Publications by authors named "Joachim Frey"

182 Publications

Galactocerebroside biosynthesis pathways of Mycoplasma species: an antigen triggering Guillain-Barré-Stohl syndrome.

Microb Biotechnol 2021 Mar 27. Epub 2021 Mar 27.

Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands.

Infection by Mycoplasma pneumoniae has been identified as a preceding factor of Guillain-Barré-Stohl syndrome. The Guillain-Barré-Stohl syndrome is triggered by an immune reaction against the major glycolipids and it has been postulated that M. pneumoniae infection triggers this syndrome due to bacterial production of galactocerebroside. Here, we present an extensive comparison of 224 genome sequences from 104 Mycoplasma species to characterize the genetic determinants of galactocerebroside biosynthesis. Hidden Markov models were used to analyse glycosil transferases, leading to identification of a functional protein domain, termed M2000535 that appears in about a third of the studied genomes. This domain appears to be associated with a potential UDP-glucose epimerase, which converts UDP-glucose into UDP-galactose, a main substrate for the biosynthesis of galactocerebroside. These findings clarify the pathogenic mechanisms underlining the triggering of Guillain-Barré-Stohl syndrome by M. pneumoniae infections.
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http://dx.doi.org/10.1111/1751-7915.13794DOI Listing
March 2021

Crisis of emerging antibiotic resistances mirroring that of the COVID-19 in the age of globalisation.

Swiss Med Wkly 2020 11 17;150:w20402. Epub 2020 Nov 17.

National Research Programme NRP 72, Swiss National Science Foundation, Bern, Switzerland.

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http://dx.doi.org/10.4414/smw.2020.20402DOI Listing
November 2020

RTX Toxins of Animal Pathogens and Their Role as Antigens in Vaccines and Diagnostics.

Authors:
Joachim Frey

Toxins (Basel) 2019 12 10;11(12). Epub 2019 Dec 10.

Vetsuisse Facutly, University of Bern, 3012 Bern, Switzerland.

Exotoxins play a central role in the pathologies caused by most major bacterial animal pathogens. The large variety of vertebrate and invertebrate hosts in the animal kingdom is reflected by a large variety of bacterial pathogens and toxins. The group of repeats in the structural toxin (RTX) toxins is particularly abundant among bacterial pathogens of animals. Many of these toxins are described as hemolysins due to their capacity to lyse erythrocytes in vitro. Hemolysis by RTX toxins is due to the formation of cation-selective pores in the cell membrane and serves as an important marker for virulence in bacterial diagnostics. However, their physiologic relevant targets are leukocytes expressing β2 integrins, which act as specific receptors for RTX toxins. For various RTX toxins, the binding to the CD18 moiety of β integrins has been shown to be host specific, reflecting the molecular basis of the host range of RTX toxins expressed by bacterial pathogens. Due to the key role of RTX toxins in the pathogenesis of many bacteria, antibodies directed against specific RTX toxins protect against disease, hence, making RTX toxins valuable targets in vaccine research and development. Due to their specificity, several structural genes encoding for RTX toxins have proven to be essential in modern diagnostic applications in veterinary medicine.
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http://dx.doi.org/10.3390/toxins11120719DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6950323PMC
December 2019

A Mesophilic Strain Isolated from an Unsuspected Host, the Migratory Bird Pied Avocet.

Microorganisms 2019 Nov 20;7(12). Epub 2019 Nov 20.

Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada.

is a Gram-negative bacterium, known as a fish pathogen since its discovery. Although the species was initially considered psychrophilic, a mesophilic subspecies () and many other mesophilic strains still not attributed to subspecies have been described in the last two decades. These mesophilic strains were sampled from various sources, including humans, and some of them are known to be pathogenic. In this study, we describe a strain, JF2480, which was isolated from the spleen, and also found the kidney and liver of a dead pied avocet (), a type of migratory bird inhabiting aquatic environments. A core genome phylogenomic analysis suggests that JF2480 is taxonomically distant from other known   subspecies. The genome sequence confirms that the strain possesses key virulence genes that are present in the typical psychrophilic subspecies, with the exception of the genes encoding the type three secretion system (T3SS). Bacterial virulence assays conducted on the surrogate host amoeba confirmed that the strain is virulent despite the lack of T3SS. Bacterial growth curves showed that strain JF2480 grow well at 40 °C, the body temperature of the pied avocet, and even faster at 41 °C, compared to other mesophilic strains. Discovery of this strain further demonstrates the extent of the phylogenomic tree of this species. This study also suggests that can infect a wider array of hosts than previously suspected and that we need to rethink the way we perceive 's natural environment.
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http://dx.doi.org/10.3390/microorganisms7120592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6955901PMC
November 2019

Genomic comparison of Clostridium chauvoei isolates from classical and visceral clinical manifestation.

Braz J Microbiol 2020 Sep 24;51(3):1327-1332. Epub 2019 Oct 24.

Laboratório de Bacteriologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil.

