Disease-Specific Enteric Microbiome Dysbiosis in Inflammatory Bowel Disease.

Inflammatory Bowel disease (IBD) is traditionally divided into Crohn's disease (CD) and ulcerative colitis (UC). UC is a relapsing non-transmural inflammatory disease that is restricted to the colon and is characterized by flare-ups of bloody diarrhea. CD is a chronic, segmental localized granulomatous disease that can affect any part of the entire gastrointestinal tract. Ileo-anal pouch is a procedure restoring functionality of the rectum after a colectomy. IBD is a multifactorial disease and flares of IBD are probably triggered by changes in the intestinal microbiota followed by an abnormal immune response. In this study, we aim to analyze the intestinal bacterial diversity in IBD patients during various stages of disease compared with healthy controls. Permission for human experiments and recruitment of participants was obtained from the Ethic Committee for Copenhagen County hospitals (Permission no. KA-03019, Permission no. KA-20060159). Stools from 26 healthy controls, 42 CD, 38 UC and 18 pouch patients were collected. Stool DNA extraction was performed using Qiagen, DNA mini stool kit Denmark. DGGE-PCR amplifying the V2-V3 region of 16S-rDNA gene of the bacteria was amplified by universal primers HDA1 and HDA2. Analysis of DGGE was performed blinded using BioNumerics version 7.5. After normalization, a DGGE gel band matching was performed. The similarities between profiles were calculated with a ranked Pearson correlation coefficient based on the band matching results using band intensities. Simpson's index of diversity and Pielou's species evenness were calculated. Based on the Shannon Diversity Index, UC patients had lower species diversity and bacterial evenness in comparison to healthy persons, p < 0.05. However, only CD and disease pouch patients had lower species diversity compared to those with inactive disease and healthy controls. Well-functioning pouch patients had decreased species evenness in comparison to diseased pouch patients and control group. During the active disease stage in CD and pouch, the patients have a low bacterial diversity in their gut when compared to the inactive stage. In UC patients, a generally low diversity was observed at all stages of the disease compared to healthy controls.

Characterization of Diarrheagenic Enteroaggregative Escherichia coli in Danish Adults-Antibiotic Treatment Does Not Reduce Duration of Diarrhea.

Enteroaggregative Escherichia coli (EAEC) is frequently isolated from sporadic cases of diarrhea and in outbreaks of gastroenteritis in several regions of the world. The pathophysiology of EAEC continues to be enigmatic, and the efficacy of antibiotic treatment in EAEC-associated diarrhea has been discussed. Since the level of antibiotic resistance is increasing, it is essential to restrict the use of antibiotics to prevent further resistance development. We aimed to investigate EAEC strains in adult Danish patients suffering from diarrhea and from healthy controls. We examined the antibiotic resistance in EAEC strains, the clinical response to antibiotic treatment in EAEC diarrheal cases, and the distribution of virulence genes in diarrheal cases. The EAEC strains were collected from patients suffering from diarrhea in a Danish multicenter study. A medical doctor interviewed the patients by using a questionnaire regarding gastrointestinal symptoms, exposures, and use of antibiotic and over-the-counter antidiarrheal drugs. Follow-up was performed after 3-5 months to inquire about differential diagnosis to gastrointestinal disease. A multiplex polymerase chain reaction characterized virulence genes in diarrheal cases. Finally, the level of antibiotic resistance was examined by using the disc diffusion method. Asymptomatic carriage of EAEC in the adult Danish population was rare, in contrast to findings in healthy Danish children. The duration of diarrhea was not shortened by antibiotic treatment, specifically ciprofloxacin treatment, or by over-the-counter antidiarrheal drugs. Follow-up revealed no pathology in diarrheal patients apart from irritable bowel syndrome in two patients. A high number of patients suffered from long-term diarrhea, which was associated with the enterotoxin EAST-1 and a high virulence factor score. A high level of antibiotic resistance was observed and 58% of the EAEC strains were multidrug resistant. Multidrug resistance was most pronounced in cases of travelers' diarrhea, and it was seen that antibiotic treatment did not reduce the duration of diarrhea.

Nonaplex PCR using Cliffhanger primers to identify diarrhoeagenic Escherichia coli from crude lysates of human faecal samples.

