scholarly journals Genomic Dissection of an Icelandic Epidemic of Equine Respiratory Disease

2016 ◽  
Author(s):  
Sigríður Björnsdóttir ◽  
Simon R. Harris ◽  
Vilhjálmur Svansson ◽  
Eggert Gunnarsson ◽  
Ólöf G. Sigurðardóttirr ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Respiratory Disease ◽  
Bacterial Species ◽  
Opportunistic Pathogen ◽  
Broad Host Range ◽  
Streptococcus Zooepidemicus ◽  
Epidemiological Investigation ◽  
Horse Population ◽  
Pathogenic Potential ◽  
Zoonotic Infections

ABSTRACTThe native horse population of Iceland has remained free of major infectious diseases. Between May and July 2010 an epidemic of respiratory disease swept through the population. Initial microbiological investigations ruled out known equine viral agents as the cause of the infections, but identified the opportunistic pathogenStreptococcus zooepidemicusas being frequently isolated from diseased animals. This diverse bacterial species has a broad host range and is usually regarded as a commensal of horses. By genome sequencingS. zooepidemicusrecovered from horses during the epidemic we show that although multiple clones ofS. zooepidemicuswere present in the population, one particular clone, ST209, was responsible for the epidemic. Concurrent with the epidemic, ST209 caused zoonotic infections, highlighting the pathogenic potential of this clone. Phylogenetic analysis suggests that the original ST209 strain entered Iceland in late 2008 or early 2009. Epidemiological investigation revealed that the incursion of this strain into a training yard that utilized a submerged treadmill between the 5thand 19thof February 2010 was a critical trigger for the ensuing epidemic of disease, provided a nidus for the infection of multiple horses, and subsequent distribution of these animals to multiple sites in Iceland.

scholarly journals Phylogenetic Analysis ofStenotrophomonasspp. Isolates Contributes to the Identification of Nosocomial and Community-Acquired Infections

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Vinicius Godoy Cerezer ◽  
Silvia Yumi Bando ◽  
Jacyr Pasternak ◽  
Marcia Regina Franzolin ◽  
Carlos Alberto Moreira-Filho
Keyword(s):  
Phylogenetic Analysis ◽  
Multidrug Resistance ◽  
Phylogenetic Profile ◽  
Opportunistic Pathogen ◽  
Clinical Isolates ◽  
Environmental Distribution ◽  
Pathogenic Potential ◽  
Clinical Strains ◽  
Specific Fragment ◽  
Clonal Variability

Stenotrophomonasssp. has a wide environmental distribution and is also found as an opportunistic pathogen, causing nosocomial or community-acquired infections. One species,S. maltophilia, presents multidrug resistance and has been associated with serious infections in pediatric and immunocompromised patients. Therefore, it is relevant to conduct resistance profile and phylogenetic studies in clinical isolates for identifying infection origins and isolates with augmented pathogenic potential. Here, multilocus sequence typing was performed for phylogenetic analysis of nosocomial isolates ofStenotrophomonasspp. and, environmental and clinical strains ofS. maltophilia. Biochemical and multidrug resistance profiles of nosocomial and clinical strains were determined. The inferred phylogenetic profile showed high clonal variability, what correlates with the adaptability process ofStenotrophomonasto different habitats. Two clinical isolates subgroups ofS. maltophiliasharing high phylogenetic homogeneity presented intergroup recombination, thus indicating the high permittivity to horizontal gene transfer, a mechanism involved in the acquisition of antibiotic resistance and expression of virulence factors. For most of the clinical strains, phylogenetic inference was made using only partialppsA gene sequence. Therefore, the sequencing of just one specific fragment of this gene would allow, in many cases, determining whether the infection withS. maltophiliawas nosocomial or community-acquired.

scholarly journals Cocirculation of Two Distinct Genetic and Antigenic Lineages of Proposed Influenza D Virus in Cattle