Clostridium chauvoei is the etiological agent of blackleg, an infectious disease affecting cattle and small ruminants worldwide. This disease can manifest as classical blackleg, a condition in which skeletal muscles are affected and visceral blackleg, which affects the heart, sublingual muscles, and the diaphragm. The pathogenesis of the visceral form of the disease is poorly understood. The objective of this study is to determine and analyze complete genomic sequences of six C. chauvoei strains, five isolates from skeletal muscle and one isolate from a visceral case of blackleg in Brazil, to provide insights into the differences in pathogenic profiles of strains causing the different forms of disease. The full genomes of the six C. chauvoei strains were sequenced and comparative analyses were performed among these genomes and the C. chauvoei reference strain JF4335. The results of this study revealed that the genomes of the C. chauvoei strains analyzed are highly conserved; no particular differences were noted that could be associated with the two different clinical manifestations of the disease.
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http://dx.doi.org/10.1007/s42770-019-00177-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7455654PMC
September 2020

Recommended rejection of the names gen. nov., gen. nov., gen. nov., fam. nov., fam. nov., ord. nov., gen. nov., gen. nov. [Gupta, Sawnani, Adeolu, Alnajar and Oren 2018] and all proposed species comb. nov. placed therein.

Int J Syst Evol Microbiol 2019 Nov;69(11):3650-3653

USDA-ARS, Beltsville, MD, USA.

The consensus of the members of the International Committee on Systematics of Prokaryotes' Subcommittee on the taxonomy of is that recently proposed sweeping changes to nomenclature of members of the , specifically involving introduction of the names gen. nov., gen. nov., gen. nov., fam. nov., fam. nov., ord. nov., gen. nov., gen. nov., and all proposed species or subspecies comb. nov. placed therein, should be rejected because they violate one or more essential points of the International Code of Nomenclature of Prokaryotes.
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http://dx.doi.org/10.1099/ijsem.0.003632DOI Listing
November 2019

Systemic infection in European perch with thermoadapted virulent Aeromonas salmonicida (Perca fluviatilis).

J Fish Dis 2019 May 26;42(5):685-691. Epub 2019 Feb 26.

Centre for Fish and Wildlife Health, University of Bern, Bern, Switzerland.

In non-salmonid fish, Aeromonas salmonicidacan cause local infections with severe skin ulcerations, known as atypical furunculosis. In this study, we present a systemic infection by a virulent A. salmonicidain European perch (Perca fluviatilis).This infection was diagnosed in a Swiss warm water recirculation aquaculture system. The isolate of A.  salmonicida encodes a type three secretion system (TTSS) most likely located on a plasmid similar to pAsa5/pASvirA, which is known to specify one of the main virulence attributes of the species A. salmonicida. However, the genes specifying the TTSS of the perch isolate show a higher temperature tolerance than strains isolated from cold-water fish. The function of the TTSS in virulence was verified in a cytotoxicity test using bluegill fry and epithelioma papulosum cyprinid cells.
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http://dx.doi.org/10.1111/jfd.12970DOI Listing
May 2019

Production of neutralizing antibodies against the secreted Clostridium chauvoei toxin A (CctA) upon blackleg vaccination.

Anaerobe 2019 Apr 14;56:78-87. Epub 2019 Feb 14.

Vetsuisse Faculty, University of Bern, Bern, Switzerland. Electronic address:

Clostridium chauvoei is the etiologic agent of blackleg in cattle, inducing fever, severe myonecrosis, oedemic lesions and ultimately death of infected animals. The pathogen often results in such rapid death that antibiotic therapy is futile and thus vaccination is the only efficient strategy in order to control the disease. The β-barrel pore forming leucocidin Clostridium chauvoei toxin A (CctA) is one of the best characterised toxins of C. chauvoei and has been shown to be an important virulence factor. It has been reported to induce protective immunity and is conserved across C. chauvoei strains collected from diverse geographical locations for more than 50 years. The aim of this study was to identify the location of the CctA toxin during liquid culture fermentation and to use CctA to develop an in vitro assay to replace the current guinea pig challenge assay for vaccine potency in standard batch release procedures. We report that CctA is fully secreted in C. chauvoei culture and show that it is found abundantly in the supernatant of liquid cultures. Sera from cattle vaccinated with a commercial blackleg vaccine revealed strong haemolysin-neutralizing activity against recombinant CctA which reached titres of 1000 times 28 days post-vaccination. Similarly, guinea pig sera from an official potency control test reached titres of 600 times 14 days post-vaccination. In contrast, ELISA was not able to specifically measure anti-CctA antibodies in cattle serum due to strong cross-reactions with antibodies against other proteins present pre-vaccination. We conclude that haemolysin-neutralizing antibodies are a valuable measurement for protective immunity against blackleg and have the potential to be a suitable replacement of the guinea pig challenge potency test, which would forego the unnecessary challenge of laboratory animals.
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http://dx.doi.org/10.1016/j.anaerobe.2019.02.011DOI Listing
April 2019

Reproduction of contagious caprine pleuropneumonia reveals the ability of convalescent sera to reduce hydrogen peroxide production in vitro.

Vet Res 2019 Feb 8;50(1):10. Epub 2019 Feb 8.

International Livestock Research Institute, Box 30709, Nairobi, 00100, Kenya.

