Shinto John - Academia.edu (original) (raw)

Papers by Shinto John

Journal of Comparative Pathology, May 1, 2023

Journal of Wildlife Diseases, Oct 9, 2019

Two adult great spotted woodpeckers (Dendrocopos major) from separate sites in Great Britain were... more Two adult great spotted woodpeckers (Dendrocopos major) from separate sites in Great Britain were examined post mortem in 2013 and 2016. A Salmonella sp. was isolated from multiple tissues in both birds. Histopathology and immunohistochemistry confirmed disseminated salmonellosis. Whole genome sequencing and biochemical analyses putatively identified both isolates as a novel variant of Salmonella enterica subsp. enterica serovar Hessarek (S. Hessarek). Salmonellosis has seldom been reported in Piciformes, and never before in association with S. Hessarek infection. These findings, therefore, add to current knowledge regarding the range of wild bird species susceptible to this Salmonella serovar, and our understanding of the pathogens affecting great spotted woodpeckers, in particular.

Scientific Reports, Oct 10, 2018

Proliferative leg skin lesions have been described in wild finches in Europe although there have ... more Proliferative leg skin lesions have been described in wild finches in Europe although there have been no large-scale studies of their aetiology or epizootiology to date. Firstly, disease surveillance, utilising public reporting of observations of live wild finches was conducted in Great Britain (GB) and showed proliferative leg skin lesions in chaffinches (Fringilla coelebs) to be widespread. Seasonal variation was observed, with a peak during the winter months. Secondly, pathological investigations were performed on a sample of 39 chaffinches, four bullfinches (Pyrrhula pyrrhula), one greenfinch (Chloris chloris) and one goldfinch (Carduelis carduelis) with proliferative leg skin lesions and detected Cnemidocoptes sp. mites in 91% (41/45) of affected finches and from all species examined. Fringilla coelebs papillomavirus (FcPV1) PCR was positive in 74% (23/31) of birds tested: a 394 base pair sequence was derived from 20 of these birds, from all examined species, with 100% identity to reference genomes. Both mites and FcPV1 DNA were detected in 71% (20/28) of birds tested for both pathogens. Histopathological examination of lesions did not discriminate the relative importance of mite or FcPV1 infection as their cause. Development of techniques to localise FcPV1 within lesions is required to elucidate the pathological significance of FcPV1 DNA detection. The epidemiology and impact of diseases of wild birds that cause morbidity, but are not typically associated with mortality, are often poorly understood. Papillomatosis and cnemidocoptosis are each diseases characterised by proliferative leg skin lesions in British finches (family Fringillidae) which, although often seen, are infrequently reported as causing mortality. The chaffinch (Fringilla coelebs) is most frequently affected and lesions typically affect the non-feathered areas of the legs, feet and digits 1-3. When severe, the skin lesions can interfere with locomotion, lead to digit distortion, loss and/or lameness and may predispose to entanglement or predation 1,3 (BL personal communication). Papillomaviruses are epitheliotropic, double-stranded DNA viruses that are generally considered hostspecific 2,3. Fringilla coelebs papillomavirus (FcPV1) is one of eight known to infect birds 4-8. The small number of avian papillomavirus species is in contrast to the high number detected in mammals. Of known papillomaviruses, 344 of 353 are found in mammals; of which 180 are known only from humans (the Papillomavirus Episteme is available at https://pave.niaid.nih.gov/). It is unclear whether the relative paucity of papillomaviruses in non-mammalian taxa is real or due to sampling bias 9. Chaffinches with proliferative leg skin lesions associated with papillomavirus infection have been described from multiple countries in western, northern and central Europe, including the Czech Republic, Germany, Great Britain, Italy, Sweden and the Netherlands 6,10-14. Papillomavirus from similar leg skin lesions has been reported less commonly in wild brambling (Fringilla montifringilla), wild bullfinch (Pyrrhula pyrrhula) and captive greenfinch (Chloris chloris) 2,6,15. The macroscopic appearance of these proliferative leg skin lesions has been described generally as (squamous) papillomas and wart-like growths and more specifically as nodular or hyperplastic

Research Square (Research Square), Sep 15, 2022

Escherichia albertii is a recently identi ed gastrointestinal bacterial pathogen of humans and an... more Escherichia albertii is a recently identi ed gastrointestinal bacterial pathogen of humans and animals which is typically misidenti ed and generally only detected during genomic surveillance of other Enterobacteriaceae. The incidence of E. albertii is likely underestimated and its epidemiology and clinical relevance are poorly characterised. Here, we whole genome sequenced E. albertii isolates from humans (n = 83) and birds (n = 79) in Great Britain and analysed a broader public dataset (n = 475) to address these gaps. We found human and avian isolates typically (90%; 148/164) belonged to host-associated monophyletic groups with distinct virulence and antimicrobial resistance pro les. Overlaid patient epidemiological data suggested that human infection was likely related to travel and possibly foodborne transmission. The Shiga toxin encoding stx2f gene was associated with clinical disease (OR = 10.27, 95% CI = 2.98-35.45 p = 0.0002) in nches. Our results suggest that improved future surveillance will further elucidate disease ecology and public and animal health risks associated with E. albertii.

