Outbreak of invasive Streptococcus pneumoniae serotype 12F among a marginalized inner-city population in Winnipeg, Canada, 2009-2011

Invasive Pneumococcal Disease and Potential Impact of Pneumococcal Conjugate Vaccines Among Adults, Including Persons Experiencing Homelessness-Alaska, 2011-2020

BACKGROUND

Adults aged ≥65 years, adults with certain underlying medical conditions, and persons experiencing homelessness are at increased risk for invasive pneumococcal disease (IPD). Two new pneumococcal conjugate vaccines, 15-valent pneumococcal conjugate vaccine (PCV15) and 20-valent pneumococcal conjugate vaccine (PCV20), were recently approved for use in US adults. We describe the epidemiology of IPD among Alaska adults and estimate the proportion of IPD cases potentially preventable by new vaccines.

METHODS

We used statewide, laboratory-based surveillance data to calculate and compare IPD incidence rates and 95% confidence intervals (CIs) among Alaska adults aged ≥18 years during 2011-2020 and estimate the proportion of IPD cases that were caused by serotypes in PCV15 and PCV20.

RESULTS

During 2011-2020, 1164 IPD cases were reported among Alaska adults for an average annual incidence of 21.3 cases per 100 000 adults per year (95% CI, 20.1-22.5). Incidence increased significantly during the study period (P < .01). IPD incidence among Alaska Native adults was 4.7 times higher than among non-Alaska Native adults (95% CI, 4.2-5.2). Among adults experiencing homelessness in Anchorage, IPD incidence was 72 times higher than in the general adult population (95% CI, 59-89). Overall, 1032 (89%) Alaska adults with IPD had an indication for pneumococcal vaccine according to updated vaccination guidelines; 456 (39%) and 700 (60%) cases were caused by serotypes in PCV15 and PCV20, respectively.

CONCLUSIONS

Use of PCV15 and PCV20 could substantially reduce IPD among adults in Alaska, including Alaska Native adults and adults experiencing homelessness.

Genomic investigation of the most common Streptococcus pneumoniae serotypes causing invasive infections in Canada: the SAVE study, 2011-2020

OBJECTIVES

To investigate the lineages and genomic antimicrobial resistance (AMR) determinants of the 10 most common pneumococcal serotypes identified in Canada during the five most recent years of the SAVE study, in the context of the 10-year post-PCV13 period in Canada.

METHODS

The 10 most common invasive Streptococcus pneumoniae serotypes collected by the SAVE study from 2016 to 2020 were 3, 22F, 9N, 8, 4, 12F, 19A, 33F, 23A and 15A. A random sample comprising ∼5% of each of these serotypes collected during each year of the full SAVE study (2011-2020) were selected for whole-genome sequencing (WGS) using the Illumina NextSeq platform. Phylogenomic analysis was performed using the SNVPhyl pipeline. WGS data were used to identify virulence genes of interest, sequence types, global pneumococcal sequence clusters (GPSC) and AMR determinants.

RESULTS

Of the 10 serotypes analysed in this study, six increased significantly in prevalence from 2011 to 2020: 3, 4, 8, 9N, 23A and 33F (P ≤ 0.0201). Serotypes 12F and 15A remained stable in prevalence over time, while serotype 19A decreased in prevalence (P < 0.0001). The investigated serotypes represented four of the most prevalent international lineages causing non-vaccine serotype pneumococcal disease in the PCV13 era: GPSC3 (serotypes 8/33F), GPSC19 (22F), GPSC5 (23A) and GPSC26 (12F). Of these lineages, GPSC5 isolates were found to consistently possess the most AMR determinants. Commonly collected vaccine serotypes 3 and 4 were associated with GPSC12 and GPSC27, respectively. However, a more recently collected lineage of serotype 4 (GPSC192) was highly clonal and possessed AMR determinants.

CONCLUSIONS

Continued genomic surveillance of S. pneumoniae in Canada is essential to monitor for the appearance of new and evolving lineages, including antimicrobial-resistant GPSC5 and GPSC162.

Distribution of Serotypes Causing Invasive Pneumococcal Disease in Children From High-Income Countries and the Impact of Pediatric Pneumococcal Vaccination

BACKGROUND

The introduction and adoption of pneumococcal conjugate vaccines (PCVs) into pediatric national immunization programs (NIPs) has led to large decreases in invasive pneumococcal disease (IPD) incidence caused by vaccine serotypes. Despite these reductions, the global IPD burden in children remains significant.

