Gross and microscopic pathology of West Indian sea eggs (Tripneustes ventricosus).

In this study, we performed comprehensive pathology examinations on 83 Tripneustes ventricosus from 11 locations on St. Kitts to build baseline data necessary for disease diagnosis in this species. Gross abnormalities were observed in 23/83 (28%) urchins and included spine loss, visceral hyperpigmentation, test discoloration, and test ulceration. Ciliates were the only protists identified in this study via examination of tissue wet mounts and histology, documented in 50/83 (60%) urchins. Microscopic observations associated with visibly abnormal status included muscle necrosis, test and appendage inflammation, appendage (tube feet, spines, and pedicellariae) degeneration, severe coelomocytosis, and generalized hypermelanosis. Enterocyte intranuclear inclusion bodies, microbial aggregates, nerve pigmentation, enteric pigmentation, integument-associated crustaceans, and encysted metazoan parasites were of uncertain pathological significance. The etiology for any lesion was not microscopically apparent, contrasting literature implicating common marine bacteria in urchin diseases. This study highlights the importance of histopathology in urchin disease investigations and facilitates the recognition of disease in T. ventricosus.

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.

Hereditary ß-mannosidosis in a dog: Clinicopathological and molecular genetic characterization.

Hereditary ß-mannosidosis causing progressive lysosomal neuropathy and other clinical signs, has been previously described in humans, Nubian goats, and Salers cattle. Here we report the clinicopathological, metabolic, and molecular genetic features of canine beta-mannosidase (MANBA, EC 3.2.1.25) deficiency. A 1-year-old male mix-breed dog from St. Kitts was presented with progressive stumbling, weakness, and regurgitation. Vacuolated lymphocytes were observed on the blood film. Postmortem findings included marked enlargement of nerves, megaesophagus, and internal hydrocephalus. Vacuolated macrophages, neurons, and secretory epithelial cells suggested an oligosaccharide storage disease. Plasma concentration of the ß-mannosidosis specific oligosaccharide was approximately 75 fold that of controls. The plasma beta-mannosidase activity was severely reduced to ~5% of controls; five other lysosomal acid hydrolase activities were increased or within their normal reference interval. Genomic sequencing of this dog's MANBA gene identified a homozygous exonic five bp tandem duplication in the penultimate exon of the MANBA gene (c.2377_2381dupTATCA) which results in a reading frame shift, altering the subsequent amino acid sequence and creating a premature stop codon. The truncated beta-mannosidase enzyme is expected to be dysfunctional. This enzyme deficiency causes the accumulation of un-degraded oligosaccharides in cells, which affect the myelination of the peripheral and central nervous systems. This insertion was not encountered in 121 and 80-screened samples from dogs on St. Kitts (all were homozygous for wild-type) and Philadelphia region (wild-type), respectively. In conclusion, canine ß-mannosidosis has similar clinicopathological features with some human patients, but milder signs than in ruminants and more severe than in knockout mice. Hence, dogs with ß-mannosidosis could become a valuable disease model for the human disease.

Extraintestinal Acanthocephalan Oncicola venezuelensis (Oligacanthorhynchidae) in Small Indian Mongooses (Herpestes auropunctatus) and African Green Monkeys (Chlorocebus aethiops sabaeus).

We identified multiple extraintestinal cystacanths during routine postmortem examination of 3 small Indian mongooses and 2 African green monkeys from the Caribbean island of St. Kitts. In mongooses, cystacanths were encysted or free in the subcutaneous tissue, skeletal muscle, or peritoneal or pericardial cavities, whereas in the monkeys, they were in the cavity and parietal layer of the, tunica vaginalis, skeletal muscle, and peritoneal cavity. Morphological, histological, and molecular characterization identified these cystacanths as Oncicola venezuelensis (Acanthocephala: Oligacanthorhynchidae). There was minimal to mild lymphoplasmacytic inflammation associated with the parasite in the mongooses and moderate inflammation, mineralization, hemorrhage, and fibrosis in the connective tissue between the testis and epididymis in 1 monkey. We identified a mature male O. venezuelensis attached in the aboral jejunum of a feral cat, confirming it as the definitive host. Termites serve as intermediate hosts and lizards as paratenic hosts. This report emphasizes the role of the small Indian mongoose and African green monkey as paratenic hosts for O. venezuelensis.

Epidemiology of Leptospira infection in livestock species in Saint Kitts.