2014 ◽  
Vol 89 (2) ◽  
pp. 1036-1042 ◽  
Author(s):  
Emily A. Collin ◽  
Zizhang Sheng ◽  
Yuekun Lang ◽  
Wenjun Ma ◽  
Ben M. Hause ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Influenza Virus ◽  
Respiratory Disease ◽  
New Genus ◽  
Cross Reactivity ◽  
Surface Glycoprotein ◽  
Clinical Samples ◽  
Genome Sequences ◽  
Antigenic Analysis ◽  
Pathogenic Potential

ABSTRACTViruses with approximately 50% homology to human influenza C virus (ICV) have recently been isolated from swine and cattle. The overall low homology to ICV, lack of antibody cross-reactivity to ICV in hemagglutination inhibition (HI) and agar gel immunodiffusion assays, and inability to productively reassort with ICV led to the proposal that these viruses represented a new genus of influenza virus, influenzavirus D (IDV). To further our understanding of the epidemiology of IDV, real-time reverse transcription-PCR was performed on a set of 208 samples from bovines with respiratory disease. Ten samples (4.8%) were positive and six viruses were successfully isolatedin vitro. Phylogenetic analysis of full-genome sequences of these six new viruses and four previously reported viruses revealed two distinct cocirculating lineages represented by D/swine/Oklahoma/1334/2011 (D/OK) and D/bovine/Oklahoma/660/2013 (D/660), which frequently reassorted with one another. Antigenic analysis using the HI assay and lineage-representative D/OK and D/660 antiserum found up to an approximate 10-fold loss in cross-reactivity against heterologous clade antiserum. One isolate, D/bovine/Texas/3-13/2011 (D/3-13), clustered with the D/660 lineage, but also had high HI titers to heterologous (D/OK) clade antiserum. Molecular modeling of the hemagglutinin esterase fusion protein of D/3-13 identified a mutation at position 212 as a possible antigenic determinant responsible for the discrepant HI results. These results suggest that IDV is common in bovines with respiratory disease and that at least two genetic and antigenically distinct clades cocirculate.IMPORTANCEA novel bovine influenza virus was recently identified. Detailed genetic and antigenic studies led to the proposal that this virus represents a new genus of influenza, influenzavirus D (IDV). Here, we show that IDV is common in clinical samples of bovine respiratory disease complex (BRDC), with a prevalence similar to that of other established BRDC etiological agents. These results are in good agreement with the near-ubiquitous seroprevalence of IDV previously found. Phylogenetic analysis of complete genome sequences found evidence for two distinct cocirculating lineages of IDV which freely reassort. Significant antigenic differences, which generally agreed with the surface glycoprotein hemagglutinin esterase phylogeny, were observed between the two lineages. Based on these results, and on the ability of IDV to infect and transmit in multiple mammalian species, additional studies to determine the pathogenic potential of IDV are warranted.

scholarly journals Genomic Dissection of an Icelandic Epidemic of Respiratory Disease in Horses and Associated Zoonotic Cases

mBio ◽  
2017 ◽  
Vol 8 (4) ◽  
Author(s):  
Sigríður Björnsdóttir ◽  
Simon R. Harris ◽  
Vilhjálmur Svansson ◽  
Eggert Gunnarsson ◽  
Ólöf G. Sigurðardóttir ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Respiratory Disease ◽  
Genome Sequencing ◽  
Causative Agent ◽  
Opportunistic Pathogen ◽  
Whole Genome ◽  
National Scale ◽  
Horse Population ◽  
Viral Pathogen ◽  
First Time

