Commercial bacterial and fungal broad-range PCR (Micro-Dx™) used on culture-negative specimens from normally sterile sites: diagnostic value and implications for antimicrobial treatment

The aim of this study was to evaluate the clinical value of partial 16S/18S rRNA gene sequencing with the commercial kit Micro-Dx™ used with the SelectNA™plus instrument on culture-negative samples. A retrospective study of microbiological and clinical data from a 2.5-year period was performed. Assessment of the clinical relevance of the 16S/18S rRNA gene sequencing results was based on evaluation of the results in the clinical context and changes in antimicrobial therapy. Included were 529 samples from 223 patients, representing 251 episodes. In 191 samples (36.1%), bacterial/fungal DNA was detected. Positive results were judged clinically relevant in 79 (31.5%) episodes. Antimicrobial treatment was adjusted according to the 16S/18S rRNA gene sequence analysis result in 42 (16.7%) episodes. The results from 16S/18S rRNA gene sequence analysis were highly clinically relevant. These findings support the use of this analysis in a routine setting.

Profiling of immune-related gene expression in children with familial hypercholesterolaemia

BACKGROUND

Innate and adaptive immune responses are pivotal in atherosclerosis, but their association with early-stage atherosclerosis in humans is incompletely understood. In this regard, untreated children with familial hypercholesterolaemia may serve as a human model to investigate the effect of elevated low-density lipoprotein (LDL)-cholesterol.

OBJECTIVES

We aimed to study the immunological and inflammatory pathways involved in early atherosclerosis by examining mRNA molecules in peripheral blood mononuclear cells (PBMCs) from children with FH.

METHODS

We analysed the level of 587 immune-related mRNA molecules using state-of-the-art Nanostring technology in PBMCs from children with (n = 30) and without (n = 21) FH, and from FH children before and after statin therapy (n = 10).

RESULTS

176 genes (30%) were differentially expressed between the FH and healthy children at P < 0.05. Compared to healthy children, the dysregulated pathways in FH children included the following: T cells (18/19); B cells (5/6); tumour necrosis factor super family (TNFSF) (6/8); cell growth, proliferation and differentiation (5/7); interleukins (5/9); toll-like receptors (2/5); apoptosis (3/7) and antigen presentation (1/7), where the ratio denotes higher expressed genes to total number of genes. Statin therapy reversed expression of thirteen of these mRNAs in FH children.

CONCLUSION

FH children display higher PBMC expression of immune-related genes mapped to several pathways, including T and B cells, and TNFSF than healthy children. Our results suggest that LDL-C plays an important role in modulating expression of different immune-related genes, and novel data on the involvement of these pathways in the early atherosclerosis may represent future therapeutic targets for prevention of atherosclerotic progression.

Typing of vancomycin-resistant enterococci with MALDI-TOF mass spectrometry in a nosocomial outbreak setting

OBJECTIVES

To investigate the usefulness of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) typing as a first-line epidemiological tool in a nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VREfm).

METHODS

Fifty-five VREfm isolates, previously characterized by whole-genome sequencing (WGS), were included and analysed by MALDI-TOF MS. To take peak reproducibility into account, ethanol/formic acid extraction and other steps of the protocol were conducted in triplicate. Twenty-seven spectra were generated per isolate, and spectra were visually inspected to determine discriminatory peaks. The presence or absence of these was recorded in a peak scheme.

RESULTS

Nine discriminatory peaks were identified. A characteristic pattern of these could distinguish between the three major WGS groups: WGS I, WGS II and WGS III. Only one of 38 isolates belonging to WGS I, WGS II or WGS III was misclassified. However, ten of the 17 isolates not belonging to WGS I, II or III displayed peak patterns indistinguishable from those of the outbreak strain.

CONCLUSIONS

Using visual inspection of spectra, MALDI-TOF MS typing proved to be useful in differentiating three VREfm outbreak clones from each other. However, as non-outbreak isolates could not be reliably differentiated from outbreak clones, the practical value of this typing method for VREfm outbreak management was limited in our setting.

