Publications by authors named "Torsten Semmler"

107 Publications

First report of NDM-1 in an Acinetobacter baumannii strain from a pet animal in Europe.

J Glob Antimicrob Resist 2021 May 24. Epub 2021 May 24.

Institute of Hygiene and Infectious Diseases of Animals (IHIT), Giessen, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jgar.2021.05.003DOI Listing
May 2021

A global metagenomic map of urban microbiomes and antimicrobial resistance.

Cell 2021 May 22. Epub 2021 May 22.

Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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http://dx.doi.org/10.1016/j.cell.2021.05.002DOI Listing
May 2021

Genome-wide insights into population structure and host specificity of Campylobacter jejuni.

Sci Rep 2021 May 14;11(1):10358. Epub 2021 May 14.

Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany.

The zoonotic pathogen Campylobacter jejuni is among the leading causes of foodborne diseases worldwide. While C. jejuni colonises many wild animals and livestock, persistence mechanisms enabling the bacterium to adapt to host species' guts are not fully understood. In order to identify putative determinants influencing host preferences of distinct lineages, bootstrapping based on stratified random sampling combined with a k-mer-based genome-wide association was conducted on 490 genomes from diverse origins in Germany and Canada. We show a strong association of both the core and the accessory genome characteristics with distinct host animal species, indicating multiple adaptive trajectories defining the evolution of C. jejuni lifestyle preferences in different ecosystems. Here, we demonstrate that adaptation towards a specific host niche ecology is most likely a long evolutionary and multifactorial process, expressed by gene absence or presence and allele variations of core genes. Several host-specific allelic variants from different phylogenetic backgrounds, including dnaE, rpoB, ftsX or pycB play important roles for genome maintenance and metabolic pathways. Thus, variants of genes important for C. jejuni to cope with specific ecological niches or hosts may be useful markers for both surveillance and future pathogen intervention strategies.
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http://dx.doi.org/10.1038/s41598-021-89683-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8121833PMC
May 2021

Frequency, Local Dynamics, and Genomic Characteristics of ESBL-Producing Isolated From Specimens of Hospitalized Horses.

Front Microbiol 2021 16;12:671676. Epub 2021 Apr 16.

Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany.

Previous research identified veterinary clinics as hotspots with respect to accumulation and spread of multidrug resistant extended-spectrum β-lactamase (ESBL)-producing (EC). Therefore, promoting the prudent use of antibiotics to decrease selective pressure in that particular clinical environment is preferable to enhance biosecurity for animal patients and hospital staff. Accordingly, this study comparatively investigated the impact of two distinct perioperative antibiotic prophylaxis (PAP) regimens (short-term versus prolonged) on ESBL-EC carriage of horses subjected to colic surgery. While all horses received a combination of penicillin/gentamicin (P/G) as PAP, they were assigned to either the "single-shot group" (SSG) or the conventional "5-day group" (5DG). Fecal samples collected on arrival (t), on the 3rd (t) and on the 10th day after surgery (t) were screened for ESBL-EC. All isolates were further investigated using whole genome sequences. In total, 81 of 98 horses met the inclusion criteria for this study. ESBL-EC identified in samples available at t, t and t were 4.8% (SSG) and 9.7% (5DG), 37% (SSG) and 47.2% (5DG) as well as 55.6% (SSG) and 56.8% (5DG), respectively. Regardless of the P/G PAP regimen, horses were 9.12 times (95% CI 2.79-29.7) more likely to carry ESBL-EC at t compared to t ( < 0.001) and 15.64 times (95% CI 4.57-53.55) more likely to carry ESBL-EC at t compared to t ( < 0.001). ESBL-EC belonging to sequence type (ST) 10, ST86, ST641, and ST410 were the most prevalent lineages, with (60%) being the dominant ESBL gene. A close spatio-temporal relationship between isolates sharing a particular ST was revealed by genome analysis, strongly indicating local spread. Consequently, hospitalization itself has a strong impact on ESBL-EC isolation rates in horses, possibly masking differences between distinct PAP regimens. The results of this study reveal accumulation and spread of multi-drug resistant ESBL-EC among horses subjected to colic surgery with different P/G PAP regimens, challenging the local hygiene management system and work-place safety of veterinary staff. Moreover, the predominance of particular ESBL-EC lineages in clinics providing health care for horses needs further investigation.
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http://dx.doi.org/10.3389/fmicb.2021.671676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085565PMC
April 2021

Whole-Genome Sequence of the () DSM 25591 Type Strain.

Microbiol Resour Announc 2021 Apr 22;10(16). Epub 2021 Apr 22.

Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany

The whole-genome sequence of the type strain () DSM 25591 is reported and compared to the available sequences of the corresponding type strains from other strain collections to ascertain conformity. Knowledge of the identity of type strains is of importance for their application in standardized test systems.
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http://dx.doi.org/10.1128/MRA.00164-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8063644PMC
April 2021

Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Strains From Healthy Food Animals Across Europe.

Front Microbiol 2021 1;12:626774. Epub 2021 Apr 1.

NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany.