ABSTRACT Iceland is free of the major infectious diseases of horses. However, in 2010 an epidemic of respiratory disease of unknown cause spread through the country’s native horse population of 77,000. Microbiological investigations ruled out known viral agents but identified the opportunistic pathogen Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) in diseased animals. We sequenced the genomes of 257 isolates of S. zooepidemicus to differentiate epidemic from endemic strains. We found that although multiple endemic clones of S. zooepidemicus were present, one particular clone, sequence type 209 (ST209), was likely to have been responsible for the epidemic. Concurrent with the epidemic, ST209 was also recovered from a human case of septicemia, highlighting the pathogenic potential of this strain. Epidemiological investigation revealed that the incursion of this strain into one training yard during February 2010 provided a nidus for the infection of multiple horses that then transmitted the strain to farms throughout Iceland. This study represents the first time that whole-genome sequencing has been used to investigate an epidemic on a national scale to identify the likely causative agent and the link to an associated zoonotic infection. Our data highlight the importance of national biosecurity to protect vulnerable populations of animals and also demonstrate the potential impact of S. zooepidemicus transmission to other animals, including humans. IMPORTANCE An epidemic of respiratory disease affected almost the entire native Icelandic horse population of 77,000 animals in 2010, resulting in a self-imposed ban on the export of horses and significant economic costs to associated industries. Although the speed of transmission suggested that a viral pathogen was responsible, only the presence of the opportunistic pathogen Streptococcus zooepidemicus was consistent with the observed clinical signs. We applied genomic sequencing to differentiate epidemic from endemic strains and to shed light on the rapid transmission of the epidemic strain throughout Iceland. We further highlight the ability of epidemic and endemic strains of S. zooepidemicus to infect other animals, including humans. This study represents the first time that whole-genome sequencing has been used to elucidate an outbreak on a national scale and identify the likely causative agent. An epidemic of respiratory disease affected almost the entire native Icelandic horse population of 77,000 animals in 2010, resulting in a self-imposed ban on the export of horses and significant economic costs to associated industries. Although the speed of transmission suggested that a viral pathogen was responsible, only the presence of the opportunistic pathogen Streptococcus zooepidemicus was consistent with the observed clinical signs. We applied genomic sequencing to differentiate epidemic from endemic strains and to shed light on the rapid transmission of the epidemic strain throughout Iceland. We further highlight the ability of epidemic and endemic strains of S. zooepidemicus to infect other animals, including humans. This study represents the first time that whole-genome sequencing has been used to elucidate an outbreak on a national scale and identify the likely causative agent.

scholarly journals Closed Genome Sequences and Antibiograms of 16 Pasteurella multocida Isolates from Bovine Respiratory Disease Complex Cases and Apparently Healthy Controls

2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Gregory P. Harhay ◽  
Dayna M. Harhay ◽  
James L. Bono ◽  
Timothy P. L. Smith ◽  
Sarah F. Capik ◽  
...  
Keyword(s):  
Respiratory Disease ◽  
Pasteurella Multocida ◽  
Bacterial Species ◽  
Bovine Respiratory Disease ◽  
Opportunistic Pathogen ◽  
Feedlot Cattle ◽  
Content Type ◽  
Disease Complex ◽  
Bovine Respiratory Disease Complex ◽  
Apparently Healthy

Pasteurella multocida is an animal-associated Gram-negative member of the Pasteurellaceae family. It is an opportunistic pathogen and is one of the principal bacterial species contributing to bovine respiratory disease complex (BRDC) in feedlot cattle.

scholarly journals Moraxella catarrhalis: from Emerging to Established Pathogen

2002 ◽  
Vol 15 (1) ◽  
pp. 125-144 ◽  
Author(s):  
Cees M. Verduin ◽  
Cees Hol ◽  
André Fleer ◽  
Hans van Dijk ◽  
Alex van Belkum
Keyword(s):  
Moraxella Catarrhalis ◽  
Current Knowledge ◽  
Bacterial Species ◽  
Bacterial Pathogen ◽  
Diagnostic Techniques ◽  
Human Infection ◽  
Molecular Diagnostic ◽  
Molecular Diagnostic Techniques ◽  
Pathogenic Potential ◽  
The Past