Contagious caprine pleuropneumonia (CCPP), caused by Mycoplasma capricolum subsp. capripneumoniae is a severe disease widespread in Africa and Asia. Limited knowledge is available on the pathogenesis of this organism, mainly due to the lack of a robust in vivo challenge model and the means to do site-directed mutagenesis. This work describes the establishment of a novel caprine challenge model for CCPP that resulted in 100% morbidity using a combination of repeated intranasal spray infection followed by a single transtracheal infection employing the recent Kenyan outbreak strain ILRI181. Diseased animals displayed CCPP-related pathology and the bacteria could subsequently be isolated from pleural exudates and lung tissues in concentrations of up to 10 bacteria per mL as well as in the trachea using immunohistochemistry. Reannotation of the genome sequence of ILRI181 and F38 revealed the existence of genes encoding the complete glycerol uptake and metabolic pathways involved in hydrogen peroxide (HO) production in the phylogenetically related pathogen M. mycoides subsp. mycoides. Furthermore, the expression of L-α-glycerophosphate oxidase (GlpO) in vivo was confirmed. In addition, the function of the glycerol metabolism was verified by measurement of production of HO in medium containing physiological serum concentrations of glycerol. Peroxide production could be inhibited with serum from convalescent animals. These results will pave the way for a better understanding of host-pathogen interactions during CCPP and subsequent vaccine development.
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http://dx.doi.org/10.1186/s13567-019-0628-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368817PMC
February 2019

Hyperinvasiveness of Listeria monocytogenes sequence type 1 is independent of lineage I-specific genes encoding internalin-like proteins.

Microbiologyopen 2019 Jan 17:e790. Epub 2019 Jan 17.

Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland.

Listeriosis is a severe disease caused by the opportunistic bacterial pathogen Listeria monocytogenes (L. monocytogenes). Previous studies indicate that of the four phylogenetical lineages known, lineage I strains are significantly more prevalent in clinical infections than in the environment. Among lineage 1, sequence type (ST1) belongs to the most frequent genotypes in clinical infections and behaves hyperinvasive in experimental in vitro infections compared to lineage II strains suggesting that yet uncharacterized virulence genes contribute to high virulence of certain lineage I strains. This study investigated the effect of four specific lineage I genes encoding surface proteins with internalin-like structures on cellular infection. CNS derived cell lines (fetal bovine brain cells, human microglia cells) and non-CNS derived cell lines (bovine macrophage cells, human adenocarcinoma cells) that represent the various target cells of L. monocytogenes were infected with the parental ST1 strain and deletion mutants of the four genes. Despite their association with lineage I, deletion of the four genes investigated did not dampen the hyperinvasiveness of the ST1 strain. Similarly, these genes did not contribute to the intracellular survival and intercellular spread of L. monocytogenes ST1, indicating that these genes may have other functions, either during the infection process or outside the host.
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http://dx.doi.org/10.1002/mbo3.790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612545PMC
January 2019

Pathogenicity, population genetics and dissemination of Bacillus anthracis.

Infect Genet Evol 2018 10 20;64:115-125. Epub 2018 Jun 20.

Dean's Office, Vetsuisse Faculty, University of Bern, Bern, Switzerland. Electronic address:

Bacillus anthracis, the etiological agent of anthrax, procures its particular virulence by a capsule and two AB type toxins: the lethal factor LF and the edema factor EF. These toxins primarily disable immune cells. Both toxins are translocated to the host cell by the adhesin-internalin subunit called protective antigen PA. PA enables LF to reach intra-luminal vesicles, where it remains active for long periods. Subsequently, LF translocates to non-infected cells, leading to inefficient late therapy of anthrax. B. anthracis undergoes slow evolution because it alternates between vegetative and long spore phases. Full genome sequence analysis of a large number of worldwide strains resulted in a robust evolutionary reconstruction of this bacterium, showing that B. anthracis is split in three main clades: A, B and C. Clade A efficiently disseminated worldwide underpinned by human activities including heavy intercontinental trade of goat and sheep hair. Subclade A.Br.WNA, which is widespread in the Northern American continent, is estimated to have split from clade A reaching the Northern American continent in the late Pleistocene epoch via the former Bering Land Bridge and further spread from Northwest southwards. An alternative hypothesis is that subclade A.Br.WNA. evolved from clade A.Br.TEA tracing it back to strains from Northern France that were assumingly dispatched by European explorers that settled along the St. Lawrence River. Clade B established mostly in Europe along the alpine axis where it evolved in association with local cattle breeds and hence displays specific geographic subclusters. Sequencing technologies are also used for forensic applications to trace unintended or criminal acts of release of B. anthracis. Under natural conditions, B. anthracis generally affects domesticated and wild ruminants in arid ecosystems. The more recently discovered B. cereus biovar anthracis spreads in tropical forests, where it threatens particularly endangered primate populations.
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http://dx.doi.org/10.1016/j.meegid.2018.06.024DOI Listing
October 2018

Corrigendum: , an Evolutionary Dead-End Pathogen.

Front Microbiol 2018 6;9:421. Epub 2018 Mar 6.

Department of Biology, Swiss Institute of Bioinformatics, University of Fribourg, Fribourg, Switzerland.

[This corrects the article on p. 1054 in vol. 8, PMID: 28649238.].
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http://dx.doi.org/10.3389/fmicb.2018.00421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5845704PMC
March 2018

Genetic Separation of Causing Central Nervous System Infections in Animals.

Front Cell Infect Microbiol 2018 5;8:20. Epub 2018 Feb 5.