The role of livestock animals as a putative source of ESBL/pAmpC for humans is a central issue of research. In a large-scale pan-European surveillance, 2,993 commensal spp. isolates were recovered from randomly collected fecal samples of healthy cattle, pigs and chickens in various abattoirs. One-hundred spp. isolates (0.5% from cattle, 1.3% pigs, 8.0% chickens) fulfilled the criteria for cefotaxime and ceftazidime non-wildtype (EUCAST). screening of WGS data of 99 isolates (98 and 1 ) revealed (32.3%), (24.2%), and (22.2%) as predominant ESBL/pAmpC types. Other types were (1.0%), (1.0/6.1/1.0%), and (5.1%). Six isolates revealed AmpC-promoter mutations (position -42 (C > T) and one carried . The majority (91.3%) of ESBL/pAmpC genes were located on plasmids. SHV-12 was mainly (50%) encoded on IncI1α plasmids (pST-3/-26/-95), followed by IncX3 (12.5%) and IncK2 (3.1%). The genes were located on IncI1α-pST-36 (60%) and IncX1 plasmids (20%). The dominant plasmid lineage among CTX-M-1 isolates was IncI1α (pST-3/-295/-317) (87.5%), followed by IncN-pST-1 (8.3%). CMY-2 was mostly identified on IncI1α (pST-12/-2) (54.5%) and IncK2 (31.8%) plasmids. Several plasmids revealed high similarity to published plasmids from human and animal Enterobacteriaceae. The isolates were assigned to phylogroups A/C (34.7/7.1%), B1 (27.6%), B2 (3.1%), D/F (9.2/10.2%), E (5.1%), and to . clades (3.0%). With 51 known and 2 novel MLST types, a wide variety of STs was found, including STs previously observed in human isolates (ST10/38/117/131/648). ESBL/AmpC types or STs were rarely correlated with the geographic origin of the isolates or animal species. Virulence gene typing identified extraintestinal pathogenic (ExPEC; 2.0%), avian pathogenic (APEC; 51.5%), and atypical enteropathogenic (EPEC; 6.1%). In conclusion, the high diversity of STs and phylogenetic groups provides hardly any hint for clonal spread of single lineages but hints toward the dissemination of cephalosporin resistance genes in livestock via distinct, globally successful plasmid lineages. Even though a number of isolates could not be assigned to a distinct pathotype, our finding of combined multidrug-resistance and virulence in this facultative pathogen should be considered an additional threat to public health.
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http://dx.doi.org/10.3389/fmicb.2021.626774DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8047082PMC
April 2021

Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase () Island.

mBio 2021 03 2;12(1). Epub 2021 Mar 2.

Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India

The genotoxin colibactin is a secondary metabolite produced by the polyketide synthase () island harbored by extraintestinal pathogenic (ExPEC) and other members of the that has been increasingly reported to have critical implications in human health. The present study entails a high-throughput whole-genome comparison and phylogenetic analysis of such pathogenic isolates to gain insights into the patterns of distribution, horizontal transmission, and evolution of the island. For the current study, 23 -positive ExPEC genomes were newly sequenced, and their virulome and resistome profiles indicated a preponderance of virulence encoding genes and a reduced number of genes for antimicrobial resistance. In addition, 4,090 genomes from the public domain were also analyzed for large-scale screening for -positive genomes, out of which a total of 530 positive genomes were studied to understand the subtype-based distribution pattern(s). The island showed a significant association with the B2 phylogroup (82.2%) and a high prevalence in sequence type 73 (ST73;  = 179) and ST95 ( = 110) and the O6:H1 ( = 110) serotype. Maximum-likelihood (ML) phylogeny of the core genome and intergenic regions (IGRs) of the ST95 model data set, which was selected because it had both -positive and -negative genomes, displayed clustering in relation to their carriage of the island. Prevalence patterns of genes encoding RM systems in the -positive and negative genomes were also analyzed to determine their potential role in island acquisition and the maintenance capability of the genomes. Further, the maximum-likelihood phylogeny based on the core genome and island sequences from 247 genomes with an intact island demonstrated horizontal gene transfer of the island across sequence types and serotypes, with few exceptions. This study vitally contributes to understanding of the lineages and subtypes that have a higher propensity to harbor the island-encoded genotoxin with possible clinical implications. Extraintestinal pathologies caused by highly virulent strains of amount to clinical implications with high morbidity and mortality rates. Pathogenic strains are evolving with the horizontal acquisition of mobile genetic elements, including pathogenicity islands such as the island, which produces the genotoxin colibactin, resulting in severe clinical outcomes, including colorectal cancer progression. The current study encompasses high-throughput comparative genomics and phylogenetic analyses to address the questions pertaining to the acquisition and evolution pattern of the genomic island in different subtypes. It is crucial to gain insights into the distribution, transfer, and maintenance of pathogenic islands, as they harbor multiple virulence genes involved in pathogenesis and clinical implications of the infection.
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http://dx.doi.org/10.1128/mBio.03634-20DOI Listing
March 2021

Population Biology and Comparative Genomics of Campylobacter Species.

Curr Top Microbiol Immunol 2021 ;431:59-78

Microbial Genomics, Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany.

The zoonotic pathogen Campylobacter is the leading cause for bacterial foodborne infections in humans. Campylobacters are most commonly transmitted via the consumption of undercooked poultry meat or raw milk products. The decreasing costs of whole genome sequencing enabled large genome-based analyses of the evolution and population structure of this pathogen, as well as the development of novel high-throughput molecular typing methods. Here, we review the evolutionary development and the population diversity of the two most clinically relevant Campylobacter species; C. jejuni and C. coli. The state-of-the-art phylogenetic studies showed clustering of C. jejuni lineages into host specialists and generalists with coexisting lifestyles in chicken and livestock-associated hosts, as well as the separation of C. coli isolates of riparian origin (waterfowl, water) from C. coli isolated from clinical and farm-related samples. We will give an overview of recombination between both species and the potential impact of horizontal gene transfer on host adaptation in Campylobacter. Additionally, this review briefly places the current knowledge of the population structure of other Campylobacter species such as C. lari, C. concisus and C. upsaliensis into perspective. We also provide an overview of how molecular typing methods such as multilocus sequence typing (MLST) and whole genome MLST have been used to detect and trace Campylobacter outbreaks along the food chain.
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http://dx.doi.org/10.1007/978-3-030-65481-8_3DOI Listing
February 2021

High-Zinc Supplementation of Weaned Piglets Affects Frequencies of Virulence and Bacteriocin Associated Genes Among Intestinal Populations.

Front Vet Sci 2020 16;7:614513. Epub 2020 Dec 16.

Robert Koch Institute, Berlin, Germany.