Danish guidelines on management of otitis media in preschool children

INTRODUCTION

Otitis media is one of the most common diseases in small children. This underlines the importance of optimizing diagnostics and treatment of the condition. Recent literature points toward a stricter approach to diagnosing acute otitis media (AOM). Moreover, ventilating tube treatment for recurrent AOM (RAOM) and chronic otitis media with effusion (COME) has become the most frequently performed surgical procedure in pre-school children. Therefore, the Danish Health and Medicines Authority and the Danish Society of Otorhinolaryngology, Head and Neck Surgery deemed it necessary to update the Danish guidelines regarding the diagnostic criteria for acute otitis media and surgical treatment of RAOM and COME.

METHODS

The GRADE system (The Grading of Recommendations Assessment, Development and Evaluation) was used in order to comply with current standards of evidence assessment in formulation of recommendations. An extensive literature search was conducted between July and December 2014. The quality of the existing literature was assessed using AGREE II (Appraisal of Guidelines for Research & Evaluation), AMSTAR (assessing the Methodological Quality of Systematic Reviews), QUADAS-2 (Quality of Diagnostic Accuracy Studies), Cochrane Risk of Bias Tool for randomized trials and ACROBAT-NRSI (A Cochrane Risk of Bias Assessment Tool for Non-Randomized Studies). The working group consisted of otolaryngologists, general practitioners, pediatricians, microbiologists and epidemiologists.

CONCLUSION

Recommendations for AOM diagnosis, surgical management for RAOM and COME, including the role of adenoidectomy and treatment of ventilating tube otorrhea, are proposed in the guideline.

Differentiation of Candida glabrata, C. nivariensis and C. bracarensis based on fragment length polymorphism of ITS1 and ITS2 and restriction fragment length polymorphism of ITS and D1/D2 regions in rDNA

Different molecular methods for the discrimination of Candida glabrata, C. bracarensis and C. nivariensis were evaluated and the prevalence of these species among Danish blood isolates investigated. Control strains were used to determine fragment length polymorphism in the ITS1, ITS2, ITS1-5.8S-ITS2 regions and in the D1/D2 domain of 26S rDNA using primers designed for this study. A total of 133 blood isolates previously identified as C. glabrata were examined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and the peptide nucleic acid-fluorescent in situ hybridization (PNA-FISH) method. The size of ITS1 allowed differentiation between C. glabrata (483), C. nivariensis (361) and C. bracarensis (385), whereas the ITS2 region was of similar size in C. nivariensis (417) and C. glabrata (418). Sequence analysis of the ITS region suggested that many restriction enzymes were suitable for RFLP differentiation of the species. Enzymatic digestion of the D1/D2 domain with TatI produced unique band sizes for each of the three species. PCR-RFLP and PNA-FISH were in agreement for all of the isolates tested. None of the 133 Danish blood isolates were C. nivariensis or C. bracarensis. Fragment size polymorphism of ITS1 and RFLP of the D1/D2 domain or the ITS region are useful methods for the differentiation of the species within the C. glabrata group. C. bracarensis and C. nivariensis are rare among Danish C. glabrata blood isolates.

European guideline for the management of chancroid, 2011

Chancroid is a sexually acquired disease caused by Haemophilus ducreyi. The infection is characterized by one or more genital ulcers, which are soft and painful, and regional lymphadenitis which may develop into buboes. The infection may easily be misidentified due to its rare occurrence in Europe and difficulties in detecting the causative pathogen. H. ducreyi is difficult to culture. Polymerase chain reaction (PCR) can demonstrate the bacterium in suspected cases. Antibiotics will usually be efficient for curing chancroid.

Cognitively unimpaired HIV-positive subjects do not have increased 11C-PiB: a case-control study

OBJECTIVES

Diagnostic challenges exist for differentiating HIV dementia from Alzheimer disease (AD) in older HIV-infected (HIV+) individuals. Similar abnormalities in brain amyloid-beta42 (Alphabeta42) metabolism may be involved in HIV-associated neuropathology and AD. We evaluated the amyloid-binding agent (11)C-Pittsburgh compound B ((11)C-PiB), a biomarker for Alphabeta42 deposition, in cognitively unimpaired HIV+ (n = 10) participants and matched community controls without dementia (n = 20).

