International circumpolar surveillance: update on the interlaboratory quality control program for Streptococcus pneumoniae, 2009 to 2020

The International Circumpolar Surveillance (ICS) program is a population-based surveillance network for invasive bacterial diseases throughout Arctic countries and territories. The ICS quality control program for Streptococcus pneumoniae serotyping and antimicrobial susceptibility testing has been ongoing since 1999. Current participating laboratories include the Provincial Laboratory for Public Health in Edmonton, Alberta; Laboratoire de santé publique du Québec in Sainte-Anne-de-Bellevue, Québec; the Centers for Disease Control's Arctic Investigations Program in Anchorage, Alaska; the Neisseria and Streptococcus Reference Laboratory at Statens Serum Institut in Copenhagen, Denmark; the Department of Clinical Microbiology, Landspitali in Reykjavik, Iceland; and Public Health Agency of Canada's National Microbiology Laboratory in Winnipeg, Manitoba. From 2009 to 2020, 140 isolates of S. pneumoniae were distributed among the six laboratories as part of the quality control program. Overall serotype concordance was 96.9%, with 99.3% concordance to pool level. All participating laboratories had individual concordance rates >92% for serotype and >97% for pool. Overall concordance by modal minimum inhibitory concentration (MIC) for testing done by broth microdilution or Etest was 99.1%, and >98% for all antimicrobials tested. Categorical concordance was >98% by both CLSI and EUCAST criteria. For two laboratories performing disc diffusion, rates of concordance by modal MIC were >97% for most antimicrobials, except chloramphenicol (>93%) and trimethoprim/sulfamethoxazole (>88%). Data collected from 12 years of the ICS quality control program for S. pneumoniae demonstrate excellent (≥95%) overall concordance for serotype and antimicrobial susceptibility testing results across six laboratories.

IMPORTANCE

Arctic populations experience several social and physical challenges that lead to the increased spread and incidence of invasive diseases. The International Circumpolar Surveillance (ICS) program was developed to monitor five invasive bacterial diseases in Arctic countries and territories. Each ICS organism has a corresponding interlaboratory quality control (QC) program for laboratory-based typing, to ensure the technical precision and accuracy of reference testing services for these regions, and identify and correct potential problems. Here, we describe the results of the ICS Streptococcus pneumoniae QC program, from 2009 to 2020. Excellent overall concordance was achieved for serotype and antimicrobial susceptibility testing results across six laboratories. Ongoing participation in these QC programs ensures the continuation of quality surveillance systems within Arctic populations that experience health disparities.

Increase in invasive Streptococcus pyogenes M1 infections with close evolutionary genetic relationship, Iceland and Scotland, 2022 to 2023

Group A Streptococcus isolates of the recently described M1UK clade have emerged to cause human infections in several European countries and elsewhere. Full-genome sequence analysis of M1 isolates discovered a close genomic relationship between some isolates from Scotland and the majority of isolates from Iceland causing serious infections in 2022 and 2023. Phylogenetic analysis strongly suggests that an isolate from or related to Scotland was the precursor to an M1UK variant responsible for almost all recent M1 infections in Iceland.

Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium

BACKGROUND

The Invasive Respiratory Infection Surveillance (IRIS) Consortium was established to assess the impact of the COVID-19 pandemic on invasive diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Streptococcus agalactiae. We aimed to analyse the incidence and distribution of these diseases during the first 2 years of the COVID-19 pandemic compared to the 2 years preceding the pandemic.

METHODS

For this prospective analysis, laboratories in 30 countries and territories representing five continents submitted surveillance data from Jan 1, 2018, to Jan 2, 2022, to private projects within databases in PubMLST. The impact of COVID-19 containment measures on the overall number of cases was analysed, and changes in disease distributions by patient age and serotype or group were examined. Interrupted time-series analyses were done to quantify the impact of pandemic response measures and their relaxation on disease rates, and autoregressive integrated moving average models were used to estimate effect sizes and forecast counterfactual trends by hemisphere.

FINDINGS

Overall, 116 841 cases were analysed: 76 481 in 2018-19, before the pandemic, and 40 360 in 2020-21, during the pandemic. During the pandemic there was a significant reduction in the risk of disease caused by S pneumoniae (risk ratio 0·47; 95% CI 0·40-0·55), H influenzae (0·51; 0·40-0·66) and N meningitidis (0·26; 0·21-0·31), while no significant changes were observed for S agalactiae (1·02; 0·75-1·40), which is not transmitted via the respiratory route. No major changes in the distribution of cases were observed when stratified by patient age or serotype or group. An estimated 36 289 (95% prediction interval 17 145-55 434) cases of invasive bacterial disease were averted during the first 2 years of the pandemic among IRIS-participating countries and territories.

INTERPRETATION

COVID-19 containment measures were associated with a sustained decrease in the incidence of invasive disease caused by S pneumoniae, H influenzae, and N meningitidis during the first 2 years of the pandemic, but cases began to increase in some countries towards the end of 2021 as pandemic restrictions were lifted. These IRIS data provide a better understanding of microbial transmission, will inform vaccine development and implementation, and can contribute to health-care service planning and provision of policies.

FUNDING

Wellcome Trust, NIHR Oxford Biomedical Research Centre, Spanish Ministry of Science and Innovation, Korea Disease Control and Prevention Agency, Torsten Söderberg Foundation, Stockholm County Council, Swedish Research Council, German Federal Ministry of Health, Robert Koch Institute, Pfizer, Merck, and the Greek National Public Health Organization.

Nasopharyngeal competition dynamics are likely to be altered following vaccine introduction: bacteriocin prevalence and diversity among Icelandic and Kenyan pneumococci

Bacteriocins are antimicrobial peptides produced by bacteria to inhibit other bacteria in the surrounding environment. Streptococcus pneumoniae is a leading cause of disease worldwide and colonises the healthy human nasopharynx, where it competes for space and nutrients. Pneumococcal conjugate vaccines have reduced the incidence of disease, but they also restructure the bacterial population, and this restructuring likely alters the nasopharyngeal competition dynamics. Here, the distribution of bacteriocins was examined in over 5000 carriage and disease-causing pneumococci from Iceland and Kenya, recovered before and after the introduction of pneumococcal vaccination. Overall, up to eleven different bacteriocin gene clusters were identified per pneumococcus. Significant differences in the prevalence of bacteriocins were observed before and after vaccine introduction, and among carriage and disease-causing pneumococci, which were largely explained by the bacterial population structure. Genetically similar pneumococci generally harboured the same bacteriocins although sometimes different repertoires of bacteriocins were observed, which suggested that horizontal transfer of bacteriocin clusters had occurred. These findings demonstrated that vaccine-mediated changes in the pneumococcal population altered the prevalence and distribution of bacteriocins. The consequences of this for pneumococcal colonisation and disease remain to be determined.

Determining SARS-CoV-2 non-infectivity state-A brief overview

From the beginning of the COVID-19 pandemic, it has claimed over 6 million lives, and globally the pandemic rages with detrimental consequences, with the emergence of new more infectious and possibly virulent variants. A clinical obstacle in this battle has been to determine when an infected individual has reached a non-infectious state. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can be transmitted under diverse circumstances, and various rules and regulations, along with different testing methods, have been applied in an attempt to confine the transmission. However, that has proven to be a difficult task. In this review, we take together recently published data on infectivity and transmission of SARS-CoV-2 and have combined it with the clinical experience that physicians in Iceland have accumulated from the pandemic. In addition, we suggest guidelines for determining when patients with COVID-19 reach a non-infectious state based on a combination of clinical experience, scientific data, and proficient use of available tests. This review has addressed some of the questions regarding contagiousness and immunity against SARS-CoV-2.

International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease

BACKGROUND

Pneumococcal disease outbreaks of vaccine preventable serotype 4 sequence type (ST)801 in shipyards have been reported in several countries. We aimed to use genomics to establish any international links between them.

METHODS

Sequence data from ST801-related outbreak isolates from Norway (n = 17), Finland (n = 11) and Northern Ireland (n = 2) were combined with invasive pneumococcal disease surveillance from the respective countries, and ST801-related genomes from an international collection (n = 41 of > 40,000), totalling 106 genomes. Raw data were mapped and recombination excluded before phylogenetic dating.

RESULTS

Outbreak isolates were relatively diverse, with up to 100 SNPs (single nucleotide polymorphisms) and a common ancestor estimated around the year 2000. However, 19 Norwegian and Finnish isolates were nearly indistinguishable (0-2 SNPs) with the common ancestor dated around 2017.

