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Biomedical subjects

Paul J Rooney

Publications and source records attributed to Paul J Rooney.

12 recordsLinked to original sources
PubMed2006

The epidemiology of antibiotic resistance in Campylobacter.

Antibiotic resistance, particularly with the fluoroquinolones and macrolide antibiotics, has now emerged globally with thermophilic campylobacters, including Campylobacter jejuni and C. coli, giving rise to concerns about how these organisms have acquired such resistance characteristics, as well as consequences for human and animal treatment. This review examines (i) the clinical epidemiology of antibiotic resistance in human and animal thermophilic campylobacters, (ii) an update on resistance rates globally, (iii) surveillance of antimicrobial resistance in campylobacters originating from animals, particularly poultry, (iv) the role of the environment in the acquisition and transmission of antibiotic-resistant campylobacters, as well as (v) issues of biocide resistance in campylobacters.

Animals↗
PubMed2006

Clinico-epidemiological features of infections caused by CTX-M type extended spectrum beta lactamase-producing Escherichia coli in hospitalised patients.

A review of medical records of 45 of 53 hospitalised patients with positive cultures for CTX-M type ESBL-producing Escherichia coli between 01 January and 31 May 2004 was conducted. The mean age of the population studied was 73.1 (+/-14.6) years and the majority (55.6%) had been under the care of the internal medicine or elderly care service. In the majority (77.8%) of instances the isolate was attributed to a clinical infection rather than colonisation and the commonest clinical specimen to yield the organism was urine, which was positive in 57.8% of patients. Acquisition of the organism was categorised as nosocomial in 68.9% of patients; in this subgroup, the median duration of inpatient stay prior to recovery of the organism was 24 (range 3-240) days. Haemodialysis-dependence was the most common of the comorbidities evaluated. The mean number of antibiotics prescribed per patient in the 30 days prior to first isolation of the organism was 1.7 (range 0-4). Furthermore, the mean number of antibiotic-days exposure per patient during this period was 13.9 (range 0-48). The most frequently received class of antibiotic was beta-lactam/beta-lactamase inhibitor combinations. Of 35 infections, 26 (74.2%) were successfully treated. Overall 12 patients with infection died (34.3%); attributable mortality was presumed in seven (20%).

Adult↗
PubMed2006

Prevalence and identity of Cryptosporidium spp. in pig slurry.

Cryptosporidium spp. were detected in 25 of 56 pig slurry samples from 33 Irish farms by PCR and DNA sequencing. The organisms detected included C. suis, Cryptosporidium pig genotype II, and C. muris. We concluded that Cryptosporidium oocysts can persist in treated slurry and potentially contaminate surface water through improper discharge or uncontrolled runoff.

Animals↗
PubMed2005

Central line-related bacteremia due to Roseomonas mucosa in a patient with diffuse large B-cell non-Hodgkin's lymphoma.

A 42-year-old male patient with a history of diffuse large B-cell non-Hodgkin's lymphoma (DLBCL) developed a central line-related bacteremia due to the presence of a Gram-negative bacillus, which was difficult to identify conventionally. Sequencing of a partial region of the 16S rRNA gene identified the organism as Roseomonas mucosa with a homology score of 100% with 1003 bases called. Due to difficulties with the phenotypic identification of this genus, coupled with its emergence in line-related bacteremia in hematology patients with malignancy, Roseomonas spp. should be considered in cases of line-related infection in such patients with atypical Gram-negative organisms. Although several cases have been reported in the literature of line-related sepsis due to Roseomonas gilardii, only a few cases have been reported of Roseomonas mucosa infection in patients with hematological malignancy. This report highlights the benefits of the integration of a sequence-based typing approach in the identification of difficult-to-identify bacterial isolates employing partial regions of the 16S rRNA gene. Continued routine adoption of such techniques by clinical diagnostic laboratories may prove beneficial for the correct identification of blood-borne infections, as well as for the correct epidemiological characterization of unusual causal agents of bacteremia in immunocompromised individuals.

Adult↗
PubMed2004

Improved laboratory diagnosis of bacterial and fungal infections in patients with hematological malignancies using PCR and ribosomal RNA sequence analysis.

During October 1999 to November 2000, 98 blood culture specimens from the same number of febrile episodes originating from 49 patients with hematological malignancies were examined for the presence of eubacteria and fungi based on 16S rRNA gene and the 5.8, 18 and 28S rRNA combined with in vitro PCR amplification and sequencing, in addition to conventional blood culture laboratory techniques. Nineteen of the samples were associated with positive blood cultures. Eubacterial (16S rRNA) PCR detected bacterial DNA in 26 febrile episodes, i.e. in an additional 7 febrile episodes than blood-culture alone. The species identified by partial 16S rRNA gene sequencing were as follows Staphylococcus spp (n = 6), Staphylococcus epidermidis (n = 5), Acinetobacter spp (n = 5), Escherichia coli (n = 2), Enterobacter agglomerans (n = 2), Campylobacter spp (n = 1), Citrobacter spp (n = 1), Corynebacterium spp (n = 1), Enterobacter faecium (n = 1), Ralstonia spp (n = 1), Acidovorax spp. (n = 1) and Stenotrophomonas maltophilia (n = 1). Gram-positive bacteria were found in 12/27 (44.6%) and gram-negative bacteria were found in 15/27 (55.6%). After optimization of a PCR-based fungal detection method, none of the febrile episodes were shown to be attributable to fungi. The results of this study suggest that fungi are not common causal agents of febrile episodes in patients with a hematological malignancy at this centre and that molecular techniques can augment cultural methods in the diagnosis of causal agents of bacteremia in patients, so that appropriate antibiotic regimens may be commenced in patients with culture-negative episodes of infection.

