Dissemination of clonally related multidrug-resistant Klebsiella pneumoniae in Ireland.

In October 2012, an outbreak of gentamicin-resistant, ciprofloxacin non-susceptible extended-spectrum ß-lactamase (ESBL)-producing Klebsiella pneumoniae occurred in a neonatal intensive care unit in Ireland. In order to determine whether the outbreak strain was more widely dispersed in the country, 137 isolates of K. pneumoniae with this resistance phenotype collected from 17 hospitals throughout Ireland between January 2011 and July 2013 were examined. ESBL production was confirmed phenotypically and all isolates were screened for susceptibility to 19 antimicrobial agents and for the presence of genes encoding bla TEM, bla SHV, bla OXA, and bla CTX-M; 22 isolates were also screened for bla KPC, bla NDM, bla VIM, bla IMP and bla OXA-48 genes. All isolates harboured bla SHV and bla CTX-M and were resistant to ciprofloxacin, gentamicin, nalidixic acid, amoxicillin-clavulanate, and cefpodoxime; 15 were resistant to ertapenem, seven to meropenem and five isolates were confirmed as carbapenemase producers. Pulsed-field gel electrophoresis of all isolates identified 16 major clusters, with two clusters comprising 61% of the entire collection. Multilocus sequence typing of a subset of these isolates identified a novel type, ST1236, a single locus variant of ST48. Data suggest that two major clonal groups, ST1236/ST48 (CG43) and ST15/ST14 (CG15) have been circulating in Ireland since at least January 2011.

Hepatitis E Virus (HEV) Infection in Ireland.

Hepatitis E virus (HEV) is a single stranded RNA virus causing infection worldwide. In developing countries HEV genotypes 1 and 2 spread faeco-orally via water. Recently, infections with HEV have been detected in Europe and North America in patients with no travel history. These are food-borne HEV genotypes 3 and 4, a pig-associated zoonosis. Most infections are asymptomatic but morbidity and chronic infection may occur with prior liver disease or immunosuppression. International seroprevalence rates vary and with improved diagnostics have increased. To determine the current prevalence in this region we studied anonymised serum samples submitted in 2015 for routine testing. We detected anti-HEV IgG in 16/198 (8%) individuals, highest rate in 40-59 year olds (43.8%). This is higher than reported for the same region in 1995 (0.4%) using a previous generation assay. This study provides evidence of HEV circulation in Ireland and reinforces the need for ongoing surveillance.

A comparison of the efficiency of ELISA and selected primer sets to detect Norovirus isolates in southern Ireland over a four-year period (2002-2006): variation in detection rates and evidence for continuing predominance of NoV GII.4 genotype.

Norovirus (NoV) gastroenteritis occurs in all age groups and is the most common cause of gastroenteritis in the community. However, detection methods and rates vary widely, and few data are available to compare these, particularly in Ireland. Detection of noroviruses through antigen and molecular-based strategies was carried out on 135 suspected NoV-positive samples, collected over the course of three NoV outbreaks, from 2002 to 2006, in the southern region of Ireland. A commercially available ELISA and a panel of six primer sets were evaluated to determine their suitability for NoV detection in Irish clinical samples. The key findings of this study were the detection of both GGI and GGII noroviruses by ELISA, but the detection of only GGII noroviruses by RT-PCR. In addition to this, a variation in the levels of detection from 9.4 % to 17.3 % was observed for conventional PCR assays, while a detection rate of 46.3 % was observed for the real-time PCR assay. A proportion (17.8 %) of samples were found to be negative by all detection strategies, suggesting the possibility of reporting false positives for these samples or low-copy positives that do not often repeat. Sequencing information from selected samples also revealed nucleotide polymorphisms, compromising efficient primer binding in the case of one primer pairing. Phylogenetic analysis of the partial polymerase gene identified NoV GII.4 as the dominant genotype, in accordance with previous NoV studies in Ireland. Investigating the NoV diversity of the circulating strains and the dynamics of strain replacement is important to better assess the efficacy of future NoV vaccines and to facilitate the early detection of changes in circulating NoV strains.