CONCLUSION

The total diversity of ST801 within the outbreaks could not be explained by recent transmission alone, suggesting that harsh environmental and associated living conditions reported in the shipyards may facilitate invasion of colonising pneumococci. However, near identical strains in the Norwegian and Finnish outbreaks does suggest that transmission between international shipyards also contributed to those outbreaks. This indicates the need for improved preventative measures in this working population including pneumococcal vaccination.

Detailed Multiplex Analysis of SARS-CoV-2 Specific Antibodies in COVID-19 Disease

A detailed understanding of the antibody response against SARS-CoV-2 is of high importance, especially with the emergence of novel vaccines. A multiplex-based assay, analyzing IgG, IgM, and IgA antibodies against the receptor binding domain (RBD), spike 1 (S1), and nucleocapsid proteins of the SARS-CoV-2 virus was set up. The multiplex-based analysis was calibrated against the Elecsys^® Anti-SARS-CoV-2 assay on a Roche Cobas^® instrument, using positive and negative samples. The calibration of the multiplex based assay yielded a sensitivity of 100% and a specificity of 97.7%. SARS-CoV-2 specific antibody levels were analyzed by multiplex in 251 samples from 221 patients. A significant increase in all antibody types (IgM, IgG, and IgA) against RBD was observed between the first and the third weeks of disease. Additionally, the S1 IgG antibody response increased significantly between weeks 1, 2, and 3 of disease. Class switching appeared to occur earlier for IgA than for IgG. Patients requiring hospital admission and intensive care had higher levels of SARS-CoV-2 specific IgA levels than outpatients. These findings describe the initial antibody response during the first weeks of disease and demonstrate the importance of analyzing different antibody isotypes against multiple antigens and include IgA when examining the immunological response to COVID-19.

The impact and cost-effectiveness of introducing the 10-valent pneumococcal conjugate vaccine into the paediatric immunisation programme in Iceland-A population-based time series analysis

INTRODUCTION

Streptococcus pneumoniae is a cause of infections that range in severity from acute otitis media (AOM) to pneumonia and invasive pneumococcal disease (IPD). The 10-valent pneumococcal conjugate vaccine (PHiD-CV10) was introduced into the Icelandic paediatric immunisation programme in 2011. The aim was to estimate the population impact and cost-effectiveness of PHiD-CV10 introduction.

METHODS

Data on primary care visits from 2005-2015 and hospitalisations from 2005-2017 were obtained from population-based registries. A Bayesian time series analysis with synthetic controls was employed to estimate the number of cases of AOM, pneumonia and IPD that would have occurred between 2013-2017, had PHiD-CV10 not been introduced. Prevented cases were calculated by subtracting the observed number of cases from this estimate. The cost of the programme was calculated accounting for cost-savings due to prevented cases.

RESULTS

The introduction of PHiD-CV10 prevented 13,767 (95% credible interval [CI] 2,511-29,410) visits for AOM from 2013-2015, and prevented 1,814 (95%CI -523-4,512) hospitalisations for pneumonia and 53 (95%CI -17-177) admissions for IPD from 2013-2017. Visits for AOM decreased both among young children and among children 4-19 years of age, with rate ratios between 0.72-0.89. Decreases were observed in both pneumonia hospitalisations (rate ratios between 0.67-0.92) and IPD (rate ratios between 0.27-0.94). The total cost of implementing PHiD-CV10 in Iceland was -7,463,176 United States Dollars (USD) (95%CI -16,159,551-582,135) with 2.1 USD (95%CI 0.2-4.7) saved for every 1 USD spent.

CONCLUSIONS

The introduction of PHiD-CV10 was associated with large decreases in visits and hospitalisations for infections commonly caused by pneumococcus and was cost-saving during the first five years of the immunisation programme.

Serotype Distribution of Remaining Pneumococcal Meningitis in the Mature PCV10/13 Period: Findings from the PSERENADE Project

Pneumococcal conjugate vaccine (PCV) introduction has reduced pneumococcal meningitis incidence. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project described the serotype distribution of remaining pneumococcal meningitis in countries using PCV10/13 for least 5-7 years with primary series uptake above 70%. The distribution was estimated using a multinomial Dirichlet regression model, stratified by PCV product and age. In PCV10-using sites (N = 8; cases = 1141), PCV10 types caused 5% of cases <5 years of age and 15% among ≥5 years; the top serotypes were 19A, 6C, and 3, together causing 42% of cases <5 years and 37% ≥5 years. In PCV13-using sites (N = 32; cases = 4503), PCV13 types caused 14% in <5 and 26% in ≥5 years; 4% and 13%, respectively, were serotype 3. Among the top serotypes are five (15BC, 8, 12F, 10A, and 22F) included in higher-valency PCVs under evaluation. Other top serotypes (24F, 23B, and 23A) are not in any known investigational product. In countries with mature vaccination programs, the proportion of pneumococcal meningitis caused by vaccine-in-use serotypes is lower (≤26% across all ages) than pre-PCV (≥70% in children). Higher-valency PCVs under evaluation target over half of remaining pneumococcal meningitis cases, but questions remain regarding generalizability to the African meningitis belt where additional data are needed.

Changes in Invasive Pneumococcal Disease Caused by Streptococcus pneumoniae Serotype 1 Following Introduction of PCV10 and PCV13: Findings from the PSERENADE Project

Streptococcus pneumoniae serotype 1 (ST1) was an important cause of invasive pneumococcal disease (IPD) globally before the introduction of pneumococcal conjugate vaccines (PCVs) containing ST1 antigen. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project gathered ST1 IPD surveillance data from sites globally and aimed to estimate PCV10/13 impact on ST1 IPD incidence. We estimated ST1 IPD incidence rate ratios (IRRs) comparing the pre-PCV10/13 period to each post-PCV10/13 year by site using a Bayesian multi-level, mixed-effects Poisson regression and all-site IRRs using a linear mixed-effects regression (N = 45 sites). Following PCV10/13 introduction, the incidence rate (IR) of ST1 IPD declined among all ages. After six years of PCV10/13 use, the all-site IRR was 0.05 (95% credibility interval 0.04–0.06) for all ages, 0.05 (0.04–0.05) for <5 years of age, 0.08 (0.06–0.09) for 5–17 years, 0.06 (0.05–0.08) for 18–49 years, 0.06 (0.05–0.07) for 50–64 years, and 0.05 (0.04–0.06) for ≥65 years. PCV10/13 use in infant immunization programs was followed by a 95% reduction in ST1 IPD in all ages after approximately 6 years. Limited data availability from the highest ST1 disease burden countries using a 3 + 0 schedule constrains generalizability and data from these settings are needed.

Humoral Immune Response to SARS-CoV-2 in Iceland

BACKGROUND

Little is known about the nature and durability of the humoral immune response to infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS

We measured antibodies in serum samples from 30,576 persons in Iceland, using six assays (including two pan-immunoglobulin [pan-Ig] assays), and we determined that the appropriate measure of seropositivity was a positive result with both pan-Ig assays. We tested 2102 samples collected from 1237 persons up to 4 months after diagnosis by a quantitative polymerase-chain-reaction (qPCR) assay. We measured antibodies in 4222 quarantined persons who had been exposed to SARS-CoV-2 and in 23,452 persons not known to have been exposed.

RESULTS

Of the 1797 persons who had recovered from SARS-CoV-2 infection, 1107 of the 1215 who were tested (91.1%) were seropositive; antiviral antibody titers assayed by two pan-Ig assays increased during 2 months after diagnosis by qPCR and remained on a plateau for the remainder of the study. Of quarantined persons, 2.3% were seropositive; of those with unknown exposure, 0.3% were positive. We estimate that 0.9% of Icelanders were infected with SARS-CoV-2 and that the infection was fatal in 0.3%. We also estimate that 56% of all SARS-CoV-2 infections in Iceland had been diagnosed with qPCR, 14% had occurred in quarantined persons who had not been tested with qPCR (or who had not received a positive result, if tested), and 30% had occurred in persons outside quarantine and not tested with qPCR.

CONCLUSIONS

Our results indicate that antiviral antibodies against SARS-CoV-2 did not decline within 4 months after diagnosis. We estimate that the risk of death from infection was 0.3% and that 44% of persons infected with SARS-CoV-2 in Iceland were not diagnosed by qPCR.

