Efficacy and Outcomes of Faecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection in Children with Inflammatory Bowel Disease.

BACKGROUND: Children with inflammatory bowel disease [IBD] are disproportionally affected by recurrent Clostridioides difficile infection [rCDI]. Although faecal microbiota transplantation [FMT] has been used with good efficacy in adults with IBD, little is known about outcomes associated with FMT in paediatric IBD. METHODS: We performed a retrospective review of FMT at 20 paediatric centres in the USA from March 2012 to March 2020. Children with and without IBD were compared with determined differences in the efficacy of FMT for rCDI. In addition, children with IBD with and without a successful outcome were compared with determined predictors of success. Safety data and IBD-specific outcomes were obtained. RESULTS: A total of 396 paediatric patients, including 148 with IBD, were included. Children with IBD were no less likely to have a successful first FMT then the non-IBD affected cohort [76% vs 81%, p = 0.17]. Among children with IBD, patients were more likely to have a successful FMT if they received FMT with fresh stool [p = 0.03], were without diarrhoea prior to FMT [p = 0.03], or had a shorter time from rCDI diagnosis until FMT [p = 0.04]. Children with a failed FMT were more likely to have clinically active IBD post-FMT [p = 0.002] and 19 [13%] patients had an IBD-related hospitalisation in the 3-month follow-up. CONCLUSIONS: Based on the findings from this large US multicentre cohort, the efficacy of FMT for the treatment of rCDI did not differ in children with IBD. Failed FMT among children with IBD was possibly related to the presence of clinically active IBD.

Detection and analysis of tick-borne infections in communal dogs of northwest Zimbabwe.

Domestic dogs (Canis familiaris) may serve as a reservoir or a sentinel for infectious disease pathogens that can affect human and wildlife health. To understand the role of tick-borne diseases in rural and lesser developed regions, we investigated the prevalence of several tick-borne pathogens in communal dogs of Zimbabwe. Blood samples from 225 dogs in northwest Zimbabwe were assessed by serology for Ehrlichia canis, Anaplasma phagocytophilum and Borrelia burgdorferi, and 241 samples were assessed by polymerase chain reaction (PCR) for Ehrlichia. There was a high seroprevalence (73%) of E. canis-specific antibodies in domestic dogs in northwest Zimbabwe, but follow up analyses via PCR and genetic sequencing indicated only 7.5% of the canines were actively infected with the organism. Whilst indicating that an organism serologically related to E. canis is likely present in the region, this data also shows that the organism is currently present in a relative minority of the domestic dogs in the region. Its presence as evidenced by both serologic and PCR analysis is significant because of the 'one health' paradigm, where humans and wildlife may be affected by the exposure to this pathogen in domestic dogs.

Effect of ultraviolet germicidal irradiation of the air on the incidence of upper respiratory tract infections in kittens in a nursery.

OBJECTIVE: To evaluate the effect of UV germicidal irradiation of the air on the incidence of upper respiratory tract infections (URIs) in kittens in a nursery. ANIMALS: 4- to 8-week-old kittens admitted to a kitten nursery in 2016 and 2018. PROCEDURES: 2 UV germicidal irradiation systems (1 within the heating, ventilation, and air conditioning system and 1 attached to the ceiling) were installed in a kitten nursery. Data were collected on the number of kittens in which a URI was diagnosed by means of a physical examination. The incidence of URIs was compared between 2016, when no UV systems were used, and 2018, when the UV systems were used. RESULTS: The overall incidence of URIs in 2016 was 12.4 cases/100 kitten admissions and in 2018 was 1.6 cases/100 kitten admissions, a significant decrease of 87.1% between the years. CONCLUSIONS AND CLINICAL RELEVANCE: A significant reduction in the incidence of URIs in kittens in a nursery was noted when the UV germicidal irradiation systems were used. Therefore, airborne transmission of feline respiratory pathogens may be more important than has been previously recognized. Ultraviolet germicidal irradiation systems that disinfect the air may be an effective adjunct to standard infection prevention and control protocols in reducing the risk of the transmission of respiratory pathogens among kittens in nurseries and shelters. However, additional studies are needed to confirm the findings reported here.

