Changing demographics and immunity to vaccine preventable diseases in people with HIV in Ireland.

BACKGROUND: HIV infection is associated with an increased risk of morbidity and mortality from vaccine preventable infections. This research describes, in the context of changing patient demographics, the seroprevalence of vaccine preventable viral infections among attendees of the largest centre for HIV positive patients in Ireland. METHODS: Baseline serum IgG results for measles, mumps, rubella, varicella zoster virus (VZV) & hepatitis A, as well as hepatitis B sAg, cAb and sAb results, were retrieved for 2534 clinic attendees attending in 2018. Results were available for between 990 and 2363 attendees (39-93%), depending on the test, and were compared with 2013 clinic data. RESULTS: There was a 35% increase in attendees in 2018 when compared to 2013. The largest increase was in attendees of South American origin. In 2018, males accounted for 73% of the entire cohort and the HIV acquisition risk for 48% of attendees was MSM. 47% of attendees were originally from Ireland. Among those tested, 33% were susceptible to at least one component of the MMR vaccine. 5% were VZV non-immune (significantly associated with younger age and the acquisition risk status of injection drug use). 21% were hepatitis A non-immune (significantly associated with younger age and being of European or South American origin). 32% were hepatitis B cAb seropositive (significantly associated with older age, injection drug use status and being originally from Africa). 3% demonstrated hepatitis B sAg positivity. 64% had hepatitis B sAb ≥ 10mIU. CONCLUSION: In a cohort of attendees to an HIV clinic in a large urban setting, the susceptibility to several common vaccine preventable viral infections, in particular MMR and hepatitis A and B, was high. These results highlight the importance of proactive screening and immunisation to help protect this high risk patient group against vaccine preventable diseases.

The Current Use of Lumbar Puncture in a General Paediatric Unit.

Aim This study evaluated the use of Lumbar Puncture (LP) in a general paediatric unit over a 3-year period. Methods Index patients, who had a successful LP, were identified from the microbiology database and failed LP procedures were identified from a chart review of the serum PCR database. Data abstracted included 1) patient age, 2) LP indication, 3) LP procedure outcome; classified as atraumatic, traumatic or failed, 4) grade of doctor undertaking the procedure and 5) the final diagnosis. Results We identified 104 paediatric patients, of whom 29(27.9%) were neonates. LP was indicated for the evaluation of acute undifferentiated illnesses, with 33 (31.7%) patients having fever without source beyond the neonatal period and 16 (15.4%) being neonates with fever. A CSF sample was obtained in 96 (92.4%) patients, with 71 (73.9%) being atraumatic. Successful LP was undertaken by Consultants in 4 (4.1%), Registrars in 83 (86.5%) and SHOs in 9 (9.4%) patients. 14 (14.6%) patients had positive CSF cultures with an additional 23 having positive cultures or serology (9 blood cultures, 11 urine cultures and 3 positive serum PCR). Conclusion Skill in LP performance is still required, to evaluate acute undifferentiated illness, in general paediatric units and ancillary methods to aid SHOs with LP skill development is desirable.

Lamivudine treatment and outcome in pregnant women with high hepatitis B viral loads.

Perinatal transmission is the most common mode of hepatitis B virus (HBV) transmission and is a leading cause of chronic infection worldwide. Maternal treatment with lamivudine (LAM) can result in a rapid and significant reduction in HBV viral load (VL) and, thus, mitigate the risk of mother-to-child transmission (MTCT). The aim of this study was to retrospectively evaluate the safety of LAM treatment administered in the third trimester of pregnancy and determine the influence, if any, on infant outcome. The medical charts of all HBV surface antigen (HBsAg)-positive women eligible for treatment with LAM and who registered for antenatal care between 2007 and 2012 were retrospectively reviewed. During the 6-year period, 45 women met the criteria for LAM treatment. Thirty-six women (80 %) accepted treatment; the remaining women declined treatment (5), defaulted from care (3) or transferred to another maternity unit (1). The median duration of treatment was 11.4 weeks (range 5.3-17.4) and the median baseline VL was 1.4 × 10(8) IU/mL (range 1.8 × 10(7)-1.7 × 10(8)). The median VL at delivery was 2.3 × 10(5) IU/mL and 60 % of women achieved a VL reduction >2 log10 IU/mL before delivery. No cases of perinatal transmission occurred in the infants born to mothers who received treatment; however, one infant, born to a mother who defaulted from care, was HBV-infected at 8 months. The results suggest that LAM therapy in highly viraemic HBV-infected pregnant women could lower the rate of vertical transmission.