SUMMARY Moraxella catarrhalis (formerly known as Branhamella catarrhalis) has emerged as a significant bacterial pathogen of humans over the past two decades. During this period, microbiological and molecular diagnostic techniques have been developed and improved for M. catarrhalis, allowing the adequate determination and taxonomic positioning of this pathogen. Over the same period, studies have revealed its involvement in respiratory (e.g., sinusitis, otitis media, bronchitis, and pneumonia) and ocular infections in children and in laryngitis, bronchitis, and pneumonia in adults. The development of (molecular) epidemiological tools has enabled the national and international distribution of M. catarrhalis strains to be established, and has allowed the monitoring of nosocomial infections and the dynamics of carriage. Indeed, such monitoring has revealed an increasing number of Β-lactamase-positive M. catarrhalis isolates (now well above 90%), underscoring the pathogenic potential of this organism. Although a number of putative M. catarrhalis virulence factors have been identified and described in detail, their relationship to actual bacterial adhesion, invasion, complement resistance, etc. (and ultimately their role in infection and immunity), has been established in a only few cases. In the past 10 years, various animal models for the study of M. catarrhalis pathogenicity have been described, although not all of these models are equally suitable for the study of human infection. Techniques involving the molecular manipulation of M. catarrhalis genes and antigens are also advancing our knowledge of the host response to and pathogenesis of this bacterial species in humans, as well as providing insights into possible vaccine candidates. This review aims to outline our current knowledge of M. catarrhalis, an organism that has evolved from an emerging to a well-established human pathogen.

scholarly journals Genetic and phenotypic analysis of the pathogenic potential of two novel Chlamydia gallinacea strains compared to Chlamydia psittaci

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marloes Heijne ◽  
Martina Jelocnik ◽  
Alexander Umanets ◽  
Michael S. M. Brouwer ◽  
Annemieke Dinkla ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Opportunistic Pathogen ◽  
Chlamydia Psittaci ◽  
Phenotypic Analysis ◽  
Pathogenic Potential ◽  
The Family ◽  
Chicken Eggs ◽  
Sequence Types ◽  
Insight Into ◽  
Embryonated Chicken

AbstractChlamydia gallinacea is an obligate intracellular bacterium that has recently been added to the family of Chlamydiaceae. C. gallinacea is genetically diverse, widespread in poultry and a suspected cause of pneumonia in slaughterhouse workers. In poultry, C. gallinacea infections appear asymptomatic, but studies about the pathogenic potential are limited. In this study two novel sequence types of C. gallinacea were isolated from apparently healthy chickens. Both isolates (NL_G47 and NL_F725) were closely related to each other and have at least 99.5% DNA sequence identity to C. gallinacea Type strain 08-1274/3. To gain further insight into the pathogenic potential, infection experiments in embryonated chicken eggs and comparative genomics with Chlamydia psittaci were performed. C. psittaci is a ubiquitous zoonotic pathogen of birds and mammals, and infection in poultry can result in severe systemic illness. In experiments with embryonated chicken eggs, C. gallinacea induced mortality was observed, potentially strain dependent, but lower compared to C. psittaci induced mortality. Comparative analyses confirmed all currently available C. gallinacea genomes possess the hallmark genes coding for known and potential virulence factors as found in C. psittaci albeit to a reduced number of orthologues or paralogs. The presence of potential virulence factors and the observed mortality in embryonated eggs indicates C. gallinacea should rather be considered as an opportunistic pathogen than an innocuous commensal.

scholarly journals Serological Survey of Leptospira Infection in Arabian Horses in Poland

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 688
Author(s):  
Bernard Wasiński ◽  
Katarzyna Paschalis-Trela ◽  
Jan Trela ◽  
Michał Czopowicz ◽  
Jerzy Kita ◽  
...  
Keyword(s):  
Companion Animals ◽  
Laboratory Diagnosis ◽  
Serological Survey ◽  
Serum Samples ◽  
Horse Population ◽  
Zoonotic Infections ◽  
Clinical Presentations ◽  
Arabian Horse ◽  
Breeding Farms

Leptospirosis is one of the most common zoonotic infections worldwide, including in most livestock, some companion animals, horses, wildlife, and humans. Epidemiological estimation of its prevalence in all species is difficult due to the variety of clinical presentations and challenges regarding laboratory diagnosis. The purpose of this study was to measure the seroprevalence of leptospiral infection in Arabian horses kept in the largest breeding farms in Poland, representing over 15% of the Polish Arabian horse population. Leptospira antibodies were detected by MAT (cut-off 1:100) in 33.2% of serum samples (204 of 615 animals) (CI 95%: 29.6–37.0%), most frequently reacting with the serovar Grippotyphosa, similar to previous reports in populations of randomly selected horses. These results indicated high Leptospira seropositivity, thus, although any form of clinical leptospirosis is rare, it may be postulated that the leptospiral exposure is widespread.