To prevent economic losses due to post-weaning diarrhea (PWD) in industrial pig production, zinc (Zn) feed additives have been widely used, especially since awareness has risen that the regular application of antibiotics promotes buildup of antimicrobial resistance in both commensal and pathogenic bacteria. In a previous study on 179 collected from piglets sacrificed at the end of a Zn feeding trial, including isolates obtained from animals of a high-zinc fed group (HZG) and a corresponding control group (CG), we found that the isolate collection exhibited three different levels of tolerance toward zinc, i.e., the minimal inhibitory concentration (MIC) detected was 128, followed by 256 and 512 μg/ml ZnCl We further provided evidence that enhanced zinc tolerance in porcine intestinal populations is clearly linked to excessive zinc feeding. Here we provide insights about the genomic make-up and phylogenetic background of these 179 genomes. Bayesian analysis of the population structure (BAPS) revealed a lack of association between the actual zinc tolerance level and a particular phylogenetic cluster or even branch for both, isolates belonging to the HZG and CG. In addition, detection rates for genes and operons associated with virulence (VAG) and bacteriocins (BAG) were lower in isolates originating from the HZG (41 vs. 65% and 22 vs. 35%, < 0.001 and = 0.002, resp.). Strikingly, harboring genes defining distinct pathotypes associated with intestinal disease, i.e., enterotoxigenic, enteropathogenic, and Shiga toxin-producing (ETEC, EPEC, and STEC) constituted 1% of the isolates belonging to the HZG but 14% of those from the CG. Notably, these pathotypes were positively associated with enhanced zinc tolerance (512 μg/ml ZnCl MIC, < 0.001). Taken together, zinc excess seems to influence carriage rates of VAGs and BAGs in porcine intestinal populations, and high-zinc feeding is negatively correlated with enteral pathotype occurrences, which might explain earlier observations concerning the relative increase of considering the overall intestinal microbiota of piglets during zinc feeding trials while PWD rates have decreased.
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http://dx.doi.org/10.3389/fvets.2020.614513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7772137PMC
December 2020

sp. nov., isolated from the respiratory tract of diseased Chacoan peccaries ().

Int J Syst Evol Microbiol 2020 Nov 17;70(11):5734-5739. Epub 2020 Sep 17.

Hessian State Laboratory, Giessen, Germany.

Novel catalase-negative, Gram-stain-positive, beta-haemolytic, coccus-shaped organisms were isolated from Chacoan peccaries that died from respiratory disease. The initial API 20 Strep profiles suggested with acceptable identification scores, but the 16S rRNA gene similarity (1548 bp) to available sequences of streptococci was below 98 %. Next taxa of the genus , displaying highest similarities to the strains from this study, were NZ1587 (97.5 %), ATCC 29178 (97.5 %), HKU30 (97.4 %), DSM 6631 (97.1 %), CAIM 1838 (97.1 %), DSM 18513 (97.0 %), DSM 15616 (96.6 %), 707-05 (96.6 %), JCM 5709 (96.5 %) and NCTC 10999 (96.4 %). All other species had sequence similarities of below 96.4 %. A gene as well as whole genome-based core genome phylogeny of three representative strains and 145 available genomes confirmed the unique taxonomic position. Interstrain average nucleotide identity (ANI) and amino acid identity (AAI) values were high (ANI >96 %; AAI 100%), but for other streptococci clearly below the proposed species boundary of 95-96 % (ANI <75 %; AAI <83 %). Results were confirmed by genome-to-genome distance calculations. Pairwise digital DNA-DNA hybridization estimates were high (>90 %) between the novel strains, but well below the species boundary of 70 % for closely related type strains (23.5-19.7 %). Phenotypic properties as obtained from extended biochemical profiles and MALDI-TOF mass spectrometry supported the outstanding rank. Based on the presented molecular and physiological data of the six strains, we propose a novel taxon for which we suggest the name sp. nov. with the type strain 99-1/2017 (=DSM 110457=CCUG 74072) and five reference strains.
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http://dx.doi.org/10.1099/ijsem.0.004471DOI Listing
November 2020

Silence as a way of niche adaptation: mecC-MRSA with variations in the accessory gene regulator (agr) functionality express kaleidoscopic phenotypes.

Sci Rep 2020 09 8;10(1):14787. Epub 2020 Sep 8.

Advanced Light and Electron Microscopy (ZBS4), Robert Koch Institute, Berlin, Germany.

Functionality of the accessory gene regulator (agr) quorum sensing system is an important factor promoting either acute or chronic infections by the notorious opportunistic human and veterinary pathogen Staphylococcus aureus. Spontaneous alterations of the agr system are known to frequently occur in human healthcare-associated S. aureus lineages. However, data on agr integrity and function are sparse regarding other major clonal lineages. Here we report on the agr system functionality and activity level in mecC-carrying methicillin resistant S. aureus (MRSA) of various animal origins (n = 33) obtained in Europe as well as in closely related human isolates (n = 12). Whole genome analysis assigned all isolates to four clonal complexes (CC) with distinct agr types (CC599 agr I, CC49 agr II, CC130 agr III and CC1943 agr IV). Agr functionality was assessed by a combination of phenotypic assays and proteome analysis. In each CC, isolates with varying agr activity levels were detected, including the presence of completely non-functional variants. Genomic comparison of the agr I-IV encoding regions associated these phenotypic differences with variations in the agrA and agrC genes. The genomic changes were detected independently in divergent lineages, suggesting that agr variation might foster viability and adaptation of emerging MRSA lineages to distinct ecological niches.
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http://dx.doi.org/10.1038/s41598-020-71640-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7479134PMC
September 2020

SCORE: Smart Consensus Of RNA Expression-a consensus tool for detecting differentially expressed genes in bacteria.

Bioinformatics 2021 04;37(3):426-428

Microbial Genomics, Robert Koch Institute, Berlin 13353, Germany.

Summary: RNA-sequencing (RNA-Seq) is the current method of choice for studying bacterial transcriptomes. To date, many computational pipelines have been developed to predict differentially expressed genes from RNA-Seq data, but no gold-standard has been widely accepted. We present the Snakemake-based tool Smart Consensus Of RNA Expression (SCORE) which uses a consensus approach founded on a selection of well-established tools for differential gene expression analysis. This allows SCORE to increase the overall prediction accuracy and to merge varying results into a single, human-readable output. SCORE performs all steps for the analysis of bacterial RNA-Seq data, from read preprocessing to the overrepresentation analysis of significantly associated ontologies. Development of consensus approaches like SCORE will help to streamline future RNA-Seq workflows and will fundamentally contribute to the creation of new gold-standards for the analysis of these types of data.