Factors associated with milking characteristics in dairy cows.

Milking characteristics, and in particular milking duration, are a known contributor to costs in dairy production systems. Results from previous studies suggest that higher-yielding animals, on average, milk for a longer duration. Culling or selection for reduced milking duration alone may, therefore, reduce milk yield. Here, we propose 2 new traits, residual milking duration (RMD) and residual milking duration including somatic cell score (RMDS). Residual milking duration is represented by the residuals from a least squares regression of milking duration on milk yield; RMDS is represented by the residuals from a least squares regression of milking duration on both milk yield and somatic cell score [i.e., logarithm (base 10) of somatic cell count]. The mathematical properties of least squares regression ensure than the residual traits are independent from the regressor variables, or, in other words, RMDS is not correlated with either milk yield or somatic cell score. Both RMD and RMDS were defined using electronically measured individual cow milking duration from 235,036 part-day milking events from 74,607 cows from 1,075 Irish dairy herds. Twenty-four percent of the variation in milking duration was explained by the multiple regression model containing both milk yield and somatic cell score. The phenotypic standard deviation of RMD and RMDS was 102.2 and 98.2s, respectively, suggesting large variation in milking duration independent of milk yield (and somatic cell score). The correlation of RMD and RMDS with average milk flow rate, which may also be considered a measure of milking efficiency, was -0.74 and -0.75, respectively. Neither RMD nor RMDS was correlated with somatic cell score. However, average milk flow rate was correlated with milk yield (0.57) and milking duration (-0.38). Both RMD and RMDS are useful traits, which exhibit considerable variation and, therefore, can be used by farmers to identify phenotypically slower milking animals irrespective of milk yield (and somatic cell score). However, because of the lack of a correlation between RMD and somatic cell score in the sample population used in the present study, RMD and RMDS values per milking were almost identical.

Effectiveness of 2010/2011 seasonal influenza vaccine in Ireland.

We conducted a case-control study to estimate the 2010/2011 trivalent influenza vaccine effectiveness (TIVE) using the Irish general practitioners' influenza sentinel surveillance scheme. Cases were influenza-like illness (ILI) patients with laboratory-confirmed influenza. Controls were ILI patients who tested negative for influenza. Participating sentinel general practitioners (GP) collected swabs from patients presenting with ILI along with their vaccination history and other individual characteristics. The TIVE was computed as (1 - odds ratiofor vaccination) x100%. Of 60 sentinel GP practices, 22 expressed interest in participating in the study and 17 (28%) recruited at least one ILI patient. In the analysis, we included 106 cases and 85 controls. Seven controls (8.2%) and one influenza case (0.9%) had been vaccinated in 2010/2011. The estimated TIVE against any influenza subtype was 89.4% [95% CI: 13.8; 99.8%], suggesting a protective effect against GP-attended laboratory confirmed influenza. This study design could be used to monitor influenza vaccine effectiveness annually but sample size and vaccination coverage should be increased to obtain precise and adjusted estimates.

First reported cases of human adenovirus serotype 14p1 infection, Ireland, October 2009 to July 2010.

We report the first nine confirmed cases of human adenovirus 14p1 infection (HAdV-14p1), identified at different locations in Ireland between October 2009 and July 2010. These were the first notifications in Ireland and all were sporadic cases. Following these notifications, the Health Protection Surveillance Centre set up an enhanced surveillance system for HAdV-14p1 infection. Seven cases were male and five were aged less than one year. Three patients died, giving a case fatality rate of 33%. It should be noted that cases presented here were diagnosed on presentation to hospital and may represent the severe end of the spectrum of HAdV 14 disease in Ireland.

Indirect impact of rotavirus vaccination on viral causes of acute gastroenteritis in the elderly.