scholarly journals No Change, No Life? What We Know about Phase Variation in Staphylococcus aureus

2021 ◽  
Vol 9 (2) ◽  
pp. 244
Author(s):  
Vishal Gor ◽  
Ryosuke L. Ohniwa ◽  
Kazuya Morikawa
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
High Frequency ◽  
Direct Evidence ◽  
Bacterial Species ◽  
Phase Variation ◽  
Opportunistic Pathogen ◽  
Adaptation Strategy ◽  
Innate Immune ◽  
Epigenetic Mechanisms

Phase variation (PV) is a well-known phenomenon of high-frequency reversible gene-expression switching. PV arises from genetic and epigenetic mechanisms and confers a range of benefits to bacteria, constituting both an innate immune strategy to infection from bacteriophages as well as an adaptation strategy within an infected host. PV has been well-characterized in numerous bacterial species; however, there is limited direct evidence of PV in the human opportunistic pathogen Staphylococcus aureus. This review provides an overview of the mechanisms that generate PV and focuses on earlier and recent findings of PV in S. aureus, with a brief look at the future of the field.

scholarly journals Phylogenetic and Haplotype Network Analyses of Diaporthe eres Species in China Based on Sequences of Multiple Loci

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 179
Author(s):  
Chingchai Chaisiri ◽  
Xiangyu Liu ◽  
Yang Lin ◽  
Yanping Fu ◽  
Fuxing Zhu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Elongation Factor ◽  
Haplotype Network ◽  
Population Diversity ◽  
Plant Diseases ◽  
Broad Host Range ◽  
Internal Transcribed Spacer Region ◽  
Chinese Populations ◽  
Network Analyses ◽  
Haplotype Networks

Diaporthe eres is considered one of the most important causal agents of many plant diseases, with a broad host range worldwide. In this study, multiple sequences of ribosomal internal transcribed spacer region (ITS), translation elongation factor 1-α gene (EF1-α), beta-tubulin gene (TUB2), calmodulin gene (CAL), and histone-3 gene (HIS) were used for multi-locus phylogenetic analysis. For phylogenetic analysis, maximum likelihood (ML), maximum parsimony (MP), and Bayesian inferred (BI) approaches were performed to investigate relationships of D. eres with closely related species. The results strongly support that the D. eres species falls into a monophyletic lineage, with the characteristics of a species complex. Phylogenetic informativeness (PI) analysis showed that clear boundaries could be proposed by using EF1-α, whereas ITS showed an ineffective reconstruction and, thus, was unsuitable for speciating boundaries for Diaporthe species. A combined dataset of EF1-α, CAL, TUB2, and HIS showed strong resolution for Diaporthe species, providing insights for the D. eres complex. Accordingly, besides D. biguttusis, D. camptothecicola, D. castaneae-mollissimae, D. cotoneastri, D. ellipicola, D. longicicola, D. mahothocarpus, D. momicola, D. nobilis, and Phomopsis fukushii, which have already been previously considered the synonymous species of D. eres, another three species, D. henanensis, D. lonicerae and D. rosicola, were further revealed to be synonyms of D. eres in this study. In order to demonstrate the genetic diversity of D. eres species in China, 138 D. eres isolates were randomly selected from previous studies in 16 provinces. These isolates were obtained from different major plant species from 2006 to 2020. The genetic distance was estimated with phylogenetic analysis and haplotype networks, and it was revealed that two major haplotypes existed in the Chinese populations of D. eres. The haplotype networks were widely dispersed and not uniquely correlated to specific populations. Overall, our analyses evaluated the phylogenetic identification for D. eres species and demonstrated the population diversity of D. eres in China.

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