METHODS

In this case-control study, all participants had an (11)C-PiB scan within 2 years of concomitant CSF studies and neuropsychometric testing. Statistical differences between HIV+ and community controls for demographic and clinical values were assessed by chi(2) tests. Participants were further divided into either low (<500 pg/mL) or normal (>or=500 pg/mL) CSF Alphabeta42 groups with Student t tests performed to determine if regional differences in fibrillar amyloid plaque deposition varied with CSF Alphabeta42.

RESULTS

Regardless of CSF Alphabeta42 level, none of the HIV+ participants had fibrillar amyloid plaques as assessed by increased (11)C-PiB mean cortical binding potential (MCBP) or binding potential within 4 cortical regions. In contrast, some community controls with low CSF Alphabeta42 (<500 pg/mL) had high (11)C-PiB MCBP with elevated binding potentials (>0.18 arbitrary units) within cortical regions.

CONCLUSIONS

Cognitively unimpaired HIV+ participants, even with low CSF Alphabeta42 (<500 pg/mL), do not have (11)C-PiB parameters suggesting brain fibrillar amyloid deposition. The dissimilarity between unimpaired HIV+ and preclinical AD may reflect differences in Abeta42 production and/or formation of diffuse plaques. Future longitudinal studies of HIV+ participants with low CSF Abeta42 and normal (11)C-PiB are required.

Substantial increase in listeriosis, Denmark 2009

In 2009, 97 cases of listeriosis were reported in Denmark (1.8 per 100,000), a significant rise over the previous year. The increase was seen both in cases of bacteraemia and meningitis and affected mainly people aged 70 years and older. A foodborne outbreak of eight cases was identified by pulsed-field gel electrophoresis typing. No explanation has so far been found for the marked increase in incidence. An increasing trend has been observed since 2003 and possible explanations are discussed.

Substantial increase in listeriosis, Denmark 2009

In 2009, 97 cases of listeriosis were reported in Denmark (1.8 per 100,000), a significant rise over the previous year. The increase was seen both in cases of bacteraemia and meningitis and affected mainly people aged 70 years and older. A foodborne outbreak of eight cases was identified by pulsed-field gel electrophoresis typing. No explanation has so far been found for the marked increase in incidence. An increasing trend has been observed since 2003 and possible explanations are discussed.

Actinomyces species: A danish survey on human infections and microbiological characteristics

This study compared phenotypic and genotypic identification of Actinomyces strains, tested susceptibility to antibiotics and evaluated their clinical importance. Thirty-four Actinomyces strains were examined; sixteen type strains, and 18 clinical strains from different hospitals in Denmark from the period 2003-2005. Partial 16S rDNA sequencing using a stretch of 526 bases was used for genotypic identification. Susceptibility testing was done by E-test. The antibiotics examined were: benzylpenicillin, piperacillin with tazobactam, ceftriaxone, meropenem, erythromycin, clindamycin, linezolid, moxifloxacin, tetracycline and tigecycline. Clinical parameters were obtained by reviewing patient records. There was poor agreement between the phenotypic and genotypic identification. Phenotypic tests were helpful in identifying strains closely related by DNA sequences. The strains were sensitive to the examined antibiotics except for moxifloxacin to which most strains were resistant, and a few strains were resistant to meropenem and tetracycline. The clinical strains were from many different types of infections and locations. None of the patients was described as having typical actinomycetic lesions, and an apparently good outcome was obtained with different treatment regimens.

Denmark: botulism in an infant or infant botulism?

A 4.5 months old, previously healthy Danish girl was admitted to a paediatric department after six days of passive behaviour and weak suck. Over the next days she became increasingly weak, developed bilateral ptosis, the muscle stretch reflexes were lost, and mydriasis with slow pupillary responses was noted. Botulism was suspected and confirmed by testing of patient serum in a bioassay. The condition of the patient improved following administration of botulism antiserum. The clinical picture was suggestive of intestinal (infant) botulism. However, botulism acquired from consumption of food with preformed neurotoxin could not be excluded.

Denmark: Botulism in an infant or infant botulism?