METHODS

We collected serotype-specific IPD data from surveillance systems or hospital networks of all 30 high-income countries that met inclusion criteria. Data sources included online databases, surveillance system reports, and peer-reviewed literature. Percentage of serotyped cases covered were calculated for all countries combined and by PCV type in the pediatric NIP.

RESULTS

We identified 8012 serotyped IPD cases in children <5 or ≤5 years old. PCV13 serotype IPD caused 37.4% of total IPD cases, including 57.1% and 25.2% for countries with PCV10 or PCV13 in the pediatric NIP, respectively, most commonly due to serotypes 3 and 19A (11.4% and 13.3%, respectively, across all countries). In PCV10 countries, PCV15 and PCV20 would cover an additional 45.1% and 55.6% of IPD beyond serotypes contained in PCV10, largely due to coverage of serotype 19A. In PCV13 countries, PCV15 and PCV20 would cover an additional 10.6% and 38.2% of IPD beyond serotypes contained in PCV13. The most common IPD serotypes covered by higher valency PCVs were 10A (5.2%), 12F (5.1%), and 22F and 33F (3.5% each).

CONCLUSIONS

Much of the remaining IPD burden is due to serotypes included in PCV15 and PCV20. The inclusion of these next generation PCVs into existing pediatric NIPs may further reduce the incidence of childhood IPD.

Invasive pneumococcal disease clusters disproportionally impact persons experiencing homelessness, injecting drug users, and the western United States

BACKGROUND

Invasive pneumococcal disease (IPD) isolates forming genomic clusters can reflect rapid disease transmission between vulnerable individuals.

METHODS

We performed whole genome sequencing of 2820 IPD isolates recovered during 2019 through CDC's Active Bacterial Core surveillance (ABCs) to provide strain information (serotypes, resistance, genotypes), and 2778 of these genomes were analyzed to detect highly related genomic clusters.

RESULTS

Isolates from persons experiencing homelessness (PEH) were more often within genomic clusters than those from persons not experiencing homelessness (PNEH) (105/198, 53.0% vs 592/2551, 23.2%, p<0.001). The 4 western sites accounted for 33.4% (929/2778) of isolates subjected to cluster analysis yet accounted for 48.7% (343/705) of clustering isolates (p<0.001) and 150/198 (75.8%) isolates recovered from PEH (p<0.001). Serotypes most frequent among PEH were (in rank order) 12F, 4, 3, 9N, 8, 20, and 22F, all of which were among the 10 serotypes exhibiting the highest proportions of clustering isolates among all cases. These serotypes accounted for 44.9% (1265/2820) of all IPD cases and are included within available vaccines.

CONCLUSIONS

We identified serotype-specific and geographic differences in IPD transmission. We show the vulnerability of PEH within different regions to rapidly spreading IPD transmission networks representing several pneumococcal serotypes included in available vaccines.

Invasive Streptococcus pneumoniae isolates from pediatric population in Argentina for the period 2006-2019. Temporal progression of serotypes distribution and antibiotic resistance

Streptococcus pneumoniae is a major cause of severe invasive disease associated with high mortality and morbidity worldwide. A total of 2908 pneumococcal isolates were analyzed between 2006 and 2019. Gold standard pneumococcal serotyping (the Neufeld-Quellung reaction) was performed to identify the serotypes associated with infection in children < 5 years in Argentina and agar dilution method was carried out to determine their profiles to 14 antimicrobial agents. In 2012, the 13-valent pneumococcal conjugate vaccine (PCV13) was included in the National Immunization Program. In this work we have analyzed the local epidemiology of invasive pneumococcal diseases before and after the introduction of this vaccine in order to understand the epidemiological relevance and impact of PCV13. During the periods compared in the present study there was a significant increase in the proportion of non-PCV13 serotypes, serogroup 24 (246.7%) and 12F (85.7%), and a significant decrease in PCV13 serotypes, including serotypes 14 (91.2%), 5 (95.6%) and 1 (84.6%) among others. Another observation was that serotypes 3 (7.4%) and 19A (4.9%) still remain among the most frequent serotypes despite being part of the PCV13 formulation. Regarding antimicrobial resistance, in the present study we observed an increase in erythromycin resistance during the period of study mainly associated to serotype 14 in the pre-PCV13 period and to serogroup 24 in the post-PCV13 period, which also was the major NVT serotype associated with antimicrobial resistance and MDR. Serotypes 14, 24A/B/F and 19A were in the first three places among isolates resistant to all the antibiotics tested. Our data highlight the importance of continuous surveillance to assess the impact of pneumococcal vaccines and the use of antibiotics in the dynamic of pneumococcal serotypes.