BUGFri Group, Swiss Institute of Bioinformatics, Fribourg, Switzerland.

is a foodborne pathogen that causes abortion, septicemia, gastroenteritis and central nervous system (CNS) infections in ruminants and humans. strains mainly belong to two distinct phylogenetic groups, named lineages I and II. In general, clinical cases in humans and animals, in particular CNS infections, are caused by lineage I strains, while most of the environmental and food strains belong to lineage II. Little is known about why lineage I is more virulent than lineage II, even though various molecular factors and mechanisms associated with pathogenesis are known. In this study, we have used a variety of whole genome sequence analyses and comparative genomic tools in order to find characteristics that distinguish lineage I from lineage II strains and CNS infection strains from non-CNS strains. We analyzed 225 strains and identified single nucleotide variants between lineages I and II, as well as differences in the gene content. Using a novel approach based on Reads Per Kilobase per Million Mapped (RPKM), we identified 167 genes predominantly absent in lineage II but present in lineage I. These genes are mostly encoding for membrane-associated proteins. Additionally, we found 77 genes that are largely absent in the non-CNS associated strains, while 39 genes are especially lacking in our defined "non-clinical" group. Based on the RPKM analysis and the metadata linked to the strains, we identified 6 genes potentially associated with CNS cases, which include a transcriptional regulator, an ABC transporter and a non-coding RNA. Although there is not a clear separation between pathogenic and non-pathogenic strains based on phylogenetic lineages, the presence of the genes identified in our study reveals potential pathogenesis traits in ruminant strains. Ultimately, the differences that we have found in our study will help steer future studies in understanding the virulence mechanisms of the most pathogenic strains.
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http://dx.doi.org/10.3389/fcimb.2018.00020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807335PMC
January 2019

Transposon-associated lincosamide resistance lnu(C) gene identified in Brachyspira hyodysenteriae ST83.

Vet Microbiol 2018 Feb 7;214:51-55. Epub 2017 Dec 7.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland. Electronic address:

Treatment of Swine Dysentery (SD) caused by Brachyspira hyodysenteriae (B. hyodysenteriae) is carried out using antimicrobials such as macrolides, lincosamides and pleuromutilins leading to the selection of resistant strains. Whole genome sequencing of a multidrug-resistant B. hyodysenteriae strain called BH718 belonging to sequence type (ST) 83 revealed the presence of the lincosamide resistance gene lnu(C) on the small 1724-bp transposon MTnSag1. The strain also contains an A to T substitution at position 2058 (A2058T) in the 23S rRNA gene which is known to be associated with macrolide and lincosamide resistance in B. hyodysenteriae. Testing of additional strains showed that those containing lnu(C) exhibited a higher minimal inhibitory concentration (MIC) of lincomycin (MIC ≥ 64 mg/L) compared to strains lacking lnu(C), even if they also harbor the A2058T mutation. Resistance to pleuromutilins could not be explained by the presence of already reported mutations in the 23S rRNA gene and in the ribosomal protein L3. This study shows that B. hyodysenteriae has the ability to acquire mobile genetic elements conferring resistance to antibiotics.
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http://dx.doi.org/10.1016/j.vetmic.2017.12.003DOI Listing
February 2018

Pooling of interdigital swab samples for PCR detection of virulent Dichelobacter nodosus.

J Vet Diagn Invest 2018 Mar 4;30(2):205-210. Epub 2017 Nov 4.

Clinic for Ruminants (Greber, Locher, Butty, Steiner), Vetsuisse-Faculty Bern, University of Bern, Bern, Switzerland.

Virulent ovine foot rot is a contagious foot disease. Given the development and validation of a real-time PCR to detect Dichelobacter nodosus isolates that contain the virulence-associated protease genes aprV2 and aprB2, the diagnosis of foot rot has made considerable progress. We evaluated pooling methods to reduce the number of samples during a foot rot control program. Samples of individual feet were compared to a 4-feet sample of the same sheep. All further analyses based on 4-feet samples (pools-of-5 and pools-of-10 4-feet samples) were compared to samples of individual sheep, and a risk-based herd sampling was evaluated and compared to the whole flock. The sensitivity and specificity of the 4-feet samples for detection of aprV2-positive strains was 93.8% (CI: 87.6-97.5%) and 98.3% (CI: 96.5-99.3%), respectively. The sensitivity and specificity of the pools-of-10 was 86.7% (CI: 78.4-92.7%) and 100.0% (CI: 97.4-100%), respectively. Pools-of-5 were not significantly more sensitive than pools-of-10. The pooling of 4 individual foot samples into one 4-feet sample is an adequate method to reduce the number of samples of individual sheep. The sensitivity of pools-of-5 and pools-of-10 is too imprecise for a control program. Risk-based sampling allowed for a substantial reduction of samples to be tested, had a sensitivity of 95.8% (CI: 78.9-99.9%) and specificity of 100.0% (CI: 88.1-100.0%) when determining the foot rot flock status, and represents an adequate methodology to predict within-flock freedom from infection.
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http://dx.doi.org/10.1177/1040638717733508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6505860PMC
March 2018

Long-term dynamics of Mycoplasma conjunctivae at the wildlife-livestock interface in the Pyrenees.

PLoS One 2017 9;12(10):e0186069. Epub 2017 Oct 9.

Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia, Universitat Autònoma de Barcelona, Bellaterra, Spain.