BACKGROUND: Rotavirus is considered a childhood infection causing acute gastroenteritis however, it also causes disease in adults which may be underestimated due to less frequent testing in this age-group. OBJECTIVES: To determine if paediatric rotavirus vaccination, introduced into Ireland in December 2016, affected the viral aetiology in those aged ≥65 yrs presenting with gastroenteritis in the pre- and post-vaccination years. Additionally, rotavirus genotypes in this age-group will be described. METHODS: Faecal samples from 2015 to 2019 for the investigation of gastroenteritis were tested by real-time (RT-) PCR for norovirus, adenovirus, rotavirus, Rotarix, astrovirus and sapovirus. Rotaviruses were genotyped by multiplex real-time RT-PCR or hemi-nested RT-PCR and a proportion confirmed by sequencing. RESULTS: 22,593 samples from adults aged ≥65 yrs were tested and 2566 (11 %) had ≥1 virus detected. Of 2566 positive samples, norovirus was detected in 82 %, rotavirus 9 %, sapovirus 6 %, astrovirus 3 % and adenovirus 1 %. Rotavirus and norovirus infections decreased between pre and post-vaccine year groups p < 0.001, whereas sapovirus, astrovirus and adenovirus remained unchanged. Between 2015-16 and 2018-19, G2P[4] increased and G4P[8] decreased, p < 0.001. In 2015-2019 there were 37 rotavirus outbreaks. Five geriatric outbreaks were genotyped and caused by G4P[8] (n = 1), G1P[8] (n = 1), G2P[4] (n = 2) and G12P[8] (n = 1). CONCLUSION: Rotavirus causes acute gastroenteritis in older people. Paediatric vaccination may have contributed to a decline in infections in the elderly; nevertheless, rotavirus continued to circulate in older people following vaccine introduction. Genotype distribution changed between the pre- and post-vaccine era however genotypes in outbreak and endemic settings were comparable.

The gut virome in Irritable Bowel Syndrome differs from that of controls.

Irritable Bowel Syndrome (IBS), the most common gastrointestinal disorder, is diagnosed solely on symptoms. Potentially diagnostic alterations in the bacterial component of the gut microbiome (the bacteriome) are associated with IBS, but despite the known role of the virome (particularly bacteriophages), in shaping the gut bacteriome, few studies have investigated the virome in IBS. We performed metagenomic sequencing of fecal Virus-Like Particles (VLPs) from 55 patients with IBS and 51 control individuals. We detected significantly lower alpha diversity of viral clusters comprising both known and novel viruses (viral 'dark matter') in IBS and a significant difference in beta diversity compared to controls, but not between IBS symptom subtypes. The three most abundant bacteriophage clusters belonged to the Siphoviridae, Myoviridae, and Podoviridae families (Order Caudovirales). A core virome (defined as a cluster present in at least 50% of samples) of 5 and 12 viral clusters was identified in IBS and control subjects, respectively. We also identified a subset of viral clusters that showed differential abundance between IBS and controls. The virome did not co-vary significantly with the bacteriome, with IBS clinical subtype, or with Bile Acid Malabsorption status. However, differences in the virome could be related back to the bacteriome as analysis of CRISPR spacers indicated that the virome alterations were at least partially related to the alterations in the bacteriome. We found no evidence for a shift from lytic to lysogenic replication of core viral clusters, a phenomenon reported for the gut virome of patients with Inflammatory Bowel Disease. Collectively, our data show alterations in the virome of patients with IBS, regardless of clinical subtype, which may facilitate development of new microbiome-based therapeutics.

The role of rhinovirus infections in young children with cystic fibrosis.

Rhinovirus (RV) is an important virus in children with chronic respiratory conditions such as asthma; however, little is known about its role in CF. Our aim was to examine the prevalence and clinical impact of different RV species in young children with CF. We collected clinical data and nasal swabs on patients at home and in the hospital setting. Parents filled out symptom diaries and collected nasal swabs when their children were symptomatic and asymptomatic. A novel RV typing PCR assay was used to determine the RV species present. We collected 55 nasal swab samples from ten preschool CF patients over a six month period. The quality of parent collected samples at home was sufficient for PCR analysis. RV was the most common virus detected in young children with CF. There was no difference in the frequency of RV species between symptomatic and asymptomatic subjects. However, parental home-sampling is an acceptable and feasible approach to monitoring young children with CF.

Analysis of integrated virological and epidemiological reports of norovirus outbreaks collected within the Foodborne Viruses in Europe network from 1 July 2001 to 30 June 2006.