Humoral Immune Response to SARS-CoV-2 in Iceland

BACKGROUND

Little is known about the nature and durability of the humoral immune response to infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS

We measured antibodies in serum samples from 30,576 persons in Iceland, using six assays (including two pan-immunoglobulin [pan-Ig] assays), and we determined that the appropriate measure of seropositivity was a positive result with both pan-Ig assays. We tested 2102 samples collected from 1237 persons up to 4 months after diagnosis by a quantitative polymerase-chain-reaction (qPCR) assay. We measured antibodies in 4222 quarantined persons who had been exposed to SARS-CoV-2 and in 23,452 persons not known to have been exposed.

RESULTS

Of the 1797 persons who had recovered from SARS-CoV-2 infection, 1107 of the 1215 who were tested (91.1%) were seropositive; antiviral antibody titers assayed by two pan-Ig assays increased during 2 months after diagnosis by qPCR and remained on a plateau for the remainder of the study. Of quarantined persons, 2.3% were seropositive; of those with unknown exposure, 0.3% were positive. We estimate that 0.9% of Icelanders were infected with SARS-CoV-2 and that the infection was fatal in 0.3%. We also estimate that 56% of all SARS-CoV-2 infections in Iceland had been diagnosed with qPCR, 14% had occurred in quarantined persons who had not been tested with qPCR (or who had not received a positive result, if tested), and 30% had occurred in persons outside quarantine and not tested with qPCR.

CONCLUSIONS

Our results indicate that antiviral antibodies against SARS-CoV-2 did not decline within 4 months after diagnosis. We estimate that the risk of death from infection was 0.3% and that 44% of persons infected with SARS-CoV-2 in Iceland were not diagnosed by qPCR.

Effect of vaccination on the use of antimicrobial agents: a systematic literature review

BACKGROUND

Antimicrobial resistance is a growing global health threat. To preserve the effectiveness of antimicrobials, it is important to reduce demand for antimicrobials.

OBJECTIVES

The objective of the study was to screen the existing peer-reviewed literature to identify articles that addressed the potential impact of influenza or Pneumococcus vaccination on antibiotic usage. Data sources: PubMed, Embase Study eligibility criteria: Clinical studies where antimicrobial prescribing was assessed in both vaccinated and unvaccinated populations. Participants and interventions: All patient populations were included (infants, children, adults and elderly), where the effects of the intervention (vaccination) was assessed.

RESULTS

We identified unique 3638 publications, of which 26 were judged to be of sufficiently high quality to allow the calculation of the potential impact of vaccination. Of these studies 23/26 found a significant reduction in antibiotic use by at least one of the parameters assessed.

LIMITATIONS

Different measures used to define anti-microbial use, studies typically focus on specific risk groups and most studies are from high-income countries. Conclusions and implications of key findings: Despite the limitations of the review, the evidence indicates that improved coverage with existing vaccines may significantly reduce antimicrobial demand. This suggests it may be a valuable tool for antimicrobial stewardship. Key messages While vaccines against a number of pathogens have been studied for their ability to reduce antimicrobial use, currently only vaccination against influenza or pneumococcus has generated sufficient data for analysis Vaccination against either influenza or pneumococcus significantly reduced overall antimicrobial prescribing rates, both in vaccinated individuals and at a population level Maintaining and expanding vaccination coverage thus appears to be a key tool for antimicrobial stewardship.

Spread of SARS-CoV-2 in the Icelandic Population

BACKGROUND

During the current worldwide pandemic, coronavirus disease 2019 (Covid-19) was first diagnosed in Iceland at the end of February. However, data are limited on how SARS-CoV-2, the virus that causes Covid-19, enters and spreads in a population.

METHODS

We targeted testing to persons living in Iceland who were at high risk for infection (mainly those who were symptomatic, had recently traveled to high-risk countries, or had contact with infected persons). We also carried out population screening using two strategies: issuing an open invitation to 10,797 persons and sending random invitations to 2283 persons. We sequenced SARS-CoV-2 from 643 samples.

RESULTS

As of April 4, a total of 1221 of 9199 persons (13.3%) who were recruited for targeted testing had positive results for infection with SARS-CoV-2. Of those tested in the general population, 87 (0.8%) in the open-invitation screening and 13 (0.6%) in the random-population screening tested positive for the virus. In total, 6% of the population was screened. Most persons in the targeted-testing group who received positive tests early in the study had recently traveled internationally, in contrast to those who tested positive later in the study. Children under 10 years of age were less likely to receive a positive result than were persons 10 years of age or older, with percentages of 6.7% and 13.7%, respectively, for targeted testing; in the population screening, no child under 10 years of age had a positive result, as compared with 0.8% of those 10 years of age or older. Fewer females than males received positive results both in targeted testing (11.0% vs. 16.7%) and in population screening (0.6% vs. 0.9%). The haplotypes of the sequenced SARS-CoV-2 viruses were diverse and changed over time. The percentage of infected participants that was determined through population screening remained stable for the 20-day duration of screening.

CONCLUSIONS

In a population-based study in Iceland, children under 10 years of age and females had a lower incidence of SARS-CoV-2 infection than adolescents or adults and males. The proportion of infected persons identified through population screening did not change substantially during the screening period, which was consistent with a beneficial effect of containment efforts. (Funded by deCODE Genetics-Amgen.).

Reduction of antimicrobial resistant pneumococci seven years after introduction of pneumococcal vaccine in Iceland

Background

Penicillin non-susceptible (PNSP) and multi-resistant pneumococci have been prevalent in Iceland since early nineties, mainly causing problems in treatment of acute otitis media. The 10-valent protein conjugated pneumococcal vaccine (PHiD-CV) was introduced into the childhood vaccination program in 2011. The aim of the study was to investigate the changes in antimicrobial susceptibility and serotype distribution of penicillin non-susceptible pneumococci (PNSP) in Iceland 2011–2017.

Methods and findings

All pneumococcal isolates identified at the Landspítali University Hospital in 2011–2017, excluding isolates from the nasopharynx and throat were studied. Susceptibility testing was done according to the EUCAST guidelines using disk diffusion with chloramphenicol, erythromycin, clindamycin, tetracycline, trimethoprim/sulfamethoxazole and oxacillin for PNSP screening. Penicillin and ceftriaxone minimum inhibitory concentrations (MIC) were measured for oxacillin resistant isolates using the E-test. Serotyping was done using latex agglutination and/or multiplex PCR. The total number of pneumococcal isolates that met the study criteria was 1,706, of which 516 (30.2%) were PNSP, and declining with time. PNSP isolates of PHiD-CV vaccine serotypes (VT) were 362/516 (70.2%) declining with time, 132/143 (92.3%) in 2011 and 17/54 (31.5%) in 2017. PNSP were most commonly of serotype 19F, 317/516 isolates declining with time, 124/143 in 2011 and 15/54 in 2017. Their number decreased in all age groups, but mainly in the youngest children. PNSP isolates of non PHiD-CV vaccine serotypes (NVT) were 154/516, increasing with time, 11/14, in 2011 and 37/54 in 2017. The most common emerging NVTs in 2011 and 2017 were 6C, 1/143 and 10/54 respectively.

Conclusions

PNSP of VTs have virtually disappeared from children with pneumococcal diseases after the initiation of pneumococcal vaccination in Iceland and a clear herd effect was observed. This was mainly driven by a decrease of PNSP isolates belonging to a serotype 19F multi-resistant lineage. However, emerging multi-resistant NVT isolates are of concern.

Impact of the 10-valent pneumococcal conjugate vaccine on hospital admissions in children under three years of age in Iceland

INTRODUCTION

Pneumococcus is an important respiratory pathogen. The 10-valent pneumococcal vaccine (PHiD-CV) was introduced into the Icelandic vaccination programme in 2011. The aim was to estimate the impact of PHiD-CV on paediatric hospitalisations for respiratory tract infections and invasive disease.

METHODS

The 2005-2015 birth-cohorts were followed until three years of age and hospitalisations were recorded for invasive pneumococcal disease (IPD), meningitis, sepsis, pneumonia and otitis media. Hospitalisations for upper- and lower respiratory tract infections (URTI, LRTI) were used as comparators. The 2005-2010 birth-cohorts were defined as vaccine non-eligible cohorts (VNEC) and 2011-2015 birth-cohorts as vaccine eligible cohorts (VEC). Incidence rates (IR) were estimated for diagnoses, birth-cohorts and age groups, and incidence rate ratios (IRR) between VNEC and VEC were calculated assuming Poisson variance. Cox regression was used to estimate the hazard ratio (HR) of hospitalisation between VNEC and VEC.

