Molecular and Phenotypic Characterization of Escherichia coli Associated with Granulomatous Colitis of Boxer Dogs

Fluorescent In Situ Hybridization for the Detection of Intracellular Bacteria in Companion Animals

FISH techniques have been applied for the visualization and identification of intracellular bacteria in companion animal species. Most frequently, these techniques have focused on the identification of adhesive-invasive Escherichia coli in gastrointestinal disease, although various other organisms have been identified in inflammatory or neoplastic gastrointestinal disease. Previous studies have investigated a potential role of Helicobacter spp. in inflammatory gastrointestinal and hepatic conditions. Other studies evaluating the role of infectious organisms in hepatopathies have received some attention with mixed results. FISH techniques using both eubacterial and species-specific probes have been applied in inflammatory cardiovascular, urinary, and cutaneous diseases to screen for intracellular bacteria. This review summarizes the results of these studies.

A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice

BACKGROUND

Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in vitro definition fully predicts mucosal colonization in vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis.

RESULTS

Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortium of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization.

CONCLUSIONS

Our findings establish the in vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in vivo colonization dynamics of patient-derived bacteria in murine models. Video Abstract.

Review article: The complex interplay between diet and Escherichia coli in inflammatory bowel disease

BACKGROUND

Although no causative microbe has been yet identified or successfully targeted in the treatment of inflammatory bowel disease (IBD), the role of Escherichia coli in the pathogenesis of Crohn's disease has attracted considerable interest.

AIM

In this review, we present a literature overview of the interactions between diet and E. coli and other Proteobacteria in the aetiology, outcomes and management of IBD and suggest future research directions.

METHODS

An extensive literature search was performed to identify in vitro studies and research in animal models that explored mechanisms by which dietary components can interact with E. coli or Proteobacteria to initiate or propagate gut inflammation. We also explored the effect diet and dietary therapies have on the levels of E. coli or Proteobacteria in patients with IBD.

RESULTS

Preclinical data suggest that the Western diet and its components influence the abundance, colonisation and phenotypic behaviour of E. coli in the gut, which may in turn initiate or contribute to gut inflammation. In contrast, the Mediterranean diet and specific dietary fibres may abrogate these effects and protect from inflammation. There are limited data from clinical trials, mostly from patients with Crohn's disease during treatment with exclusive enteral nutrition, with findings often challenging observations from preclinical research. Data from patients with ulcerative colitis are sparse.

CONCLUSIONS

Preclinical and some clinical trial data suggest that E. coli and other Proteobacteria interact with certain dietary components to promote gut inflammation. Well-designed clinical trials are required before dietary recommendations for disease management can be made.

A case of canine intestinal malakoplakia

Malakoplakia is a rare chronic granulomatous disease usually affecting the urinary bladder and other locations. In humans, the gastrointestinal tract is the second most common location but there are no reports of intestinal malakoplakia in animals. A 10-month-old female French Bulldog was presented with chronic haemorrhagic diarrhoea and anorexia with normochromic-normocytic anaemia and hypoalbuminaemia. Grossly, there was mucosal thickening and ulceration of the caecum, colon and rectum. Microscopically, transmural sheets of foamy macrophages were seen in these tissues. Macrophages were periodic acid-Schiff, vimentin and ionized calcium-binding adaptor molecule 1 positive and contained von Kossa- and Prussian blue-positive Michaelis-Gutmann bodies. Giemsa staining revealed rod-shaped bacterial colonies and fluorescence in-situ hybridization demonstrated Escherichia coli within macrophages. This is the first reported case of intestinal malakoplakia in domestic animals. Pathological features of intestinal malakoplakia share many similarities with ulcerative histiocytic colitis in dogs but it is unclear if they are different forms of the same pathological process or distinct entities.

