Team » Konrad Sachse

@article{nokey_75,

title = {\textit{Trichosporon asahii}: A Potential Growth Promoter for \textit{C. gallinacea}? Implications for Chlamydial Infections and Cell Culture},

author = {Erika Ornelas-Eusebio and Fabien Vorimore and Rachid Aaziz and Maria-Lucia Mandola and Francesca Rizzo and Monica Marchino and Chiara Nogarol and Veronica Risco-Castillo and Gina Zanella and Christiane Schnee and Konrad Sachse and Karine Laroucau},

doi = {10.3390/microorganisms13020288},

year  = {2025},

date = {2025-01-27},

urldate = {2025-01-27},

journal = {Microorganisms},

volume = {13},

number = {2},

abstract = {The cultivation of Chlamydia gallinacea, a recently identified species, is challenging due to the lack of an optimized protocol. In this study, several infection protocols were tested, including different cell lines, incubation temperatures, centrifugation methods and culture media. However, none were successful in field samples. The only exception was a chance co-culture with Trichosporon asahii, a microorganism commonly found in the chicken gut. This suggests that current in vitro methods may not be optimized for this species and that host-associated microorganisms may influence the in vivo growth of C. gallinacea, which is typically found in the chicken gut. These findings raise new questions and highlight the need for further investigation of microbial interactions within the host, particularly to understand their role in the proliferation of chlamydial species.},

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}

@article{nokey_63,

title = {RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level},

author = {Kevin Lamkiewicz and Lisa-Marie Barf and Konrad Sachse and Martin Hölzer},

doi = {10.1186/s13059-024-03312-9},

year  = {2024},

date = {2024-07-01},

journal = {Genome Biology},

volume = {25},

issue = {1},

abstract = {Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when analyzing species with higher sequence diversity or higher taxonomic orders such as genera or families. The Roary ILP Bacterial core Annotation Pipeline (RIBAP) uses an integer linear programming approach to refine gene clusters predicted by Roary for identifying core genes. RIBAP successfully handles the complexity and diversity of Chlamydia, Klebsiella, Brucella, and Enterococcus genomes, outperforming other established and recent pangenome tools for identifying all-encompassing core genes at the genus level. RIBAP is a freely available Nextflow pipeline at github.com/hoelzer-lab/ribap and zenodo.org/doi/10.5281/zenodo.10890871.},

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pubstate = {published},

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}

@article{nokey_60,

title = {Detection of a novel genotype of \textit{Chlamydia buteonis} in falcons from the Emirates},

author = {F. Vorimore and R. Aaziz and L. {Al Qaysi} and U. Wernery and N. Borel and Konrad Sachse and K. Laroucau},

doi = {10.1016/j.vetmic.2024.110027},

year  = {2024},

date = {2024-02-16},

journal = {Veterinary Microbiology},

volume = {291},

pages = {110027},

abstract = {Chlamydiaceae are a family of obligate intracellular bacterial pathogens that affect both humans and animals. Recently, a new species named Chlamydia (C.) buteonis was isolated from hawks. In this study, we aimed to investigate the prevalence of Chlamydiaceae in 60 falcons that underwent a routine health check at a specialized clinic in Dubai, United Arab Emirates. Using real-time PCR, we analyzed cloacal and tracheal swabs from these birds and found that 39 of them tested positive for Chlamydiaceae. Subsequent real-time PCR assays specific for C. psittaci, C. abortus, C. avium, and C. gallinacea yielded negative results, while testing positive for C. buteonis. Analysis of ompA and MLST sequences indicated a highly conserved group of strains within this set of samples, but with sequences distinct from the C. buteonis RSHA reference strains and other C. buteonis strains isolated from hawks in the United States. Two strains were further isolated by cell culture and sequenced using whole-genome sequencing, confirming the clustering of these falcon strains within the C. buteonis species, but in a separate clade from the previously identified hawk strains. We also developed a SNP-based PCR-HRM assay to distinguish between these different genotypes. Overall, our findings suggest a high prevalence of C. buteonis in falcons in Dubai and highlight the importance of monitoring this pathogen in birds of prey.},

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@article{nokey_44,

title = {\textit{De novo} genome assembly resolving repetitive structures enables genomic analysis of 35 European \textit{Mycoplasmopsis bovis} strains},

author = {Sandra Triebel and Konrad Sachse and Michael Weber and Martin Heller and Celia Diezel and Martin Hölzer and Christiane Schnee and Manja Marz },