Availability And Implementation: https://github.com/SiWolf/SCORE.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btaa681DOI Listing
April 2021

Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital.

PLoS One 2020 24;15(6):e0235160. Epub 2020 Jun 24.

Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany.

Vancomycin-resistant E. faecium (VRE) are an important cause of nosocomial infections, which are rapidly transmitted in hospitals. To identify possible transmission routes, we applied combined genomics and contact-network modeling to retrospectively evaluate routine VRE screening data generated by the infection control program of a hemato-oncology unit. Over 1 year, a total of 111 VRE isolates from 111 patients were collected by anal swabs in a tertiary care hospital in Southern Germany. All isolated VRE were whole-genome sequenced, followed by different in-depth bioinformatics analyses including genotyping and determination of phylogenetic relations, aiming to evaluate a standardized workflow. Patient movement data were used to overlay sequencing data to infer transmission events and strain dynamics over time. A predominant clone harboring vanB and exhibiting genotype ST117/CT469 (n = 67) was identified. Our comprehensive combined analyses suggested intra-hospital spread, especially of clone ST117/CT469, despite of extensive screening, single room placement, and contact isolation. A new interactive tool to visualize these complex data was designed. Furthermore, a patient-contact network-modeling approach was developed, which indicates both the periodic import of the clone into the hospital and its spread within the hospital due to patient movements. The analyzed spread of VRE was most likely due to placement of patients in the same room prior to positivity of screening. We successfully demonstrated the added value for this combined strategy to extract well-founded knowledge from interdisciplinary data sources. The combination of patient-contact modeling and high-resolution typing unraveled the transmission dynamics within the hospital department and, additionally, a constant VRE influx over time.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0235160PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7314025PMC
September 2020

Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon.

Dis Aquat Organ 2020 May 14;139:161-174. Epub 2020 May 14.

Discipline of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway H91TK33, Ireland.

During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.
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http://dx.doi.org/10.3354/dao03478DOI Listing
May 2020

sp. nov. isolated from a dog.

Int J Syst Evol Microbiol 2020 Apr 25;70(4):2648-2656. Epub 2020 Mar 25.

Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, 35392 Giessen, Germany.

From a phlegmon in a dog an aerobic and facultatively anaerobic, indole-, oxidase- and catalase-negative, non-motile bacterium was isolated in 2019 in Germany that stained Gram-negative and showed a pleomorphic, rod-shaped, non-spore-forming appearance. Based on the results of 16S rRNA gene sequence analyses, strain IHIT1603-19 was assigned to the genus with sequence similarities of 98.6, 98.0, 97.9, 97.1 and 94.4 % to the type strains of , , , and , respectively. Strain IHIT1603-19 could also clearly be differentiated from other species by , and gene, nucleotide and amino acid sequence analyses as well as by core genome phylogeny. Regarding DNA-DNA relatedness, strain IHIT1603-19 demonstrated an average nucleotide identity of 83.00 and 82.28 % compared to 131000547 and DSM 12112, respectively. Chemotaxonomic and physiological data of strain IHIT1603-19 were in congruence with other closely related members of the family , represented by highly similar enzyme profiles and fatty acid patterns. MALDI-TOF MS analysis also proved suitable in unequivocally discriminating strain IHIT1603-19 from all currently described taxa of the genus . On the basis of these data, we propose the novel species sp. nov. with the type strain IHIT1603-19 (=DSM 110501=CCUG 74118=CIP 111795). The G+C content of the DNA of the type strain is 26.6 mol%, genome size is 1.60 Mbp.
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http://dx.doi.org/10.1099/ijsem.0.004086DOI Listing
April 2020

Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential.

Sci Rep 2020 02 28;10(1):3686. Epub 2020 Feb 28.

German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany.

Campylobacter is the major bacterial agent of human gastroenteritis worldwide and represents a crucial global public health burden. Species differentiation of C. jejuni and C. coli and phylogenetic analysis is challenged by inter-species horizontal gene transfer. Routine real-time PCR on more than 4000 C. jejuni and C. coli field strains identified isolates with ambiguous PCR results for species differentiation, in particular, from the isolation source eggs. K-mer analysis of whole genome sequencing data indicated the presence of C. coli hybrid strains with huge amounts of C. jejuni introgression. Recombination events were distributed over the whole chromosome. MLST typing was impaired, since C. jejuni sequences were also found in six of the seven housekeeping genes. cgMLST suggested that the strains were phylogenetically unrelated. Intriguingly, the strains shared a stress response set of C. jejuni variant genes, with proposed roles in oxidative, osmotic and general stress defence, chromosome maintenance and repair, membrane transport, cell wall and capsular biosynthesis and chemotaxis. The results have practical impact on routine typing and on the understanding of the functional adaption to harsh environments, enabling successful spreading and persistence of Campylobacter.
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http://dx.doi.org/10.1038/s41598-020-60320-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048796PMC
February 2020

Comparison of different technologies for the decipherment of the whole genome sequence of BfR-CA-14430.

Gut Pathog 2019 16;11:59. Epub 2019 Dec 16.

1NG1-Microbial Genomics, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.

Background: is a zoonotic pathogen that infects the human gut through the food chain mainly by consumption of undercooked chicken meat, raw chicken cross-contaminated ready-to-eat food or by raw milk. In the last decades, has increasingly become the most common bacterial cause for food-born infections in high income countries, costing public health systems billions of euros each year. Currently, different whole genome sequencing techniques such as short-read bridge amplification and long-read single molecule real-time sequencing techniques are applied for in-depth analysis of bacterial species, in particular, Illumina MiSeq, PacBio and MinION.