Molecular characterization of group A rotaviruses detected in children with gastroenteritis in Ireland in 2006-2009.

Community and hospital-acquired cases of human rotavirus are responsible for millions of gastroenteritis cases in children worldwide, chiefly in developing countries, and vaccines are now available. During surveillance activity for human rotavirus infections in Ireland, between 2006 and 2009, a total of 420 rotavirus strains were collected and analysed. Upon either PCR genotyping and sequence analysis, a variety of VP7 (G1-G4 and G9) and VP4 (P[4], P[6], P[8] and P[9]) genotypes were detected. Strains G1P[8] were found to be predominant throughout the period 2006-2008, with slight fluctuations seen in the very limited samples available in 2008-2009. Upon either PCR genotyping and sequence analysis of selected strains, the G1, G3 and G9 viruses were found to contain E1 (Wa-like) NSP4 and I1 VP6 genotypes, while the analysed G2 strains possessed E2 NSP4 and I2 VP6 genotypes, a genetic make-up which is highly conserved in the major human rotavirus genogroups Wa- and Kun-like, respectively. Upon sequence analysis of the most common VP4 genotype, P[8], at least two distinct lineages were identified, both unrelated to P[8] Irish rotaviruses circulating in previous years, and more closely related to recent European humans rotaviruses. Moreover, sequence analysis of the VP7 of G1 rotaviruses revealed the onset of a G1 variant, previously unseen in the Irish population.

Emergence of group B Streptococcus serotype IV in women of child-bearing age in Ireland.

This study determined the carriage rate and serotype distribution of group B Streptococcus (GBS) in women of child-bearing age in the southern region of Ireland. A total of 2000 vaginal swabs collected in two periods in 2004 and 2006 were examined and revealed a GBS carriage rate of 16·1%. Serotyping of isolates showed that serotypes Ia, II, III, IV, and V were the most prevalent. A high prevalence of serotype IV was found, increasing from 7·6% to 15·2% between 2004 and 2006. Random amplified polymorphic DNA analysis demonstrated considerable genetic heterogeneity in the serotype IV isolates. This serotype should be considered for inclusion in potential vaccines for use in Ireland.

First detection of a class 2 integron among clinical isolates of Serratia marcescens.

Serratia marcescens is a frequent nosocomial isolate and is associated with a variety of clinical sources, including blood, urine and sputum, and can cause significant infection. Infections can be difficult to treat due to its resistance to a variety of antimicrobial agents. An investigation of a population of 30 clinical strains revealed the presence of a class 2 integron among nine of the isolates, which represents the first isolation of this integron in Serratia species. This integron contained the gene cassettes dfrA1, sat1 and aadA1, conferring resistance to trimethoprim, streptothricin and streptomycin/ spectinomycin, respectively. One of these isolates also carried a class 1 integron identified by sequence analysis as containing the open reading frames aacC1 (encoding gentamicin resistance), ORFX, ORFY and aadA1. Polymerase chain reaction analysis confirmed the presence of the qac epsilon delta1 and sul1 markers, which are common among class 1 integrons.

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.

Prosthetic valve endocarditis caused by Veillonella parvula.

Veillonella species is a rare cause of endocarditis. We report a case of a 49-year-old man with Veillonella parvula prosthetic valve endocarditis who presented with acute cardiac failure due to valvular dehiscence. His clinical course was complicated by cortical blindness and limb paresis as a result of cerebral embolism. The endocarditis was successfully treated with urgent valve replacement surgery and a prolonged course of metronidazole.

Rotavirus in Ireland: national estimates of disease burden, 1997 to 1998.