This pilot study describes the prevalence of Leptospira infection and exposure in livestock species, cattle, pig, sheep, and goats in Saint Kitts in the Caribbean region. Serum and kidney samples were collected from cattle, pigs, sheep, and goats at a local abattoir between September 2016 and March 2017. Cattle had the highest seroprevalence (79.8%) followed by pigs (64.8%), sheep (39.4%), and goats (24.8%). Highest seroprevalence was observed to serovars, Mankarso in cattle, Bratislava in pigs, Hardjo in sheep, and goats. Leptospira DNA was amplified from kidney samples of 18/99 cattle (18.2%), 11/106 pigs (10.4%), 4/106 sheep (3.8%), and 2/105 goats (1.9%). Our findings warrant further studies to assess leptospirosis associated economic burden to subsistence farmers and public health impact.

Evaluation of Grower-Friendly, Science-Based Sampling Approaches for the Detection of Salmonella in Ponds Used for Irrigation of Fresh Produce.

The recognition that irrigation water sources contribute to preharvest contamination of produce has led to new regulations on testing microbial water quality. To best identify contamination problems, growers who depend on irrigation ponds need guidance on how and where to collect water samples for testing. In this study, we evaluated several sampling strategies to identify Salmonella and Escherichia coli contamination in five ponds used for irrigation on produce farms in southern Georgia. Both Salmonella and E. coli were detected regularly in all the ponds over the 19-month study period, with overall prevalence and concentrations increasing in late summer and early fall. Of 507 water samples, 217 (42.8%) were positive for Salmonella, with a very low geometric mean (GM) concentration of 0.06 most probable number (MPN)/100 mL, and 442 (87.1%) tested positive for E. coli, with a GM of 6.40 MPN/100 mL. We found no significant differences in Salmonella or E. coli detection rates or concentrations between sampling at the bank closest to the pump intake versus sampling from the bank around the pond perimeter, when comparing with results from the pump intake, which we considered our gold standard. However, samples collected from the bank closest to the intake had a greater level of agreement with the intake (Cohen's kappa statistic = 0.53; p < 0.001) than the samples collected around the pond perimeter (kappa = 0.34; p = 0.009). E. coli concentrations were associated with increased odds of Salmonella detection (odds ratio = 1.31; 95% confidence interval = 1.10-1.56). All the ponds would have met the Produce Safety Rule standards for E. coli, although Salmonella was also detected. Results from this study provide important information to growers and regulators about pathogen detection in irrigation ponds and inform best practices for surface water sampling.

Multilaboratory Survey To Evaluate Salmonella Prevalence in Diarrheic and Nondiarrheic Dogs and Cats in the United States between 2012 and 2014.

Eleven laboratories collaborated to determine the periodic prevalence of Salmonella in a population of dogs and cats in the United States visiting veterinary clinics. Fecal samples (2,965) solicited from 11 geographically dispersed veterinary testing laboratories were collected in 36 states between January 2012 and April 2014 and tested using a harmonized method. The overall study prevalence of Salmonella in cats (3 of 542) was <1%. The prevalence in dogs (60 of 2,422) was 2.5%. Diarrhea was present in only 55% of positive dogs; however, 3.8% of the all diarrheic dogs were positive, compared with 1.8% of the nondiarrheic dogs. Salmonella-positive dogs were significantly more likely to have consumed raw food (P = 0.01), to have consumed probiotics (P = 0.002), or to have been given antibiotics (P = 0.01). Rural dogs were also more likely to be Salmonella positive than urban (P = 0.002) or suburban (P = 0.001) dogs. In the 67 isolates, 27 unique serovars were identified, with three dogs having two serovars present. Antimicrobial susceptibility testing of 66 isolates revealed that only four of the isolates were resistant to one or more antibiotics. Additional characterization of the 66 isolates was done using pulsed-field gel electrophoresis and whole-genome sequencing (WGS). Sequence data compared well to resistance phenotypic data and were submitted to the National Center for Biotechnology Information (NCBI). This study suggests an overall decline in prevalence of Salmonella-positive dogs and cats over the last decades and identifies consumption of raw food as a major risk factor for Salmonella infection. Of note is that almost half of the Salmonella-positive animals were clinically nondiarrheic.

The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.