A 4.5 months old, previously healthy Danish girl was admitted to a paediatric department after six days of passive behaviour and weak suck. Over the next days she became increasingly weak, developed bilateral ptosis, the muscle stretch reflexes were lost, and mydriasis with slow pupillary responses was noted. Botulism was suspected and confirmed by testing of patient serum in a bioassay. The condition of the patient improved following administration of botulism antiserum. The clinical picture was suggestive of intestinal (infant) botulism. However, botulism acquired from consumption of food with preformed neurotoxin could not be excluded. The food history revealed consumption of a commercially produced banana/peach puree which was suspected as a possible source, and based on a precautionary principle this product was recalled. The case description illustrates a risk-management dilemma between suspected foodborne versus intestinal botulism. Taking the potentially very serious consequences of foodborne botulism into consideration, the measures taken were justified.

Semi-national surveillance of fungaemia in Denmark 2004-2006: increasing incidence of fungaemia and numbers of isolates with reduced azole susceptibility

A semi-national laboratory-based surveillance programme for fungaemia was initiated in 2003 that now covers c. 3.5 million inhabitants (64%) of the Danish population. In total, 1089 episodes of fungaemia were recorded during 2004-2006, corresponding to an annual incidence of 10.4/100 000 inhabitants. The annual number of episodes increased by 17% during the study period. Candida spp. accounted for 98% of the fungal pathogens. Although Candida albicans remained predominant, the proportion of C. albicans decreased from 66.1% in 2004 to 53.8% in 2006 (p <0.01), and varied considerably among participating departments, e.g., from 51.1% at a university hospital in Copenhagen to 67.6% in North Jutland County. Candida glabrata ranked second, and increased in proportion from 16.7% to 22.7% (p 0.04). Candida krusei was isolated rarely (4.1%), but the proportion doubled during the study period from 3.2% to 6.4% (p 0.06). MIC distributions of amphotericin B and caspofungin were in close agreement with the patterns predicted by species identification; however, decreased susceptibility to voriconazole, defined as an MIC of >1 mg/L, was detected in one (2.5%) C. glabrata isolate in 2004 and in 12 (14.0%) isolates in 2006 (p 0.03). Overall, the proportion of isolates with decreased susceptibility to fluconazole exceeded 30% in 2006. The incidence of fungaemia in Denmark was three-fold higher than that reported from other Nordic countries and is increasing. Decreased susceptibility to fluconazole is frequent, and a new trend towards C. glabrata isolates with elevated voriconazole MICs was observed.

Invasive listeriosis in Denmark 1994-2003: a review of 299 cases with special emphasis on risk factors for mortality

Listeriosis is a rare, but serious, foodborne infection which, in the invasive form, presents as bloodstream (BS) infection, an infection of the central nervous system (CNS), a maternofetal infection or a focal infection. The disease is notifiable in Denmark. This paper reviews the results of the Danish surveillance of invasive listeriosis from 1994 to 2003, excluding maternofetal cases. In total, 299 invasive cases of listeriosis were reported. Two-thirds of the cases were caused by isolates of serogroup 1/2, and one-third by serogroup 4. Most (70%) cases had conditions known to predispose to listeriosis. More patients with BS infection were predisposed because of concurrent underlying illness than were patients with CNS infection. Half of the patients were aged > 70 years, and 21% died of the disease. There was no change in the case fatality rate (CFR) during the 10-year period. The CFR was identical for men and women. BS and CNS infection caused the same incidence of mortality, but no mortality was observed in patients with focal infections at normally sterile body sites. In a multivariate analysis, isolates belonging to serogroup 4 were associated with a higher CFR than were isolates of serogroup 1/2. In patients aged < 70 years, underlying conditions predisposing to disease were related strongly to mortality, which was not the case in patients aged > 70 years. The underlying conditions associated most strongly with mortality in the younger age group were non-haematological malignancies.

Aerococcus urinae: polyphasic characterization of the species

A polyphasic characterization of Aerococcus urinae is presented. In this study the intraspecies relationships between 26 strains of varying geographical origin were examined by phenotypic tests, ribotyping and multilocus enzyme electrophoresis. The results demonstrated two main phenotypic patterns that could be distinguished in tests for hydrolysis of aesculin, and acid production from amygdalin and salicin. Strains were either negative (n=19) or positive (n=6) in these tests. One strain had a deviating pattern. Heterogeneity within the 19 pattern I strains was demonstrated especially by phenotypic tests (acid production from ribose, mannitol, sorbitol, sucrose and D-arabitol) and by multilocus enzyme electrophoresis. However, DNA sequence analysis of the 16S rRNA (n=7) and gyrB genes (n=3) from strains representing the two main patterns showed no variation in sequences among strains. Comparison of A. urinae and representatives of related taxa by 16S rDNA sequence analysis showed that the taxon is related to, but distinct from, other Aerococcus spp.