Is there a need for pneumococcal vaccination programs for the homeless to prevent invasive pneumococcal disease?

INTRODUCTION

Homeless are a vulnerable segment of society at risk for infections. Invasive pneumococcal disease (IPD) infections are increasingly identified in homeless as a major contributor of morbidity and mortality. Very few countries have recommended pneumococcal vaccination programs for the homeless.

AREAS COVERED

A literature review of IPD in the homeless from 1980 to 2020 in PubMed and Scopus using terms, 'homeless,' and 'homelessness,' and after 'chronic' or 'transitory' homeless was conducted. Gray literature from the CDC, WHO and major governmental agencies/organizations were included. Terms for IPD eligible for inclusion in the database search included 'pneumococcal disease,' 'invasive pneumococcal disease,' 'Streptococcus pneumoniae.' This included outbreaks of pneumococcal disease in the homeless, clinical characteristics associated with pneumococcal disease in the homeless, pneumococcal vaccines and vaccination recommendations for the homeless.

EXPERT OPINION

Homeless populations are at increased risk for IPD in comparison to the general population. This is due to clinical conditions experienced by the homeless including alcoholism and cigarette smoking. In addition, a collection of specific pneumococcal serotypes are associated with IPD in this group. Pneumococcal vaccine programs aimed at this population would likely decrease the incidence of IPD for this group and contribute to better overall health for the homeless.

Invasive Pneumococcal Strain Distributions and Isolate Clusters Associated With Persons Experiencing Homelessness During 2018

BACKGROUND

We aimed to characterize invasive pneumococcal disease (IPD) isolates collected from multistate surveillance in the United States during 2018 and examine within-serotype propensities of isolates to form related clusters.

METHODS

We predicted strain features using whole genome sequencing obtained from 2885 IPD isolates obtained through the Center for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs), which has a surveillance population of approximately 34.5 million individuals distributed among 10 states. Phylogenetic analysis was provided for serotypes accounting for ≥27 isolates.

RESULTS

Thirteen-valent pneumococcal conjugate vaccine (PCV13) serotypes together with 6C accounted for 23 of 105 (21.9%) of isolates from children aged <5 years and 820 of 2780 (29.5%) isolates from those aged ≥5 years. The most common serotypes from adult IPD isolates were serotypes 3 (413/2780 [14.9%]), 22F (291/2780 [10.5%]), and 9N (191/2780 [6.9%]). Among child IPD isolates, serotypes 15BC (18/105 [17.1%]), 3 (11/105 [10.5%]), and 33F (10/105 [9.5%]) were most common. Serotypes 4, 12F, 20, and 7F had the highest proportions of isolates that formed related clusters together with the highest proportions of isolates from persons experiencing homelessness (PEH). Among 84 isolates from long-term care facilities, 2 instances of highly related isolate pairs from co-residents were identified.

CONCLUSIONS

Non-PCV13 serotypes accounted for >70% of IPD in ABCs; however, PCV13 serotype 3 is the most common IPD serotype overall. Serotypes most common among PEH were more often associated with temporally related clusters identified both among PEH and among persons not reportedly experiencing homelessness.

Effectiveness of 23-Valent Pneumococcal Polysaccharide Vaccine against Invasive Pneumococcal Disease in Adults, Japan, 2013-2017

The decline in the proportion of pneumococcal conjugate vaccine (PCV)–covered serotypes among adult invasive pneumococcal disease (IPD) patients might change the overall effectiveness of the 23-valent pneumococcal polysaccharide vaccine (PPSV23) because its effectiveness differs according to serotype. Using the indirect cohort method, we calculated the effectiveness of PPSV23 against IPD among adults in Japan to assess the impact of the national pediatric PCV program. Clinical and epidemiologic information and pneumococcal isolates were collected from IPD patients >20 years of age through enhanced IPD surveillance during April 2013–December 2017. Adjusted effectiveness against PPSV23-serotype IPD was 42.2%. Despite a substantial decline in the proportion of 13-valent PCV serotypes during the study period (45% to 31%), the change in effectiveness for PPSV23-serotype IPD was limited (47.1% to 39.3%) and only marginal in the elderly population (39.9% to 39.4%). The pediatric PCV program had limited impact on PPSV23 effectiveness against IPD in adults.

Incidence of Invasive Pneumococcal Disease Higher Among People Notified With Markers of Hepatitis C Virus Infection: Population-based Surveillance in Victoria, Australia, 2001-2017

BACKGROUND

Worse outcomes from invasive pneumococcal disease (IPD) have been reported among those coinfected with hepatitis C. We aimed to establish if IPD notification rates are higher among people notified with markers of hepatitis C virus infection than the general population.