Functional roles of domestic and wild host populations in infectious keratoconjunctivitis (IKC) epidemiology have been extensively discussed claiming a domestic reservoir for the more susceptible wild hosts, however, based on limited data. With the aim to better assess IKC epidemiology in complex host-pathogen alpine systems, the long-term infectious dynamics and molecular epidemiology of Mycoplasma conjunctivae was investigated in all host populations from six study areas in the Pyrenees and one in the Cantabrian Mountains (Northern Spain). Detection of M. conjunctivae was performed by qPCR on 3600 eye swabs collected during seven years from hunted wild ungulates and sympatric domestic sheep (n = 1800 animals), and cluster analyses of the strains were performed including previous reported local strains. Mycoplasma conjunctivae was consistently detected in three Pyrenean chamois (Rupicapra p. pyrenaica) populations, as well as in sheep flocks (17.0% of sheep) and occasionally in mouflon (Ovis aries musimon) from the Pyrenees (22.2% in one year/area); statistically associated with ocular clinical signs only in chamois. Chamois populations showed different infection dynamics with low but steady prevalence (4.9%) and significant yearly fluctuations (0.0%- 40.0%). Persistence of specific M. conjunctivae strain clusters in wild host populations is demonstrated for six and nine years. Cross-species transmission between chamois and sheep and chamois and mouflon were also sporadically evidenced. Overall, independent M. conjunctivae sylvatic and domestic cycles occurred at the wildlife-livestock interface in the alpine ecosystems from the Pyrenees with sheep and chamois as the key host species for each cycle, and mouflon as a spill-over host. Host population characteristics and M. conjunctivae strains resulted in different epidemiological scenarios in chamois, ranging from the fading out of the mycoplasma to the epidemic and endemic long-term persistence. These findings highlight the capacity of M. conjunctivae to establish diverse interactions and persist in host populations, also with different transmission conditions.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0186069PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5633175PMC
October 2017

Infectious keratoconjunctivitis and occurrence of and Chlamydiaceae in small domestic ruminants from Central Karakoram, Pakistan.

Vet Rec 2017 Sep 1;181(9):237. Epub 2017 Aug 1.

Servei d'Ecopatologia de Fauna Salvatge, Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain.

Infectious keratoconjunctivitis (IKC) is a contagious eye disease primarily caused by in domestic and wild Caprinae. species have also been detected in ruminants with IKC. The objectives of this study are to investigate the ocular infection of and Chlamydiaceae and assess its interaction in relation to IKC in sheep and goats from remote communities around the Central Karakoram National Park in Pakistan, performing a combination of cross-sectional and case-control study design. Mostly asymptomatic and endemic infections of and Chlamydiaceae were found in sheep (19.3 per cent and 4.5 per cent, respectively) and goats (9.5 per cent and 1.9 per cent, respectively) from all communities, assessed by qPCR. Prevalence significantly differed between species only for (P=0.0184), which was also more prevalent in younger sheep (P<0.01). was identified by sequencing and was related with IKC only when coinfection with occurred, which suggest a synergic interaction. Cluster analysis of strains revealed higher diversity of strains than expected, evidenced interspecific transmission and suggested a higher local livestock trade than previously assumed. These results highlight the widespread occurrence of in sheep worldwide and its implications for wildlife should be assessed from a conservation perspective.
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http://dx.doi.org/10.1136/vr.103948DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738590PMC
September 2017

A review of methods used for studying the molecular epidemiology of Brachyspira hyodysenteriae.

Vet Microbiol 2017 Aug 19;207:181-194. Epub 2017 Jun 19.

Department of Clinical Sciences, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Box 7054, 750 07 Uppsala, Sweden. Electronic address:

Brachyspira (B.) spp. are intestinal spirochaetes isolated from pigs, other mammals, birds and humans. In pigs, seven Brachyspira spp. have been described, i.e. B. hyodysenteriae, B. pilosicoli, B. intermedia, B. murdochii, B. innocens, B. suanatina and B. hampsonii. Brachyspira hyodysenteriae is especially relevant in pigs as it causes swine dysentery and hence considerable economic losses to the pig industry. Furthermore, reduced susceptibility of B. hyodysenteriae to antimicrobials is of increasing concern. The epidemiology of B. hyodysenteriae infections is only partially understood, but different methods for detection, identification and typing have supported recent improvements in knowledge and understanding. In the last years, molecular methods have been increasingly used. Molecular epidemiology links molecular biology with epidemiology, offering unique opportunities to advance the study of diseases. This review is based on papers published in the field of epidemiology and molecular epidemiology of B. hyodysenteriae in pigs. Electronic databases were screened for potentially relevant papers using title and abstract and finally, Barcellos et al. papers were systemically selected and assessed. The review summarises briefly the current knowledge on B. hyodysenteriae epidemiology and elaborates on molecular typing techniques available. Results of the studies are compared and gaps in the knowledge are addressed. Finally, potential areas for future research are proposed.
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http://dx.doi.org/10.1016/j.vetmic.2017.06.011DOI Listing
August 2017

Hyperinvasiveness and increased intercellular spread of Listeria monocytogenes sequence type 1 are independent of listeriolysin S, internalin F and internalin J1.

J Med Microbiol 2017 Jul 31;66(7):1053-1062. Epub 2017 Jul 31.

Division of Neurological Sciences, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland.

Purpose: Listeria monocytogenes is a genetically heterogeneous species, which is divided into evolutionary lineages and clonal complexes (CCs). Not all L. monocytogenes isolates are equally likely to cause disease, with CC1, and in particular sequence type (ST) 1, being the most prevalent complex in human and ruminant infections and more specifically in neurolisteriosis. While the major factors that determine neurotropism are unknown, the L. monocytogenes CC1 strains harbour listeriolysin S (lls) and particular alleles of internalin (inl) F and inlJ, which are not present in CCs commonly isolated from food and the environment. The aim of this study was to analyse the role of these factors in cellular infection.

Methodology: A ST1 field strain (JF5203) from CC1 isolated from a bovine rhombencephalitis case was used to create deletion mutants. These were tested alongside the parental strain and EGD-e (CC9), in different culture models representing L. monocytogenes targets (neurons, microglia, placenta, intestine and macrophages). The phenotype was assessed by quantification of c.f.u. from cell lysates and immunofluorescence analysis.