Sensitive, probe-based detection of multiple DNA targets is limited by the competitive reannealing of the antiparallel duplex DNA helix with the complementary DNA strand. To address this, we developed Cliffhanger primers, which create single-stranded DNA overhangs on PCR amplicons while simultaneously increasing the multiplex PCR efficacy and allowing PCR amplification using crude lysates of human faecal samples. A multiplex PCR that targeted eight genes from diarrhoeagenic Escherichia coli plus an internal control was performed and compared to a routine method that consisted of culture followed by multiplex PCR with fragment length separation. A total of 2515 clinical faecal samples from patients with diarrhoea were tested using both methods, and there was a significant increase in clinical sensitivity and negative predictive value with the Cliffhanger method for seven out of eight genes. All Cliffhanger-only positive samples were confirmed by Sanger sequencing of the PCR amplicon. Notably, the Cliffhanger method reduced the total sample turn-around time in the laboratory from 20 hours to 6 hours. Hence, use of Cliffhanger primers increased assay robustness, decreased turn-around time and increased PCR efficacy. This increased the overall clinical sensitivity without the loss of specificity for a heavily multiplexed PCR assay.

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid.

Advances in genomics have the potential to revolutionize clinical diagnostics. Here, we examine the microbiome of vitreous (intraocular body fluid) from patients who developed endophthalmitis following cataract surgery or intravitreal injection. Endophthalmitis is an inflammation of the intraocular cavity and can lead to a permanent loss of vision. As controls, we included vitreous from endophthalmitis-negative patients, balanced salt solution used during vitrectomy and DNA extraction blanks. We compared two DNA isolation procedures and found that an ultraclean production of reagents appeared to reduce background DNA in these low microbial biomass samples. We created a curated microbial genome database (>5700 genomes) and designed a metagenomics workflow with filtering steps to reduce DNA sequences originating from: (i) human hosts, (ii) ambiguousness/contaminants in public microbial reference genomes and (iii) the environment. Our metagenomic read classification revealed in nearly all cases the same microorganism that was determined in cultivation- and mass spectrometry-based analyses. For some patients, we identified the sequence type of the microorganism and antibiotic resistance genes through analyses of whole genome sequence (WGS) assemblies of isolates and metagenomic assemblies. Together, we conclude that genomics-based analyses of human ocular body fluid specimens can provide actionable information relevant to infectious disease management.

Genetic Virulence Profile of Enteroaggregative Escherichia coli Strains Isolated from Danish Children with Either Acute or Persistent Diarrhea.

Enteroaggregative Escherichia coli (EAEC) is frequently found in diarrheal stools worldwide. It has been associated with persistent diarrhea, weight loss, and failure to thrive in children living in developing countries. A number of important EAEC virulence genes are identified; however, their roles in acute and persistent diarrhea have not been previously investigated. The aim of this study was to identify specific EAEC virulence genes associated with duration and type of diarrhea in Danish children. We aimed to improve the current diagnostics of EAEC and enable targeting of strains with an expected severe disease course. Questionnaires answered by parents provided information regarding duration of diarrhea and presence of blood or mucus. A total of 295 EAEC strains were collected from children with acute (≤7 days) and persistent diarrhea (≥14 days) and were compared by using multiplex PCR targeting the genes sat, sepA, pic, sigA, pet, astA, aatA, aggR, aaiC, aap, agg3/4C, ORF3, aafA, aggA, agg3A, agg4A, and agg5A. Furthermore, the distribution of EAEC genes in strains collected from cases of bloody, mucoid, and watery diarrhea was investigated. The classification and regression tree analysis (CART) was applied to investigate the relationship between EAEC virulence genes and diarrheal duration and type. Persistent diarrhea was associated with strains lacking the pic gene (p = 0.002) and with the combination of the genes pic, sat, and absence of the aggA gene (p = 0.05). Prolonged diarrhea was associated with the combination of the genes aatA and astA (p = 0.03). Non-mucoid diarrhea was associated with strains lacking the aatA gene (p = 0.004). Acute diarrhea was associated with the genes aggR, aap, and aggA by individual odds ratios. Resistance toward gentamicin and ciprofloxacin was observed in 7.5 and 3% of strains, respectively. Multi-drug resistance was observed in 38% of strains. Genetic host factors have been associated with an increased risk of EAEC-associated disease. Therefore, we investigated a panel of risk factors in two groups of children-EAEC-positive and EAEC-negative-to identify additional factors predisposing to disease. The duration of breastfeeding was positively correlated with the likelihood of belonging to the EAEC-negative group of children.

A Prospective Study on the Clinical and Microbiological Spectrum of Endophthalmitis in a Specific Region in Denmark.