Results: In this study, we analyzed a recently isolated strain from chicken meat by short- and long-read data from Illumina, PacBio and MinION sequencing technologies. For comparability, this strain is used in the German PAC-CAMPY research consortium in several studies, including phenotypic analysis of biofilm formation, natural transformation and in vivo colonization models. The complete assembled genome sequence most likely consists of a chromosome of 1,645,980 bp covering 1665 coding sequences as well as a plasmid sequence with 41,772 bp that encodes for 46 genes. Multilocus sequence typing revealed that the strain belongs to the clonal complex CC-21 (ST-44) which is known to be involved in human infections, including outbreaks. Furthermore, we discovered resistance determinants and a point mutation in the DNA gyrase () that render the bacterium resistant against ampicillin, tetracycline and (fluoro-)quinolones.

Conclusion: The comparison of Illumina MiSeq, PacBio and MinION sequencing and analyses with different assembly tools enabled us to reconstruct a complete chromosome as well as a circular plasmid sequence of the strain BfR-CA-14430. Illumina short-read sequencing in combination with either PacBio or MinION can substantially improve the quality of the complete chromosome and epichromosomal elements on the level of mismatches and insertions/deletions, depending on the assembly program used.
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http://dx.doi.org/10.1186/s13099-019-0340-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6913002PMC
December 2019

Genomic and Functional Characterization of Poultry From India Revealed Diverse Extended-Spectrum β-Lactamase-Producing Lineages With Shared Virulence Profiles.

Front Microbiol 2019 3;10:2766. Epub 2019 Dec 3.

International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.

Extended-spectrum β-lactamases (ESBLs) form the most important resistance determinants prevalent worldwide. Data on ESBL-producing from poultry and livestock are scarce in India. We present data on the functional and genomic characterization of ESBL-producing obtained from poultry in India. The whole genome sequences of 28 ESBL-producing were analyzed comprising of 12 broiler chicken isolates, 11 free-range chicken isolates, and 5 human extraintestinal pathogenic . All of the 28 ESBL-producing isolates were tested for antibiotic susceptibilities, conjugation, and virulence-associated phenotypic characteristics. A total of 13 sequence types were identified from the poultry , which included globally successful sequence types such as ST117 (9%), ST131 (4.3%), and ST10 (4.3%). The most common ESBL gene detected in poultry genomes was (17%). Also, FIB (73%) and FII (73%) were the most common plasmid replicons identified. Conjugation experiments demonstrated 54 (7/13), 30 (3/10), and 40% (2/5) of broiler, free-range, and human ExPEC to be able to transfer their ESBL genes, respectively. The virulence-associated phenotypic tests revealed the broiler, free-range, and human ExPEC isolates to be comparable in biofilm formation, resistance to serum bactericidal activity, adherence, and invasion capabilities. Our overall results showed prevalence of virulence phenotypes among the diverse ESBL-producing from poultry; while certain clones from broiler-poultry may indeed have the potential to cause infection in humans.
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http://dx.doi.org/10.3389/fmicb.2019.02766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901389PMC
December 2019

Effects of a Four-Week High-Dosage Zinc Oxide Supplemented Diet on Commensal of Weaned Pigs.

Front Microbiol 2019 28;10:2734. Epub 2019 Nov 28.

Robert Koch Institute, Berlin, Germany.

Strategies to reduce economic losses associated with post-weaning diarrhea in pig farming include high-level dietary zinc oxide supplementation. However, excessive usage of zinc oxide in the pig production sector was found to be associated with accumulation of multidrug resistant bacteria in these animals, presenting an environmental burden through contaminated manure. Here we report on zinc tolerance among a random selection of intestinal comprising of different antibiotic resistance phenotypes and sampling sites isolated during a controlled feeding trial from 16 weaned piglets: In total, 179 isolates from "pigs fed with high zinc concentrations" (high zinc group, [HZG]: = 99) and a corresponding "control group" ([CG]: = 80) were investigated with regard to zinc tolerance, antimicrobial- and biocide susceptibilities by determining minimum inhibitory concentrations (MICs). In addition, whole genome screening (WGSc) for antibiotic resistance genes (ARGs) as well as biocide- and heavy metal tolerance genes was performed using an in-house BLAST-based pipeline. Overall, porcine isolates showed three different ZnCl MICs: 128 μg/ml (HZG, 2%; CG, 6%), 256 μg/ml (HZG, 64%; CG, 91%) and 512 μg/ml ZnCl (HZG, 34%, CG, 3%), a unimodal distribution most likely reflecting natural differences in zinc tolerance associated with different genetic lineages. However, a selective impact of the zinc-rich supplemented diet seems to be reasonable, since the linear mixed regression model revealed a statistically significant association between "higher" ZnCl MICs and isolates representing the HZG as well as "lower ZnCl MICs" with isolates of the CG ( = 0.005). None of the zinc chloride MICs was associated with a particular antibiotic-, heavy metal- or biocide- tolerance/resistance phenotype. Isolates expressing the 512 μg/ml MIC were either positive for ARGs conferring resistance to aminoglycosides, tetracycline and sulfamethoxazole-trimethoprim, or harbored no ARGs at all. Moreover, WGSc revealed a ubiquitous presence of zinc homeostasis and - detoxification genes, including B, A, and . In conclusion, we provide evidence that zinc-rich supplementation of pig feed selects for more zinc tolerant , including isolates harboring ARGs and biocide- and heavy metal tolerance genes - a putative selective advantage considering substances and antibiotics currently used in industrial pork production systems.
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http://dx.doi.org/10.3389/fmicb.2019.02734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892955PMC
November 2019

The gut microbiome of horses: current research on equine enteral microbiota and future perspectives.

Anim Microbiome 2019 Nov 13;1(1):14. Epub 2019 Nov 13.

Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.

Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease is still an expanding research field in both, human and veterinary medicine. GIT disorders and their consequences are among the most important diseases of domesticated Equidae, but current gaps of knowledge hinder adequate progress with respect to disease prevention and microbiome-based interventions. Current literature on enteral microbiomes mirrors a vast data and knowledge imbalance, with only few studies tackling archaea, viruses and eukaryotes compared with those addressing the bacterial components.Until recently, culture-dependent methods were used for the identification and description of compositional changes of enteral microorganisms, limiting the outcome to cultivatable bacteria only. Today, next generation sequencing technologies provide access to the entirety of genes (microbiome) associated with the microorganisms of the equine GIT including the mass of uncultured microbiota, or "microbial dark matter".This review illustrates methods commonly used for enteral microbiome analysis in horses and summarizes key findings reached for bacteria, viruses and fungi so far. Moreover, reasonable possibilities to combine different explorative techniques are described. As a future perspective, knowledge expansion concerning beneficial compositions of microorganisms within the equine GIT creates novel possibilities for early disorder diagnostics as well as innovative therapeutic approaches. In addition, analysis of shotgun metagenomic data enables tracking of certain microorganisms beyond species barriers: transmission events of bacteria including pathogens and opportunists harboring antibiotic resistance factors between different horses but also between humans and horses will reach new levels of depth concerning strain-level distinctions.
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http://dx.doi.org/10.1186/s42523-019-0013-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7807895PMC
November 2019

Sindbis virus polyarthritis outbreak signalled by virus prevalence in the mosquito vectors.

PLoS Negl Trop Dis 2019 08 29;13(8):e0007702. Epub 2019 Aug 29.

Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, Leipzig, Germany.

Polyarthritis and rash caused by Sindbis virus (SINV), was first recognised in northern Europe about 50 years ago and is known as Ockelbo disease in Sweden and Pogosta disease in Finland. This mosquito-borne virus occurs mainly in tropical and sub-tropical countries, and in northern Europe it is suggested to cause regularly reoccurring outbreaks. Here a seven-year cycle of SINV outbreaks has been referred to in scientific papers, although the hypothesis is based solely on reported human cases. In the search for a more objective outbreak signal, we evaluated mosquito abundance and SINV prevalence in vector mosquitoes from an endemic area in central Sweden. Vector mosquitoes collected in the River Dalälven floodplains during the years before, during, and after the hypothesised 2002 outbreak year were assayed for virus on cell culture. Obtained isolates were partially sequenced, and the nucleotide sequences analysed using Bayesian maximum clade credibility and median joining network analysis. Only one SINV strain was recovered in 2001, and 4 strains in 2003, while 15 strains were recovered in 2002 with significantly increased infection rates in both the enzootic and the bridge-vectors. In 2002, the Maximum Likelihood Estimated infection rates were 10.0/1000 in the enzootic vectors Culex torrentium/pipiens, and 0.62/1000 in the bridge-vector Aedes cinereus, compared to 4.9/1000 and 0.0/1000 in 2001 and 0.0/1000 and 0.32/1000 in 2003 Sequence analysis showed that all isolates belonged to the SINV genotype I (SINV-I). The genetic analysis revealed local maintenance of four SINV-I clades in the River Dalälven floodplains over the years. Our findings suggest that increased SINV-I prevalence in vector mosquitoes constitutes the most valuable outbreak marker for further scrutinising the hypothesized seven-year cycle of SINV-I outbreaks and the mechanisms behind.
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http://dx.doi.org/10.1371/journal.pntd.0007702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6738656PMC
August 2019

Type I interferon induced by TLR2-TLR4-MyD88-TRIF-IRF3 controls Mycobacterium abscessus subsp. abscessus persistence in murine macrophages via nitric oxide.

Int J Med Microbiol 2019 Jul 1;309(5):307-318. Epub 2019 Jun 1.

Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany. Electronic address:

Mycobacterium abscessus (MAB) is an emerging, rapidly growing non-tuberculous Mycobacterium causing therapy-resistant pulmonary disease especially in patients with cystic fibrosis (CF). Smooth and rough colony type MAB can be isolated from infected patients whereby rough colony type MAB are more often associated with severe disease. Disease severity is also associated with an alternated type I interferon (IFN-I) response of the MAB-infected patients. However the relevance of this response for the outcome of MAB infection is still unknown. In this study, we analyzed the IFNβ expression of murine macrophages infected with a MAB rough colony strain (MAB-R) isolated from a patient with progressive CF and compared it to macrophages infected with the MAB smooth colony type reference strain (MAB-S). We found that MAB-R infected macrophages expressed significantly more IFNβ mRNA and protein than MAB-S infected macrophages. Higher IFNβ induction by MAB-R was associated with higher TNF expression and intracellular killing while low IFNβ induction was associated with lower TNF expression and persistence of MAB-S. IFNβ induction was independent of the intracellular cGAS-STING recognition pathway. MAB appeared to be recognized extracellularly and induced IFNβ expression via TLR2-TLR4-MyD88-TRIF-IRF3 dependent pathways. By using macrophages lacking the IFN-I receptor we demonstrate that MAB induced IFN-I response essentially contributed to restricting MAB-R and MAB-S infections by activating macrophage Nos2 expression and nitric oxide production. Thus IFN-I seem to influence the intrinsic ability of macrophages to control MAB infections. As MAB persists over long time periods in susceptible patients, our findings suggest that virulence of MAB strains is promoted by an insufficient IFN-I response of the host.
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http://dx.doi.org/10.1016/j.ijmm.2019.05.007DOI Listing
July 2019

Corrigendum to 'Impact of the colistin resistance gene mcr-1 on bacterial fitness' [International Journal of Antimicrobial Agents 51/4 (2018) 554-561].

Int J Antimicrob Agents 2019 06 13;53(6):878. Epub 2019 Apr 13.

Institute of Medical Microbiology and Infection Control, Hospital of the Johann Wolfgang von Goethe University, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ijantimicag.2019.04.001DOI Listing
June 2019

Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Lineage Sequence Type 648.

Antimicrob Agents Chemother 2019 06 24;63(6). Epub 2019 May 24.