Shotgun metagenomic sequencing analysis is widely used for microbial profiling of biological specimens and pathogen detection. However, very little is known about the technical biases caused by the choice of analysis software and databases on the biological specimen. In this study, we evaluated different direct read shotgun metagenomics taxonomic profiling software to characterize the microbial compositions of simulated mice gut microbiome samples and of biological samples collected from wild rodents across multiple taxonomic levels. Using ten of the most widely used metagenomics software and four different databases, we demonstrated that obtaining an accurate species-level microbial profile using the current direct read metagenomics profiling software is still a challenging task. We also showed that the discrepancies in results when different databases and software were used could lead to significant variations in the distinct microbial taxa classified, in the characterizations of the microbial communities, and in the differentially abundant taxa identified. Differences in database contents and read profiling algorithms are the main contributors for these discrepancies. The inclusion of host genomes and of genomes of the interested taxa in the databases is important for increasing the accuracy of profiling. Our analysis also showed that software included in this study differed in their ability to detect the presence of Leptospira, a major zoonotic pathogen of one health importance, especially at the species level resolution. We concluded that using different databases and software combinations can result in confounding biological conclusions in microbial profiling. Our study warrants that software and database selection must be based on the purpose of the study.

Leptospira transcriptome sequencing using long-read technology reveals unannotated transcripts and potential polyadenylation of RNA molecules.

IMPORTANCE: Leptospirosis, caused by the spirochete bacteria Leptospira, is a zoonotic disease of humans and animals, accounting for over 1 million annual human cases and over 60,000 deaths. We have characterized operon transcriptional units, identified novel RNA coding regions, and reported evidence of potential posttranscriptional polyadenylation in the Leptospira transcriptomes for the first time using Oxford Nanopore Technology RNA sequencing protocols. The newly identified RNA coding regions and operon transcriptional units were detected only in the pathogenic Leptospira transcriptomes, suggesting their significance in virulence-related functions. This article integrates bioinformatics, infectious diseases, microbiology, molecular biology, veterinary sciences, and public health. Given the current knowledge gap in the regulation of leptospiral pathogenicity, our findings offer valuable insights to researchers studying leptospiral pathogenicity and provide both a basis and a tool for researchers focusing on prokaryotic molecular studies for the understanding of RNA compositions and prokaryotic polyadenylation for their organisms of interest.

Galleria mellonella infection model to evaluate pathogenic and nonpathogenic Leptospira strains.

The Galleria mellonella larvae infection model is emerging as a valuable tool for studying various characteristics of infectious agents and host-pathogen interaction. This system has been widely recognized as a high throughput, ethical, and cost-effective invertebrate infection model to study the virulence and pathogenesis of various bacterial pathogens. In this study, we compared the effect of Leptospira infection in G. mellonella larvae infected with Leptospira interrogans serovar Copenhageni (pathogenic) or Leptospira biflexa serovar Patoc (saprophytic) strains. We observed significant pathologic changes such as decreased activity, complete melanization, and lower survival rate in the G. mellonella larvae infected with a pathogenic strain L. interrogans serovar Copenhageni compared to those infected with a nonpathogenic strain L. biflexa serovar Patoc. Our study demonstrates the feasibility and the potential of using G. mellonella larvae as an alternative model to study virulence mechanisms and pathogenesis of Leptospira strains. Once optimized, the G. mellonella infection model can be a potential substitute for hamsters to explore various host and pathogen-related mechanistic events in Leptospira infection.

Leptospira enrichment culture followed by ONT metagenomic sequencing allows better detection of Leptospira presence and diversity in water and soil samples.

BACKGROUND: Leptospirosis, a life-threatening disease in humans and animals, is one of the most widespread global zoonosis. Contaminated soil and water are the major transmission sources in humans and animals. Clusters of disease outbreaks are common during rainy seasons. METHODOLOGY/PRINCIPAL FINDINGS: In this study, to detect the presence of Leptospira, we applied PCR, direct metagenomic sequencing, and enrichment culture followed by PCR and metagenomic sequencing on water and soil samples. Direct sequencing and enrichment cultures followed by PCR or sequencing effectively detected pathogenic and nonpathogenic Leptospira compared to direct PCR and 16S amplification-based metagenomic sequencing in soil or water samples. Among multiple culture media evaluated, Ellinghausen-McCullough-Johnson-Harris (EMJH) media containing antimicrobial agents was superior in recovering and detecting Leptospira from the environmental samples. Our results show that enrichment culture followed by PCR can be used to confirm the presence of pathogenic Leptospira in environmental samples. Additionally, metagenomic sequencing on enrichment cultures effectively detects the abundance and diversity of Leptospira spp. from environmental samples. CONCLUSIONS/SIGNIFICANCE: The selection of methodology is critical when testing environmental samples for the presence of Leptospira. Selective enrichment culture improves Leptospira detection efficacy by PCR or metagenomic sequencing and can be used successfully to understand the presence and diversity of pathogenic Leptospira during environmental surveillance.