PURPOSE: To study the clinical and microbiological spectrum of endophthalmitis with emphasis on clinical features, visual outcomes and risks of surgical complications. METHODS: A prospective observational study was conducted between 2012 and 2013 in a specific region in Denmark. Patients were clinically examined before, during and after surgical intervention for endophthalmitis. RESULTS: Fifty eyes with endophthalmitis were included. Endophthalmitis after cataract surgery (post-cataract), anti-VEGF (vascular endothelial growth factor) intravitreal injections (post-injection) and cases of endogenous endophthalmitis were responsible for 40, 28 and 18% of all cases, respectively. There was no difference in the microbiological spectrum in post-cataract patients and post-injection patients, but patients with post-cataract endophthalmitis presented statistically significantly more frequently with hypopyon and fibrin in the anterior chamber. Between 20 and 25% of post-cataract and post-injection endophthalmitis patients developed a surgical complication after primary surgical intervention for endophthalmitis, and this was statistically significantly associated with a poor visual outcome. There was no statistically significant difference in the risk of surgical complications in phakic and pseudophakic eyes with post-injection endophthalmitis. Of the 8 patients with endogenous endophthalmitis, 67% developed a surgical complication, and these patients had a high mortality. The visual outcome in the most common types of endophthalmitis was good, with 60% of post-cataract patients achieving a visual outcome ≥ 0.5, and 64% of post-injection patients only had a mild vision loss (1-14 ETDRS letters) or even gained vision. CONCLUSIONS: The endophthalmitis cases had a broad clinical spectrum. Surprisingly, endogenous endophthalmitis accounted for almost one fifth of all cases. Patients with post-cataract endophthalmitis had a clinically different presentation than patients with post-injection endophthalmitis. In general, the bacteria were low-virulent and the visual outcomes good, but a substantial part of the patients developed a surgical complication which was associated with a poor visual outcome.

Phenotypic and genotypic characteristics of Arcanobacterium haemolyticum isolated from clinical samples in a Danish hospital.

Six Arcanobacterium haemolyticum strains isolated from six patients of two hospitals in Denmark were identified phenotypically, also including matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, and by genotypic methods. The latter were performed by sequencing 16S rDNA and glyceraldehyde 3-phosphate dehydrogenase encoding gene gap and by amplification of an A. haemolyticum specific region of 16S-23S rDNA intergenic spacer region and 23S rDNA. The six A. haemolyticum strains were further investigated for the presence of seven potential virulence genes encoding arcanolysin, phospholipase D, hemolysin A, CAMP factor family protein, collagen binding protein, neuraminidase A and neuraminidase H which appeared to be present in two (seven virulence genes), two (six virulence genes) and two strains (four virulence genes), respectively. The phenotypic and genotypic properties described in the present study might help to reliably identify and further characterize A. haemolyticum isolated from human patients, a species which seems to be of increasing importance.

Genital and extra-genital screening for gonorrhoea using the BD Probetec ET system with an in-house PCR method targeting the porA pseudogene as confirmatory test.

Diagnosing gonorrhoea from extra-genital as well as genital sites is important in managing this sexually transmitted disease. In this study we evaluated a screening procedure for Neisseria gonorrhoeae (GC) from all sample sites in a low-prevalence setting. A total of 69,252 specimens submitted for Chlamydia trachomatis testing were also examined for GC on the BD Viper™ platform using the BD Probetec ET system. In order to avoid false-positive results all GC BD reactive samples were re-tested using a PCR method with the porA pseudogene as target. Using this method we screened 170% more samples for GC than in the previous year, in the same population, and diagnosed more than twice as many GC-positive episodes. The BD system can be used successfully to screen extra-genital as well as genital specimen types for GC in a low-prevalence area if it is combined with a validated confirmatory PCR test.

Seroreactivity to E. coli outer membrane protein C antibodies in active inflammatory bowel disease; diagnostic value and correlation with phylogroup B2 E. coli infection.

BACKGROUND: Several serologic tests, including anti-outer membrane porin C antibody (Omp C), are used for screening and as marker of disease course in inflammatory bowel diseases (IBD). Our aim was to investigate possible differences in Omp C level in patients with active and inactive IBD compared to controls. METHODS: All blood samples were tested for Omp C. Disease activity was evaluated by Harvey Bradshaw Index, Simple Clinical Activity Index and Modified Pouchitis Disease Activity Index. RESULTS: Blood samples were collected from 113 patients and 60 controls. Patients with active IBD did not have a higher level of Omp C than patients in remission. Surprisingly, in patients with active Crohn's disease a significantly lower level of Omp C was found compared with patients with inactive Crohn's disease (p < 0.05). All other groups among patients with IBD did have a significantly higher level of Omp C, compared with controls, including patients with acute gastroenteritis (p < 0.05). Although IBD patients with phylogroup B2 E. coli cultured from their fecal samples, were more likely to have a positive Omp C test (p < 0.05), this could not explain the low Omp C level in the subgroup of patients with active Crohn's disease. CONCLUSIONS: Omp C titer was not raised in patients with active IBD compared with patients in remission. In addition, there was no difference in Omp C level in patients with active Crohn's disease compared with controls. These observations do not support the use of Omp C serology testing, either in disease activity assessment, or in screening for active Crohn's disease.