Epidemiology and Infection, 2019

Disease surveillance in wildlife populations presents a logistical challenge, yet is critical in ... more Disease surveillance in wildlife populations presents a logistical challenge, yet is critical in gaining a deeper understanding of the presence and impact of wildlife pathogens. Erinaceus coronavirus (EriCoV), a clade C Betacoronavirus, was first described in Western European hedgehogs (Erinaceus europaeus) in Germany. Here, our objective was to determine whether EriCoV is present, and if it is associated with disease, in Great Britain (GB). An EriCoV-specific BRYT-Green® real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Viral RNA was detected in 10.8% (38) samples; however, the virus was not detected in any of the 61 samples tested from Scotland. The full genome sequence of the British EriCoV strain was determined using next generation sequencing; it shared 94% identity with a German EriCoV sequence. Multivariate statistical models using hedgehog case history data, faecal specimen descriptions and post-mortem examination findings found no significant associations indicative of disease associated with EriCoV in hedgehogs. These findings indicate that the Western European hedgehog is a reservoir host of EriCoV in the absence of apparent disease.

Journal of Avian Medicine and Surgery, Dec 1, 2005

Ecohealth, Jun 20, 2014

The significance of chlamydiosis as a cause of mortality in wild passerines (Order Passeriformes)... more The significance of chlamydiosis as a cause of mortality in wild passerines (Order Passeriformes), and the role of these birds as a potential source of zoonotic Chlamydia psittaci infection, is unknown. We reviewed wild bird mortality incidents (2005-2011). Where species composition or post-mortem findings were indicative of chlamydiosis, we examined archived tissues for C. psittaci infection using PCR and ArrayTube Microarray assays. Twenty-one of 40 birds tested positive: 8 dunnocks (Prunella modularis), 7 great tits (Parus major), 3 blue tits (Cyanistes caeruleus), 2 collared doves (Streptopelia decaocto, Order Columbiformes), and 1 robin (Erithacus rubecula). Chlamydia psittaci genotype A was identified in all positive passerines and in a further three dunnocks and three robins diagnosed with chlamydiosis from a previous study. Two collared doves had genotype E. Ten of the 21 C. psittaci-positive birds identified in the current study had histological lesions consistent with chlamydiosis and co-localizing Chlamydia spp. antigens on immunohistochemistry. Our results indicate that chlamydiosis may be a more common disease of British passerines than was previously recognized. Wild passerines may be a source of C. psittaci zoonotic infection, and people should be advised to take appropriate hygiene precautions when handling bird feeders or wild birds.

Applied and Environmental Microbiology, Nov 15, 2011

Salmonellosis is a frequently diagnosed infectious disease of passerine birds in garden habitats ... more Salmonellosis is a frequently diagnosed infectious disease of passerine birds in garden habitats within Great Britain with potential implications for human and domestic animal health. Postmortem examinations were performed on 1,477 garden bird carcasses of circa 50 species from England and Wales, 1999 to 2007 inclusive. Salmonellosis was confirmed in 263 adult birds of 10 passerine species in this 11-year longitudinal study. A subset of 124 fully biotyped Salmonella enterica subsp. enterica serovar Typhimurium isolates was examined using pulsed-field gel electrophoresis to investigate the hypothesis that these strains are host adapted and to determine whether this molecular technique offers greater resolution in understanding the epidemiology of Salmonella Typhimurium infection than phage typing alone. For the two most common phage types, definitive type (DT) 40 and DT56v, which together accounted for 97% (120/124) of isolates, pulsed-field gel electrophoresis groupings closely correlated with phage type with remarkably few exceptions. A high degree of genetic similarity (>90%) was observed within and between the two most common pulsed-field gel electrophoresis groups. No clustering or variation was found in the pulsed-field gel electrophoresis groupings by bird species, year, or geographical region beyond that revealed by phage typing. These findings support the hypothesis that there are currently two host-adapted Salmonella phage types, S. Typhimurium DT40 and DT56v, circulating widely in British garden birds and that the reservoir of infection is maintained within wild bird populations. Large-scale multilocus sequence typing studies are required to further investigate the epidemiology of this infection.

Infection, Genetics and Evolution, Oct 1, 2011

Trichomonas gallinae is a protozoan parasite that is well characterised as a cause of trichomonos... more Trichomonas gallinae is a protozoan parasite that is well characterised as a cause of trichomonosis in columbid and raptor species worldwide. The parasite emerged as a novel infection of British passerines in 2005, leading to epidemic mortality associated with significant declines of breeding populations of greenfinches (Carduelis chloris) and chaffinches (Fringilla coelebs). We characterised the extent of T. gallinae genotypic heterogeneity within the affected wild British avifauna by analysing individual isolates from 17 of the species affected. To do so, we employed improved platform-based multilocus typing tools as well as the hydrogenosomal Fe-hydrogenase gene as a single marker locus for fine-typing. We found no evidence of heterogeneity amongst the parasites infecting British passerines, indicating that a clonal strain of T. gallinae is the causative agent of this emerging infectious disease.