In vitro and in vivo assessment of caprine origin Staphylococcus aureus ST398 strain UTCVM1 as an osteomyelitis pathogen.

Staphylococcus aureus (SA) is a significant and well-recognized causative organism of bacterial osteomyelitis. Osteomyelitis is an inflammatory bone disease characterized by progressive bone destruction and loss. This disease causes significant morbidity and mortality to the patient and poses therapeutic challenges for clinicians. To improve the efficacy of therapeutic strategies to combat bacterial osteomyelitis, there is a need to define the molecular epidemiology of bacterial organisms more clearly and further the understanding of the pathogenesis of SA osteomyelitis. We conducted in vitro characterization of the pathogenic capabilities of an isolate of SA ST398 derived from a clinical case of osteomyelitis in a goat. We also report a rodent mandibular defect model to determine the ability of ST398 to cause reproducible osteomyelitis. Our results indicate that ST398 can invade and distort pre-osteoblastic cells in culture, induce significant inflammation and alter expression of osteoregulatory cytokines. We also demonstrate the ability of ST398 to induce osteomyelitis in a rat mandibular model. When compiled, these data support ST398 as a competent osteomyelitis pathogen.

Corrigendum: In vitro and In vivo assessment of caprine origin Staphylococcus aureus ST398 strain UTCVM1 as an osteomyelitis pathogen.

[This corrects the article DOI: 10.3389/fcimb.2022.1015655.].

Meningoencephalitis caused by Mycoplasma edwardii in a dog.

A 6-week-old, female, mixed-breed dog with a clinical history of sudden onset of neurologic signs was presented for necropsy. The dog was diagnosed with suppurative and histiocytic meningoencephalitis based on necropsy findings and histopathology. Mycoplasma sp. was isolated in pure culture from the brain and meninges and was identified as Mycoplasma edwardii using DNA sequencing.

Comparison of fluorescent antibody and microscopic agglutination testing for Leptospira in pregnant and nonpregnant cows.

Serum and urine samples from 30 cows (15 pregnant and 15 nonpregnant) from each of 10 Georgia dairy herds (total cows = 300) were examined by microscopic agglutination testing (MAT) and direct fluorescent antibody testing (FAT), respectively. Seven of the 10 herds had at least 1 cow with a positive FAT, and all of the herds had at least 1 cow with a reciprocal MAT titer > or =100 for 1 or more serovars. Serological testing was not helpful in identifying the infecting serovar for cows with a positive FAT result. The MAT titers for all 7 of the serovars evaluated were significantly correlated with one another, with 17 (81%) of the 21 Spearman rank correlation coefficients > or =0.4 in magnitude. Twenty (56%) of 36 FAT-positive cows did not have a titer that was highest for any particular serovar. Four of the 7 herds that reported using a Leptospira borgpetersenii serovar Hardjo-bovis vaccine had one or more FAT-positive cows compared with 3 out of 3 herds that reported they were not using this type of vaccine, although this difference was not statistically significant.

First Whole Genome Sequence of Anaplasma platys, an Obligate Intracellular Rickettsial Pathogen of Dogs.

We have assembled the first genome draft of Anaplasma platys, an obligate intracellular rickettsia, and the only known bacterial pathogen infecting canine platelets. A. platys is a not-yet-cultivated bacterium that causes infectious cyclic canine thrombocytopenia, a potentially fatal disease in dogs. Despite its global distribution and veterinary relevance, no genome sequence has been published so far for this pathogen. Here, we used a strategy based on metagenome assembly to generate a draft of the A. platys genome using the blood of an infected dog. The assembled draft is similar to other Anaplasma genomes in size, gene content, and synteny. Notable differences are the apparent absence of rbfA, a gene encoding a 30S ribosome-binding factor acting as a cold-shock protein, as well as two genes involved in biotin metabolism. We also observed differences associated with expanded gene families, including those encoding outer membrane proteins, a type IV secretion system, ankyrin repeat-containing proteins, and proteins with predicted intrinsically disordered regions. Several of these families have members highly divergent in sequence, likely to be associated with survival and interactions within the host and the vector. The sequence of the A. platys genome can benefit future studies regarding invasion, survival, and pathogenesis of Anaplasma species, while paving the way for the better design of treatment and prevention strategies against these neglected intracellular pathogens.

Potential use of a canine whole blood culture system to evaluate the immune response to Leptospira.