The Foodborne Viruses in Europe network has developed integrated epidemiological and virological outbreak reporting with aggregation and sharing of data through a joint database. We analyzed data from reported outbreaks of norovirus (NoV)-caused gastroenteritis from 13 European countries (July 2001 to July 2006) for trends in time and indications of different epidemiology of genotypes and variants. Of the 13 countries participating in this surveillance network, 11 were capable of collecting integrated epidemiological and virological surveillance data and 10 countries reported outbreaks throughout the entire period. Large differences in the numbers and rates of reported outbreaks per country were observed, reflecting the differences in the focus and coverage of national surveillance systems. GII.4 strains predominated throughout the 5-year surveillance period, but the proportion of outbreaks associated with GII.4 rose remarkably during years in which NoV activity was particularly high. Spring and summer peaks indicated the emergence of genetically distinct variants within GII.4 across Europe and were followed by increased NoV activity during the 2002-2003 and 2004-2005 winter seasons. GII.4 viruses predominated in health care settings and in person-to-person transmission. The consecutive emergence of new GII.4 variants is highly indicative of immune-driven selection. Their predominance in health care settings suggests properties that facilitate transmission in settings with a high concentration of people such as higher virus loads in excreta or a higher incidence of vomiting. Understanding the mechanisms driving the changes in epidemiology and clinical impact of these rapidly evolving RNA viruses is essential to design effective intervention and prevention measures.

Data quality of 5 years of central norovirus outbreak reporting in the European Network for food-borne viruses.

BACKGROUND: The food-borne viruses in Europe (FBVE) network database was established in 1999 to monitor trends in outbreaks of gastroenteritis due to noroviruses (NoVs), to identify major transmission routes of NoV infections within and between participating countries and to detect diffuse international food-borne outbreaks. METHODS: We reviewed the total of 9430 NoV outbreak reports from 13 countries with date of onset between 1 January 2002 and 1 January 2007 for representativeness, completeness and timeliness against these objectives. RESULTS: Rates of reporting ranged from a yearly average of 1.8 in 2003 to 11.6 in 2006. Completeness of reporting of an agreed minimum dataset improved over the years, both for epidemiological and virological data. For the 10 countries that provided integrated (epidemiological AND virological) reporting over the 5-year period, the completeness of the minimum dataset rose from 15% in 2003 to 48% in 2006. Two countries have not been able to combine both data types due to the structure of the national surveillance system (England and Wales and Germany). Timeliness of reporting (median days between the onset of an outbreak and the date of reporting to the FBVE database) differed greatly between countries, but gradually improved to 47 days in 2006. CONCLUSION: The outbreaks reported to the FBVE reflect the lack of standardization of surveillance systems across Europe, making direct comparison of data between countries difficult. However, trends in reported outbreaks per country, distribution of NoV genotypes, and detection of diffuse international outbreaks were used as background data in acute questions about NoV illness and the changing genotype distribution during the 5-year period, shown to be of added value. Integrated reporting is essential for these objectives, but could be limited to sentinel countries with surveillance systems that allow this integration. For successful intervention in case of diffuse international outbreaks, completeness and timeliness of reporting would need to be improved and expanded to countries that presently do not participate.

Diagnosis of rotavirus infection in a vaccinated population: Is a less sensitive immunochromatographic method more suitable for detecting wild-type rotavirus than real-time RT-PCR?

BACKGROUND: Diagnosis of wild-type rotavirus disease may be complicated by the detection of vaccine-derived virus which can be detected in stool samples following immunisation. We evaluate an immunochromatographic assay and real-time RT-PCR to determine which is more suitable for the detection of wild-type rotavirus. OBJECTIVES: To compare the Ct values of wild-type rotavirus and Rotarix determined by real-time RT-PCR. To establish the Ct value corresponding to the limit of detection of the immunochromatographic Combi-Strip method (Coris, BioConcept). STUDY DESIGN: Retrospective review of real-time RT-PCR Ct values was performed on 100 samples tested by a pan-rotavirus assay (n = 50 wild-type, n = 50 Rotarix). Secondly the limit of detection of the Combi-Strip assay was determined by testing; wild-type rotavirus (n = 33, Ct range 6.85-34.26) samples, Rotarix (n = 9, Ct range 20.86-34.26) samples and rotavirus negative (n = 21) samples. RESULTS: The median Ct of 50 wild-type rotavirus was Ct 12.43; range 6.11-32.66 compared with the median of 50 Rotarix, Ct 29.09; range 18.91-35.28, p=<0.0001. The limit of detection of the Combi-Strip method was approximately Ct 18. The 21 rotavirus negative samples were negative by real-time RT-PCR and Combi-Strip. CONCLUSIONS: We found the Ct value was significantly lower, and therefore the viral load higher, for wild-type rotavirus compared to detectable Rotarix. The Combi-Strip assay detects most wild-type infections; however, it lacks sensitivity to detect low-level wild-type rotavirus and, beneficially, is unlikely to detect Rotarix. It is not a more suitable method than real-time RT-PCR when a definitive rotavirus result is required.