RESULTS

51,264 children were followed for 142,315 person-years, accumulating 1,703 hospitalisations for the respective study diagnoses. Hospitalisations for pneumonia decreased by 20% (HR 0.80, 95%CI:0.67-0.95) despite a 32% increase in admissions for LRTI (HR 1.32, 95%CI:1.14-1.53). Hospital admissions for culture-confirmed IPD decreased by 93% (HR 0.07, 95%CI:0.01-0.50) and no hospitalisations for IPD with vaccine-type pneumococci were observed in the VEC. Hospitalisations for meningitis and sepsis did not change. A decrease in hospital admissions for otitis media was observed, but did not coincide with PHiD-CV introduction.

CONCLUSION

Following the introduction of PHiD-CV in Iceland, hospitalisations for pneumonia and culture confirmed IPD decreased. Admissions for other LRTIs and URTIs increased during this period.

MRSA outbreak in a tertiary neonatal intensive care unit in Iceland

Introduction: Preventing the spread of methicillin-resistant Staphylococcus aureus (MRSA) and understanding the pathophysiology and transmission is essential. This study describes an MRSA outbreak in a neonatal intensive care unit in Reykjavik, Iceland at a time where no screening procedures were active. Materials and methods: After isolating MRSA in the neonatal intensive care unit in 2015, neonates, staff members and parents of positive patients were screened and environmental samples collected. The study period was from 14 April 2015 until 31 August 2015. Antimicrobial susceptibility testing, spa-typing and whole genome sequencing were done on MRSA isolates. Results: During the study period, 96/143 admitted patients were screened for colonization. Non-screened infants had short admissions not including screening days. MRSA was isolated from nine infants and seven parents. All tested staff members were negative. Eight infants and six parents carried MRSA ST30-IVc with spa-type t253 and one infant and its parent carried MRSA CC9-IVa (spa-type t4845) while most environmental samples were MRSA CC9-IVa (spa-type t4845). Whole genome sequencing revealed close relatedness between all ST30-IVc and CC9-IVa isolates, respectively. All colonized infants received decolonization treatment, but 3/9 were still positive when last sampled. Discussion: The main outbreak source was a single MRSA ST30-IVc (spa-type t253), isolated for the first time in Iceland. A new CC9-IVa (spa-type t4845) was also identified, most abundant on environmental surfaces but only in one patient. The reason for the differences in the epidemiology of the two strains is not clear. The study highlights a need for screening procedures in high-risk settings and guidelines for neonatal decolonization.

Increase in tympanostomy tube placements despite pneumococcal vaccination, a population-based study

AIM

The aim was to estimate the impact of the 10-valent pneumococcal vaccine (PHiD-CV) on tympanostomy tube placements (TTP) in children under five years of age in Iceland.

METHODS

This population-based observational cohort study followed 11 consecutive birth-cohorts 2005-2015 from birth until their fifth birthday. Population registries were merged using national identification numbers. The risk of TTP was compared between birth-cohorts adjusted for the number of previous otitis media diagnoses and antimicrobial prescriptions. A Cox regression model was applied and the hazard ratio (HR) of TTP was estimated between each birth-cohort and the last vaccine non-eligible birth-cohort. The vaccine impact of PHiD-CV10 on TTP was estimated as 1-HR ×100%.

RESULTS

In total, 51 247 children were followed for 210 724 person-years, of which 14 351 underwent 20 373 procedures. The estimated vaccine impact on TTP was -6% (95% CI -16% to 2.7%). Children in the vaccine-eligible cohorts had fewer previous otitis media diagnoses and had been prescribed fewer antimicrobials prior to the procedure than children in the vaccine non-eligible cohorts.

CONCLUSION

Despite high uptake of PHiD-CV10, tympanostomy procedures increased in Iceland during the study period. Vaccine-eligible children had milder disease prior to the procedure. The reason underlying these findings are speculative.

Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions

Understanding the structure of a bacterial population is essential in order to understand bacterial evolution. Estimating the core genome (those genes common to all, or nearly all, strains of a species) is a key component of such analyses. The size and composition of the core genome varies by dataset, but we hypothesized that the variation between different collections of the same bacterial species would be minimal. To investigate this, we analyzed the genome sequences of 3,118 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (United States), and Maela (Thailand). The analyses revealed a “supercore” genome (genes shared by all 3,118 pneumococci) of 558 genes, although an additional 354 core genes were shared by pneumococci from Reykjavik, Southampton, and Boston. Overall, the size and composition of the core and pan-genomes among pneumococci recovered in Reykjavik, Southampton, and Boston were similar. Maela pneumococci were distinctly different in that they had a smaller core genome and larger pan-genome. The pan-genome of Maela pneumococci contained several >25 Kb sequence regions (flanked by pneumococcal genes) that were homologous to genomic regions found in other bacterial species. Overall, our work revealed that some subsets of the global pneumococcal population are highly heterogeneous, and our hypothesis was rejected. This is an important finding in terms of understanding genetic variation among pneumococci and is also an essential point of consideration before generalizing the findings from a single dataset to the wider pneumococcal population.

Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5405 pneumococcal genomes

The pneumococcus is a leading global pathogen and a key virulence factor possessed by the majority of pneumococci is an antigenic polysaccharide capsule (‘serotype’), which is encoded by the capsular (cps) locus. Approximately 100 different serotypes are known, but the extent of sequence diversity within the cps loci of individual serotypes is not well understood. Investigating serotype-specific sequence variation is crucial to the design of sequence-based serotyping methodology, understanding pneumococcal conjugate vaccine (PCV) effectiveness and the design of future PCVs. The availability of large genome datasets makes it possible to assess population-level variation among pneumococcal serotypes and in this study 5405 pneumococcal genomes were used to investigate cps locus diversity among 49 different serotypes. Pneumococci had been recovered between 1916 and 2014 from people of all ages living in 51 countries. Serotypes were deduced bioinformatically, cps locus sequences were extracted and variation was assessed within the cps locus, in the context of pneumococcal genetic lineages. Overall, cps locus sequence diversity varied markedly: low to moderate diversity was revealed among serogroups/types 1, 3, 7, 9, 11 and 22; whereas serogroups/types 6, 19, 23, 14, 15, 18, 33 and 35 displayed high diversity. Putative novel and/or hybrid cps loci were identified among all serogroups/types apart from 1, 3 and 9. This study demonstrated that cps locus sequence diversity varied widely between serogroups/types. Investigation of the biochemical structure of the polysaccharide capsule of major variants, particularly PCV-related serotypes and those that appear to be novel or hybrids, is warranted.

Impact of the 10-valent pneumococcal conjugate vaccine on antimicrobial prescriptions in young children: a whole population study

Background

Antimicrobial resistance is a public-health threat and antimicrobial consumption is the main contributor. The ten-valent pneumococcal conjugate vaccine (PHiD-CV10) was introduced into the Icelandic vaccination program in 2011.

The aim was to estimate the vaccine impact of PHiD-CV10 on outpatient antimicrobial prescriptions in children.

Methods

Eleven Icelandic birth-cohorts (2005–2015) were followed from birth until three years of age or to the end of the study period (December 31, 2016). Birth-cohorts were grouped as vaccine non-eligible (VNEC, 2005–2010) or vaccine eligible (VEC, 2011–2015). Data on primary care visits for respiratory infections and antimicrobial prescriptions were extracted from two national registers. Using national identification numbers, prescriptions were linked to physician visits if filled within three days of the visit. Incidence rates and incidence rate ratios between VNEC and VEC were calculated. An Andersen-Gill model was used to model the individual level data, accounting for repeated events and censoring. Vaccine impact was calculated as (1 – Hazard Ratio) × 100%.

Results

Included were 53,510 children who contributed 151,992 person-years of follow-up and filled 231,660 antimicrobial prescriptions. The incidence rate was significantly lower in the VEC compared to the VNEC, 144.5 and 157.2 prescriptions per 100 person-years respectively (IRR 0.92, 95%CI 0.91–0.93). Children in VEC were more likely to have filled zero (IRR 1.16 (95%CI 1.10–1.23) and 1–4 (IRR 1.08 95%CI 1.06–1.11) prescriptions compared to children in VNEC. The vaccine impact of PHiD-CV10 against all-cause antimicrobial prescriptions was 5.8% (95%CI 1.6–9.8%).When only considering acute otitis media-associated prescriptions, the vaccine impact was 21.8% (95%CI 11.5–30.9%).

Conclusion

The introduction of PHiD-CV10 lead to reduced antimicrobial use in children, mainly by reducing acute otitis media episodes. This intervention therefore reduces both disease burden and could slow the spread of antimicrobial resistance.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3416-y) contains supplementary material, which is available to authorized users.

