Assessment of the comparability of CLSI, EUCAST and Stokes antimicrobial susceptibility profiles for Escherichia coli uropathogenic isolates.

BACKGROUND: As many clinical laboratories convert between Stokes, Clinical and Laboratory Standards Institute (CLSI) and European Committee for Antimicrobial Susceptibility Testing (EUCAST) methods, the problem of comparing differently derived sets of antimicrobial susceptibility testing (AST) data with each other arises, owing to a scarcity of knowledge of inter-method comparability. The purpose of the current study was to determine the comparability of CLSI, EUCAST and Stokes AST methods for determining susceptibility of uropathogenic Escherichia coli to ampicillin, amoxicillin-clavulanate, trimethoprim, cephradine/cephalexin, ciprofloxacin and nitrofurantoin. METHODS: A total of 100 E. coli isolates were obtained from boric acid urine samples from patients attending GP surgeries. For EUCAST and CLSI, the Kirby-Bauer disc diffusion method was used and results interpreted using the respective breakpoint guidelines. For the Stokes method, direct susceptibility testing was performed on the urine samples. RESULTS: The lowest levels of agreement were for amoxicillin-clavulanate (60%) and ciprofloxacin (89%) between the three AST methods, when using 2017 interpretive guidelines for CLSI and EUCAST. A comparison of EUCAST and CLSI without Stokes showed 82% agreement for amoxicillin-clavulanate and 94% agreement for ciprofloxacin. Discrepancies were compounded by varying breakpoint susceptibility guidelines issued during the period 2011-2017, and through the inclusion of a definition of intermediate susceptibility in some cases. CONCLUSIONS: Our data indicate that the discrepancies generated through using different AST methods and different interpretive guidelines may result in confusion and inaccuracy when prescribing treatment for urinary tract infection.

Three-centre evaluation of laboratory Clostridium difficile detection algorithms and the EntericBio® realtime C. difficile assay.

The comparatively high cost of laboratory detection methods for Clostridium difficile infection (CDI) coupled to a low prevalence rate has resulted in testing algorithms that use cheaper and relatively sensitive screening methods, followed by more specific confirmatory methods. The aim of this prospectively-conducted study from two centres in the UK, and one in the Republic of Ireland was to determine the efficacy of the EntericBio® realtime C. difficile Assay (EBCD) for the detection of toxigenic C. difficile in stool samples. The EBCD was compared to the in-use testing methods for Clostridium difficile (CD) detection in each centre. In the two UK centres, the EBCD was compared to the C.diff Quik Chek Complete® kit (Techlab), and discrepancies were tested further using The Xpert®C. difficile PCR assay (Cepheid) and PCR ribotyping after cultivation using the spore culture method, respectively. In the Irish centre, EBCD comparison was to an algorithm of C. DIFF CHEK™-60 test (Techlab) for screening followed by C. difficile Premier ™ Toxins A&B assay (Meridian Bioscience®) in the case of positive results; discrepancies were tested using the Xpert®C. difficile PCR assay. In a retrospective analysis of data, a total of 947 stool samples were tested, of which eight (0.8%) proved inhibitory to the EBCD assay. Of the 939 valid tests conducted, reported sensitivities of the EBCD were 94.7%, 100% and 97.9%, respectively; specificities were 99.6%, 100% and 100%, respectively; positive predictive values were 94.7%, 100% and 100%, respectively, and negative predictive values were 99.6%, 100% and 99.8%, respectively. The CD positivity rates in the current study ranged between 6.6% and 8.2%.

Mycobacterium diagnostics: from the primitive to the promising.

The field of clinical microbiology has been revolutionised by genomic and proteomic methods, which have facilitated more rapid diagnosis and characterisation of infection in many cases. In contrast, mycobacteriological evolution has tended to retain the traditional methods of smear microscopy for detection of acid-fast bacilli to indicate mycobacteria, along with culture, and in synergy with more modern molecular methods. Thus, efforts have been focused on reducing the time to diagnosis of infection, while increasing the amount of diagnostic information available, including more definitive speciation, and more rapid susceptibility test results. Although smear microscopy remains a mainstay for the laboratory-based diagnosis of mycobacterial infection, molecular testing has vastly reduced the time needed for identification of Mycobacterium tuberculosis in particular, when compared with traditional culture-based techniques. Molecular methods may also yield antimicrobial susceptibility results through testing for the most common resistance-inducing mutations to some of the antimicrobial agents of choice. However, the diversity of resistance mutations already characterised suggests that these currently-available molecular detection systems should be accompanied by culture-based susceptibility testing. This review compares the efficacy of microscopic, phenotypic, proteomic and genotypic methods available for mycobacterial diagnosis. The diversity of methods currently in use reflects the complexity of this area of diagnostic microbiology.

Vancomycin-resistant enterococci carriage in an acute Irish hospital.