Nature Communications, Mar 27, 2023

Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and a... more Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and animals which is typically misidentified as pathotypes of diarrhoeagenic Escherichia coli or Shigella species and is generally only detected during genomic surveillance of other Enterobacteriaceae. The incidence of E. albertii is likely underestimated, and its epidemiology and clinical relevance are poorly characterised. Here, we whole genome sequenced E. albertii isolates from humans (n = 83) and birds (n = 79) isolated in Great Britain between 2000 and 2021 and analysed these alongside a broader public dataset (n = 475) to address these gaps. We found human and avian isolates typically (90%; 148/ 164) belonged to host-associated monophyletic groups with distinct virulence and antimicrobial resistance profiles. Overlaid patient epidemiological data suggested that human infection was likely related to travel and possibly foodborne transmission. The Shiga toxin encoding stx2f gene was associated with clinical disease (OR = 10.27, 95% CI = 2.98-35.45 p = 0.0002) in finches. Our results suggest that improved future surveillance will further elucidate disease ecology and public and animal health risks associated with E. albertii. Escherichia albertii, a Gram-negative gastrointestinal pathogen of humans and animals, was first confirmed as a novel bacterium in 2003 1-3. This pathogen is often misidentified because it is difficult to differentiate from Shigella species as they are morphologically, colonially, metabolically and biochemically similar; for example, both are non-lactose fermenting and lysine decarboxylase negative 4,5. Implementation of PCR for the detection of a wide range of gastrointestinal (GI) pathogens, including diarrhoeagenic E. coli (DEC), and the use of whole genome sequencing (WGS) for identification and typing has provided a more robust and reliable approach for the detection and characterisation of E. albertii 6-8. As a result of the implementation of routine WGS for microbiological surveillance by the United Kingdom Health Security Agency (UKHSA, formerly Public Health England), we now have the capacity to accurately identify E. albertii in individuals presenting to primary healthcare settings with gastrointestinal symptoms. Although detection and speciation prior to the genomic era were challenging, the pathogenic traits of E. albertii are well described 4. Like certain DEC pathotypes, specifically the enteropathogenic E. coli (EPEC) and a subset of Shiga toxin-producing E. coli (STEC), the genome of E. albertii contains the locus of enterocyte effacement (LEE) pathogenicity island encoding a type III secretion system involved in the attachment of the pathogen to the gut mucosa 9,10. Colonisation of EPEC and eae gene positive (a marker of LEE) STEC in both humans and

Diseases of Aquatic Organisms, Feb 7, 2019

Fatal phaeohyphomycosis due to Exophiala sp. infection in a free-living common toad (Bufo bufo).

Genome Biology and Evolution, Jul 30, 2019

In Europe, Trichomonas gallinae recently emerged as a cause of epidemic disease in songbirds. A c... more In Europe, Trichomonas gallinae recently emerged as a cause of epidemic disease in songbirds. A clonal strain of the parasite, first found in the United Kingdom, has become the predominant strain there and spread to continental Europe. Discriminating this epidemic strain of T. gallinae from other strains necessitated development of multilocus sequence typing (MLST). Development of the MLST was facilitated by the assembly and annotation of a 54.7 Mb draft genome of a cloned stabilate of the A1 European finch epidemic strain (isolated from Greenfinch, Chloris chloris, XT-1081/07 in 2007) containing 21,924 protein coding genes. This enabled construction of a robust 19 locus MLST based on existing typing loci for Trichomonas vaginalis and T. gallinae. Our MLST has the sensitivity to discriminate strains within existing genotypes confidently, and resolves the American finch A1 genotype from the European finch epidemic A1 genotype. Interestingly, one isolate we obtained from a captive black-naped fruit dove Ptilinopsus melanospilus, was not truly T. gallinae but a hybrid of T. gallinae with a distant trichomonad lineage. Phylogenetic analysis of the individual loci in this fruit dove provides evidence of gene flow between distant trichomonad lineages at 2 of the 19 loci examined and may provide precedence for the emergence of other hybrid trichomonad genomes including T. vaginalis.

Journal of Wildlife Diseases, Oct 1, 2014

A European Robin (Erithacus rubecula) found dead in England had marked blepharitis and periocular... more A European Robin (Erithacus rubecula) found dead in England had marked blepharitis and periocular alopecia associated with Aprocta cylindrica (Nematoda: Aproctidae) and concurrent mixed fungal infections. Aprocta cylindrica should be considered a differential diagnosis in periocular abnormalities of robins and other insectivorous, migratory passerines in Western Europe.

Parasitology, May 16, 2016

Finch trichomonosis is an emerging infectious disease affecting European passerines caused by a c... more Finch trichomonosis is an emerging infectious disease affecting European passerines caused by a clonal strain of Trichomonas gallinae. Migrating chaffinches (Fringilla coelebs) were proposed as the likely vector of parasite spread from Great Britain to Fennoscandia. To test for such parasite carriage, we screened samples of oesophagus/crop from 275 Apodiform, Passeriform and Piciform birds (40 species) which had no macroscopic evidence of trichomonosis (i.e. necrotic ingluvitis). These birds were found dead following the emergence of trichomonosis in Great Britain, 2009-2012, and were examined post-mortem. Polymerase chain reactions were used to detect (ITS1/5.8S rRNA/ITS2 region and single subunit rRNA gene) and to subtype (Fe-hydrogenase gene) T. gallinae. Trichomonas gallinae was detected in six finches (three chaffinches, two greenfinches (Chloris chloris) and a bullfinch (Pyrrhula pyrrhula)). Sequence data had 100% identity to the European finch epidemic A1 strain for each species. While these results are consistent with finches being vectors of T. gallinae, alternative explanations include the presence of incubating or resolved T. gallinae infections. The inclusion of histopathological examination would help elucidate the significance of T. gallinae infection in the absence of macroscopic lesions.