Streptococcus pneumoniae: Antimicrobial Resistance and Serotypes of Strains Carried by Children and Causing Invasive Disease in the Faroe Islands

Knowledge about pneumococcal carriage, antibacterial resistance, serotype prevalence, and prevalence of invasive pneumococcal disease (IPD) after introduction of pneumococcal conjugate vaccines (PCVs) is lacking in the Faroe Islands. PCV-7 was introduced in 2008 and PCV-13 in 2010. The aim was to obtain knowledge on serotypes and antimicrobial resistance in pneumococci from carriage in children attending day-care centers (DCCs) and invasive isolates. Nasopharyngeal swabs were collected from 607 healthy children attending DCCs in the Faroe Islands in January to March in 2009, 2010, and 2011. Pneumococci were cultured selectively, tested for antibacterial susceptibility, and serotyped. Data from IPD isolates from 1974 to 2016 from the Department of Microbiology, National Hospital of the Faroe Islands, and typed and stored at Staten Serum Institute were also analyzed. Of the 607 screened children, 45% were pneumococcal carriers, 50% in 2009, 40% in 2010, and 42% in 2011. Antibiotic resistance in pneumococci was rare both in carriers and patients. Five penicillin nonsusceptible pneumococci were found in carriers (1.8%) and one among the invasive isolates (1.7%). The most common serotypes in carriage were 6B and 6A in 2009, serotype 3 and 6C in 2010, and serotype 11 and 6C in 2011. Serotype 6B was not found in 2011. The most common serotypes among IPD were 7F and 3. Pneumococcal carriage prevalence in healthy children attending DCCs in the Faroe Islands was low and antibacterial resistance was rare, compared with Iceland. The results suggest a possible serotype shift, reduction in antibacterial use, and PCV-7/13 serotype decrease in IPD after the introduction of pneumococcal vaccinations in children.

Incidence, Etiology, and Outcomes of Community-Acquired Pneumonia: A Population-Based Study

Background

The microbial etiology of community-acquired pneumonia (CAP) is often unclear in clinical practice, and previous studies have produced variable results. Population-based studies examining etiology and incidence are lacking. This study examined the incidence and etiology of CAP requiring hospitalization in a population-based cohort as well as risk factors and outcomes for specific etiologies.

Methods

Consecutive admissions due to CAP in Reykjavik, Iceland were studied. Etiologic testing was performed with cultures, urine-antigen detection, and polymerase chain reaction analysis of airway samples. Outcomes were length of stay, intensive care unit admission, assisted ventilation, and mortality.

Results

The inclusion rate was 95%. The incidence of CAP requiring hospitalization was 20.6 cases per 10000 adults/year. A potential pathogen was detected in 52% (164 of 310) of admissions and in 74% (43 of 58) with complete sample sets. Streptococcuspneumoniae was the most common pathogen (61 of 310, 20%; incidence: 4.1/10000). Viruses were identified in 15% (47 of 310; incidence: 3.1/10000), Mycoplasmapneumoniae were identified in 12% (36 of 310; incidence: 2.4/10000), and multiple pathogens were identified in 10% (30 of 310; incidence: 2.0/10000). Recent antimicrobial therapy was associated with increased detection of M pneumoniae (P < .001), whereas a lack of recent antimicrobial therapy was associated with increased detection of S pneumoniae (P = .02). Symptoms and outcomes were similar irrespective of microbial etiology.

Conclusions

Pneumococci, M pneumoniae, and viruses are the most common pathogens associated with CAP requiring hospital admission, and they all have a similar incidence that increases with age. Symptoms do not correlate with specific agents, and outcomes are similar irrespective of pathogens identified.

Antibacterial Susceptibilities of Escherichia coli from Community-Acquired Urinary Tract Infections in the Faroe Islands, Associations with Antibacterial Sales, and Comparison with Iceland and Denmark

Currently, data on Escherichia coli antibacterial susceptibilities in the Faroe Islands are lacking. The aim was to investigate the antibacterial susceptibilities of E. coli from patients with community-acquired urinary tract infections in the Faroe Islands, correlate with antibacterial sales, and compare with Iceland and Denmark. From 2009 to 2010 and in 2012, 12 general practitioners from the Faroe Islands were recruited to provide urine samples from patients. Antibacterial susceptibilities were determined by disc diffusion testing according to the Clinical and Laboratory Standards Institute methods and criteria. Logistic regression (quasibinomial) of the antibacterial resistance proportions versus mean sales during the period of 2008-2011 was used to determine association. Nonsusceptibility to at least 1 of the 14 antibacterial drugs investigated was found in 54% of the E. coli isolates and was most common to ampicillin (46%), followed by sulfamethoxazole (39%), trimethoprim (27%), trimethoprim/sulfamethoxazole (27%), and <10% to the remaining 10 antibiotics. The resistance prevalence did not change significantly with time. From logistic regression modeling, we find significant associations between antibacterial mean sales and antibacterial resistances. For the resistances in the Faroe Islands compared with data from Denmark and Iceland, we infer two groups of resistances indicating different responses-one steep and one gradual-to antibacterial sales. For these two groups, we find β₁ = 4.77 (Std. Error = 0.624, p-value = 0.002) and β₁ = 0.26 (Std. Error = 0.020, p-value = 4e-7) for the steep and gradual groups, respectively. This knowledge can potentially be used to predict and control the future increase in E. coli resistance with antibacterial sales.

Utility of oropharyngeal real-time PCR for S. pneumoniae and H. influenzae for diagnosis of pneumonia in adults

A lack of sensitive tests and difficulties obtaining representative samples contribute to the challenge in identifying etiology in pneumonia. Upper respiratory tract swabs can be easily collected and analyzed with real-time PCR (rtPCR). Common pathogens such as S. pneumoniae and H. influenzae can both colonize and infect the respiratory tract, complicating the interpretation of positive results. Oropharyngeal swabs were collected (n = 239) prospectively from adults admitted to hospital with pneumonia. Analysis with rtPCR targeting S. pneumoniae and H. influenzae was performed and results compared with sputum cultures, blood cultures, and urine antigen testing for S. pneumoniae. Different Ct cutoff values were applied to positive tests to discern colonization from infection. Comparing rtPCR with conventional testing for S. pneumoniae in patients with all tests available (n = 57) resulted in: sensitivity 87 %, specificity 79 %, PPV 59 % and NPV 94 %, and for H. influenzae (n = 67): sensitivity 75 %, specificity 80 %, PPV 45 % and NPV 94 %. When patients with prior antimicrobial exposure were excluded sensitivity improved: 92 % for S. pneumoniae and 80 % for H. influenzae. Receiver operating characteristic curve analysis demonstrated for S. pneumoniae: AUC = 0.65 (95 % CI 0.51-0.80) and for H. influenzae: AUC = 0.86 (95 % CI 0.72-1.00). Analysis of oropharyngeal swabs using rtPCR proved both reasonably sensitive and specific for diagnosing pneumonia caused by S. pneumoniae and H. influenzae. This method may be a useful diagnostic adjunct to other methods and of special value in patients unable to provide representative lower airway samples.

Comparison of Serotype Prevalence of Pneumococci Isolated from Middle Ear, Lower Respiratory Tract and Invasive Disease Prior to Vaccination in Iceland

Background

Information on pneumococcal serotype distribution before vaccination is a prerequisite for evaluation of vaccine effect. The aim was to investigate the prevalence of pneumococcal serotypes isolated from middle ear (ME), lower respiratory tract (LRT) and from invasive disease (IPD) in Iceland prior to implementation of ten-valent pneumococcal Haemophilus influenzae protein D conjugate vaccine (PHiD-CV-10) into the infant vaccination program (April 2011).

Methods and findings

All isolates cultured 2007–2011 from ME, LRT and IPD identified as pneumococci were serotyped and tested for susceptibility at the Clinical Microbiology Department, Landspitali University Hospital that serves approximately 85% of the Icelandic population. Pneumococcal isolates were 1711 and 1616 (94.4%) were available for serotyping and included. Isolates belonging to PHiD-CV10 serotypes (VTs) were 1052 (65.1%). Isolates from ME were 879 (54.4%), with 639 (72.7%) from 0–1 year old patients and 651 of VTs (74%). Isolates from LRT were 564 (34.9%), with 292 (51.8%) from ≥65 years old patients, and 300 (53.2%) of VTs. IPD isolates were 173 (10.7%), although more evenly distributed according to age than isolates from the other sites most were from adults and the youngest age group,101 (58.4%) isolates were of VTs. The most common serotype was 19F, 583 (36.1%). Its prevalence was highest in ME, 400 (45.5%), 172 (30.5%) in LRT and 11 isolates (6.4%), in IPD. Penicillin non-susceptible isolates were 651 (40.3%), mainly belonging to VTs, 611 (93.9%), including 535 (82.2%) of 19F.