Bacteriological aetiology and antimicrobial treatment of pleural empyema.

BACKGROUND: Our aims were to describe the aetiologies of culture-positive pleural infections and to evaluate the choice of empiric antimicrobial treatment regimens according to antimicrobial sensitivity, and to evaluate the possible influence of this on outcome. METHODS: All cases over a 9-y period were identified from 3 hospitals using the laboratory databases of the clinical microbiology departments, and were verified by evaluating the medical records. RESULTS: We identified 291 isolates in pleural fluid cultures from 158 patients. These included viridans streptococci (25%), Staphylococcus aureus (18%), anaerobic bacteria (17%), Enterobacteriaceae (12%), Staphylococcus epidermidis (10%), and Streptococcus pneumoniae (7%), with differences between nosocomial and community-acquired infections. The mortality (overall 27%) was highest among the patients with Enterobacteriaceae (50%) and S. aureus (36%) infections, and in patients with mixed infections (34%). The actual empiric treatment or the recommended penicillin plus metronidazole had low antimicrobial coverage (49%) compared to the proposed cefuroxime plus metronidazole (78%). Thoracentesis was often delayed (median 2 days). The adequacy of empiric antimicrobial therapy was independently correlated with mortality (odds ratio 0.43, 95% confidence interval 0.30-0.62). CONCLUSIONS: The early diagnosis of pleural infection could be optimized. In this North-European patient population, we suggest that the recommended empiric antimicrobial treatment be changed to cefuroxime plus metronidazole for community-acquired and nosocomial infections.

The prevalence and clinical significance of intestinal parasites in HIV-infected patients in Denmark.

To investigate the prevalence and clinical significance of intestinal parasites in human immunodeficiency virus (HIV)-infected patients, faecal specimens from 96 HIV-infected patients were submitted to microbiological analyses, including microscopy and polymerase chain reaction for protozoa and enteropathogenic bacteria. Results of microbiological analyses were compared with self-reported gastrointestinal complaints collected using a validated questionnaire. Thirty-two (33%) patients were positive for parasites. However, opportunistic parasites (Isospora and Cryptosporidium) were detected in only 2 instances. Entamoeba dispar was detected in 10 cases, 9 of which represented men who have sex with men (MSM). Despite generally low HIV RNA loads and high CD4+ T-cell counts, 42% of the 76 patients reporting symptoms complained of diarrhoea, 31% of whom were parasite-positive. The presence of diarrhoea was not associated with the presence or absence of parasites; neither was it associated with receiving highly active anti-retroviral therapy (HAART) in general, or protease inhibitors (PI) in particular. A CD4+ T-cell count <200 cells/mm³ was not associated with parasitic infection or with diarrhoea. The data show that diarrhoea is a common symptom among HIV-infected patients in Denmark, but do not indicate that the diarrhoea is due to intestinal parasites.

Prevalence and molecular characterization of clinical isolates of Escherichia coli expressing an AmpC phenotype.

OBJECTIVES: To establish the prevalence of the AmpC beta-lactamase phenotype in clinical isolates of Escherichia coli and characterize the genetic resistance mechanisms causing the observed phenotype. METHODS: Clinical E. coli (n = 74) with reduced susceptibility to third-generation cephalosporins and resistance to cefoxitin were collected from the Department of Clinical Microbiology at Hvidovre Hospital, Denmark, in 2006. The AmpC disc test was used to confirm expression of AmpC, and test-positive strains were selected for further antimicrobial susceptibility testing and molecular characterization. Hyperproduction of AmpC beta-lactamase was confirmed by isoelectric focusing (IEF). The presence of a plasmid-mediated ampC gene (pAmpC) was detected by multiplex PCR. The promoter and the entire reading frame of the chromosomal ampC gene were sequenced to identify promoter mutations associated with hyperproduction and gene mutations associated with extended-spectrum AmpC (ESAC) beta-lactamase activity. RESULTS: Twenty-four isolates exhibited a positive AmpC disc test. IEF confirmed AmpC expression in all isolates except one. Four isolates contained a bla(CMY-2) gene. These were not clonally related by multilocus sequence typing (MLST). The remaining isolates all had mutations or insertions in the promoter region, which could explain increased expression of the chromosomal AmpC enzyme. Mutations in the ampC gene associated with extended activity were rare and did not cause resistance to cefepime. Sequencing of ampC showed that most isolates were not clonally related. CONCLUSIONS: E. coli expressing an AmpC phenotype occur sporadically and cause significant resistance to cephalosporins. The majority of these are hyperproducing chromosomal ampC although some isolates have acquired pAmpC.