PLOS ONE, 2013

<p>(a) Necrotic ingluvitis lesions (arrow) with a characteristic yellow caseous appearance ... more <p>(a) Necrotic ingluvitis lesions (arrow) with a characteristic yellow caseous appearance in a greenfinch caused by <i>Trichomonas gallinae</i> infection. (b) Morphology of the greenfinch trichomonad parasite. Scanning electron micrograph. Arrows indicate anterior flagella and axostyle.</p

Journal of Zoo and Wildlife Medicine, Apr 5, 2019

Listeria monocytogenes is a ubiquitous environmental bacterium that causes disease in a wide rang... more Listeria monocytogenes is a ubiquitous environmental bacterium that causes disease in a wide range of species. Infection with this pathogen is most frequently diagnosed in ruminant livestock, but is also known to infect people and occasionally wildlife. Post-mortem examinations of Western European hedgehogs (Erinaceus europaeus) in Great Britain (2011-2017) identified five (5/266, 2%, 95% confidence interval: 0.8-4.3%) animals with L. monocytogenes infection. The L. monocytogenes isolates comprised three serogroup 1/2a and two serogroup 4 from three Multilocus Sequence Types (2, 37 and 121), all of which were different by single nucleotide polymorphism analysis indicating they were distinct and epidemiologically-unrelated. These findings are consistent with hedgehogs contracting sporadic infection from the environment, perhaps through eating soil-dwelling invertebrates. Examination of data from scanning surveillance programs focused on other British wildlife species indicates that the hedgehog is one of the wildlife species from which L. monocytogenes has been most frequently identified to date in Great Britain. However, further studies of multiple taxa with comparable sampling efforts are required to assess the relative frequency of L. monocytogenes infection in different wildlife species. The bacterium was isolated from extra-intestinal sites in multiple hedgehogs which may indicate septicemia. However, histological examination was limited and could not discriminate subclinical infection from disease (i.e. listeriosis). Whilst L. monocytogenes is a source of zoonotic infection, disease in people is typically contracted from the ingestion of contaminated foods. The risk to immunocompetent people of contracting listeriosis from hedgehogs is considered very low to negligible.

Eurosurveillance, Oct 15, 2020

Scientific Reports

Following the first detection in the United Kingdom of Usutu virus (USUV) in wild birds in 2020, ... more Following the first detection in the United Kingdom of Usutu virus (USUV) in wild birds in 2020, we undertook a multidisciplinary investigation that combined screening host and vector populations with interrogation of national citizen science monitoring datasets to assess the potential for population impacts on avian hosts. Pathological findings from six USUV-positive wild passerines were non-specific, highlighting the need for molecular and immunohistochemical examinations to confirm infection. Mosquito surveillance at the index site identified USUV RNA in Culex pipiens s.l. following the outbreak. Although the Eurasian blackbird (Turdus merula) is most frequently impacted by USUV in Europe, national syndromic surveillance failed to detect any increase in occurrence of clinical signs consistent with USUV infection in this species. Furthermore, there was no increase in recoveries of dead blackbirds marked by the national ringing scheme. However, there was regional clustering of blac...

Diseases of Aquatic Organisms, 2021

Microbiology records for 1127 cetaceans stranded on English and Welsh beaches and examined at the... more Microbiology records for 1127 cetaceans stranded on English and Welsh beaches and examined at the Institute of Zoology between 1990 and 2019 were reviewed to identify cases of Erysipelothrix rhusiopathiae, an uncommon but potentially fatal zoonotic pathogen. Once cases were identified, prevalence was calculated, corresponding postmortem reports were reviewed, common gross and histopathological findings were identified, and antibiotic susceptibilities were determined. Overall prevalence for E. rhusiopathiae was 0.62% (7/1127; 95% CI: 0.30-1.28%). It was isolated from 3 bottlenose dolphins Tursiops truncatus, 3 harbor porpoises Phocoena phocoena, and 1 short-beaked common dolphin Delphinus delphis, with a prevalence of 21.4% (3/14; 95% CI: 7.6-47.9%), 0.39% (3/779; 95% CI: 0.13-1.13%), and 0.47% (1/212; 95% CI: 0.08-2.62%) for each species, respectively. E. rhusiopathiae resulted in septicemia in all cases from which it was isolated. Gross necropsy findings included pulmonary edema (5...

Scientific Reports

The influence of supplementary feeding of wildlife on disease transmission and its consequent imp... more The influence of supplementary feeding of wildlife on disease transmission and its consequent impacts on population dynamics are underappreciated. In Great Britain, supplementary feeding is hypothesised to have enabled the spread of the protozoan parasite, Trichomonas gallinae, from columbids to finches, leading to epidemic finch trichomonosis and a rapid population decline of greenfinch (Chloris chloris). More recently, chaffinch (Fringilla coelebs), has also declined markedly from the second to fifth commonest bird in Britain. Using citizen science data, we show that both declines were driven primarily by reduced adult survival, with the greatest reductions occurring in peri-domestic habitats, where supplementary food provision is common. Post-mortem examinations showed a proportional increase in chaffinch trichomonosis cases, near-contemporaneous with its population decline. Like greenfinches, chaffinches often use supplementary food, but are less associated with human habitation...