Conclusions

Multiresistant isolates of serotype 19F were highly prevalent, especially from ME of young children but also from LRT of adults. Serotype 14 was the most common serotype in IPD. The rate of VTs was high and almost all PNSP were of VTs. There was great difference in vaccine coverage between sampling sites, also reflecting difference in vaccine coverage by age groups.

HLA class II sequence variants influence tuberculosis risk in populations of European ancestry

Mycobacterium tuberculosis infections cause 9 million new tuberculosis cases and 1.5 million deaths annually. To identify variants conferring risk of tuberculosis, we tested 28.3 million variants identified through whole-genome sequencing of 2,636 Icelanders for association with tuberculosis (8,162 cases and 277,643 controls), pulmonary tuberculosis (PTB) and M. tuberculosis infection. We found association of three variants in the region harboring genes encoding the class II human leukocyte antigens (HLAs): rs557011[T] (minor allele frequency (MAF) = 40.2%), associated with M. tuberculosis infection (odds ratio (OR) = 1.14, P = 3.1 × 10(-13)) and PTB (OR = 1.25, P = 5.8 × 10(-12)), and rs9271378[G] (MAF = 32.5%), associated with PTB (OR = 0.78, P = 2.5 × 10(-12))--both located between HLA-DQA1 and HLA-DRB1--and a missense variant encoding p.Ala210Thr in HLA-DQA1 (MAF = 19.1%, rs9272785), associated with M. tuberculosis infection (P = 9.3 × 10(-9), OR = 1.14). We replicated association of these variants with PTB in samples of European ancestry from Russia and Croatia (P < 5.9 × 10(-4)). These findings show that the HLA class II region contributes to genetic risk of tuberculosis, possibly through reduced presentation of protective M. tuberculosis antigens to T cells.

Antibacterial resistance in Streptococcus pyogenes (GAS) from healthy carriers and tonsillitis patients and association with antibacterial sale in the Faroe Islands

The aim of this study was to investigate the antibacterial resistance of Streptococcus pyogenes (GAS), and correlate the findings with the sales of erythromycin and tetracycline. General practitioners in the Faroe Islands were recruited to send oropharyngeal swabs. From an ongoing pneumococcal study, nasopharyngeal swabs were sampled from healthy children 0-7 years of age. Erythromycin susceptibility data from Iceland were obtained from the reference laboratory at the Landspitali University Hospital. Susceptibility testing in the Faroe Islands and Iceland was performed according to CLSI methods and criteria. The resistance rate to erythromycin and tetracycline found in patients in the Faroe Islands in 2009/2010 was 6% and 30% respectively. Tetracycline resistance in patients declined significantly from 2009 to 2010 (37-10%, p-value = 0.006 < 0.05) and differed significantly between age groups (p-value = 0.03 < 0.05). In Iceland, there was a peak in erythromycin resistance in 2008 (44%) and a substantial decrease in 2009 (5%). Although the prevalence of erythromycin and tetracycline resistance in the Faroe Islands and Iceland may be associated with antimicrobial use, sudden changes can occur with the introduction of new resistant clones.

Changing epidemiology of group B streptococcal infections among adults in Iceland: 1975-2014

We studied the bacterial characteristics and incidence of invasive infections caused by group B streptococci (GBS) in adults in Iceland in 1975-2014. A total of 145 isolates were characterized by serotyping, antimicrobial susceptibility, multilocus sequence typing and surface protein gene profiling. Disease incidence increased during the studied period (p <0.001), reaching 2.17 cases/100 000 person-years in 2013-14. Overall, serotype Ia was the most frequently found (23%), but serotypes Ib, II, III and V showed similar prevalence (14%-17%). Although there were notable changes in the proportion of most serotypes during the study period, only the decline of serotype III was statistically supported (p = 0.003) and was reflected in a decrease of clonal complexes CC17 and CC19 that included most serotype III isolates (p <0.04). On the other hand, the increase in frequency of CC1 was caused by two lineages expressing distinct serotypes: ST1/V/alp3 and ST196/IV/eps. Underlying the relative stability of serotype Ia were major changes in the lineages expressing this serotype, with an increase in the relative importance of CC23, including both ST23/Ia/eps and ST24/Ia/bca lineages, and a decrease in CC7. Nine cases of invasive GBS disease were caused by ST7, of possible zoonotic origin. All isolates were susceptible to penicillin. Rates of erythromycin and clindamycin resistance were 8.3% and 9.7%, respectively. An over-representation of resistance solely to clindamycin was associated with the unusual lsaC gene and serotype III ST19/rib lineage (p <0.001).

A molecular trigger for intercontinental epidemics of group A Streptococcus

The identification of the molecular events responsible for strain emergence, enhanced virulence, and epidemicity has been a long-pursued goal in infectious diseases research. A recent analysis of 3,615 genomes of serotype M1 group A Streptococcus strains (the so-called "flesh-eating" bacterium) identified a recombination event that coincides with the global M1 pandemic beginning in the early 1980s. Here, we have shown that the allelic variation that results from this recombination event, which replaces the chromosomal region encoding secreted NADase and streptolysin O, is the key driver of increased toxin production and enhanced infection severity of the M1 pandemic strains. Using isoallelic mutant strains, we found that 3 polymorphisms in this toxin gene region increase resistance to killing by human polymorphonuclear leukocytes, increase bacterial proliferation, and increase virulence in animal models of pharyngitis and necrotizing fasciitis. Genome sequencing of an additional 1,125 streptococcal strains and virulence studies revealed that a highly similar recombinational replacement event underlies an ongoing intercontinental epidemic of serotype M89 group A Streptococcus infections. By identifying the molecular changes that enhance upper respiratory tract fitness, increased resistance to innate immunity, and increased tissue destruction, we describe a mechanism that underpins epidemic streptococcal infections, which have affected many millions of people.

[Infection risks associated with importation of fresh food in Iceland]

Access to safe food is a privilege for people living in Iceland. Rapid increase in antimicrobial resistance, related to factory farming and antimicrobial use in agriculture, is a major threat to public health. Increasing food trade between countries and continents facilitates global spread of pathogens and resistance. Icelandic agriculture has benefitted from its isolation and small size. After interventions to reduce the prevalence of Campylobacter and Salmonella at poultry farms, the incidence of human campylobacteriolsis is 17-43/100.000, of which about half is domestically acquired and Salmonella infections 10-15/100.000 mainly acquired abroad. Since Enterohaemorrhagic E. coli (EHEC) has not been detected in domestic cattle, the low incidence of infections is not surprising (0-0.6/100.000/year). A recent outbreak due to a multiresistant EHEC strain was traced to imported lettuce. Antimicrobial use in Icelandic agriculture is among the lowest in Europe and domestic infections caused by Salmonella and Campylobacter are rarely caused by resistant strains. Carbapenemase producing Enterobacteriaceae have not been found in Iceland. Low use of antimicrobials in Icelandic agriculture and actions to limit the spread of Campylobacter and Salmonella have been successful. The public should be informed of the importance of the origin of food and that Icelandic food products are among the safest.

Prevalence of pilus genes in pneumococci isolated from healthy preschool children in Iceland: association with vaccine serotypes and antibiotic resistance

OBJECTIVES

The objective of this study was to investigate the prevalence of pilus islets [pilus islet 1 (PI-1) and pilus islet 2 (PI-2)] in pneumococcal isolates from healthy Icelandic preschool children attending day care centres, prior to the introduction of conjugated pneumococcal vaccine, and the association of the pilus islets with vaccine serotypes and antibiotic resistance.

METHODS

Nasopharyngeal swabs were collected from 516 healthy children attending day care centres in Reykjavik in March and April 2009. Infant vaccination was started in 2011, thus the great majority of the children were unvaccinated. Pneumococci were cultured selectively, tested for antimicrobial susceptibility and serotyped. The presence of PI-1 and PI-2 was detected using PCR.

RESULTS

A total of 398 viable isolates were obtained of which 134 (33.7%) showed the presence of PI-1. PI-1-positive isolates were most often seen in serotype 19F [30/31 (96.8%)] and were of clade I, and in 6B [48/58 (82.8%)] of clade II. PI-2-positive isolates were most common in serotype 19F [27/31 (87.1%)]; all of them were also PI-1 positive. Of the PI-1-positive and PI-2-positive isolates, 118 (88.1%) and 31 (81.6%), respectively, were of vaccine serotypes. Both PI-1 and PI-2 were more often present in penicillin-non-susceptible pneumococci (PNSP) than in penicillin-susceptible pneumococci [PI-1 in 41/58 (70.7%) and 93/340 (27.4%), respectively, and PI-2 in 28/58 (48.3%) and 10/340 (2.9%), respectively].