Demonstration by PCR and DNA sequencing of Corynebacterium pseudodiphtheriticum as a cause of joint infection and isolation of the same organism from a surface swab specimen from the patient

A case of infectious arthritis following arthroscopy is described. Real-time PCR, using universal bacterial primers targeting the 16S rRNA gene, and subsequent DNA sequencing of the PCR product demonstrated the presence of DNA from Corynebacterium pseudodiphtheriticum in the synovial fluid from the affected knee. Culture from a surface swab from the site of purulent discharge from the knee was initially reported as growing normal skin microbiota. Knowing the result of the DNA analysis, the specimen was re-examined and a diphtheroid bacterium was isolated. The DNA sequence of the isolated bacterium was identical to that of the DNA in the joint. The isolated bacterium was tested for susceptibility to relevant antibiotics. Demonstration and identification of bacterial DNA by PCR and gene sequencing may not by itself give information on important characteristics such as susceptibility to antibiotics of the infecting bacterium. The present case illustrates that the results obtained by the method can be used to isolate the relevant bacterium in culture from other sites and thereby characterize it. It furthermore demonstrates that C. pseudodiphtheriticum can cause severe arthritis when inoculated into joints.

A simple method to test if the internal mammary lymph nodes are covered by the wide tangent technique in radiotherapy for high-risk breast cancer

AIM

It is often complicated to include the internal mammary lymph nodes in the radiation field after breast-conserving therapy. Using the wide tangent technique the internal mammary lymph nodes are generally presumed to be included if the medial tangential field border is placed 3 cm across the midline. The current study was designed to test the validity of this assumption, and if possible, to correct the wide tangents without using computed tomography (CT) scanning.

PATIENTS AND METHODS

Twenty-one consecutive, high-risk, post-lumpectomy patients were included. An arrangement of three copper wires was mounted in wax placed perpendicular to the skin surface at the ipsilateral border of sternum at intercostal spaces 2 to 4. During a standard simulation for wide tangents, it was examined if the length of the copper wires projected beneath the skin surface (representing the depth of the internal mammary lymph nodes, measured by ultrasound) were included in the wide tangent fields.

RESULTS

In only one patient were the internal mammary lymph nodes covered by the wide tangent technique. In 14 of the remaining 20 patients the lateral tangential field border was subsequently moved in the posterior direction, and the internal mammary lymph nodes could be included without unacceptable normal tissue involvement. In the last six patients the irradiated heart and lung volumes exceeded acceptable tolerance levels with this correction, and these patients were referred for three-dimensional CT dose planning.

CONCLUSION

The presented simple technique may be helpful if CT scanning is not available. In all other cases CT-based dose plan should ideally be used as a standard in the planning of radiotherapy after breast-conserving surgery to assure optimal inclusion of the relevant target, and to avoid irradiation of large volumes of critical normal tissue.

Short-term tools to measure responsiveness to growth hormone replacement

Growth hormone (GH) replacement is a prolonged and expensive treatment modality which involves daily subcutaneous injections in children and adults. Efforts have been made, therefore, to develop short-term tests to predict long-term clinical response. The so-called insulin-like growth factor I (IGF-I) generation test was originally introduced in order to select responders to GH among short children without classical GH deficiency. A positive correlation between short-term increase in serum IGF-I and linear growth has, however, only been reported in a minority of studies. There is no single outcome measure available in GH-deficient adults, and no evidence of a correlation between IGF-I and the effects of GH replacement on factors such as body composition or physical fitness. In conclusion, no reliable short-term test to predict long-term response to GH replacement is available in either children or adults. For safety reasons, however, measurement of serum IGF-I concentrations in GH-deficient patients remains an important means of monitoring during GH replacement.