Journal of Comparative Pathology, May 1, 2023

Journal of Wildlife Diseases, Oct 9, 2019

Two adult great spotted woodpeckers (Dendrocopos major) from separate sites in Great Britain were... more Two adult great spotted woodpeckers (Dendrocopos major) from separate sites in Great Britain were examined post mortem in 2013 and 2016. A Salmonella sp. was isolated from multiple tissues in both birds. Histopathology and immunohistochemistry confirmed disseminated salmonellosis. Whole genome sequencing and biochemical analyses putatively identified both isolates as a novel variant of Salmonella enterica subsp. enterica serovar Hessarek (S. Hessarek). Salmonellosis has seldom been reported in Piciformes, and never before in association with S. Hessarek infection. These findings, therefore, add to current knowledge regarding the range of wild bird species susceptible to this Salmonella serovar, and our understanding of the pathogens affecting great spotted woodpeckers, in particular.

Scientific Reports, Oct 10, 2018

Proliferative leg skin lesions have been described in wild finches in Europe although there have ... more Proliferative leg skin lesions have been described in wild finches in Europe although there have been no large-scale studies of their aetiology or epizootiology to date. Firstly, disease surveillance, utilising public reporting of observations of live wild finches was conducted in Great Britain (GB) and showed proliferative leg skin lesions in chaffinches (Fringilla coelebs) to be widespread. Seasonal variation was observed, with a peak during the winter months. Secondly, pathological investigations were performed on a sample of 39 chaffinches, four bullfinches (Pyrrhula pyrrhula), one greenfinch (Chloris chloris) and one goldfinch (Carduelis carduelis) with proliferative leg skin lesions and detected Cnemidocoptes sp. mites in 91% (41/45) of affected finches and from all species examined. Fringilla coelebs papillomavirus (FcPV1) PCR was positive in 74% (23/31) of birds tested: a 394 base pair sequence was derived from 20 of these birds, from all examined species, with 100% identity to reference genomes. Both mites and FcPV1 DNA were detected in 71% (20/28) of birds tested for both pathogens. Histopathological examination of lesions did not discriminate the relative importance of mite or FcPV1 infection as their cause. Development of techniques to localise FcPV1 within lesions is required to elucidate the pathological significance of FcPV1 DNA detection. The epidemiology and impact of diseases of wild birds that cause morbidity, but are not typically associated with mortality, are often poorly understood. Papillomatosis and cnemidocoptosis are each diseases characterised by proliferative leg skin lesions in British finches (family Fringillidae) which, although often seen, are infrequently reported as causing mortality. The chaffinch (Fringilla coelebs) is most frequently affected and lesions typically affect the non-feathered areas of the legs, feet and digits 1-3. When severe, the skin lesions can interfere with locomotion, lead to digit distortion, loss and/or lameness and may predispose to entanglement or predation 1,3 (BL personal communication). Papillomaviruses are epitheliotropic, double-stranded DNA viruses that are generally considered hostspecific 2,3. Fringilla coelebs papillomavirus (FcPV1) is one of eight known to infect birds 4-8. The small number of avian papillomavirus species is in contrast to the high number detected in mammals. Of known papillomaviruses, 344 of 353 are found in mammals; of which 180 are known only from humans (the Papillomavirus Episteme is available at https://pave.niaid.nih.gov/). It is unclear whether the relative paucity of papillomaviruses in non-mammalian taxa is real or due to sampling bias 9. Chaffinches with proliferative leg skin lesions associated with papillomavirus infection have been described from multiple countries in western, northern and central Europe, including the Czech Republic, Germany, Great Britain, Italy, Sweden and the Netherlands 6,10-14. Papillomavirus from similar leg skin lesions has been reported less commonly in wild brambling (Fringilla montifringilla), wild bullfinch (Pyrrhula pyrrhula) and captive greenfinch (Chloris chloris) 2,6,15. The macroscopic appearance of these proliferative leg skin lesions has been described generally as (squamous) papillomas and wart-like growths and more specifically as nodular or hyperplastic

Research Square (Research Square), Sep 15, 2022

Escherichia albertii is a recently identi ed gastrointestinal bacterial pathogen of humans and an... more Escherichia albertii is a recently identi ed gastrointestinal bacterial pathogen of humans and animals which is typically misidenti ed and generally only detected during genomic surveillance of other Enterobacteriaceae. The incidence of E. albertii is likely underestimated and its epidemiology and clinical relevance are poorly characterised. Here, we whole genome sequenced E. albertii isolates from humans (n = 83) and birds (n = 79) in Great Britain and analysed a broader public dataset (n = 475) to address these gaps. We found human and avian isolates typically (90%; 148/164) belonged to host-associated monophyletic groups with distinct virulence and antimicrobial resistance pro les. Overlaid patient epidemiological data suggested that human infection was likely related to travel and possibly foodborne transmission. The Shiga toxin encoding stx2f gene was associated with clinical disease (OR = 10.27, 95% CI = 2.98-35.45 p = 0.0002) in nches. Our results suggest that improved future surveillance will further elucidate disease ecology and public and animal health risks associated with E. albertii.