Institute of Microbiology and Epizootics, Free University Berlin, Berlin, Germany

The pathogenic extended-spectrum-beta-lactamase (ESBL)-producing lineage ST648 is increasingly reported from multiple origins. Our study of a large and global ST648 collection from various hosts (87 whole-genome sequences) combining core and accessory genomics with functional analyses and experiments suggests that ST648 is a nascent and generalist lineage, lacking clear phylogeographic and host association signals. By including large numbers of ST131 ( = 107) and ST10 ( = 96) strains for comparative genomics and phenotypic analysis, we demonstrate that the combination of multidrug resistance and high-level virulence are the hallmarks of ST648, similar to international high-risk clonal lineage ST131. Specifically, our , , and results demonstrate that ST648 is well equipped with biofilm-associated features, while ST131 shows sophisticated signatures indicative of adaption to urinary tract infection, potentially conveying individual ecological niche adaptation. In addition, we used a recently developed NFDS (negative frequency-dependent selection) population model suggesting that ST648 will increase significantly in frequency as a cause of bacteremia within the next few years. Also, ESBL plasmids impacting biofilm formation aided in shaping and maintaining ST648 strains to successfully emerge worldwide across different ecologies. Our study contributes to understanding what factors drive the evolution and spread of emerging international high-risk clonal lineages.
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http://dx.doi.org/10.1128/AAC.00243-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535536PMC
June 2019

Seasonal Occurrence and Carbapenem Susceptibility of Bovine in Germany.

Front Microbiol 2019 22;10:272. Epub 2019 Feb 22.

Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany.

is one of the leading causes of nosocomial infections in humans. To investigate its prevalence, distribution of sequence types (STs), and antimicrobial resistance in cattle, we sampled 422 cattle, including 280 dairy cows, 59 beef cattle, and 83 calves over a 14-month period. Metadata, such as the previous use of antimicrobial agents and feeding, were collected to identify putative determining factors. Bacterial isolates were identified via MALDI-TOF/MS and PCR, antimicrobial susceptibility was evaluated via VITEK2 and antibiotic gradient tests, resistance genes were identified by PCR. Overall, 15.6% of the cattle harbored , predominantly in the nose (60.3% of the isolates). It was more frequent in dairy cows (21.1%) than in beef cattle (6.8%) and calves (2.4%). A seasonal occurrence was shown with a peak between May and August. The rate of occurrence of was correlated with a history of use of 3rd generation cephalosporins in the last 6 months prior to sampling Multilocus sequence typing (Pasteur scheme) revealed 83 STs among 126 unique isolates. Nine of the bovine STs have previously been implicated in human infections. Besides known intrinsic resistance of the species, the isolates did not show additional resistance to the antimicrobial substances tested, including carbapenems. Our data suggest that cattle are not a reservoir for nosocomial but carry a highly diverse population of this species. Nevertheless, some STs seem to be able to colonize both cattle and humans.
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http://dx.doi.org/10.3389/fmicb.2019.00272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395434PMC
February 2019

Equine Methicillin-Resistant Sequence Type 398 (MRSA) Harbor Mobile Genetic Elements Promoting Host Adaptation.

Front Microbiol 2018 24;9:2516. Epub 2018 Oct 24.

Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany.

Continuing introduction of multi-drug resistant, zoonotic pathogens such as methicillin-resistant (MRSA) in horse clinics challenges the biosafety of employees and animal patients. This study was aimed to determine the occurrence of mobile genetic elements facilitating survival in the early stages of invasive infection in different host species, including humans and horses, in MRSA carried by equine patients admitted to a large horse clinic. A total of 341 equine patients were investigated for carriage of MRSA by hygiene screening directly at hospital admission. MRSA were further investigated by antimicrobial susceptibility testing, whole-genome sequencing and genomic composition, including virulence factors involved in immune evasion and host adaption. From a total of 340 validated specimens from equine nostrils, 3.5% yielded positive results for MRSA. All MRSA were found to be closely related belonging to sequence type (ST) 398_t011 with up to four additional antimicrobial resistances. All MRSA harbored a specific Staphylococcal Pathogenicity Island (SaPIbov5) involved in facilitating survival in ruminant and equine plasma. Moreover, a β-hemolysin () converting ΦSa3 phage encoding the human-specific Immune Evasion Cluster (IEC) was present in 72% of the isolates. An equid-specific leukotoxin encoded by a further temperate phage (Saeq1) was only rarely detected (22%). Despite the absence of β-hemolysin production for all IEC-positive ST398, a prominent hemolysis zone was demonstrable on sheep blood agar. Thus, IEC might remain undetected among the ST398 lineage, since the presence of IEC is commonly associated with reduction of hemolysis in belonging to other genetic backgrounds. Here we describe MRSA-ST398 harboring different mobile genetic elements encoding variants of immune evasion factors and toxins previously shown to contribute to invasive diseases in specific host species or ecologic niches. We suggest these combinations contribute to the adaptation of MRSA belonging to ST398 with respect to epidemic spread across different habitats and hosts, and may therefore confer a host "generalist" phenotype.
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http://dx.doi.org/10.3389/fmicb.2018.02516DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6207647PMC
October 2018

Bringing together what belongs together: Optimizing murine infection models by using mouse-adapted Staphylococcus aureus strains.

Int J Med Microbiol 2019 Jan 22;309(1):26-38. Epub 2018 Oct 22.