In susceptible hosts, protection from Leptospira infection is mediated by the innate immune response at the point of entry and humoral immunity. Thus, identifying and segregating the initial host response at the representative host-pathogen interface is needed to understand the typical outcomes of Leptospira infection, clearance, persistence, or disease. An in vitro whole blood culture system to study the overall immune response using pathogenic and non-pathogenic Leptospira strains was explored in this study. Using an ELISA, increased IL-8, TNF alpha, and IL-1 in blood samples stimulated with pathogenic and nonpathogenic Leptospira compared to unstimulated controls were detected. In RT2 Profiler PCR Array assays, consistent upregulation of 22 genes and downregulation of 25 genes were observed. Few of the notable upregulated genes included BPI, CCL3, CXCL2, IL-6, IL-8, TLR1, TLR2, TLR6, and TNF and downregulated genes included, LBP, LYZ, MPO, MYD88. IFNß was upregulated in samples treated with pathogenic Leptospira and IL-1ß was upregulated in samples treated with nonpathogenic Leptospira. Toll- like Receptor signaling and expression of pattern recognition receptors were two of the five prominent canonical pathways observed. Individual deconvolution of each of the specific and significant pathways observed in this study may improve the understanding of the pathogenesis of this important zoonotic agent. The use of this system in conjunction with whole transcriptome analysis in a larger population, may unveil the robust nature of host/Leptospira interaction.

Complete Genome Sequence of a Virulent Leptospira interrogans Serovar Copenhageni Strain, Assembled with a Combination of Nanopore and Illumina Reads.

Here, we present the complete genome sequence of a highly virulent Leptospira interrogans serovar Copenhageni strain isolated from a dog with severe leptospirosis. In this work, a gapless genome draft was assembled with a combination of Nanopore and Illumina data of relatively low coverage.

Leptospira Infection in African Green Monkeys in an Endemic Area: An Opportunity for Comparative Studies in a Natural Environment.

This study was performed to investigate the potential asymptomatic Leptospira reservoir status among African green monkeys (AGMs) in the Caribbean island of Saint Kitts, and whether there is any renal pathology associated with Leptospira exposure. Forty-eight percent of AGMs tested were positive for Leptospira antibodies by the microscopic agglutination test. Leptospira DNA was detected in 4% of kidney samples tested using a lipl32 gene based PCR. We observed minimal to severe microscopic renal lesions in 85% of the AGM kidneys evaluated. The majority of the AGMs (n = 26) had only minimal to mild interstitial nephritis and a few (n = 3) had moderate to severe lesions. The presence of interstitial nephritis was not significantly associated with Leptospira exposure. The presence of infected AGMs in a small surface limited geographic region may pose zoonotic threat to humans and animals. The impact of Leptospira infection in renal pathology in AGMs warrants further investigation. AGMs residing in a natural setting in an insular, surface limited Leptospira endemic geographic region may offer opportunities for comparative studies to advance the field of leptospirosis. Due to their similarity to humans, such studies in AGMs may also provide translational opportunities to advance Leptospira research.

Detection and Characterization of Leptospira Infection and Exposure in Rats on the Caribbean Island of Saint Kitts.

In this study, we detected and characterized Leptospira infection and exposure in rats on the Caribbean island of Saint Kitts for the first time. We detected Leptospira infection in 17/29 (59%), 14/29 (48)%, and 11/29 (38)% of rats by RT-PCR, culture, and immunofluorescence assay, respectively. Whole genome sequencing (WGS) and analysis and serogrouping of 17 Leptospira strains isolated from rats revealed their close relationship with L. interrogans serogroup Icterohaemorrhagiae (n = 10) and L. borgpetersenii serogroup Ballum (n = 7). WGS, serogrouping, and additional PCR tests on rat kidneys confirmed mixed infections with L. interrogans and L. borgpetersenii in the kidneys of three rats. Microscopic agglutination test (MAT) was positive for 25/29 (87%) of the rats tested, and the response was restricted to serovars Icterohaemorrhagiae {24/29(83%)}, Mankarso {4/29(14%)}, Copenhageni {4/29(14%)}, Grippotyphosa {2/29(7%)}, and Wolffi {1/29(3%)}. Interestingly, there was no agglutinating antibody response to serovar Ballum. We observed a similar pattern in the serologic response using Leptospira isolates obtained from this study with each of the rat sera, with strong response to L. interrogans isolates but minimal reactivity to L. borgpetersenii isolates. Our findings suggest the use of multiple complementary diagnostic tests for Leptospira surveillance and diagnosis to improve the accuracy of the data.