Epidemiology and Infection, 2019

Disease surveillance in wildlife populations presents a logistical challenge, yet is critical in ... more Disease surveillance in wildlife populations presents a logistical challenge, yet is critical in gaining a deeper understanding of the presence and impact of wildlife pathogens. Erinaceus coronavirus (EriCoV), a clade C Betacoronavirus, was first described in Western European hedgehogs (Erinaceus europaeus) in Germany. Here, our objective was to determine whether EriCoV is present, and if it is associated with disease, in Great Britain (GB). An EriCoV-specific BRYT-Green® real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Viral RNA was detected in 10.8% (38) samples; however, the virus was not detected in any of the 61 samples tested from Scotland. The full genome sequence of the British EriCoV strain was determined using next generation sequencing; it shared 94% identity with a German EriCoV sequence. Multivariate statistical models using hedgehog case history data, faecal specimen descriptions and post-mortem examination findings found no significant associations indicative of disease associated with EriCoV in hedgehogs. These findings indicate that the Western European hedgehog is a reservoir host of EriCoV in the absence of apparent disease.

Journal of Avian Medicine and Surgery, Dec 1, 2005

Ecohealth, Jun 20, 2014

The significance of chlamydiosis as a cause of mortality in wild passerines (Order Passeriformes)... more The significance of chlamydiosis as a cause of mortality in wild passerines (Order Passeriformes), and the role of these birds as a potential source of zoonotic Chlamydia psittaci infection, is unknown. We reviewed wild bird mortality incidents (2005-2011). Where species composition or post-mortem findings were indicative of chlamydiosis, we examined archived tissues for C. psittaci infection using PCR and ArrayTube Microarray assays. Twenty-one of 40 birds tested positive: 8 dunnocks (Prunella modularis), 7 great tits (Parus major), 3 blue tits (Cyanistes caeruleus), 2 collared doves (Streptopelia decaocto, Order Columbiformes), and 1 robin (Erithacus rubecula). Chlamydia psittaci genotype A was identified in all positive passerines and in a further three dunnocks and three robins diagnosed with chlamydiosis from a previous study. Two collared doves had genotype E. Ten of the 21 C. psittaci-positive birds identified in the current study had histological lesions consistent with chlamydiosis and co-localizing Chlamydia spp. antigens on immunohistochemistry. Our results indicate that chlamydiosis may be a more common disease of British passerines than was previously recognized. Wild passerines may be a source of C. psittaci zoonotic infection, and people should be advised to take appropriate hygiene precautions when handling bird feeders or wild birds.

Applied and Environmental Microbiology, Nov 15, 2011

Salmonellosis is a frequently diagnosed infectious disease of passerine birds in garden habitats ... more Salmonellosis is a frequently diagnosed infectious disease of passerine birds in garden habitats within Great Britain with potential implications for human and domestic animal health. Postmortem examinations were performed on 1,477 garden bird carcasses of circa 50 species from England and Wales, 1999 to 2007 inclusive. Salmonellosis was confirmed in 263 adult birds of 10 passerine species in this 11-year longitudinal study. A subset of 124 fully biotyped Salmonella enterica subsp. enterica serovar Typhimurium isolates was examined using pulsed-field gel electrophoresis to investigate the hypothesis that these strains are host adapted and to determine whether this molecular technique offers greater resolution in understanding the epidemiology of Salmonella Typhimurium infection than phage typing alone. For the two most common phage types, definitive type (DT) 40 and DT56v, which together accounted for 97% (120/124) of isolates, pulsed-field gel electrophoresis groupings closely correlated with phage type with remarkably few exceptions. A high degree of genetic similarity (>90%) was observed within and between the two most common pulsed-field gel electrophoresis groups. No clustering or variation was found in the pulsed-field gel electrophoresis groupings by bird species, year, or geographical region beyond that revealed by phage typing. These findings support the hypothesis that there are currently two host-adapted Salmonella phage types, S. Typhimurium DT40 and DT56v, circulating widely in British garden birds and that the reservoir of infection is maintained within wild bird populations. Large-scale multilocus sequence typing studies are required to further investigate the epidemiology of this infection.

Infection, Genetics and Evolution, Oct 1, 2011

Trichomonas gallinae is a protozoan parasite that is well characterised as a cause of trichomonos... more Trichomonas gallinae is a protozoan parasite that is well characterised as a cause of trichomonosis in columbid and raptor species worldwide. The parasite emerged as a novel infection of British passerines in 2005, leading to epidemic mortality associated with significant declines of breeding populations of greenfinches (Carduelis chloris) and chaffinches (Fringilla coelebs). We characterised the extent of T. gallinae genotypic heterogeneity within the affected wild British avifauna by analysing individual isolates from 17 of the species affected. To do so, we employed improved platform-based multilocus typing tools as well as the hydrogenosomal Fe-hydrogenase gene as a single marker locus for fine-typing. We found no evidence of heterogeneity amongst the parasites infecting British passerines, indicating that a clonal strain of T. gallinae is the causative agent of this emerging infectious disease.