Bacteriology in acute exacerbation of chronic obstructive pulmonary disease in patients admitted to hospital.

We investigated the bacterial flora and antimicrobial sensitivity in sputum from patients admitted to hospital with acute exacerbation of chronic obstructive pulmonary disease (AECOPD) in order to recommend the best empirical treatment for these patients. The survey was a retrospective study of all patients admitted to Hvidovre hospital with the diagnosis AECOPD during 2004. A total of 118 patients were included. Microscopy, culture and sensitivity testing investigated their sputums. Clinical and paraclinical features were collected from the patients' files. Among the 118 patients, 59 (50%) had a positive sputum culture. The group with positive cultures had a higher blood neutrophil count (p=0.03). There were no other clinical differences between the groups with and without positive sputum culture. The majority of patients with positive sputum cultures were infected with bacteria other than S. pneumonia, mostly H. influenzae and Moraxella catarrhalis. Patients with low FEV(1)<1.0 litre were more likely to be infected with Pseudomonas aeruginosa (p=0.03). The sensitivity patterns of the bacteria showed that the majority were resistant to penicillin. If antibiotics are initiated empirically for AECOPD we recommend either cefuroxime for intravenous treatment or amoxicillin-clavulanate for oral treatment.

[A study of the validity of urinary tract infection diagnosis in children younger than two years of age at Hvidovre Hospital]. / Undersøgelse af validiteten af diagnosen urinvejsinfektion hos børn under to år på Hvidovre Hospital.

INTRODUCTION: The aim of this study is to validate the diagnosis of urinary tract infection (UTI) concerning false-positive diagnoses in children younger than two years of age at Hvidovre Hospital. MATERIALS AND METHODS: The material consists of 89 children (50 girls and 39 boys) diagnosed with acute pyelonephritis from September 2002 until October 2004. Two patients dropped out as they were diagnosed in other countries. The patient records were investigated to identify the children who fulfilled the UTI criteria used in the department: 1) Two mid-stream urine samples with bacterial growth of = 10.000 cfu (colony forming units)/cc, 2) growth of = 100 cfu/cc in urine obtained by a suprapubic puncture of the bladder or 3) a mid-stream urine sample with bacterial growth of = 10.000 cfu/cc and a clinical picture of UTI together with elevated inflammatory laboratory parameters. RESULTS: 70 out of 87 patients (80%, 95% confidence limits 70-88%) had a valid UTI diagnosis. CONCLUSION: We consider a diagnostic validity of 80% as satisfactory although our aim is to increase the validity to 90%.

New species in the genus Francisella (Gammaproteobacteria; Francisellaceae); Francisella piscicida sp. nov. isolated from cod (Gadus morhua).

A Francisella strain, GM2212, previously isolated from moribund farmed Atlantic cod (Gadus morhua) in Norway, is closely related to Francisella philomiragia among Francisella spp. according to its complete 16S rDNA, 16S-23S intergenic spacer, 23S rDNA, 23S-5S intergenic spacer, 5S rDNA, FopA, lipoprotein TUL4 (LpnA), malate dehydrogenase and hypothetical lipoprotein (LpnB) sequences. A comparison between GM2212 and the type strain of Francisella philomiragia were performed by DNA-DNA hybridization and fatty acid analysis. The DNA-DNA hybridization showed a 70% similarity. The fatty acid analysis showed only minor differences between the Francisella isolates. Due to the inconclusive result from the DNA-DNA hybridisation, major emphasis concerning the status of this isolate is made on previously published molecular, phenotypic and biochemical characters. All characteristics taken together support the establishment of GM2212 as a novel species, for which the name Francisella piscicida sp. nov. is proposed (=CNCM I-3511(T) = DSM 18777(T) = LMG registration number not yet available).

[Necrotizing fasciitis after arthroscopic synovectomy of an infected prepatellar bursa]. / Fasciitis necroticans efter artroskopi af praepatellar bursitis.

Necrotizing fasciitis (NF) is a life-threatening soft tissue infection in superficial and deep fascias. NF is most often caused by mixed aerobic and anaerobic bacteria. The treatment is early and aggressive surgical debridement, antibiotics and hyperbaric oxygen. In this case description, a nearly 60-year-old man developed NF after arthroscopic synovectomy of an infected prepatellar bursa. We stress the point that the endoscopic technique itself might be responsible for the spreading of bacteria to the fascias. This is a subject for further investigation.