Betacoronavirus Genomes: How Genomic Information has been Used to Deal with Past Outbreaks and the COVID-19 Pandemic.

In the 21st century, three highly pathogenic betacoronaviruses have emerged, with an alarming rate of human morbidity and case fatality. Genomic information has been widely used to understand the pathogenesis, animal origin and mode of transmission of coronaviruses in the aftermath of the 2002-2003 severe acute respiratory syndrome (SARS) and 2012 Middle East respiratory syndrome (MERS) outbreaks. Furthermore, genome sequencing and bioinformatic analysis have had an unprecedented relevance in the battle against the 2019-2020 coronavirus disease 2019 (COVID-19) pandemic, the newest and most devastating outbreak caused by a coronavirus in the history of mankind. Here, we review how genomic information has been used to tackle outbreaks caused by emerging, highly pathogenic, betacoronavirus strains, emphasizing on SARS-CoV, MERS-CoV and SARS-CoV-2. We focus on shared genomic features of the betacoronaviruses and the application of genomic information to phylogenetic analysis, molecular epidemiology and the design of diagnostic systems, potential drugs and vaccine candidates.

Feline Infectious Peritonitis: Update on Pathogenesis, Diagnostics, and Treatment.

Feline infectious peritonitis (FIP) is a mysterious and lethal disease of cats. The causative agent, feline coronavirus (FCoV), is ubiquitous in most feline populations, yet the disease is sporadic in nature. Mutations in the infecting virus combined with an inappropriate immune response to the FCoV contribute to the development of FIP. Diagnosis can be challenging because signs may be vague, clinical pathology parameters are nonspecific, and the gold standard for diagnosis is invasive: histopathology of affected tissue. This article discusses the developments in the understanding of this disease as well as the progress in diagnosis and treatment.

Investigation of the effects of an ultraviolet germicidal irradiation system on concentrations of aerosolized surrogates for common veterinary pathogens.

OBJECTIVE: To determine whether exposure to UV germicidal irradiation (UVGI) reduces concentrations of viable aerosolized microorganisms (attenuated strains of common veterinary pathogens) in a simulated heating, ventilation, and air conditioning (HVAC) system. SAMPLE: 42 air samples seeded with bacteriophage MS2 or attenuated strains of Bordetella bronchiseptica, feline calicivirus, feline herpesvirus-1, canine parvovirus, or canine distemper virus (6/microorganism) or with no microorganisms added (6). PROCEDURES: A simulated HVAC unit was built that included a nebulizer to aerosolize microorganisms suspended in phosphate-buffered water, a fan to produce airflow, 2 UVGI bulb systems, and an impinger for air sampling. Ten-minute trials (3 with UVGI, 3 without UVGI, and 1 negative control) were conducted for each microorganism. Impingers collected microorganisms into phosphate-buffered water for subsequent quantification with culture-based assays. Results for samples yielding no target microorganisms were recorded as the assay's lower limit of detection. Statistical analysis was not performed. RESULTS: The UVGI treatment resulted in subjectively lower concentrations of viable MS2, B bronchiseptica, and canine distemper virus (arithmetic mean ± SD log10 microorganism reduction, 2.57 ± 0.47, ≥ 3.45 ± 0.24, and ≥ 1.50 ± 0.25, respectively) collected from air. Feline herpesvirus-1 was detected in only 1 sample without and no samples with UVGI treatment. Feline calicivirus and canine parvovirus were not detectable in any collected samples. CONCLUSIONS AND CLINICAL RELEVANCE: Results for some surrogates of veterinary pathogens suggested a potential benefit to supplementing manual disinfection practices with UVGI-based air cleaning systems in animal care environments. Further research is needed to investigate the utility of UVGI in operating HVAC systems.