Nature Communications, Mar 27, 2023

Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and a... more Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and animals which is typically misidentified as pathotypes of diarrhoeagenic Escherichia coli or Shigella species and is generally only detected during genomic surveillance of other Enterobacteriaceae. The incidence of E. albertii is likely underestimated, and its epidemiology and clinical relevance are poorly characterised. Here, we whole genome sequenced E. albertii isolates from humans (n = 83) and birds (n = 79) isolated in Great Britain between 2000 and 2021 and analysed these alongside a broader public dataset (n = 475) to address these gaps. We found human and avian isolates typically (90%; 148/ 164) belonged to host-associated monophyletic groups with distinct virulence and antimicrobial resistance profiles. Overlaid patient epidemiological data suggested that human infection was likely related to travel and possibly foodborne transmission. The Shiga toxin encoding stx2f gene was associated with clinical disease (OR = 10.27, 95% CI = 2.98-35.45 p = 0.0002) in finches. Our results suggest that improved future surveillance will further elucidate disease ecology and public and animal health risks associated with E. albertii. Escherichia albertii, a Gram-negative gastrointestinal pathogen of humans and animals, was first confirmed as a novel bacterium in 2003 1-3. This pathogen is often misidentified because it is difficult to differentiate from Shigella species as they are morphologically, colonially, metabolically and biochemically similar; for example, both are non-lactose fermenting and lysine decarboxylase negative 4,5. Implementation of PCR for the detection of a wide range of gastrointestinal (GI) pathogens, including diarrhoeagenic E. coli (DEC), and the use of whole genome sequencing (WGS) for identification and typing has provided a more robust and reliable approach for the detection and characterisation of E. albertii 6-8. As a result of the implementation of routine WGS for microbiological surveillance by the United Kingdom Health Security Agency (UKHSA, formerly Public Health England), we now have the capacity to accurately identify E. albertii in individuals presenting to primary healthcare settings with gastrointestinal symptoms. Although detection and speciation prior to the genomic era were challenging, the pathogenic traits of E. albertii are well described 4. Like certain DEC pathotypes, specifically the enteropathogenic E. coli (EPEC) and a subset of Shiga toxin-producing E. coli (STEC), the genome of E. albertii contains the locus of enterocyte effacement (LEE) pathogenicity island encoding a type III secretion system involved in the attachment of the pathogen to the gut mucosa 9,10. Colonisation of EPEC and eae gene positive (a marker of LEE) STEC in both humans and

Diseases of Aquatic Organisms, Feb 7, 2019

Fatal phaeohyphomycosis due to Exophiala sp. infection in a free-living common toad (Bufo bufo).

Genome Biology and Evolution, Jul 30, 2019

In Europe, Trichomonas gallinae recently emerged as a cause of epidemic disease in songbirds. A c... more In Europe, Trichomonas gallinae recently emerged as a cause of epidemic disease in songbirds. A clonal strain of the parasite, first found in the United Kingdom, has become the predominant strain there and spread to continental Europe. Discriminating this epidemic strain of T. gallinae from other strains necessitated development of multilocus sequence typing (MLST). Development of the MLST was facilitated by the assembly and annotation of a 54.7 Mb draft genome of a cloned stabilate of the A1 European finch epidemic strain (isolated from Greenfinch, Chloris chloris, XT-1081/07 in 2007) containing 21,924 protein coding genes. This enabled construction of a robust 19 locus MLST based on existing typing loci for Trichomonas vaginalis and T. gallinae. Our MLST has the sensitivity to discriminate strains within existing genotypes confidently, and resolves the American finch A1 genotype from the European finch epidemic A1 genotype. Interestingly, one isolate we obtained from a captive black-naped fruit dove Ptilinopsus melanospilus, was not truly T. gallinae but a hybrid of T. gallinae with a distant trichomonad lineage. Phylogenetic analysis of the individual loci in this fruit dove provides evidence of gene flow between distant trichomonad lineages at 2 of the 19 loci examined and may provide precedence for the emergence of other hybrid trichomonad genomes including T. vaginalis.

Journal of Wildlife Diseases, Oct 1, 2014

A European Robin (Erithacus rubecula) found dead in England had marked blepharitis and periocular... more A European Robin (Erithacus rubecula) found dead in England had marked blepharitis and periocular alopecia associated with Aprocta cylindrica (Nematoda: Aproctidae) and concurrent mixed fungal infections. Aprocta cylindrica should be considered a differential diagnosis in periocular abnormalities of robins and other insectivorous, migratory passerines in Western Europe.

Parasitology, May 16, 2016

Finch trichomonosis is an emerging infectious disease affecting European passerines caused by a c... more Finch trichomonosis is an emerging infectious disease affecting European passerines caused by a clonal strain of Trichomonas gallinae. Migrating chaffinches (Fringilla coelebs) were proposed as the likely vector of parasite spread from Great Britain to Fennoscandia. To test for such parasite carriage, we screened samples of oesophagus/crop from 275 Apodiform, Passeriform and Piciform birds (40 species) which had no macroscopic evidence of trichomonosis (i.e. necrotic ingluvitis). These birds were found dead following the emergence of trichomonosis in Great Britain, 2009-2012, and were examined post-mortem. Polymerase chain reactions were used to detect (ITS1/5.8S rRNA/ITS2 region and single subunit rRNA gene) and to subtype (Fe-hydrogenase gene) T. gallinae. Trichomonas gallinae was detected in six finches (three chaffinches, two greenfinches (Chloris chloris) and a bullfinch (Pyrrhula pyrrhula)). Sequence data had 100% identity to the European finch epidemic A1 strain for each species. While these results are consistent with finches being vectors of T. gallinae, alternative explanations include the presence of incubating or resolved T. gallinae infections. The inclusion of histopathological examination would help elucidate the significance of T. gallinae infection in the absence of macroscopic lesions.