Circulating rotavirus genotypes in the Irish paediatric population prior to the introduction of the vaccination programme.

BACKGROUND: Rotavirus is the leading cause of viral gastroenteritis in children, and it is anticipated that the introduction of the Rotarix™ vaccine (GlaxoSmithKline Biologicals S.A., Rixensart, Belgium) into the Irish immunisation schedule will result in a significant reduction of rotavirus-associated disease. In the pre- and post-vaccination eras, it is important to determine circulating strains of rotavirus to assess vaccine effectiveness, to monitor vaccine failures, and to detect potential emerging strains. AIM: This study was a collaboration between the Temple Street Children's University Hospital (TSCUH), Dublin, and the National Virus Reference Laboratory (NVRL), Dublin, to determine the then circulating rotavirus strains in a paediatric hospital. METHOD: In the 2015/2016 period (July 2015-June 2016) 89 faecal samples from paediatric patients (53 from TSCUH, 36 from other hospitals) were characterised. RESULTS: The results showed G1P[8] to be the predominant genotype (57%), followed by G9P[8] (34%), G4P[8] (6%), G2P[4] (2%), and G12P[8] (1%). CONCLUSION: This distribution of genotypes is comparable to those found in other European countries prior to vaccination suggesting that the vaccine should be highly efficacious in the Irish population.

Ovarian carcinoma-associated TaqI restriction fragment length polymorphism in intron G of the progesterone receptor gene is due to an Alu sequence insertion.

Alu sequences, short, repetitive transposable DNA elements, are factors in a number of genetic diseases. We previously identified a germline TaqI RFLP, located in intron G of the human progesterone receptor gene, that showed an association with the incidence of sporadic ovarian carcinoma. Furthermore, the polymorphism was characterized as a small (approximately 300-bp) insertion that was inherited in a Mendelian fashion. Because of its insertional character, we named this polymorphism PROGINS. We report the identification of PROGINS as a 306-bp Alu element of the PV or HS-1 Alu subfamily.

Contribution of an aspartate residue, D114, in the active site of clostridial glutamate dehydrogenase to the enzyme's unusual pH dependence.

Glutamate dehydrogenase from Clostridium symbiosum displays unusual kinetic behaviour at high pH when compared with other members of this enzyme family. Structural and sequence comparisons with GDHs from other organisms have indicated that the Asp residue at position 114 in the clostridial enzyme may account for these differences. By replacing this residue by Asn, a mutant protein has been created with altered functional properties at high pH. This mutant protein can be efficiently overexpressed in Escherichia coli, and several criteria, including mobility in non-denaturing electrophoresis, circular dichroism (CD) spectra and initial crystallisation studies, suggest a folding and an assembly comparable to those of the wild-type protein. The D114N mutant enzyme shows a higher optimum pH for activity than the wild-type enzyme, and both CD data and activity measurements show that the distinctive time-dependent reversible conformational inactivation seen at high pH in the wild-type enzyme is abolished in the mutant.

Hepatitis C viral clearance in an intravenous drug-using cohort in the Dublin area.