BACKGROUND: We estimated the disease burden caused by rotavirus hospitalizations in the Republic of Ireland by using national data on the number of hospitalizations for diarrhea in children and laboratory surveillance of confirmed rotavirus detections. METHODS: We examined trends in diarrheal hospitalizations among children <5 years old as coded by ICD-9-CM for the period January, 1997, to December, 1998. We collated data on laboratory-confirmed rotavirus detections nationally for the same period among children <2 years old. We calculated the overall contribution of rotavirus to laboratory-confirmed intestinal disease in children <5 years old from INFOSCAN, a disease bulletin for one-third of the population. We compared data from all sources and estimated the proportion of diarrheal hospitalizations that are likely the result of rotavirus in children <5 years old. RESULTS: In children <5 years old, 9% of all hospitalizations are for diarrheal illness. In this age group 1 in 8 are hospitalized for a diarrheal illness, and 1 in 17 are hospitalized for rotavirus by 5 years of age. In hospitalized children <2 years old, 1 in 38 have a laboratory confirmed rotavirus infection. CONCLUSIONS: The disease burden of rotavirus hospitalizations is higher than in other industrialized countries. Access to comprehensive national databases may have contributed to the high hospitalization rates, as well as a greater tendency to hospitalize children with diarrhea in Ireland.

Antibiotic prescribing policy and Clostridium difficile diarrhoea.

BACKGROUND: Broad-spectrum antibiotics, particularly intravenous cephalosporins, are associated with Clostridium difficile diarrhoea. Diarrhoea due to C. difficile is a growing problem in hospitals, especially among elderly patients. AIM: To establish whether changing an antibiotic policy with the aim of reducing the use of injectable cephalosporins leads to a reduction in the incidence of C. difficile diarrhoea in elderly patients. DESIGN: Retrospective analysis. METHODS: A group of patients who were subject to the new antibiotic policy from the period following July 2000, were compared with patients who were admitted prior to July 2000 and were not subject to the new policy. Infections, antibiotic prescriptions and mortality rates were determined from case notes, and C. difficle diarrhoea rates from microbiological data. RESULTS: Intravenous cephalosporin use fell from 210 to 28 defined daily doses (p < 0.001) following the change in antibiotic policy, with a corresponding increase in piperacillin-tazobactam (p < 0.001) and moxifloxacin (p < 0.001) use. The new policy led to a significant reduction in C. difficile diarrhoea cases. The relative risk of developing C. difficile infection with the old policy compared to the new policy was 3.24 (95%CI 1.07-9.84, p = 0.03). DISCUSSION: The antibiotic policy was successfully introduced into an elderly care service. It reduced both intravenous cephalosporin use and C. difficile diarrhoea.

Investigation of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak in an Irish hospital: triplex PCR and DNA amplification fingerprinting.

Methicillin-resistant Staphylococcus aureus (MRSA) is becoming a problematic nosocomial pathogen. A continuing increase in numbers of isolates is reported from Irish hospitals each year. Preventing cross-infection and the further spread of endemic strains requires effective control measures. This necessitates the development of sensitive methods for both detection and genetic identification of MRSA isolates. In this study, 48 MRSA strains isolated in the Cork University Hospital were analysed between January and July 1995 using a one-tube triplex-polymerase chain reaction (PCR), wherein three genes, the methicillin-resistance gene (mecA), femA and the extracellular thermonuclease gene, nuc, were simultaneously amplified. Methicillin-sensitive S. aureus (MSSA) and coagulase-negative staphylococci (CNS) were also tested and the assay was found to be MRSA specific. The genetic relationship among this collection of MRSA isolates was also investigated. A single primer, RW3A, derived from a well-characterized, repetitive sequence found in Mycoplasma pneumoniae produced discriminating DNA fragment arrays with all the study organisms. The patterns were reproducible, even after several passages of the isolates. Quantitative analysis of the patterns divided the collection into two main groups, DAF group I representing 48% of the collection and DAF group II a further 19%. The remaining strains showed unrelated patterns. To fully outline the distribution of MRSA in this area a larger study will be necessary. This paper outlines the applicability of both the identification and fingerprinting techniques to local strains.

Genomic fingerprinting Acinetobacter baumannii: amplification of multiple inter-repetitive extragenic palindromic sequences.