BACKGROUND: Ireland has been shown to have the highest rate of vancomycin-resistant enterococci (VRE) in cases of bacteraemia in Europe, according to a report in 2014 from the European Antimicrobial Resistance Surveillance System Network. AIM: To investigate the prevalence of VRE gut colonization in a cohort of patients in 2014 at Cork University Hospital (CUH) by performing a cross-sectional study using faecal samples submitted to the microbiology laboratory for routine investigation from both hospital inpatients and community-based patients. METHODS: Faeces were examined for VRE colonization using selective cultivation, antimicrobial susceptibility testing, and speciation using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. All VRE isolates were evaluated by molecular means for resistance determinants, type, and Insertion Sequence 16 as an indicator of Clonal Complex 17 (CC17). FINDINGS: From the 350 specimens investigated, 67 (19.1%) specimens were positive for VRE [95% confidence interval (CI): 15.0-23.2]. The prevalence of VRE colonization among CUH patients tested in this study (N = 194) was 31.4% (95% CI: 24.7-38.1). By contrast, the general practitioner patient samples (N=29) showed a prevalence of 0%, whereas 22.2% of samples from other hospitals (N=27) were positive for VRE. All isolates were Enterococcus faecium (VREfm) and were indicated to contain CC17, though with considerable heterogeneity among the isolates. CONCLUSION: This high prevalence goes some way towards providing an explanation for the current high rates of VRE bacteraemia in Ireland, as well as highlighting the benefits of screening and enhanced infection control practices by all hospitals to control the high rates of VRE observed.

Molecular epidemiology of Mycobacterium abscessus complex isolates in Ireland.

BACKGROUND: The Mycobacterium abscessus complex are the rapidly growing mycobacteria (RGM) most commonly causing lung disease, especially in cystic fibrosis (CF) patients. Ireland has the world's highest CF incidence. The molecular epidemiology of M. abscessus complex in Ireland is unreported. METHODS: We performed rpoB gene sequencing and multi-locus sequence typing (MLST) on M. abscessus complex strains isolated from thirty-six patients in 2006-2012 (eighteen known CF patients). RESULTS: Twenty-eight strains (78%) were M. abscessus subsp. abscessus, eight M. abscessus subsp. massiliense, none were M. abscessus subsp. bolletii. Sequence type 1 (ST1) and ST26 (M. abscessus subsp. abscessus) were commonest. Seven M. abscessus subsp. abscessus STs (25%) were novel (two with novel alleles). Seven M. abscessus subsp. massiliense STs were previously reported (88%), including two ST23, the globally successful clone. In 2012, of 552 CF patients screened, eleven were infected with M. abscessus complex strains (2%). CONCLUSIONS: The most prevalent M. abscessus subsp. abscessus and M. abscessus subsp. massiliense strains in Ireland belong to widely-distributed STs, but there is evidence of high M. abscessus subsp. abscessus diversity.

Detection and identification of gastrointestinal microsporidia using non-invasive techniques.

AIMS: To detect enteric microsporidia in faecal specimens from patients with the acquired immunodeficiency syndrome (AIDS), and to identify the spores to species level without using invasive procedures. METHODS: Formalised faecal preparations were examined using a modification of the strong trichrome staining method to demonstrate microsporidian spores. Six positive specimens were prepared for electron microscopy by emulsification and separation using a 9% Ficoll gradient. RESULTS: The modified staining technique readily identified microsporidian spores. Spores of different species showed variation in size. Identification using electron microscopy was successful for five of the six positive specimens examined. It was unsuccessful for one specimen in which spores were less abundant on initial staining. CONCLUSIONS: The modified strong trichrome staining method is a useful way of detecting spores of intestinal microsporidia in faecal specimens. Variation in spore size may permit provisional identification by light microscopy. Electron microscopic examination of faecal preparations is useful for identifying spores to species level.

Endoscope decontamination: a comparison of the Wolf 35100 and DSD-91 systems.

The Wolf 35100 and DSD-91 endoscope disinfection machines were compared. Using a total viable count method, the degree of contamination of an Olympus GIFXQ20 endoscope was assessed following inoculation with a suspension of Pseudomonas aeruginosa and again following disinfection cycles in each machine, using 2% glutaraldehyde as the disinfectant. Both machines performed satisfactorily, with an average reduction of between 7 and 8 log10 cfu ml-1 P. aeruginosa following disinfection. The dilution effect on the glutaraldehyde of repeated disinfection cycles was also assessed for each machine. After 40 cycles in the DSD-91 and 25 cycles in the Wolf 35100 machines, the dilution of glutaraldehyde may give rise to concern, especially if adequate pre-cleaning of the endoscope is not carried out. The DSD-91 machine has certain advantages over the Wolf 35100 in terms of endoscope capacity, running costs and ease of maintenance. Both machines give similar results for endoscope disinfection.

Application and assessment of cloacin typing of Enterobacter cloacae.

Three methods, O-serotyping, phage typing and susceptibility to bacteriocins, were used to type 357 clinical isolates of Enterobacter cloacae cultured from 219 patients. One hundred and sixty isolates were typed by serology and phage typing. When these two methods were used, primary classification of isolates was based on serology (65.7% typable) and phage typing for further subdivision (94.1% typable). When all the isolates were typed by cloacin susceptibility, 81.5% of them were typable. Maximum discrimination between cultures was achieved when the three methods were used together; no single method was sufficiently discriminatory. There was a close parallel between serotyping and bacteriocin lysis pattern. The latter was easy to perform and the results were achieved within 48 h. By applying this typing system two episodes of cross-infection were identified in a haematology/oncology unit and intensive care unit.