Complete Genome Sequence of Bovine Viral Diarrhea Virus-1 Strain Egy/Ismailia/2014, Subtype 1b.

Here, we report the complete genome sequence of bovine viral diarrhea virus-1b (BVDV-1b), strain Egy/Ismailia/2014. The virus genome is composed of 12,217 nucleotides organized as one open reading frame encoding 3,898 amino acids. This report will assist efforts in diagnostics, studying molecular epidemiology, and control of BVDV in Egypt.

Circulation of bovine viral diarrhea virus--1 (BVDV-1) in dairy cattle and buffalo farms in Ismailia Province, Egypt.

INTRODUCTION: Bovine viral diarrhea (BVD) is one of the most economically significant diseases in the bovine industry causing losses due to diarrhea, reproductive disorders, immunosuppression and mortalities. The aim of our investigation was to detect and subtype BVDV from calves on two dairy cattle and two buffalo farms in Ismailia province, Egypt as an indicator of BVDV infection status in the province. METHODOLOGY: A total of 298 blood samples were collected and tested using an optimized one-step, real-time multiplex Taqman-based RT-PCR. All the positive samples by the multiplex real-time RT-PCR were tested using conventional RT-PCR to amplify multiple areas of the genome for further phylogenetic analysis and subtyping. RESULTS: Thirty one (10.4%) of the tested samples were positive for BVDV-1. Only three samples, all from a single dairy cattle farm, had enough viral RNA to be amplified by RT-PCR. The PCR products were sequenced and phylogenetic analysis revealed detection of BVDV-1b. The detected strain is closely related to worldwide BVDV-1b strains, making it difficult to trace its origin. Nucleotide and amino acid alignments of the E2 glycoprotein region of the detected strain with other BVDV-1b strains showed high divergence, with identity ranging from 81.3% to 93.6% and 85.3% to 93.6%, respectively. CONCLUSION: To our knowledge, this is the first report describing the circulation of BVDV-1b in Egyptian dairy cattle populations.

Effect of small interfering RNAs on in vitro replication and gene expression of feline coronavirus.

OBJECTIVE: To evaluate the ability of small interfering RNAs (siRNAs) to inhibit in vitro viral replication and gene expression of feline coronavirus (FCoV). SAMPLE: Cell cultures of Crandell-Rees feline kidney cells. PROCEDURES: 5 synthetic siRNAs that each targeted a different region of the FCoV genome were tested individually and in various combinations for their antiviral effects against 2 strains of FCoV (feline infectious peritonitis virus WSU 79-1146 and feline enteric coronavirus WSU 79-1683) in cell cultures. Tested combinations targeted the FCoV leader and 3' untranslated region, FCoV leader region and nucleocapsid gene, and FCoV leader region, 3' untranslated region, and nucleocapsid gene. For each test condition, assessments included relative quantification of the inhibition of intracellular viral genomic RNA synthesis by means of real-time, reverse-transcription PCR analysis; flow cytometric evaluation of the reduction of viral protein expression in infected cells; and assessment of virus replication inhibition via titration of extracellular virus with a TCID50 infectivity assay. RESULTS: The 5 siRNAs had variable inhibitory effects on FCoV when used singly. Combinations of siRNAs that targeted different regions of the viral genome resulted in more effective viral inhibition than did individual siRNAs that targeted a single gene. The tested siRNA combinations resulted in approximately 95% reduction in viral replication (based on virus titration results), compared with findings in negative control, nontargeting siRNA-treated, FCoV-infected cells. CONCLUSIONS AND CLINICAL RELEVANCE: In vitro replication of FCoV was specifically inhibited by siRNAs that targeted coding and noncoding regions of the viral genome, suggesting a potential therapeutic application of RNA interference in treatment of feline infectious peritonitis.