Acinetobacter species are important nosocomial pathogens. A rapid and sensitive identification system, capable of providing strain identity at the genetic level, is required to identify outbreak strains and facilitate the early implementation of infection control procedures. Repetitive extragenic palindromic (REP) elements, have been identified in numerous bacteria and these genomic sequences provide useful targets for DNA amplification. A method for amplifying inter-REP DNA sequences, REP-multiple arbitrary amplicon profiling (REP-MAAP), is described and applied to 29 Acinetobacter baumannii from clinical samples. Amplified polymorphic DNA patterns were demonstrated for all isolates and those displaying identical REP-MAAP patterns were considered identical at the genetic level. In the spring of 1993, 10 intensive care unit patients had endotracheal colonization with A. baumannii (five with REP-MAAP I and five with REP-MAAP II patterns). These findings suggested nosocomial transmission of organisms which was terminated by standard infection control measures. No further A. baumannii were detected until the winter of 1993 when isolates of different REP-MAAP groups emerged, suggesting that factors other than nosocomial transmission were implicated.

Nontuberculous mycobacteria: incidence in Southwest Ireland from 1987 to 2000.

SETTING: The Southwest of Ireland (Counties Cork and Kerry) 1987-2000, average population 549,500. OBJECTIVE: Nontuberculous mycobacteria (NTM) cause significant morbidity worldwide and the study of epidemiology and characteristics helps in their prevention and treatment. This study was performed to determine the incidence of NTM disease in comparison to Mycobacterium tuberculosis (M. tuberculosis) and Mycobacterium bovis (M. bovis) in Southwest Ireland, over the above time period. DESIGN: A retrospective study was carried out in all human isolates of NTM, M. tuberculosis and M. bovis between 1987 and 2000, in the Southwest Region of Ireland. RESULTS: The mean incidence of NTM (0.4/100,000 population) has risen since 1995, principally of pulmonary Mycobacterium avium intracellulare complex (MAC). The annual incidence of M. tuberculosis in humans over 14 years in the same region was 971/100,000 population with a significant reduction since 1994 and M. bovis remained constant at 0.5/100,000 population. CONCLUSION: The increasing incidence of disease causing NTM noted in Southwest Ireland reflects global data and is surmised to be due to an ageing population, increased incidence related to chronic fibrotic lung disease, and environmental mycobacterial factors.

A competitive enzyme-linked immunosorbent assay for detecting Escherichia coli heat-stable enterotoxin and its application to clinical isolates.

Enterotoxigenic Escherichia coli (ETEC) are well recognised enteric pathogens. The epidemiology of heat-stable enterotoxin (STa) producing strains has not been established due mainly to difficulties encountered in performing bioassays on a large scale in baby mice. This study describes a competitive enzyme-linked immunosorbent assay (ELISA) for detecting STa and its application to clinical isolates. Compared to the bioassay, the ELISA had a specificity of 93.7% and a sensitivity of 90.9%. It detected as little as 1 microgram/l STa. Of 720 E. coli isolates from children with diarrhoea, 69 (9.6%) were positive for STa by ELISA.

Isolation of Campylobacter sputorum biovar sputorum from an axillary abscess.

Campylobacter sputorum biovar sputorum is a rarely isolated organism, particularly from human clinical specimens. Its pathogenic potential is unknown. We present here what we believe to be the first report of this organism being isolated from a clinically significant source, an axillary abscess. To our knowledge, this organism has not been reported previously as one of clinical relevance in the U.K.

Actinomyces pyogenes septic arthritis in a diabetic farmer.

We report a case of septic arthritis and osteomyelitis of the left ankle due to Actinomyces pyogenes in a diabetic farmer. Few confirmed human cases of A. pyogenes infection have been reported, partly because of inadequate identification of this bacterium. Bacteriological characteristics of the organism, which resembles Arcanobacterium haemolyticum, are described with a review of previous case reports.

Salmonella tel-el-kebir and terrapins.