Neonatal osteomyelitis in Down's syndrome due to non-encapsulated Haemophilus influenzae.

A case of neonatal osteomyelitis in a baby with Down's syndrome is described. The causative organism was a non-encapsulated Haemophilus influenzae biotype I, which was isolated from pus at the site of infection. This organism has not previously been reported as a cause of neonatal osteomyelitis.

Septicaemia caused by Pediococcus pentosaceus: a new opportunistic pathogen.

A case of septicaemia caused by Pediococcus pentosaceus is described. The role played by pediococci, and other vancomycin-resistant Gram-positive cocci, in disease states is examined. We suggest that in immunocompromised patients these organisms act as opportunist pathogens. This would appear to be the first reported case of P. pentosaceus septicaemia.

Salmonella dublin infection of a prosthetic vascular graft successfully treated with ciprofloxacin.

The treatment of an infected vascular graft invariably requires an extra-anatomic bypass through a non-infected tissue plane, as simple drainage with antibiotics is rarely successful. We report a case in which an established infection of a prosthetic vascular graft with Salmonella dublin was successfully treated with simple drainage and a prolonged course of oral ciprofloxacin.

Fusobacterium nucleatum bacteraemia with multiple liver abscesses in an HIV-I antibody positive man with IgG2 deficiency.

Liver abscess formation due to Fusobacterium nucleatum is rare. We describe an HIV-I antibody positive man, with normal surrogate markers of cell-mediated immunity, who presented with F. nucleatum bacteraemia and liver abscess formation. He was found to have IgG2 subclass deficiency. This case illustrates the clinical importance of altered B-cell function in patients who are at an early stage of HIV disease.

Hepatitis C virus infection in haemodialysis patients: a clinical and virological study.

A cohort of 66 patients on maintenance haemodialysis was examined for serological (anti-HCV) and virological (HCV-RNA) evidence of infection with hepatitis C virus (HCV). Nine (13.6%) were anti-HCV positive, all of whom had detectable HCV-RNA in their serum. Statistical analysis of various risk factors (including length of time on haemodialysis, history of blood transfusion, history of renal transplantation and of previous hepatitis B infection) showed that only the length of time on haemodialysis was significantly associated with the acquisition of HCV infection. Genotypic analysis showed that five patients were infected with genotype 1 and a further two were infected with genotype 4. The latter finding is of significance because strains of genotype 4 are extremely uncommon in Western Europe. These results demonstrate that intra-unit transmission of HCV-infection took place in a group of patients on maintenance haemodialysis.

Antibiotic chemotherapy of bacterial sexually transmitted diseases in adults: a review.

Treatment regimens for sexually transmitted infections continue to evolve. The natural history of syphilis in HIV-infected patients is leading to more aggressive policies in terms of both investigation and treatment. In particular, treatment protocols for late syphilis, especially neurosyphilis, are under scrutiny. Epidemiological change typified by the spread of penicillinase-producing Neisseria gonorrhoeae (PPNG) has led to a search for new agents to treat gonorrhoea, with a more extensive use of cephalosporin and quinolone antibiotics emerging. The problem of compliance with the antibiotic courses presently required for chlamydial infection may be close to being solved with the development of newer macrolide agents. Single dose azithromycin, although expensive, seems to be as effective as longer courses with other agents. Furthermore, its efficacy in gonococcal infection is also encouraging. Increased understanding of the pathogenesis and natural history of pelvic inflammatory disease (PID) and bacterial vaginosis (BV) has led to rationalization of treatment policies for these conditions.

Listeriosis: a community problem?

Three epidemiologically distinct cases of listeriosis, one perinatal and two adult, presented in hospital over a three day period. Clinical signs were non-specific with pyrexia and respiratory distress. Diagnosis in all three was made by blood cultures. Such cases reflect the general increase in reporting of listeriosis and suggest that the condition is increasing in incidence in the community, most likely due to food contamination. Raw vegetables, milk, soft cheeses, pre-cooked and inadequately cooked meats have all been implicated. Regular public health inspection of foods and food storage facilities with increased public awareness of the hazards of inadequate cooking and storage of food are the most effective means of preventing listeriosis and its potentially disastrous consequences especially for pregnant women and immunosuppressed patients.

Severe pneumococcal infection: a one year survey.

Invasive pneumococcal infection is a major health problem with considerable mortality. In most patients the diagnosis is relatively straightforward but this study points out that in many, especially children, it is difficult because of a lack of clinical signs of septicaemia. While chronic respiratory disease is a major predisposing factor, malignancy and immune disorders are also common underlying features. Certain risk groups may benefit considerably from vaccination. The treatment of established infection is now complicated by the emergence of resistant strains, but penicillin remains the mainstay of therapy.