Real-time reverse transcription polymerase chain reaction method for detection of Canine distemper virus modified live vaccine shedding for differentiation from infection with wild-type strains.

Canine distemper virus (CDV) remains a common cause of infectious disease in dogs, particularly in high-density housing situations such as shelters. Vaccination of all dogs against CDV is recommended at the time of admission to animal shelters and many use a modified live virus (MLV) vaccine. From a diagnostic standpoint for dogs with suspected CDV infection, this is problematic because highly sensitive diagnostic real-time reverse transcription polymerase chain reaction (RT-PCR) tests are able to detect MLV virus in clinical samples. Real-time PCR can be used to quantitate amount of virus shedding and can differentiate vaccine strains from wild-type strains when shedding is high. However, differentiation by quantitation is not possible in vaccinated animals during acute infection, when shedding is low and could be mistaken for low level vaccine virus shedding. While there are gel-based RT-PCR assays for differentiation of vaccine strains from field strains based on sequence differences, the sensitivity of these assays is unable to match that of the real-time RT-PCR assay currently used in the authors' laboratory. Therefore, a real-time RT-PCR assay was developed that detects CDV MLV vaccine strains and distinguishes them from wild-type strains based on nucleotide sequence differences, rather than the amount of viral RNA in the sample. The test is highly sensitive, with detection of as few as 5 virus genomic copies (corresponding to 10(-1) TCID(50)). Sequencing of the DNA real-time products also allows phylogenetic differentiation of the wild-type strains. This test will aid diagnosis during outbreaks of CDV in recently vaccinated animals.

Serological detection of infection with canine distemper virus, canine parvovirus and canine adenovirus in communal dogs from Zimbabwe.

Domestic dogs are common amongst communities in sub-Saharan Africa and may serve as important reservoirs for infectious agents that may cause diseases in wildlife. Two agents of concern are canine parvovirus (CPV) and canine distemper virus (CDV), which may infect and cause disease in large carnivore species such as African wild dogs and African lions, respectively. The impact of domestic dogs and their diseases on wildlife conservation is increasing in Zimbabwe, necessitating thorough assessment and implementation of control measures. In this study, domestic dogs in north-western Zimbabwe were evaluated for antibodies to CDV, CPV, and canine adenovirus (CAV). These dogs were communal and had no vaccination history. Two hundred and twenty-five blood samples were collected and tested using a commercial enzyme-linked immunosorbent assay (ELISA) for antibodies to CPV, CDV, and CAV. Of these dogs, 75 (34%) had detectable antibodies to CDV, whilst 191 (84%) had antibodies to CPV. Antibodies to canine adenovirus were present in 28 (13%) dogs. Canine parvovirus had high prevalence in all six geographic areas tested. These results indicate that CPV is circulating widely amongst domestic dogs in the region. In addition, CDV is present at high levels. Both pathogens can infect wildlife species. Efforts for conservation of large carnivores in Zimbabwe must address the role of domestic dogs in disease transmission.

Complete genome sequence of an astrovirus identified in a domestic rabbit (Oryctolagus cuniculus) with gastroenteritis.

A colony of domestic rabbits in Tennessee, USA, experienced a high-mortality (~90%) outbreak of enterocolitis. The clinical characteristics were one to six days of lethargy, bloating, and diarrhea, followed by death. Heavy intestinal coccidial load was a consistent finding as was mucoid enteropathy with cecal impaction. Preliminary analysis by electron microscopy revealed the presence of virus-like particles in the stool of one of the affected rabbits. Analysis using the Virochip, a viral detection microarray, suggested the presence of an astrovirus, and follow-up PCR and sequence determination revealed a previously uncharacterized member of that family. Metagenomic sequencing enabled the recovery of the complete viral genome, which contains the characteristic attributes of astrovirus genomes. Attempts to propagate the virus in tissue culture have yet to succeed. Although astroviruses cause gastroenteric disease in other mammals, the pathogenicity of this virus and the relationship to this outbreak remains to be determined. This study therefore defines a viral species and a potential rabbit pathogen.