OBJECTIVES: An outbreak of Salmonella tel-el-kebir occurring over a 6-month period is described in this report. This is the first outbreak of S. tel-el-kebir in the reported literature. METHODS: S. tel-el-kebir was isolated from human faecal samples using conventional laboratory methods. RESULTS: Eight patients had S. tel-el-kebir isolated from faeces. All patients were owners of, or in close contact with, pet terrapins. The terrapins were purchased in the same pet shop, where they were imported from America. The epidemiological link with these pets was confirmed, as S. tel-el-kebir was isolated from cloacal swabs from the terrapins, and from terrapin water. Molecular biology studies using DNA amplification fingerprinting (DAF) gave identical fingerprint patterns for all human and terrapin isolates. CONCLUSIONS: Salmonellosis associated with exotic pets is a re-emerging disease in the 1990s, and measures to reduce this are discussed.

Epidemiology and clinical impact of Pseudomonas aeruginosa infection in cystic fibrosis using AP-PCR fingerprinting.

Arbitrarily primed PCR (AP-PCR) was utilized to genetically fingerprint 252 Pseudomonas aeruginosa strains isolated from the sputa of 50 cystic fibrosis (CF) patients attending the Cork CF clinic over a period of 3 years. Ten distinct P. aeruginosa strains were identified and the distribution, temporal trends and clinical impact of colonization with these individual P. aeruginosa clones was studied. A number of random isolates from each AP-PCR group were analysed using pulsed field gel electrophoresis (PFGE) in order to confirm the discriminatory power of the AP-PCR technique. The majority of patients were colonized with a single strain over the time period of the study, but it was also possible to harbour two or more strains transiently or simultaneously. Four main strains were relatively evenly distributed throughout the CF population, and it was noted that patients from the same family or attending the same school tended to harbour the same P. aeruginosa clone. Disease severity was significantly associated with the age of the patient (P < 0.001), clearly indicating an increase in severity with increase in age. The general clinical status of the CF patients was not significantly associated with the P. aeruginosa variant isolated from their sputa. Lung status was defined by FEV1 measurement and chest X-ray score (CXR). The non parametric Kruskal-Wallis significance test of FEV1, CXR and age by colonizing P. aeruginosa clone indicated that FEV1 (P = 0.017), but not CXR (P = 0.19) or age (P = 0.842), differed significantly across the clones of P. aeruginosa isolated. Patients harbouring P. aeruginosa strains B, F or G clearly had lower FEV1 scores while those harbouring clones A, C, D or H generally had higher FEV1 scores. Thus, the sub-species variant of P. aeruginosa colonizing CF patients may be associated with the severity of progressive lung disease.

Rotavirus in Ireland.

Acute diarrhoeal disease is the commonest single cause of morbidity and mortality worldwide. Infectious diarrhoea has been estimated to cause at least 5 million deaths each year in the developing world. Very young children are particularly susceptible to

Motif-dependent DNA analysis of a methicillin-resistant Staphylococcus aureus collection.

Methicillin-resistant Staphylococcus aureus (MRSA) has become a major nosocomial pathogen in recent years. Once introduced into the hospital environment, MRSA can spread rapidly, and its subsequent treatment is often difficult as it may be simultaneously resistant to several antibiotics. A useful strategy both to identify the source of infection and to monitor specific infecting strains would be beneficial, facilitating the implementation of control and preventive measures. In this study, a typing strategy, based on the amplification of a conserved repeat-motif in the bacterial genome, was applied in a hospital setting to analyse an MRSA collection. Using a fluorescent-labelled oligonucleotide primer RW3A, which annealed to several dispersed short-repeat sequences occurring throughout the bacterial genome, DNA amplification fingerprint patterns were produced by polymerase chain reaction (PCR). Thirty-nine MRSA isolates were successfully analysed using conventional agarose gel electrophoresis and GeneScan technology. The latter method provides a finer resolution, making use of capillary electrophoresis in an ABI Prism 310 genetic analyser. The fluorescent detection approach can facilitate the construction of a fingerprint database which can be accessed for comparison of any isolate. Quantitative analysis of all patterns divided the MRSA isolates into four different groups, based on their RW3A fingerprints. Most of the isolates (88%) were assigned to one of three main groups, while the remaining isolates (12%) comprised a fourth, miscellaneous group.