of glucose caused a dramatic increase in Cr(VI)-reduction by Ochrobactrum sp. CSCr-3, while the presence of sulfate or nitrate had no influence. The presence of other metals, such as Cu, Co, Mn, etc., significantly stimulated Cr(VI)-reduction ability by the strain CSCr-3. The results obtained in this study have significance for the bioremediation of chromate pollution.
Zdeněk Hubalek - One of the best experts on this subject based on the ideXlab platform.
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brucellosis of the common vole microtus arvalis
Vector-borne and Zoonotic Diseases, 2007Co-Authors: Zdeněk Hubalek, Holger C Scholz, Ivo Sedlacek, Falk Melzer, Yibairii Sanogo, J NesvadbovaAbstract:A systemic disease occurred in a wild population of the common vole Microtus arvalis in South Moravia. From the clinical samples, small Gram-negative coccobacilli were isolated and identified as Ochrobactrum intermedium, on the other hand the sequencing analysis identified both isolates as Brucella sp. This study demonstrates the limitations of commercial biochemical test systems in accurately differentiating among Ochrobactrum and Brucella.
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brucellosis of the common vole microtus arvalis
Vector-borne and Zoonotic Diseases, 2007Co-Authors: Zdeněk Hubalek, Holger C Scholz, Ivo Sedlacek, Falk Melzer, Yibairii Sanogo, J NesvadbovaAbstract:A systemic disease occurred in a wild population of the common vole Microtus arvalis in South Moravia (Czech Republic) during the years 1999-2003. Acute infections were characterized by edema of extremities, occasionally with colliquating abscesses, arthritis, lymphadenitis, perforations of the skin resulting from colliquated abscesses, orchitis, and peritoneal granulomas. From the clinical samples, small Gram-negative coccobacilli were isolated and identified as Ochrobactrum intermedium by API 20NE and colistin sensitivity profiles. However, subsequent rrs (16S rRNA) and recA (recombinase A) gene sequencing analysis of two isolates (CCM 4915=CAPM 6434; CCM 4916=CAPM 6435) identified them as Brucella sp. with sequence identities of 100% to other Brucella spp. Analysis of the omp2a/b genes confirmed the two isolates as Brucella. In AMOS polymerase chain reaction (PCR), a 2000-bp fragment was generated that was not seen in other brucellae. Experimental infection of outbred ICR mice with these isolates resulted in a mortality rate of 50%. Based on the results of the molecular investigations and the mortality observed in experimentally infected mice we conclude that the epizootic was caused by Brucella sp. and not by Ochrobactrum intermedium. The study demonstrates the limitations of commercial biochemical test systems in accurately differentiating among Ochrobactrum and Brucella.