Results: Compared to EGD-e, the ST1 strain JF5203 was hyperinvasive and exhibited increased intercellular spread. However, deletion of llsB, inlF or inlJ1, had no significant effect on infection or growth in the culture models tested.

Conclusion: Our results underline the importance of using relevant clinical strains when investigating L. monocytogenes virulence. We show that despite the association with CC1, llsB, inlF and inlJ1 are not involved in the hyperinvasiveness and efficient intercellular spread of ST1 in various cell types.
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http://dx.doi.org/10.1099/jmm.0.000529DOI Listing
July 2017

, an Evolutionary Dead-End Pathogen.

Front Microbiol 2017 9;8:1054. Epub 2017 Jun 9.

Department of Biology, Swiss Institute of Bioinformatics, University of FribourgFribourg, Switzerland.

Full genome sequences of 20 strains of , the etiological agent of blackleg of cattle and sheep, isolated from four different continents over a period of 64 years (1951-2015) were determined and analyzed. The study reveals that the genome of the species is highly homogeneous compared to the closely related species , a widespread pathogen that affects human and many animal species. Analysis of the CRISPR locus is sufficient to differentiate most strains and is the most heterogenous region in the genome, containing in total 187 different spacer elements that are distributed as 30 - 77 copies in the various strains. Some genetic differences are found in the 3 allelic variants of , and genes that encode structural flagellin proteins, and certain strains do only contain one or two alleles. However, the major virulence genes including the highly toxic , the sialidase and the two hyaluronidases are fully conserved as are the metabolic and structural genes of . These data indicate that is a strict ruminant-associated pathogen that has reached a dead end in its evolution.
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http://dx.doi.org/10.3389/fmicb.2017.01054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465433PMC
June 2017

Postepizootic Persistence of Asymptomatic Mycoplasma conjunctivae Infection in Iberian Ibex.

Appl Environ Microbiol 2017 08 17;83(15). Epub 2017 Jul 17.

Servei d'Ecopatologia de Fauna Salvatge, Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Barcelona, Spain

The susceptibility of the Iberian ibex () to ocular infection and the changes in their interaction over time were studied in terms of clinical outcome, molecular detection, and IgG immune response in a captive population that underwent a severe infectious keratoconjunctivitis (IKC) outbreak. was detected in the Iberian ibex, coinciding with the IKC outbreak. Its prevalence had a decreasing trend in 2013 that was consistent with the clinical resolution (August, 35.4%; September, 8.7%; November, 4.3%). Infections without clinical outcome were, however, still detected in the last handling in November. Sequencing and cluster analyses of the strains found 1 year later in the ibex population confirmed the persistence of the same strain lineage that caused the IKC outbreak but with a high prevalence (75.3%) of mostly asymptomatic infections and with lower DNA load of in the eyes (mean quantitative PCR [qPCR] cycle threshold [ ], 36.1 versus 20.3 in severe IKC). Significant age-related differences of prevalence were observed only under IKC epizootic conditions. No substantial effect of systemic IgG on DNA in the eye was evidenced with a linear mixed-models selection, which indicated that systemic IgG does not necessarily drive the resolution of infection and does not explain the epidemiological changes observed. The results show how both epidemiological scenarios, i.e., severe IKC outbreak and mostly asymptomatic infections, can consecutively occur by entailing mycoplasma persistence. infections are reported in a wide range of epidemiological scenarios that involve severe disease to asymptomatic infections. This study allows a better understanding of the transition between two different epidemiological scenarios described in wild host populations and highlights the ability of to adapt, persist, and establish diverse interactions with its hosts. The proportion of asymptomatic and clinical infections in a host population may not be regarded only in response to intrinsic host species traits (i.e., susceptibility) but also to a specific host-pathogen interaction, which in turn influences the infection dynamics. Both epidemic infectious keratoconjunctivitis and a high prevalence of asymptomatic infections may occur in the same host population, depending on the circulation of , its maintenance, and the progression of the host-pathogen interactions.
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http://dx.doi.org/10.1128/AEM.00690-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5514678PMC
August 2017

Remote Sensing of Potential Biosignatures from Rocky, Liquid, or Icy (Exo)Planetary Surfaces.

Astrobiology 2017 03 10;17(3):231-252. Epub 2017 Mar 10.

4 Physikalisches Institut, Universität Bern , Bern, Switzerland .

To detect signs of life by remote sensing on objects of our Solar System and on exoplanets, the characterization of light scattered by surface life material could complement possible clues given by the atmospheric composition. We reviewed the reflectance spectra of a broad selection of major biomolecules that constitute terrestrial carbon-based life from 0.4 to 2.4 μm, and we discuss their detectability through atmospheric spectral windows. Biomolecule features in the near-infrared (0.8-2.4 μm) will likely be obscured by water spectral features and some atmospheric gases. The visible range (0.4-0.8 μm), including the strong spectral features of pigments, is the most favorable. We investigated the detectability of a pigmented microorganism (Deinococcus radiodurans) when mixed with silica sand, liquid water, and water-ice particles representative of diverse surfaces of potentially habitable worlds. We measured the visible to near-infrared reflectance spectra (0.4-2.4 μm) and the visible phase curves (at 0.45 and 0.75 μm) of the mixtures to assess how the surface medium and the viewing geometry affect the detectability of the microorganisms. The results show that ice appears to be the most favorable medium for the detection of pigments. Water ice is bright and featureless from 0.4 to 0.8 μm, allowing the absorption of any pigment present in the ice to be well noticeable. We found that the visible phase curve of water ice is the most strongly affected by the presence of pigments, with variations of the spectral slope by more than a factor of 3 with phase angles. Finally, we show that the sublimation of the ice results in the concentration of the biological material onto the surface and the consequent increase of its signal. These results have applications to the search for life on icy worlds, such as Europa or Enceladus. Key Words: Remote sensing-Biosignatures-Reflectance spectroscopy-Exoplanets-Spectroscopic biosignatures-Pigments. Astrobiology 17, 231-252.
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http://dx.doi.org/10.1089/ast.2016.1523DOI Listing
March 2017

Infectious keratoconjunctivitis in wild Caprinae: merging field observations and molecular analyses sheds light on factors shaping outbreak dynamics.