doi = {10.1186/s12864-023-09618-5},

isbn = {1471-2164},

year  = {2023},

date = {2023-09-16},

urldate = {2023-09-16},

journal = {BMC Genomics},

volume = {24},

number = {548},

issue = {1},

abstract = {Mycoplasmopsis (M.) bovis, the agent of mastitis, pneumonia, and arthritis in cattle, harbors a small genome of approximately 1 Mbp. Combining data from Illumina and Nanopore technologies, we sequenced and assembled the genomes of 35 European strains and isolate DL422_88 from Cuba. While the high proportion of repetitive structures in M. bovis genomes represent a particular challenge, implementation of our own pipeline Mycovista (available on GitHub www.github.com/sandraTriebel/mycovista ) in a hybrid approach enabled contiguous assembly of the genomes and, consequently, improved annotation rates considerably. To put our European strain panel in a global context, we analyzed the new genome sequences together with 175 genome assemblies from public databases. Construction of a phylogenetic tree based on core genes of these 219 strains revealed a clustering pattern according to geographical origin, with European isolates positioned on clades 4 and 5. Genomic data allowing assignment of strains to tissue specificity or certain disease manifestations could not be identified. Seven strains isolated from cattle with systemic circular condition (SCC), still a largely unknown manifestation of M. bovis disease, were located on both clades 4 and 5. Pairwise association analysis revealed 108 genomic elements associated with a particular clade of the phylogenetic tree. Further analyzing these hits, 25 genes are functionally annotated and could be linked to a M. bovis protein, e.g. various proteases and nucleases, as well as ten variable surface lipoproteins (Vsps) and other surface proteins. These clade-specific genes could serve as useful markers in epidemiological and clinical surveys.},

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pubstate = {published},

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@article{nokey_35,

title = {Genomic analysis of 61 \textit{Chlamydia psittaci} strains reveals extensive divergence associated with host preference},

author = {Konrad Sachse and Martin Hölzer and Fabien Vorimore and Lisa-Marie Barf and Carsten Sachse and Karine Laroucau and Manja Marz and Kevin Lamkiewicz },

doi = {10.1186/s12864-023-09370-w},

isbn = {1471-2164},

year  = {2023},

date = {2023-05-29},

urldate = {2023-05-29},

journal = {BMC Genomics},

volume = {24},

issue = {1},

pages = {288},

abstract = {Background

Chlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains, 47 of which carrying a 7.6-kbp plasmid.



Results

Following clean-up, reassembly and polishing of poorly assembled genomes from public databases, phylogenetic analyses using C. psittaci whole-genome sequence alignment revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Strains from different non-psittacine hosts clustered in Clades 2– 4. We found that clade membership correlates with typing schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin MOMP can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps).



Conclusions

Our study identified a number of genomic features that can be correlated with the phylogeny and host preference of C. psittaci strains. Our data show that intra-species genomic divergence is associated with past host change and includes deletions in the plasticity zone, structural variations in immunogenic domains and distinct repertoires of virulence factors.},

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pubstate = {published},

tppubtype = {article}

}

@article{Collatz:20,

title = {EpiDope: A Deep Neural Network for linear B-cell epitope prediction},

author = {Maximilian Collatz and Florian Mock and Emanuel Barth and Martin Hölzer and Konrad Sachse and Manja Marz},

editor = {Lenore Cowen},

url = {https://github.com/rnajena/EpiDope},

doi = {10.1093/bioinformatics/btaa773},

year  = {2020},

date = {2020-09-11},

urldate = {2020-09-11},

journal = {Bioinformatics},

volume = {37},

number = {4},

pages = {448–455},

publisher = {Oxford University Press (OUP)},

abstract = {By binding to specific structures on antigenic proteins, the so-called epitopes, B-cell antibodies can neutralize pathogens. The identification of B-cell epitopes is of great value for the development of specific serodiagnostic assays and the optimization of medical therapy. However, identifying diagnostically or therapeutically relevant epitopes is a challenging task that usually involves extensive laboratory work. In this study, we show that the time, cost and labor-intensive process of epitope detection in the lab can be significantly reduced using in silico prediction.

Here, we present EpiDope, a python tool which uses a deep neural network to detect linear B-cell epitope regions on individual protein sequences. With an area under the curve between 0.67 ± 0.07 in the receiver operating characteristic curve, EpiDope exceeds all other currently used linear B-cell epitope prediction tools. Our software is shown to reliably predict linear B-cell epitopes of a given protein sequence, thus contributing to a significant reduction of laboratory experiments and costs required for the conventional approach.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hölzer:20,

title = {Comparative Genome Analysis of 33 \textit{Chlamydia} Strains Reveals Characteristic Features of \textit{Chlamydia Psittaci} and Closely Related Species},

author = {Martin Hölzer and Lisa-Marie Barf and Kevin Lamkiewicz and Fabien Vorimore and Marie Lataretu and Alison Favaroni and Christiane Schnee and Karine Laroucau and Manja Marz and Konrad Sachse},

url = {github.com/hoelzer-lab/ribap},

doi = {10.3390/pathogens9110899},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Pathogens},

volume = {9},

number = {11},

pages = {899},

publisher = {MDPI AG},

abstract = {To identify genome-based features characteristic of the avian and human pathogen Chlamydia (C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.},