A brief review of the basics of immunology: the innate and adaptive response.

The role of the immune system is simple yet challenging: to eliminate pathogenic agents. The immune system contains nonspecific and specific components; that is, some constituents act without precise recognition of the target, others have exquisite specificity. Regulation of the immune response and maintenance of tolerance to self are critical to the health of the animal. To properly evaluate or control immune function, knowledge of the basic components of the normal immune system is essential. This review covers the current knowledge of individual components of the immune system and how they interact to protect the host from infectious disease agents.

Vulvovaginal Candidiasis Caused by Non-albicans Candida Species: New Insights.

Non-albicans Candida species have increasingly been identified as the cause of vulvovaginitis. In vitro and in vivo data indicate that the various non-albicans Candida species identified in the lower genital tract differ considerably with regard to epidemiology, virulence or vaginal pathogenicity, and antimycotic drug susceptibility. Clinical experience indicates reduced virulence of these organisms in the lower genital tract, and their causal role in a symptomatic patient requires careful case-by-case determination rather than routine administration of antimycotic therapy. Accordingly, vaginal Candida isolates deserve species identification and consideration of pathogenic potential and antifungal susceptibility before therapeutic decisions are made.

Development and validation of a TaqMan real-time reverse transcription-PCR for rapid detection of feline calicivirus.

Feline calicivirus (FCV) is a common cause of upper respiratory tract disease in cats and is associated with interstitial pneumonia, oral ulceration and polyarthritis. Recently, outbreaks have involved a highly virulent FCV that leads to multisystemic signs. Virus isolation and conventional RT-PCR are the most common methods used for FCV diagnosis. However, real-time RT-PCR offers a rapid, sensitive, specific and easy tool for nucleic acid detection. The objective of this study was to design a TaqMan probe-based, real-time RT-PCR assay for detection of FCV. It was determined in our previous study that the first 120 nucleotides of the 5' region of the genome are highly conserved among FCV isolates. Primers and a probe specific for this region were designed for a real-time RT-PCR assay to detect FCV. Initial validation was done using 15 genetically diverse isolates. Also, 122 samples were tested by the new assay and virus isolation. The real-time RT-PCR assay was as sensitive and specific as virus isolation and was far more rapid. This real-time RT-PCR assay targeting the conserved 5' region of the genome is a fast, economical and accurate method for detection of FCV.

Detection of feline panleukopenia virus using a commercial ELISA for canine parvovirus.

Feline panleukopenia virus (FPV) is a significant pathogen of cats. Rapid virus detection is critical for treatment and management, especially in populations in which spread may occur. This study investigated the ability of the SNAP Canine Parvovirus Antigen Test Kit (SNAP Parvo, IDEXX Laboratories) to detect FPV with confirmation of viral identity by polymerase chain reaction (PCR) assay and genetic sequencing on fecal samples (n = 97) from cats with suspected FPV infection. Fifty-five samples were positive by SNAP Parvo; 54 of 55 were also positive by conventional PCR assay and were identified as FPV by genetic sequencing. This study demonstrates that SNAP Parvo can detect FPV in clinical samples.

Evaluation of antibodies against feline coronavirus 7b protein for diagnosis of feline infectious peritonitis in cats.