PLOS ONE, 2013

<p>(a) Necrotic ingluvitis lesions (arrow) with a characteristic yellow caseous appearance ... more <p>(a) Necrotic ingluvitis lesions (arrow) with a characteristic yellow caseous appearance in a greenfinch caused by <i>Trichomonas gallinae</i> infection. (b) Morphology of the greenfinch trichomonad parasite. Scanning electron micrograph. Arrows indicate anterior flagella and axostyle.</p

Journal of Zoo and Wildlife Medicine, Apr 5, 2019

Listeria monocytogenes is a ubiquitous environmental bacterium that causes disease in a wide rang... more Listeria monocytogenes is a ubiquitous environmental bacterium that causes disease in a wide range of species. Infection with this pathogen is most frequently diagnosed in ruminant livestock, but is also known to infect people and occasionally wildlife. Post-mortem examinations of Western European hedgehogs (Erinaceus europaeus) in Great Britain (2011-2017) identified five (5/266, 2%, 95% confidence interval: 0.8-4.3%) animals with L. monocytogenes infection. The L. monocytogenes isolates comprised three serogroup 1/2a and two serogroup 4 from three Multilocus Sequence Types (2, 37 and 121), all of which were different by single nucleotide polymorphism analysis indicating they were distinct and epidemiologically-unrelated. These findings are consistent with hedgehogs contracting sporadic infection from the environment, perhaps through eating soil-dwelling invertebrates. Examination of data from scanning surveillance programs focused on other British wildlife species indicates that the hedgehog is one of the wildlife species from which L. monocytogenes has been most frequently identified to date in Great Britain. However, further studies of multiple taxa with comparable sampling efforts are required to assess the relative frequency of L. monocytogenes infection in different wildlife species. The bacterium was isolated from extra-intestinal sites in multiple hedgehogs which may indicate septicemia. However, histological examination was limited and could not discriminate subclinical infection from disease (i.e. listeriosis). Whilst L. monocytogenes is a source of zoonotic infection, disease in people is typically contracted from the ingestion of contaminated foods. The risk to immunocompetent people of contracting listeriosis from hedgehogs is considered very low to negligible.

Eurosurveillance, Oct 15, 2020

Scientific Reports

Following the first detection in the United Kingdom of Usutu virus (USUV) in wild birds in 2020, ... more Following the first detection in the United Kingdom of Usutu virus (USUV) in wild birds in 2020, we undertook a multidisciplinary investigation that combined screening host and vector populations with interrogation of national citizen science monitoring datasets to assess the potential for population impacts on avian hosts. Pathological findings from six USUV-positive wild passerines were non-specific, highlighting the need for molecular and immunohistochemical examinations to confirm infection. Mosquito surveillance at the index site identified USUV RNA in Culex pipiens s.l. following the outbreak. Although the Eurasian blackbird (Turdus merula) is most frequently impacted by USUV in Europe, national syndromic surveillance failed to detect any increase in occurrence of clinical signs consistent with USUV infection in this species. Furthermore, there was no increase in recoveries of dead blackbirds marked by the national ringing scheme. However, there was regional clustering of blac...

Diseases of Aquatic Organisms, 2021

Microbiology records for 1127 cetaceans stranded on English and Welsh beaches and examined at the... more Microbiology records for 1127 cetaceans stranded on English and Welsh beaches and examined at the Institute of Zoology between 1990 and 2019 were reviewed to identify cases of Erysipelothrix rhusiopathiae, an uncommon but potentially fatal zoonotic pathogen. Once cases were identified, prevalence was calculated, corresponding postmortem reports were reviewed, common gross and histopathological findings were identified, and antibiotic susceptibilities were determined. Overall prevalence for E. rhusiopathiae was 0.62% (7/1127; 95% CI: 0.30-1.28%). It was isolated from 3 bottlenose dolphins Tursiops truncatus, 3 harbor porpoises Phocoena phocoena, and 1 short-beaked common dolphin Delphinus delphis, with a prevalence of 21.4% (3/14; 95% CI: 7.6-47.9%), 0.39% (3/779; 95% CI: 0.13-1.13%), and 0.47% (1/212; 95% CI: 0.08-2.62%) for each species, respectively. E. rhusiopathiae resulted in septicemia in all cases from which it was isolated. Gross necropsy findings included pulmonary edema (5...

Scientific Reports

The influence of supplementary feeding of wildlife on disease transmission and its consequent imp... more The influence of supplementary feeding of wildlife on disease transmission and its consequent impacts on population dynamics are underappreciated. In Great Britain, supplementary feeding is hypothesised to have enabled the spread of the protozoan parasite, Trichomonas gallinae, from columbids to finches, leading to epidemic finch trichomonosis and a rapid population decline of greenfinch (Chloris chloris). More recently, chaffinch (Fringilla coelebs), has also declined markedly from the second to fifth commonest bird in Britain. Using citizen science data, we show that both declines were driven primarily by reduced adult survival, with the greatest reductions occurring in peri-domestic habitats, where supplementary food provision is common. Post-mortem examinations showed a proportional increase in chaffinch trichomonosis cases, near-contemporaneous with its population decline. Like greenfinches, chaffinches often use supplementary food, but are less associated with human habitation...