Heterogeneity among Clinical Intestinal Escherichia coli Isolates upon Acquired Streptomycin Resistance

Escherichia coli isolates from inflammatory bowel disease (IBD) patients are often multidrug resistant, including to streptomycin. Streptomycin resistance (StrR) mutations can alter bacterial behavior, which may influence intestinal disease. We generated a spontaneous StrR strain of the intestinal adherent-invasive E. coli (AIEC) strain NC101. Whole-genome sequencing revealed a single missense mutation in rpsL that commonly confers StrR, rpsL-K43N. StrR NC101 exhibited a striking loss of aggregation and significantly increased motility, behaviors that can impact host-microbe interactions. Behavioral changes were associated with reduced transcription of csgA, encoding the biofilm component curli, and increased transcription of fliC, encoding flagellin. Scanning electron microscopy (SEM) detailed morphologic changes consistent with the observed alterations in multicellular behavior. Because intestinal E. coli isolates exhibit remarkable strain-specific differences, we generated spontaneous StrR mutants of 10 clinical E. coli phylotype B2 strains from patients with IBD, colorectal cancer, and urinary tract infection. Out of these 10 StrR clinical strains, two had altered colony morphology on Congo red agar (suggesting changes in extracellular products), and three had significant changes in motility. These changes were not associated with a particular rpsL mutation nor with the presence of virulence genes encoding the inflammation-associated E. coli metabolites yersiniabactin or colibactin. We conclude that common mutations in rpsL, which confer StrR, can differentially alter disease-associated phenotypes across intestinal E. coli strains. These findings highlight the heterogeneity among seemingly similar intestinal E. coli strains and reveal the need to carefully study the strain-specific effects of antibiotic resistance mutations, particularly when using these mutations during strain selection studies. IMPORTANCE We demonstrate that StrR, commonly acquired through a single point mutation in rpsL (a gene encoding part of the 30S bacterial ribosome), strikingly alters the morphology and behavior of a key intestinal AIEC strain, NC101. These changes include remarkably diminished aggregation and significantly increased motility, traits that are linked to AIEC-defining features and disease development. Phenotypic changes were heterogeneous among other StrR clinical E. coli strains, underscoring the need to evaluate the strain-specific effects of commonly acquired antibiotic resistance mutations. This is important, as the results of studies using mutant StrR Enterobacteriaceae strains (e.g., for cloning or in vivo selection) may be confounded beyond our demonstrated effects. Long term, these findings can help researchers better distinguish the contribution of specific E. coli traits to functional changes in the microbiota. Evaluating these strain-level differences could provide insight into the diversity of IBD symptoms and lead to improved therapies for microbiota-driven intestinal disorders.

A consortia of clinical E. coli strains with distinct in-vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice

Background

Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in-vitro definition fully predicts mucosal colonization in-vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis.

Results

Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortia of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization.

Conclusions

Our findings establish the in-vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in-vivo colonization dynamics of patient-derived bacteria in murine models.

Canine chronic enteropathy—Current state-of-the-art and emerging concepts

Over the last decade, chronic inflammatory enteropathies (CIE) in dogs have received great attention in the basic and clinical research arena. The 2010 ACVIM Consensus Statement, including guidelines for the diagnostic criteria for canine and feline CIE, was an important milestone to a more standardized approach to patients suspected of a CIE diagnosis. Great strides have been made since understanding the pathogenesis and classification of CIE in dogs, and novel diagnostic and treatment options have evolved. New concepts in the microbiome-host-interaction, metabolic pathways, crosstalk within the mucosal immune system, and extension to the gut-brain axis have emerged. Novel diagnostics have been developed, the clinical utility of which remains to be critically evaluated in the next coming years. New directions are also expected to lead to a larger spectrum of treatment options tailored to the individual patient. This review offers insights into emerging concepts and future directions proposed for further CIE research in dogs for the next decade to come.

Malakoplakia of the urinary bladder in a young French Bulldog

CASE DESCRIPTION

A 4-month-old 5.9-kg sexually intact female French Bulldog was presented because of recurrent urinary tract infections in combination with pollakiuria, hematuria, and urinary incontinence.

CLINICAL FINDINGS

A diagnosis of malakoplakia was made on the basis of results of hematologic and serum biochemical testing, abdominal ultrasonography, bacterial culture, and cystoscopic biopsies of the urinary bladder wall. Biopsy samples were sent for routine histologic examination and fluorescence in situ hybridization to confirm the presence of intracellular and subendothelial bacteria.