BMC Vet Res 2017 Mar 4;13(1):67. Epub 2017 Mar 4.

Centre for Fish and Wildlife Health (FIWI), Vetsuisse Faculty, University of Bern, Bern, Switzerland.

Background: Infectious keratoconjunctivitis (IKC) is an ocular infectious disease caused by Mycoplasma conjunctivae which affects small domestic and wild mountain ruminants. Domestic sheep maintain the pathogen but the detection of healthy carriers in wildlife has raised the question as to whether M. conjunctivae may also persist in the wild. Furthermore, the factors shaping the dynamics of IKC outbreaks in wildlife have remained largely unknown. The aims of this study were (1) to verify the etiological role of M. conjunctivae in IKC outbreaks recorded between 2002 and 2010 at four study sites in different regions of France (Pyrenees and Alps, samples from 159 Alpine ibex Capra ibex, Alpine chamois Rupicapra rupicapra and Pyrenean chamois Rupicapra pyrenaica); (2) to establish whether there existed any epidemiological links between the different regions through a cluster analysis of the detected strains (from 80 out of the 159 animals tested); (3) to explore selected pathogen, host and environmental factors potentially influencing the dynamics of IKC in wildlife, by joining results obtained by molecular analyses and by field observations (16,609 animal observations). All of the samples were tested for M. conjunctivae by qPCR, and cluster analysis was based on a highly variable part of the lppS gene.

Results: We documented infections with M. conjunctivae in epidemic and endemic situations, both in symptomatic and asymptomatic animals. The identified M. conjunctivae strains were site-specific and persisted in the local wild population for at least 6 years. In epidemic situations, peaks of cases and disease resurgence were associated with the emergence of new similar strains in a given area. Social interactions, seasonal movements and the landscape structure such as natural and anthropogenic barriers influenced the spatio-temporal spread of IKC. Adults were more affected than young animals and host susceptibility differed depending on the involved strain.

Conclusion: Our study indicates that IKC is a multifactorial disease and that M. conjunctivae can persist in wildlife populations. The disease course in individual animals and populations is influenced by both host and mycoplasma characteristics, and the disease spread within and among populations is shaped by host behavior and landscape structure.
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http://dx.doi.org/10.1186/s12917-017-0972-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5336646PMC
March 2017

Assessing Fifty Years of General Health Surveillance of Roe Deer in Switzerland: A Retrospective Analysis of Necropsy Reports.

PLoS One 2017 19;12(1):e0170338. Epub 2017 Jan 19.

Centre for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland.

General wildlife health surveillance is a valuable source of information on the causes of mortality, disease susceptibility and pathology of the investigated hosts and it is considered to be an essential component of early warning systems. However, the representativeness of data from such surveillance programs is known to be limited by numerous biases. The roe deer (Capreolus capreolus capreolus) is the most abundant ungulate and a major game species all over Europe. Yet, internationally available literature on roe deer pathology is scarce. The aims of this study were (1) to provide an overview of the causes of mortality or morbidity observed in roe deer in Switzerland and to assess potential changes in the disease pattern over time; and (2) to evaluate the value and limitations of a long term dataset originating from general wildlife health surveillance. We compiled 1571 necropsy reports of free ranging roe deer examined at the Centre for Fish and Wildlife Health in Switzerland from 1958 to 2014. Descriptive data analysis was performed considering animal metadata, submitter, pathologist in charge, laboratory methods, morphological diagnoses and etiologies. Recurrent causes of mortality and disease pictures included pneumonia, diarrhea, meningoencephalitis, actinomycosis, blunt trauma, predation, neoplasms and anomalies. By contrast, other diagnoses such as fatal parasitic gastritis, suspected alimentary intoxication and reproductive disorders appeared only in earlier time periods. Diseases potentially relevant for other animals or humans such as caseous lymphadenitis (or pseudotuberculosis), salmonellosis, paratuberculosis and listeriosis were sporadically observed. The disease pattern in roe deer from Switzerland was largely in accordance with previous reports. The observed fluctuations were consistent with methodical and/or personnel changes and varying disease awareness. Nevertheless, despite such limitations, the compiled data provide a valuable baseline. To facilitate comparison among studies, we recommend systematically archiving all case documents and fixed tissues and to perform data analyses more regularly and in a harmonized way.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170338PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5245894PMC
August 2017

Whole genome SNP analysis of bovine B. anthracis strains from Switzerland reflects strict regional separation of Simmental and Swiss Brown breeds in the past.

Vet Microbiol 2016 Nov 11;196:1-8. Epub 2016 Oct 11.