CONCLUSIONS

Genes for PI-1 and/or PI-2 in pneumococci isolated from healthy Icelandic children are mainly found in isolates of vaccine serotypes and in PNSP isolates belonging to multiresistant international clones that have been endemic in the country.

Mortality in healthcare-associated pneumonia in a low resistance setting: a prospective observational study

BACKGROUND

The classification of pneumonia as community-acquired pneumonia (CAP) or healthcare-associated pneumonia (HCAP) has implications for selection of initial antimicrobial therapy. HCAP has been associated with an increased prevalence of multidrug-resistant (MDR) pathogens and with high mortality leading to recommendations for broad empiric therapy.

METHODS

We performed a prospective, population-based study on consecutive adults (≥ 18 years) admitted for pneumonia over 1 calendar year. Patients were classified by pneumonia type and severity. Microbial etiologic testing was performed on all patients. Treatment, length of stay, and mortality rates were compared.

RESULTS

A total of 373 admissions were included, 94% of all eligible patients. They were classified as CAP (n = 236, 63%) or HCAP (n = 137, 37%). Chronic underlying disease was more commonly found among patients with HCAP compared with CAP (74% vs 51%, p < 0.001). Mycoplasma pneumoniae was more common among CAP patients (p < 0.01), while gram-negative bacteria were more often found among HCAP patients (p = 0.02). No MDR pathogens were detected, and rates of Staphylococcus aureus were similar in the two groups. HCAP patients were not more likely to receive ineffective initial antimicrobial therapy. HCAP patients had worse prognostic scores on admission and higher in-house mortality than CAP patients (10% vs 1%, respectively, p < 0.01).

CONCLUSIONS

Even in a low resistance setting, patients with HCAP have increased mortality compared with patients with CAP. This is most likely explained by a higher prevalence of co-morbidities. Our data do not support broad-spectrum empiric antibiotic therapy for HCAP.

Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone

BACKGROUND

Pneumococcal β-lactam resistance was first detected in Iceland in the late 1980s, and subsequently peaked at almost 25% of clinical isolates in the mid-1990s largely due to the spread of the internationally-disseminated multidrug-resistant PMEN2 (or Spain6B-2) clone of Streptococcus pneumoniae.

RESULTS

Whole genome sequencing of an international collection of 189 isolates estimated that PMEN2 emerged around the late 1960s, developing resistance through multiple homologous recombinations and the acquisition of a Tn5253-type integrative and conjugative element (ICE). Two distinct clades entered Iceland in the 1980s, one of which had acquired a macrolide resistance cassette and was estimated to have risen sharply in its prevalence by coalescent analysis. Transmission within the island appeared to mainly emanate from Reykjavík and the Southern Peninsular, with evolution of the bacteria effectively clonal, mainly due to a prophage disrupting a gene necessary for genetic transformation in many isolates. A subsequent decline in PMEN2's prevalence in Iceland coincided with a nationwide campaign that reduced dispensing of antibiotics to children in an attempt to limit its spread. Specific mutations causing inactivation or loss of ICE-borne resistance genes were identified from the genome sequences of isolates that reverted to drug susceptible phenotypes around this time. Phylogenetic analysis revealed some of these occurred on multiple occasions in parallel, suggesting they may have been at least temporarily advantageous. However, alteration of 'core' sequences associated with resistance was precluded by the absence of any substantial homologous recombination events.

CONCLUSIONS

PMEN2's clonal evolution was successful over the short-term in a limited geographical region, but its inability to alter major antigens or 'core' gene sequences associated with resistance may have prevented persistence over longer timespans.

Invasive infections due to Streptococcus pyogenes: seasonal variation of severity and clinical characteristics, Iceland, 1975 to 2012

Epidemiology and clinical characteristics of invasive Group A streptococcal infections (IGASI) are highly variable. Long-term studies are needed to understand the interplay between epidemiology and virulence. In a population-based study of IGASI in Iceland from 1975 to 2012, 288 cases were identified by positive cultures from normally sterile body sites. Charts were reviewed retrospectively and emm-types of viable Streptococcus pyogenes isolates (n=226) determined. Comparing the first and last decade of the study period, IGASI incidence increased from 1.09 to 3.96 cases per 100,000 inhabitants per year. The most common were emm types 1 (25%), 28 (11%) and 89 (11%); emm1 strains were most likely to cause severe infections. Infections in adults were significantly more likely to be severe during the seasonal peak from January to April (risk ratio: 2.36, 95% confidence interval: 1.34–4.15). Significant seasonal variability in severity was noted among patients with diagnosis of sepsis, respiratory infection and cellulitis, with 38% of severe infections in January to April compared with 16% in other months (p<0.01). A seasonal increase in severity of IGASI suggested that generalised seasonal increase in host susceptibility, rather than introduction of more virulent strains may play a role in the pathogenesis of these potentially fatal infections.

Invasive infections due to Streptococcus pyogenes: seasonal variation of severity and clinical characteristics, Iceland, 1975 to 2012

Epidemiology and clinical characteristics of invasive Group A streptococcal infections (IGASI) are highly variable. Long-term studies are needed to understand the interplay between epidemiology and virulence. In a population-based study of IGASI in Iceland from 1975 to 2012, 288 cases were identified by positive cultures from normally sterile body sites. Charts were reviewed retrospectively and emm-types of viable Streptococcus pyogenes isolates (n=226) determined. Comparing the first and last decade of the study period, IGASI incidence increased from 1.09 to 3.96 cases per 100,000 inhabitants per year. The most common were emm types 1 (25%), 28 (11%) and 89 (11%); emm1 strains were most likely to cause severe infections. Infections in adults were significantly more likely to be severe during the seasonal peak from January to April (risk ratio: 2.36, 95% confidence interval: 1.34–4.15). Significant seasonal variability in severity was noted among patients with diagnosis of sepsis, respiratory infection and cellulitis, with 38% of severe infections in January to April compared with 16% in other months (p<0.01). A seasonal increase in severity of IGASI suggested that generalised seasonal increase in host susceptibility, rather than introduction of more virulent strains may play a role in the pathogenesis of these potentially fatal infections.

Epidemiology of penicillin-non-susceptible pneumococci in Iceland, 1995-2010

OBJECTIVES

The first penicillin-non-susceptible pneumococci (PNSP) were identified in Iceland in 1988. A rapid increase followed, associated with expansion of a single multiresistant clone, Spain(6B)-2, peaking at 19.8% in 1993. After interventions led to reduced antimicrobial use in children, the prevalence of PNSP decreased until 1995. The aim of this study was to follow the evolution of PNSP from 1995 to 2010, the period preceding the introduction of conjugated pneumococcal vaccines into the vaccination programme.

METHODS

The laboratory at the Landspitali University Hospital serves ∼ 85% of the Icelandic population. All pneumococci isolated from 1995 to 2010 (n = 13,937) were stored (-80 °C). Oxacillin-resistant isolates were serotyped and penicillin MICs were determined. Selected strains were genotyped by PFGE and multilocus sequence typing.

RESULTS

In 1995, the rate of PNSP was 24.2%, declining to 13.6% in 2001, and then increasing to 38.6% in 2010. Similar changes were observed for resistance to erythromycin and tetracycline. In 1995, 60.7% of PNSP were serotype 6B, mainly the Spain(6B)-2 clone, declining to 5.7% in 2010. PNSP of serotype 19F rapidly increased after 2004 to comprise 85.8% of all serogrouped PNSP in 2010, with most isolates belonging to a single multiresistant PFGE clone identified as sequence type (ST) 271 and ST1968, representing single- and double-locus variants of the international clone Taiwan(19F)-14, respectively. PNSP were most common among young children, from the nasopharynx, middle ear and lower respiratory tract.

CONCLUSIONS

The epidemiology of PNSP was dominated by two multiresistant clones. The second expanded rapidly when the first one was disappearing, causing higher antibiotic resistance rates among pneumococci than seen before in Iceland.

Does hygiene intervention at day care centres reduce infectious illnesses in children? An intervention cohort study

BACKGROUND

Day care attendance is a major risk factor for respiratory and gastrointestinal illnesses in preschool children. In this study, we describe the results of a hygiene intervention cohort trial at day care centres (DCCs) on the rates of febrile, respiratory, and gastrointestinal illnesses in preschool children.