In vitro antimicrobial susceptibility of Aerococcus urinae to 14 antibiotics, and time-kill curves for penicillin, gentamicin and vancomycin

Aerococcus urinae is a newcomer in clinical and microbiological practice, causing urinary tract infections, bacteraemia/septicaemia and/or endocarditis. This study presents for the first time an evaluation of the activity of a representative panel of antibiotics against a large number of A. urinae isolates. The in vitro susceptibilities (MICs) of 56 isolates of A. urinae to 14 antibiotics were determined by agar dilution. In general, A. urinae isolates showed little inter-isolate variability, and had low MICs of penicillin, amoxicillin, piperacillin, cefepime, vancomycin and rifampicin. High-level aminoglycoside resistance was not found for any of the isolates. Moderate to good activity was seen with quinolones, erythromycin and tetracycline. Isolates from two patients with endocarditis were studied with time-kill curves for penicillin, gentamicin and vancomycin. Penicillin and vancomycin alone exhibited slow or no bactericidal activity against the two strains. When combining either penicillin or vancomycin with gentamicin, rapid bactericidal activity was obtained for both strains with both combinations. The treatment options for A. urinae seem to include penicillins for less severe cases. In severe cases, i.e. endocarditis, the time-kill investigations suggest a beneficial effect of combination with gentamicin. In the penicillin-allergic patient vancomycin in combination with gentamicin represents the most obvious alternative.

Granulicatella and Abiotrophia species from human clinical specimens

One hundred one isolates of nutritionally variant streptococci from 97 patients were phenotypically characterized and compared with the type strains of Granulicatella adiacens (formerly Abiotrophia adiacens) (ATCC 49175(T)) Abiotrophia defectiva (ATCC 49176(T)), and Granulicatella elegans (formerly Abiotrophia elegans) (DSM 11693(T)). Of the isolates, 55 and 43 resembled G. adiacens and A. defectiva, respectively, while 3 strains resembled G. elegans. Phenotypic characteristics useful in differentiating between species within the genera Granulicatella and Abiotrophia (G. adiacens, G. elegans, Granulicatella balaenopterae, and A. defectiva) were production of alpha- and beta-galactosidase; production of beta-glucuronidase; hippurate hydrolysis; arginine dihydrolase activity; and acid production from trehalose, sucrose, pullulan, and tagatose. From the reports submitted with the specimens, the clinical diagnosis was endocarditis in 58% of patients and septicemia or bacteremia in 26% of patients.

Granulicatella and Abiotrophia species from human clinical specimens

One hundred one isolates of nutritionally variant streptococci from 97 patients were phenotypically characterized and compared with the type strains of Granulicatella adiacens (formerly Abiotrophia adiacens) (ATCC 49175(T)) Abiotrophia defectiva (ATCC 49176(T)), and Granulicatella elegans (formerly Abiotrophia elegans) (DSM 11693(T)). Of the isolates, 55 and 43 resembled G. adiacens and A. defectiva, respectively, while 3 strains resembled G. elegans. Phenotypic characteristics useful in differentiating between species within the genera Granulicatella and Abiotrophia (G. adiacens, G. elegans, Granulicatella balaenopterae, and A. defectiva) were production of alpha- and beta-galactosidase; production of beta-glucuronidase; hippurate hydrolysis; arginine dihydrolase activity; and acid production from trehalose, sucrose, pullulan, and tagatose. From the reports submitted with the specimens, the clinical diagnosis was endocarditis in 58% of patients and septicemia or bacteremia in 26% of patients.

A case of Moraxella canis-associated wound infection

Moraxella canis was isolated from an infected foot ulcer in a patient suffering from diabetes mellitus with neuropathy. Bacteriological findings and 16S rDNA data are presented.

Clinical significance and taxonomy of Actinobacillus hominis

Clinical findings in 36 immunosuppressed patients with lower respiratory tract infection or bacteremia with Actinobacillus hominis are described. Animal contact was only recorded for three patients; nine patients died despite appropriate antimicrobial treatment. Although infections with this microorganism seem to be rare, the fact that 37 of 46 strains characterized in this study have been found in Copenhagen indicates that under-reporting may occur. A. hominis is phenotypically relatively homogeneous but can be difficult to differentiate from other Actinobacillus species unless extensive biochemical testing is performed. Mannose-positive strains of A. hominis are especially difficult to differentiate from A. equuli. Attempts to identify A. hominis by automatic identification systems may lead to misidentifications. Ribotyping and DNA-DNA hybridization data show that A. hominis is a homogeneous species clearly separated from other species within the genus Actinobacillus.