Department of Immunology, University Medicine Greifswald, Greifswald, Germany. Electronic address:

Staphylococcus (S.) aureus is a leading cause of bacterial infection world-wide, and currently no vaccine is available for humans. Vaccine development relies heavily on clinically relevant infection models. However, the suitability of mice for S. aureus infection models has often been questioned, because experimental infection of mice with human-adapted S. aureus requires very high infection doses. Moreover, mice were not considered to be natural hosts of S. aureus. The latter has been disproven by our recent findings, showing that both laboratory mice, as well as wild small mammals including mice, voles, and shrews, are naturally colonized with S. aureus. Here, we investigated whether mouse-and vole-derived S. aureus strains show an enhanced virulence in mice as compared to the human-adapted strain Newman. Using a step-wise approach based on the bacterial genotype and in vitro assays for host adaptation, we selected the most promising candidates for murine infection models out of a total of 254 S. aureus isolates from laboratory mice as well as wild rodents and shrews. Four strains representing the clonal complexes (CC) 8, 49, and 88 (n = 2) were selected and compared to the human-adapted S. aureus strain Newman (CC8) in murine pneumonia and bacteremia models. Notably, a bank vole-derived CC49 strain, named DIP, was highly virulent in BALB/c mice in pneumonia and bacteremia models, whereas the other murine and vole strains showed virulence similar to or lower than that of Newman. At one tenth of the standard infection dose DIP induced disease severity, bacterial load and host cytokine and chemokine responses in the murine bacteremia model similar to that of Newman. In the pneumonia model, DIP was also more virulent than Newman but the effect was less pronounced. Whole genome sequencing data analysis identified a pore-forming toxin gene, lukF-PV(P83)/lukM, in DIP but not in the other tested S. aureus isolates. To conclude, the mouse-adapted S. aureus strain DIP allows a significant reduction of the inoculation dose in mice and is hence a promising tool to develop clinically more relevant infection models.
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http://dx.doi.org/10.1016/j.ijmm.2018.10.007DOI Listing
January 2019

Determination of virulence and fitness genes associated with the , and integration sites of LEE-negative food-borne Shiga toxin-producing strains.

Gut Pathog 2018 8;10:43. Epub 2018 Oct 8.

1Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstr. 28, 70599 Stuttgart, Germany.

Background: In the current study, nine foodborne "Locus of Enterocyte Effacement" (LEE)-negative Shiga toxin-producing (STEC) strains were selected for whole genome sequencing and analysis for yet unknown genetic elements within the already known LEE integration sites , and . Foreign DNA ranging in size from 3.4 to 57 kbp was detected and further analyzed. Five STEC strains contained an insertion of foreign DNA adjacent to the tRNA gene and five and seven strains contained foreign DNA adjacent to the and tRNA genes, respectively. We characterized the foreign DNA insertion associated with (STEC O91:H21 strain 17584/1), (STEC O8:H4 strain RF1a and O55:Hnt strain K30) and (STEC O91:H21 strain 17584/1 and O113:H21 strain TS18/08) as examples.

Results: In total, 293 open reading frames partially encoding putative virulence factors such as TonB-dependent receptors, DNA helicases, a hemolysin activator protein precursor, antigen 43, anti-restriction protein KlcA, ShiA, and phosphoethanolamine transferases were detected. A virulence type IV toxin-antitoxin system was detected in three strains. Additionally, the system was found in one strain. In strain 17584/1 we were able to define a new genomic island which we designated GI. The island contained integrases and mobile elements in addition to genes for increased fitness and those playing a putative role in pathogenicity.

Conclusion: The data presented highlight the important role of the three tRNAs , and for the genomic flexibility of .
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http://dx.doi.org/10.1186/s13099-018-0271-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174562PMC
October 2018

ESBL-Producing in the Broiler Production Chain and the First Description of ST3128.

Front Microbiol 2018 3;9:2302. Epub 2018 Oct 3.

Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany.

ESBL-producing represent an increasing problem both in human and veterinary medicine. As SHV-2 - encoding were recently detected in the broiler production we were interested in investigating a possible transmission along the broiler production chain and furthermore, in evaluating their possible impact on human health. Therefore, 41 ESBL-producing originating from a parent flock, from the hatcherys' environment during the hatching of that parent flocks' chickens, and from an associated fattening flock were investigated on an Illumina Miseq. Whole genome sequences were analyzed concerning their MLST-type, cgMLST-type, genotypic and phenotypic resistance, plasmid profiles and virulence genes. Irrespective of the origin of isolation all investigated isolates were multi-drug resistant, harbored the same ESBL-gene , shared the same sequence type (ST3128) and displayed 100% similarity in core genome multilocus sequence typing (cgMLST). In addition, plasmid typing found several Inc/Rep types associated with ESBL-plasmids. Summarizing, identical clones of SHV-2-producing were detected in different stages of the industrial broiler production in one out of seven investigated broiler chains. This proves the possibility of pseudo-vertical transmission of multi-resistant human pathogens from parent flocks to hatcheries and fattening flocks. Furthermore, the importance of cross-contamination along the production chain was shown. Although the ESBL-producing clone detected here in the broiler production has not been associated with clinical settings so far, our findings present a potential public health threat.
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http://dx.doi.org/10.3389/fmicb.2018.02302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178893PMC
October 2018

Contamination of chicken meat with extended-spectrum beta-lactamase producing- Klebsiella pneumoniae and Escherichia coli during scalding and defeathering of broiler carcasses.

Food Microbiol 2019 Feb 18;77:185-191. Epub 2018 Sep 18.

Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany.

Extended-spectrum beta-lactamase- (ESBL-) producing Klebsiella (K.) pneumoniae and Escherichia (E.) coli are of critical importance in human and veterinary medicine. Animal food products, especially broiler chickens, are discussed as a possible source for the exposure of humans with antibiotic resistant bacteria. Although the occurrence and vertical transmission of ESBL-/AmpC-producing Enterobacteriaceae in the broiler production has been reported before, detailed investigations concerning the dissemination along the slaughter processing line are missing. In this study, we investigated cross-contamination with ESBL-producing Enterobacteriaceae during the processing of two different broiler flocks in one slaughterhouse. The ESBL-status during the fattening period of the flocks was determined and environmental samples from the slaughterhouse were taken before processing of the respective flocks. These isolates were compared to those found in samples from the carcasses after processing using whole genome sequencing. Phylogenetic analyses of seven ESBL-producing K. pneumoniae and 14 E. coli revealed close relationships between isolates from scalding water and the defeathering machine, respectively, which were collected before the processing of the broiler flocks, to those isolates found in samples from skin and filet of the respective flock carcasses. In conclusion, using high resolution molecular data we found evidence for the cross-contamination of carcasses with ESBL-producing Enterobacteriaceae during scalding and defeathering in the slaughterhouse.
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http://dx.doi.org/10.1016/j.fm.2018.09.010DOI Listing
February 2019