METHODS

Thirty DCCs in 2 communities were included. The number of illness episodes was registered for each child every 6 months, as well as potential risk factors. The hygiene intervention was introduced in half of the DCCs and the results analysed using a multivariate mixed effects hierarchical Poisson regression model.

RESULTS

The study lasted 2.5 y, of which the hygiene intervention lasted 1.5 y. Two thousand three hundred and forty-nine children participated, delivering 2832 person-y. Adjusted incidence rate ratios of the illnesses at the intervention and non-intervention DCCs were not significantly different for any of the illnesses. The intervention was not more effective in children less than 3 y of age than in older children and no significant effects were seen with time. Compliance with the hygiene protocol was good as measured by the use of hygiene products and by a survey among the staff at the DCCs.

CONCLUSIONS

The most likely explanation for the lack of effects of the intervention is that the baseline standard of hygiene at the DCCs was probably too high for the intervention to demonstrate significant results, but recall bias cannot be excluded. Even though hygiene is important for minimizing the spread of microbes at DCCs, other risk factors need to be studied.

Pneumococcal capsular switching: a historical perspective

Background.Changes in serotype prevalence among pneumococcal populations result from both serotype replacement and serotype (capsular) switching. Temporal changes in serotype distributions are well documented, but the contribution of capsular switching to such changes is unknown. Furthermore, it is unclear to what extent vaccine-induced selective pressures drive capsular switching.

Methods.Serotype and multilocus sequence typing data for 426 pneumococci dated from 1937 through 2007 were analyzed. Whole-genome sequence data for a subset of isolates were used to investigate capsular switching events.

Results.We identified 36 independent capsular switch events, 18 of which were explored in detail with whole-genome sequence data. Recombination fragment lengths were estimated for 11 events and ranged from approximately 19.0 kb to ≥58.2 kb. Two events took place no later than 1960, and the imported DNA included the capsular locus and the nearby penicillin-binding protein genes pbp2x and pbp1a.

Conclusions.Capsular switching has been a regular occurrence among pneumococcal populations throughout the past 7 decades. Recombination of large DNA fragments (>30 kb), sometimes including the capsular locus and penicillin-binding protein genes, predated both vaccine introduction and widespread antibiotic use. This type of recombination has likely been an intrinsic feature throughout the history of pneumococcal evolution.

The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success

BACKGROUND

Streptococcus pneumoniae, also called the pneumococcus, is a major bacterial pathogen. Since its introduction in the 1940s, penicillin has been the primary treatment for pneumococcal diseases. Penicillin resistance rapidly increased among pneumococci over the past 30 years, and one particular multidrug-resistant clone, PMEN1, became highly prevalent globally. We studied a collection of 426 pneumococci isolated between 1937 and 2007 to better understand the evolution of penicillin resistance within this species.

RESULTS

We discovered that one of the earliest known penicillin-nonsusceptible pneumococci, recovered in 1967 from Australia, was the likely ancestor of PMEN1, since approximately 95% of coding sequences identified within its genome were highly similar to those of PMEN1. The regions of the PMEN1 genome that differed from the ancestor contained genes associated with antibiotic resistance, transmission and virulence. We also revealed that PMEN1 was uniquely promiscuous with its DNA, donating penicillin-resistance genes and sometimes many other genes associated with antibiotic resistance, virulence and cell adherence to many genotypically diverse pneumococci. In particular, we describe two strains in which up to 10% of the PMEN1 genome was acquired in multiple fragments, some as long as 32 kb, distributed around the recipient genomes. This type of directional genetic promiscuity from a single clone to numerous unrelated clones has, to our knowledge, never before been described.

CONCLUSIONS

These findings suggest that PMEN1 is a paradigm of genetic success both through its epidemiology and promiscuity. These findings also challenge the existing views about horizontal gene transfer among pneumococci.

Clinical significance of Staphylococcus aureus bacteriuria in a nationwide study of adults with S. aureus bacteraemia

OBJECTIVES

To evaluate the clinical significance of Staphylococcus aureus bacteriuria (SABU) in adults with S. aureus bacteraemia (SAB).

METHODS

All individuals ≥18 years old diagnosed with SAB in Iceland between December 1st 2003 and November 30th 2008 were retrospectively identified. Data was collected from medical records. Concomitant SABU was defined as growth of S. aureus in a urine sample taken within 24 h of the index blood culture.

RESULTS

SABU was seen in 27 of 166 (16.3%) SAB patients having urine cultured before administration of antibiotics, but after excluding those with SAB of urinary tract origin SABU was seen in 16 of 152 (10.5%). In this latter cohort SABU was independently associated with having endocarditis (RR 6.68; 95% CI 1.53-17.3) and admission to intensive-care unit (RR 2.84; 95% CI 1.25-4.44), while for having complicated SAB the RR was 1.56 (95% CI 0.96-1.80). No correlation was seen with mortality or relapse rates.

CONCLUSIONS

SABU appears to be secondary to SAB in some cases while it is the primary infection causing SAB in others. In patients with SAB of non-urinary tract origin SABU should probably be regarded as distant haematogenous seeding and a marker of deep tissue dissemination, thus affecting general management and treatment duration.

Staphylococcus aureus bacteraemia--Nationwide assessment of treatment adequacy and outcome

OBJECTIVES

To assess the treatment adequacy for Staphylococcus aureus bacteraemia (SAB) and its association with outcome on a whole population basis.

METHODS

All individuals ≥18 years old diagnosed with SAB in Iceland between December 1 2003 and November 30 2008 were retrospectively identified. Clinical data was collected from medical records and adequacy of antibiotic treatment based on antibiotic choice, dose, administration route and treatment duration.

RESULTS

Empirical therapy was considered adequate in 262 of 325 (81%) SAB episodes, with no correlation to outcome. The complete antibiotic treatment was deemed adequate in 147 of 279 (53%) episodes. Among patients with complicated SAB median duration of active intravenous therapy was 14 days in those experiencing relapse compared to 30 days in patients without relapse (p = 0.03). No patient died after completing adequate treatment compared to 4 (3.0%) following inadequate therapy (p = 0.01). Despite no overall change being seen in antibiotic treatment, 30-day mortality decreased from 25.0 to 6.8% from first to last year of study (p = 0.001).

CONCLUSION

Appropriate antibiotic therapy for SAB was associated with lower relapse rates and mortality. Although treatment adequacy was regarded as insufficient in half of cases, mortality of SAB in Iceland is amongst the lowest recorded.

SUMMARY

In a national study of S. aureus bacteraemia the antibiotic treatment was judged inadequate in 53% of episodes, while appropriate treatment was associated with lower relapse rate and mortality. Despite this, the mortality in Iceland is among the lowest reported.

Bacteraemia in children in Iceland 1994-2005

AIM

To investigate the aetiology of bacteraemia in children in Iceland, the antibiotic resistance and possible preventive measures.

METHODS

All positive bacterial blood cultures from children 0-18 years old isolated at Landspítali University Hospital Iceland from 1994 to 2005 were included in the study. Epidemiological and microbiological data were registered. The blood cultures were categorized according to likelihood of infection or contamination.

RESULTS

During the study period 1253 positive blood cultures were obtained from 974 children; 647 from boys and 606 from girls. Positive blood cultures were most common during the first year of life (594; 47.4%) with 252 of them from neonates. Coagulase negative staphylococci were most common (37%). Of probable or definite infections Streptococcus pneumoniae was the most common (19.3%) followed by Staphylococcus aureus (17.6%) and Neisseria meningitidis (13.5%). The most common pneumococcal serogroups were 23, 6, 7, 19 and 14. Commercially available vaccines contain up to 88% of all pneumococcal strains and 67% of all multi-resistant strains. N. meningitidis group C was not isolated after vaccinations were started in 2002.

CONCLUSION

Our study provides important epidemiological data on bacterial bloodstream infections in children in Iceland. The results demonstrate the excellent efficacy of meningococcal group C vaccination.

Broiler chickens as source of human fluoroquinolone-resistant Escherichia coli, Iceland

To investigate feed as a source for fluoroquinolone-resistant Escherichia coli in broiler chickens, we compared antimicrobial drug–resistant E. coli from broiler feed and broilers with ciprofloxacin-resistant human clinical isolates by using pulsed-field gel electrophoresis. Feed was implicated as a source for ciprofloxacin-resistant broiler-derived E. coli and broilers as a source for ciprofloxacin-resistant human-derived E. coli.