Institute of Veterinary Bacteriology, Vetsuisse, University of Bern, Laenggasstrasse 122, 3001 Bern, Switzerland. Electronic address:

Bacillus anthracis is an evolutionarily young species that presents an extremely low genetic diversity due to its slow mode of propagation, determined by short replication phases and long sporulation periods. In our ongoing efforts to elucidate phylogenetic relationships between European B. anthracis isolates, the genomes of five strains from Switzerland belonging to lineages B.Br.CNEVA and A.Br.Aust94 were sequenced. Comparative analysis with additional, available genomes from both lineages, were used to reconstruct the substructure of these populations. Genome-wide single-nucleotide polymorphism analysis revealed two phylogeographical different groups among the Swiss B.Br.CNEVA strains (central and eastern Switzerland), that define the oldest most recent common ancestor of the B.Br.CNEVA lineage currently known. Age-old practices of livestock selection, breeding and preservation of unique traits of local breeds in Alpine valleys have likely favored differentiation of regional B. anthracis populations over centuries and the emergence of genetically distinct strains in an otherwise similar environment.
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http://dx.doi.org/10.1016/j.vetmic.2016.10.014DOI Listing
November 2016

Listeria monocytogenes sequence type 1 is predominant in ruminant rhombencephalitis.

Sci Rep 2016 11 16;6:36419. Epub 2016 Nov 16.

Division of Neurological Sciences, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Switzerland.

Listeria (L.) monocytogenes is an opportunistic pathogen causing life-threatening infections in diverse mammalian species including humans and ruminants. As little is known on the link between strains and clinicopathological phenotypes, we studied potential strain-associated virulence and organ tropism in L. monocytogenes isolates from well-defined ruminant cases of clinical infections and the farm environment. The phylogeny of isolates and their virulence-associated genes were analyzed by multilocus sequence typing (MLST) and sequence analysis of virulence-associated genes. Additionally, a panel of representative isolates was subjected to in vitro infection assays. Our data suggest the environmental exposure of ruminants to a broad range of strains and yet the strong association of sequence type (ST) 1 from clonal complex (CC) 1 with rhombencephalitis, suggesting increased neurotropism of ST1 in ruminants, which is possibly related to its hypervirulence. This study emphasizes the importance of considering clonal background of L. monocytogenes isolates in surveillance, epidemiological investigation and disease control.
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http://dx.doi.org/10.1038/srep36419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111077PMC
November 2016

Comparative genomics of Bacillus anthracis from the wool industry highlights polymorphisms of lineage A.Br.Vollum.

Infect Genet Evol 2016 12 25;46:50-58. Epub 2016 Oct 25.

Institute of Veterinary Bacteriology, Vetsuisse, University of Bern, Laenggasstrasse 122, 3001 Bern, Switzerland. Electronic address:

Background: With the advent of affordable next-generation sequencing (NGS) technologies, major progress has been made in the understanding of the population structure and evolution of the B. anthracis species. Here we report the use of whole genome sequencing and computer-based comparative analyses to characterize six strains belonging to the A.Br.Vollum lineage. These strains were isolated in Switzerland, in 1981, during iterative cases of anthrax involving workers in a textile plant processing cashmere wool from the Indian subcontinent.

Results: We took advantage of the hundreds of currently available B. anthracis genomes in public databases, to investigate the genetic diversity existing within the A.Br.Vollum lineage and to position the six Swiss isolates into the worldwide B. anthracis phylogeny. Thirty additional genomes related to the A.Br.Vollum group were identified by whole-genome single nucleotide polymorphism (SNP) analysis, including two strains forming a new evolutionary branch at the basis of the A.Br.Vollum lineage. This new phylogenetic lineage (termed A.Br.H9401) splits off the branch leading to the A.Br.Vollum group soon after its divergence to the other lineages of the major A clade (i.e. 6 SNPs). The available dataset of A.Br.Vollum genomes were resolved into 2 distinct groups. Isolates from the Swiss wool processing facility clustered together with two strains from Pakistan and one strain of unknown origin isolated from yarn. They were clearly differentiated (69 SNPs) from the twenty-five other A.Br.Vollum strains located on the branch leading to the terminal reference strain A0488 of the lineage. Novel analytic assays specific to these new subgroups were developed for the purpose of rapid molecular epidemiology.

Conclusions: Whole genome SNP surveys greatly expand upon our knowledge on the sub-structure of the A.Br.Vollum lineage. Possible origin and route of spread of this lineage worldwide are discussed.
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http://dx.doi.org/10.1016/j.meegid.2016.10.019DOI Listing
December 2016

Design of an Immersion Vaccine Against Aeromonad Septicemia in Perch (Perca fluviatilis L.).

Methods Mol Biol 2016 ;1404:203-209

Centre for Fish and Wildlife Health, Vetsuisse, University of Bern, Bern, Switzerland.

The production of an immersion vaccine and the vaccination procedure to immunize fry of perch (Perca fluviatilis L.) against pathogenic Aeromonas sobria that harbor a type III secretion system is described. The vaccine, based on chemically inactivated A. sobria, enables rapid vaccination of a large number of fish by immersion of fry in an aqueous vaccine suspension during 5 min, giving them high protection during fattening under open water conditions in a freshwater lake for at least 4 months.
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http://dx.doi.org/10.1007/978-1-4939-3389-1_14DOI Listing
December 2016

Erratum for Henke et al., Listeria monocytogenes Spreads within the Brain by Actin-Based Intra-Axonal Migration.

Infect Immun 2016 Mar 24;84(3):866. Epub 2016 Feb 24.

Division of Neurological Sciences, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland.

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http://dx.doi.org/10.1128/IAI.00003-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4771342PMC
March 2016