TREATMENT AND OUTCOME

Treatment with enrofloxacin was started after the diagnosis of malakoplakia was confirmed. During treatment, polypoid changes in the urinary bladder decreased dramatically but did not disappear. On follow-up ultrasonography after 12 weeks of treatment, marked improvement was visible and results of repeated bacterial culture and fluorescence in situ hybridization of bladder wall samples were negative. The patient was free from clinical signs and had an ultrasonographically normal urinary bladder 59 weeks after antimicrobial treatment was discontinued.

CLINICAL RELEVANCE

Malakoplakia, a granulomatous disease characterized by impaired histiocytes that are unable to completely digest phagocytized bacteria, is a very rare disease in dogs, but early suspicion of the condition is essential to allow timely diagnosis and avoid disease progression and the need for prolonged treatment. Malakoplakia should be considered in young dogs with chronic urinary tract infections; the diagnosis can be made through a combination of histologic examination and fluorescence in situ hybridization of bladder wall biopsy samples.

Correlation of cytology to histology in a case of canine granulomatous colitis in a Boxer dog

A 2-year-old castrated male mixed breed dog presented to the North Carolina State Veterinary Teaching Hospital for chronic diarrhea with hematochezia and weight loss. Cytology performed on a rectal scraping revealed macrophages containing magenta, light pink, and variably blue granular inclusions, and phagocytosed material concerning for infectious organisms. Histopathology was consistent with granulomatous colitis and identified intra-histiocytic bacterial organisms, confirmed by fluorescent in situ hybridization (FISH)-tissue culture-confirmed Escherichia coli. Based on these findings, a diagnosis of granulomatous colitis was made. The patient was successfully treated with oral enrofloxacin, and near-complete remission of signs was achieved within 6 weeks. This report describes a case of granulomatous colitis in a mixed breed dog, and is the first published description of the cytologic features of this uncommon disease, offering a valuable cytologic-histologic correlation. In this case, the cytology was helpful in identifying features consistent with granulomatous colitis and prioritizing the differential diagnoses and diagnostic plan.

Inflammation-Associated Microbiota Composition Across Domestic Animals

Domestic animals represent important resources for understanding shared mechanisms underlying complex natural diseases that arise due to both genetic and environmental factors. Intestinal inflammation, particularly inflammatory bowel disease (IBD), is a significant health challenge in humans and domestic animals. While the etiology of IBD is multifactorial, imbalance of symbiotic gut microbiota has been hypothesized to play a central role in disease pathophysiology. Advances in genomic sequencing and analytical pipelines have enabled researchers to decipher the composition of the intestinal microbiota during health and in the context of naturally occurring diseases. This review compiles microbiome genomic data across domestic species and highlights a common occurrence of gut microbiome dysbiosis during idiopathic intestinal inflammation in multiple species, including dogs, cats, horses, cows, and pigs. Current microbiome data obtained from animals with intestinal inflammation are mostly limited to taxonomical analyses in association with broad clinical phenotype. In general, a pathogen or pathosymbiont were not detected. Rather, functional potential of the altered microbiota has been suggested to be one of the key etiologic factors. Among the domestic species studied, canine analyses are currently the most advanced with incorporation of functional profiling of microbiota. Canine IBD parallels features of the disease in humans, thus canines represent a strong natural model for human IBD. While deeper analyses of metagenomic data, coupled with host molecular analyses are needed, comparative studies across domestic species can reveal shared microbial alterations and regulatory mechanisms that will improve our understanding of intestinal inflammation in both animals and humans.

Clinical characteristics and long-term outcome of E. coli-associated granulomatous ileocolitis in dogs: five cases (2010-2014)

OBJECTIVES

To describe the clinical characteristics and long-term outcome of Escherichia coli-associated granulomatous ileocolitis in dogs.