BACKGROUND: The rate of spontaneous HCV viral clearance is reported as 20-25% but recent data indicate a higher frequency in some cohorts. The rate of spontaneous clearance in intravenous drug users has not been reported in an Irish setting. AIMS: To determine the rate of spontaneous hepatitis C viral clearance and genotype in an Irish intravenous drug-using cohort. METHODS: Drug users attending five drug treatment clinics in the Dublin were investigated. Data were prospectively recorded from January 1997 to June 2001 and follow-up testing completed in 2003. There were 496 HCV antibody positive patients identified and assessed for HCV RNA clearance. All were HIV and hepatitis B negative, 68.8% were male. RESULTS: HCV RNA negativity (viral clearance) was documented in 38% of patients. Viral clearance was 47.4% in females and 34.5% in males (p = 000.6). Clearance was independent of age or duration of intravenous drug use. Viral clearance as defined as two negative consecutive HCV RNA tests, a minimum of one year apart, was sustained in 82.2% at two-year follow-up, giving an overall viral clearance of 31.1%. HCV genotype 1 and 3 were most commonly identified at 48.8% and 48.5% respectively in those with chronic infection. CONCLUSIONS: Spontaneous HCV viral clearance occurs at a higher frequency than previously reported. Genotype 1 and 3 are commonest in the patient cohort.

Enhanced proliferation of CD4+ T cells induced by dendritic cells following antigen uptake in the presence of specific antibody.

Afferent lymph dendritic cells bear an Fc gamma receptor which binds antigen/antibody complexes thereby enhancing uptake of antigen. In this report, we have addressed the question of whether the enhanced uptake of antigen results in augmented antigen presentation and T cell proliferation in in vitro secondary responses in sheep. Inclusion of affinity-purified IgG anti-ovalbumin antibody in cultures of afferent lymph dendritic cells, purified CD4+ T cells, and substimulating amounts of ovalbumin resulted in a five- to 169-fold enhancement of T cell proliferation. This effect was antigen-specific as replacement of the anti-ovalbumin antibody with an IgG anti-human serum albumin specific antibody did not cause enhanced T cell responses. The antigen-specific augmentation required intact antibody Fc portions as F(ab')2 fragments of the anti-ovalbumin antibodies were ineffective. The enhanced antigen presentation was found to be maximal with immune complexes in moderate antibody excess (three- to 30-fold), but still occurred at antibody/antigen ratios of 300. The augmented responses were inhibitable with anti-MHC Class II specific antibodies, indicating that at least some of the antigen taken in via Fc gamma receptors entered a Class II processing pathway. The results thus show that antigen uptake via Fc gamma receptors on dendritic cells results in functional augmentation of antigen presentation and T cell proliferation.

Nurses' knowledge, experiences, and attitudes concerning living wills.

A random sample of 974 registered nurses in Nova Scotia were surveyed during the 1995-96 registration year to determine their understanding of living wills legislation; their experiences, roles, and attitudes related to living wills; and their perceptions of the barriers to and resources for using living wills in their practice. Responses from 157 nurses indicated that they were unfamiliar with the Medical Consent Act, the Hospitals Act, and the Powers of Attorney Act. Although they revealed that they had a positive attitude towards living wills, and they identified nurses as the appropriate health professional to initiate discussions about living wills with patients, very few had any actual experience in this role. Respondents rated their understanding of living wills as low, and many indicated that they were uncomfortable discussing the topic with clients. Respondents saw both the individual nurse and the practice environment as barriers to the use of living wills, and they clearly indicated the need for interdisciplinary educational strategies to facilitate the use of living wills in their nursing practice.

Development and review of the voluntary phase of a national BVD eradication programme in Ireland.

The voluntary phase of an industry-led national Bovine Viral Diarrhoea (BVD) eradication programme began in Ireland on January 1, 2012 with the goal of progressing to a compulsory programme in 2013. The development and implementation of the programme in 2012 was informed by a review of current and prior eradication programmes elsewhere in Europe and extensive stakeholder consultation. The programme was based on tissue tag testing of newborn calves in participating herds, with the status of the mothers of calves with positive or inconclusive results requiring clarification. Participating herd owners were required to comply with a series of guidelines, including not selling cattle suspected of being persistently infected. For herds compliant with the guidelines, the results from 2012 counted as one of three years of tag testing anticipated in the compulsory phase of the programme. Testing was carried out in laboratories designated for this purpose by the cross-industry BVD Implementation Group that oversees the programme. Results were reported to a central database managed by the Irish Cattle Breeding Federation, and the majority of results were reported to farmers' mobile telephones by SMS message. A detailed review of the programme was conducted, encompassing the period between January 1, 2012 and July 15, 2012, based on results from approximately 500,000 calves. This paper describes the establishment and structure of the programme, and the outcomes of the review, including findings at herd and animal level.