Adolescent↗
PubMed2002

Fluorescent amplified fragment length polymorphism probabilistic database for identification of bacterial isolates from urinary tract infections.

The ability of the fluorescent amplified fragment length polymorphism (FAFLP) technique to identify bacterial isolates from urinary tract infections (UTIs) was investigated. FAFLP was carried out using the single primer combination MseI plus CT and EcoRI plus 0, and information-rich FAFLP profiles were generated from all 69 UTI isolates studied, which comprised both gram-negative and gram-positive bacteria encompassing eight genera. The genetic relatedness of these 69 bacteria was determined by cluster analysis, and this revealed eight main groups corresponding to the eight bacterial genera. Finer discrimination on the same dendrogram showed species and subspecies differentiations, thus demonstrating the potential of FAFLP for describing a wide diversity range within microbial populations. The interpretation of FAFLP profiles is often complicated because it relies upon the investigator interpreting dendrograms; this process may be subjective if the tree is complicated, particularly if it includes polytomies (unresolved nodes). Therefore, we have developed a method based on Bayes' theorem for the identification of bacteria against an FAFLP probabilistic identification matrix. Thus, FAFLP is suitable for the objective identification of causal agents of UTI, and the procedure offers great potential in the clinical laboratory.

Bacterial Infections↗
PubMed2002

Three drinking-water-associated cryptosporidiosis outbreaks, Northern Ireland.

Three recent drinking-water-associated cryptosporidiosis outbreaks in Northern Ireland were investigated by using genotyping and subgenotyping tools. One Cryptosporidium parvum outbreak was caused by the bovine genotype, and two were caused by the human genotype. Subgenotyping analyses indicate that two predominant subgenotypes were associated with these outbreaks and had been circulating in the community.

Animals↗
PubMed1998

Rapid identification of urinary tract infection bacteria using hyperspectral whole-organism fingerprinting and artificial neural networks.

Three rapid spectroscopic approaches for whole-organism fingerprinting-pyrolysis mass spectrometry (PyMS), Fourier transform infra-red spectroscopy (FT-IR) and dispersive Raman microscopy--were used to analyse a group of 59 clinical bacterial isolates associated with urinary tract infection. Direct visual analysis of these spectra was not possible, highlighting the need to use methods to reduce the dimensionality of these hyperspectral data. The unsupervised methods of discriminant function and hierarchical cluster analyses were employed to group these organisms based on their spectral fingerprints, but none produced wholly satisfactory groupings which were characteristic for each of the five bacterial types. In contrast, for PyMS and FT-IR, the artificial neural network (ANN) approaches exploiting multi-layer perceptrons or radial basis functions could be trained with representative spectra of the five bacterial groups so that isolates from clinical bacteriuria in an independent unseen test set could be correctly identified. Comparable ANNs trained with Raman spectra correctly identified some 80% of the same test set. PyMS and FT-IR have often been exploited within microbial systematics, but these are believed to be the first published data showing the ability of dispersive Raman microscopy to discriminate clinically significant intact bacterial species. These results demonstrate that modern analytical spectroscopies of high intrinsic dimensionality can provide rapid accurate microbial characterization techniques, but only when combined with appropriate chemometrics.

Bacterial Typing Techniques↗
PubMedDate not supplied

Campylobacter.

Species within the genus, Campylobacter, have emerged over the last three decades as significant clinical pathogens, particularly of human public health concern, where the majority of acute bacterial enteritis in the Western world is due to these organisms. Of particular concern are the species, C. jejuni and C. coli, which are responsible for most of these gastrointestinal-related infections. Although these organisms have already emerged as causative agents of zoonoses, several aspects of their epidemiology and pathophysiology are only beginning to emerge. Trends in increasing antibiotic resistance are beginning to emerge with oral antibiotics, which may be the drug of choice for when it is necessary to intervene chemotherapeutically. This review wishes to examine (i) emerging clinical aspects of the disease, such as Guillain Barre syndrome (GBS), (ii) the association between these organisms and poultry as a natural host, (iii) environmental aspects of Campylobacter epidemiology, (iv) the emergence of atypical campylobacters (v) emerging trends in antibiotic resistance, (vi) adoption of modern methods for the detection of campylobacters.

Animals↗