OBJECTIVE: To determine whether expression of feline coronavirus (FCoV) 7b protein, as indicated by the presence of specific serum antibodies, consistently correlated with occurrence of feline infectious peritonitis (FIP) in cats. SAMPLE POPULATION: 95 serum samples submitted for various diagnostic assays and 20 samples from specific-pathogen-free cats tested as negative control samples. PROCEDURES: The 7b gene from a virulent strain of FCoV was cloned into a protein expression vector. The resultant recombinant protein was produced and used in antibody detection assays via western blot analysis of serum samples. Results were compared with those of an immunofluorescence assay (IFA) for FCoV-specific antibody and correlated with health status. RESULTS: Healthy IFA-seronegative cats were seronegative for antibodies against the 7b protein. Some healthy cats with detectable FCoV-specific antibodies as determined via IFA were seronegative for antibodies against the 7b protein. Serum from cats with FIP had antibodies against the 7b protein, including cats with negative results via conventional IFA. However, some healthy cats, as well as cats with conditions other than FIP that were seropositive to FCoV via IFA, were also seropositive for the 7b protein. CONCLUSIONS AND CLINICAL RELEVANCE: Expression of the 7b protein, as indicated by detection of antibodies against the protein, was found in most FCoV-infected cats. Seropositivity for this protein was not specific for the FCoV virulent biotype or a diagnosis of FIP.

Analysis of genetic mutations in the 7a7b open reading frame of coronavirus of cheetahs (Acinonyx jubatus).

OBJECTIVE: To analyze the 7a7b genes of the feline coronavirus (FCoV) of cheetahs, which are believed to play a role in virulence of this virus. SAMPLE POPULATION: Biologic samples collected during a 4-year period from 5 cheetahs at the same institution and at 1 time point from 4 cheetahs at different institutions. PROCEDURES: Samples were first screened for FCoV via a reverse transcription-PCR procedure involving primers that encompassed the 3'-untranslated region. Samples that yielded positive assay results were analyzed by use of primers that targeted the 7a7b open reading frames. The nucleotide sequences of the 7a7b amplification products were determined and analyzed. RESULTS: In most isolates, substantial deletional mutations in the 7a gene were detected that would result in aberrant or no expression of the 7a product because of altered reading frames. Although the 7b gene was also found to contain mutations, these were primarily point mutations resulting in minor amino acid changes. The coronavirus associated with 1 cheetah with feline infectious peritonitis had intact 7a and 7b genes. CONCLUSIONS AND CLINICAL RELEVANCE: The data suggest that mutations arise readily in the 7a region and may remain stable in FCoV of cheetahs. In contrast, an intact 7b gene may be necessary for in vivo virus infection and replication. Persistent infection with FCoV in a cheetah population results in continued virus circulation and may lead to a quasispecies of virus variants.

Effect of intranasal vaccination against bovine enteric coronavirus on the occurrence of respiratory tract disease in a commercial backgrounding feedlot.

OBJECTIVE: To measure antibody titers against bovine coronavirus (BCV), determine frequency of BCV in nasal swab specimens, and compare calves treated for bovine respiratory tract disease (BRD) between those given an intranasally administered vaccine and control calves. DESIGN: Randomized clinical trial. ANIMALS: 414 heifer calves. PROCEDURE: Intranasal BCV antigen concentration and antibody titer against BCV were measured on entry to a feedlot. Calves were randomly assigned to receive 3.0 mL of a modified-live virus vaccine against bovine enteric coronavirus and rotavirus or 3.0 mL of saline (0.9% NaCl) solution. Calves were confined to 1 of 2 pens, depending on vaccination status, for a minimum of 17 days of observation (range, 17 to 99). Selection of calves for treatment of BRD and scoring for severity of disease were done by veterinarians unaware of treatment status. RESULTS: Intranasal BCV (125/407 [31%]) and serum antibody titers > or = 20 against BCV (246/396 [62%]) were identified in calves entering the feedlot. Vaccination was associated with significant decrease in risk of treatment for BRD; intranasal BCV on entry to the feedlot was associated with increased risk of treatment. Univariate analysis revealed that control calves with intranasal BRD on entry to the feedlot and those with antibody titer < 20 were significantly more likely to be treated for BRD. CONCLUSIONS AND CLINICAL RELEVANCE: These data provide further evidence of an association between BCV and respiratory tract disease in feedlot calves. An intranasally administered vaccine appeared to reduce risk of treatment for BRD.