METHODS

Retrospective review of medical records from dogs with periodic acid-Schiff positive (PAS+) granulomatous ileocolitis and mucosally invasive E. coli in the ileum and colon. Initial bacterial colonisation was evaluated using fluorescence in situ hybridization (FISH) in all dogs and corroborated with colonic and/or ileal culture, when performed.

RESULTS

Four boxer dogs and 1 French Bulldog with PAS+ granulomatous ileocolitis (GIC) were evaluated. All dogs had chronic diarrhoea refractory to empirical therapy. Ileocolonoscopy revealed mucosal haemorrhage and ulceration in the ileum (3/4) and colon (5/5). E. coli were visualised as clusters within the ileal and colonic mucosa. Complete (CR, 4/5) or partial (PR, 1/5) clinical response to fluoroquinolones was noted in all dogs within 30 days. CR was sustained in three of four dogs (median disease-free interval 40 months, range 16 to 60). Two dogs relapsed while receiving fluoroquinolones. Repeat biopsy isolated multidrug-resistant, mucosally invasive E. coli in the ileum (1/2) and colon (2/2). Targeted antimicrobial therapy was associated with long-term PR (78 months) in both dogs.

CLINICAL SIGNIFICANCE

Concurrent E. coli-associated granulomatous inflammation in the ileum and colon did not impart a poor clinical outcome or lack of response to the conventional standard of care for granulomatous colitis in dogs that were aggressively diagnosed and treated. Clinical outcome was influenced by antimicrobial resistance, with response dependent upon antimicrobial therapy informed by susceptibility testing.

Special Issue: Pathogenic Escherichia coli: Infections and Therapies

Escherichia coli is a facultative anaerobic Gram-negative bacterium from the Enterobacteriaceae family that colonizes the gastrointestinal tract of warm-blooded animals shortly after birth, and it is a lifelong colonizer of adults [...].

Escherichia coli-associated granulomatous colitis in dogs treated according to antimicrobial susceptibility profiling

Background

Eradication of intramucosal Escherichia coli correlates with remission of periodic acid‐Schiff‐positive E coli‐associated granulomatous colitis (GC). Treatment failures attributed to multidrug resistant (MDR) bacteria necessitate alternative approaches.

Hypothesis/objectives

Determine clinical outcome of E coli‐associated GC in dogs treated based on antimicrobial susceptibility profiling and characterize E coli phylogeny and resistance mechanisms.

Animals

Twenty Boxers and 4 French Bulldogs with E coli‐associated GC.

Methods

Culture, antimicrobial susceptibility profiling, and molecular characterization of E coli were performed and response to treatment was evaluated.

Results

Initial biopsy sample culture yielded fluoroquinolone‐sensitive (FQ‐S) E coli from 9/24 dogs and fluoroquinolone‐resistant (FQ‐R) E coli from 15/24. All but 1 FQ‐R E coli were MDR with susceptibility to macrophage‐penetrating antimicrobials restricted to carbapenems in 13/15 dogs. Of 22/24 treated based on susceptibility profiling, 8/9 FQ‐S dogs had complete initial clinical response (CR) during fluoroquinolone (FQ) treatment, whereas 9/13 FQ‐R dogs had complete or partial response (PR) during meropenem or doxycycline treatment. In 5/9 FQ‐S and 12/13 FQ‐R dogs with follow‐up ≥3 months, CR was sustained in 5/5 FQ‐S (median, 25 months; range, 4‐46) whereas 6/12 FQ‐R had long‐term CR (median, 59 months; range 15‐102), 4/12 PR (median, 19 months; range, 5‐65), and 2/12 had no response (NR). Four dogs with long‐term follow‐up died within 4 years of diagnosis, including 2 euthanized for refractory colitis. Escherichia coli were genetically diverse. Fluoroquinolone resistance was associated with mutations in gyrA and parC, with plasmid‐mediated resistance less common.

Conclusions and Clinical Importance

Antimicrobial treatment guided by susceptibility profiling was associated with positive long‐term outcomes in >80% of cases. Fluoroquinolone‐resistance was widespread and not clonal. Further study is required to optimize treatment for dogs with MDR E coli‐associated GC.