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pubstate = {published},

tppubtype = {article}

}

@article{Liebler-Tenorio:20,

title = {Regeneration of Pulmonary Tissue in a Calf Model of Fibrinonecrotic Bronchopneumonia Induced by Experimental Infection with Chlamydia psittaci},

author = {Elisabeth M. Liebler-Tenorio and Jacqueline Lambertz and Carola Ostermann and Konrad Sachse and Petra Reinhold},

doi = {10.3390/ijms21082817},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Int J Mol Sci},

volume = {21},

number = {8},

pages = {2817},

publisher = {MDPI AG},

abstract = {Pneumonia is a cause of high morbidity and mortality in humans. Animal models are indispensable to investigate the complex cellular interactions during lung injury and repair in vivo. The time sequence of lesion development and regeneration is described after endobronchial inoculation of calves with Chlamydia psittaci. Calves were necropsied 2–37 days after inoculation (dpi). Lesions and presence of Chlamydia psittaci were investigated using histology and immunohistochemistry. Calves developed bronchopneumonia at the sites of inoculation. Initially, Chlamydia psittaci replicated in type 1 alveolar epithelial cells followed by an influx of neutrophils, vascular leakage, fibrinous exudation, thrombosis and lobular pulmonary necrosis. Lesions were most extensive at 4 dpi. Beginning at 7 dpi, the number of chlamydial inclusions declined and proliferation of cuboidal alveolar epithelial cells and sprouting of capillaries were seen at the periphery of necrotic tissue. At 14 dpi, most of the necrosis had been replaced with alveoli lined with cuboidal epithelial cells resembling type 2 alveolar epithelial cells and mild fibrosis, and hyperplasia of organized lymphoid tissue were observed. At 37 dpi, regeneration of pulmonary tissue was nearly complete and only small foci of remodeling remained. The well-defined time course of development and regeneration of necrotizing pneumonia allows correlation of morphological findings with clinical data or treatment regimen.

},

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tppubtype = {article}

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@article{Hoelzer:16a,

title = {Whole-Genome Sequence of \textit{Chlamydia gallinacea} Type Strain 08-1274/3},

author = {Martin Hölzer and Karine Laroucau and Heather Huot Creasy and Sandra Ott and Fabien Vorimore and Patrik M. Bavoil and Manja Marz and Konrad Sachse},

doi = {10.1128/genomeA.00708-16},

year  = {2016},

date = {2016-07-21},

urldate = {2016-07-21},

journal = {Genome Announc},

volume = {4},

number = {4},

abstract = {The recently introduced bacterial species Chlamydia gallinacea is known to occur in domestic poultry and other birds. Its potential as an avian pathogen and zoonotic agent is under investigation. The whole-genome sequence of its type strain, 08-1274/3, consists of a 1,059,583-bp chromosome with 914 protein-coding sequences (CDSs) and a plasmid (p1274) comprising 7,619 bp with 9 CDSs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sachse:14,

title = {Evidence for the existence of two new members of the family Chlamydiaceae and proposal of \textit{Chlamydia avium} sp. nov. and \textit{Chlamydia gallinacea} sp. nov.},

author = {Konrad Sachse and Karine Laroucau and Konstantin Riege and Stefanie Wehner and Meik Dilcher and Heather Huot Creasy and Manfred Weidmann and Garry Myers and Fabien Vorimore and Nadia Vicari and Simone Magnino and Elisabeth Liebler-Tenorio and Anke Ruettger and Patrik M. Bavoil and Frank T. Hufert and Ramon Rosselló-Móra and Manja Marz},

doi = {10.1016/j.syapm.2013.12.004},

year  = {2014},

date = {2014-01-22},

urldate = {2014-01-22},

journal = {Syst Appl Microbiol},

volume = {37},

pages = {79--88},

abstract = {The family Chlamydiaceae with the recombined single genus Chlamydia currently comprises nine species, all of which are obligate intracellular organisms distinguished by a unique biphasic developmental cycle. Anecdotal evidence from epidemiological surveys in flocks of poultry, pigeons and psittacine birds have indicated the presence of non-classified chlamydial strains, some of which may act as pathogens. In the present study, phylogenetic analysis of ribosomal RNA and ompA genes, as well as multi-locus sequence analysis of 11 field isolates were conducted. All independent analyses assigned the strains into two different clades of monophyletic origin corresponding to pigeon and psittacine strains or poultry isolates, respectively. Comparative genome analysis involving the type strains of currently accepted Chlamydiaceae species and the designated type strains representing the two new clades confirmed that the latter could be classified into two different species as their average nucleotide identity (ANI) values were always below 94%, both with the closest relative species and between themselves. In view of the evidence obtained from the analyses, we propose the addition of two new species to the current classification: Chlamydia avium sp. nov. comprising strains from pigeons and psittacine birds (type strain 10DC88(T); DSMZ: DSM27005(T), CSUR: P3508(T)) and Chlamydia gallinacea sp. nov. comprising strains from poultry (type strain 08-1274/3(T); DSMZ: DSM27451(T), CSUR: P3509(T)).},

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}