METHODS

IPD cases notified in Victoria, Australia, from July 2001-December 2017 were linked with hepatitis C cases (diagnosed by serology or PCR testing) notified from January 1991-December 2017. IPD incidence was calculated using population data and the estimated number of Victorians with hepatitis C.

RESULTS

From July 2001-December 2017, 6407 IPD cases were notified. Hepatitis C infection was notified in 342 (5.3%) of IPD cases overall, and 24.4% among IPD cases aged 45-49 years. Among IPD cases also notified with hepatitis C, 55.3% were infected with 13-valent pneumococcal conjugate vaccine serotypes and 82.8% with 23-valent pneumococcal polysaccharide vaccine serotypes. Compared with IPD cases without hepatitis C, IPD cases also notified with hepatitis C were younger (mean age, 45.7 vs 49.4 years; P = .011) and more often male (65.5% vs 55.5%, P < .001). Annual IPD notification incidence was 6.8/100 000 among people without hepatitis C and 39.4/100 000 among people with hepatitis C (IRR, 5.8; 95% CI, 5.2-6.4; P < .001).

CONCLUSIONS

IPD notification incidence was 5 times higher among people notified with markers of hepatitis C than the general population. Pneumococcal vaccination should be offered to people with markers of hepatitis C virus infection. To facilitate appropriate treatment, young and middle-aged adults with IPD should be tested for hepatitis C.

Vaccine-preventable diseases other than tuberculosis, and homelessness: A scoping review of the published literature, 1980 to 2020

BACKGROUND

Homelessness may result in the breakdown of regular health services, including routine vaccination programmes. A scoping review was conducted to describe vaccine-preventable diseases (VPD) other than tuberculosis in people experiencing homelessness (PEH).

METHODS

We followed the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). We searched peer-reviewed literature published in English, French, Spanish or Portuguese reporting the outbreak of VPD or VPD prevalence in both infant and adult homeless populations published between 1980 and 2020, using PubMed/Medline, SciELO, Google Scholar, and Web of Science databases. Relevant information from the studies was charted in Microsoft Excel and results were summarised using a descriptive analytical method.

RESULTS

Eighty-one articles were included. A high prevalence of past hepatitis B virus (HBV) and hepatitis A virus (HAV) infections were observed through serosurveys, mostly in high income countries or high-middle income countries (USA, Canada, France, Iran or Brazil). Ten outbreaks of HAV infection were also reported, with lethality rates ranging from 0 to 4.8%. The studies identified numerous risk factors positively associated with HBV infection, including older age, homosexual or bisexual practice, injected drug use (IDU), and, with HAV infection including IDU, having sexual partner(s) with a history of unspecified hepatitis, insertive anal penetration, or originating from a country with a high prevalence of anti-HAV antibody. Eleven outbreaks of pneumococcal infection affecting PEH were reported in Canada and USA, with lethality rates from 0 to 15.6%. Six diphtheria outbreaks were reported. Vaccination status was rarely documented in these studies.

CONCLUSIONS

The literature suggests that homeless populations generally experience a high VPD burden suggesting the need for a national vaccination programme and planning for delivering vaccines in this population.

A Nationwide Outbreak of Invasive Pneumococcal Disease in Israel Caused by Streptococcus Pneumoniae Serotype 2

BACKGROUND

Invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae serotype 2 (Sp2) is infrequent. Large scale outbreaks have not been reported following pneumococcal conjugate vaccine (PCV) implementation. We describe a Sp2 IPD outbreak in Israel, in the 13-valent PCV (PCV13) era, with focus on Sp2 population structure and evolutionary dynamics.

METHODS

The data derived from a population-based, nationwide active surveillance of IPD since 2009. 7-valent PCV (PCV7)/PCV13 vaccines were introduced in July 2009 and November 2010, respectively. Sp2 isolates were tested for antimicrobial susceptibility, Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) analysis.

RESULTS

Overall, 170 Sp2 IPD cases were identified during 2009-2019; Sp2 increased in 2015 and caused 6% of IPD during 2015-2019, a 7-fold increase compared with 2009-2014.The outbreak was caused by a previously unreported molecular type (ST-13578), initially observed in Israel in 2014. This clone caused 88% of Sp2 during 2015-2019. ST-13578 is a single-locus variant of ST-1504, previously reported globally, including in Israel. WGS analysis confirmed clonality among the ST-13578 population. Single-nucleotide polymorphisms-dense regions support a hypothesis that the ST-13578 outbreak clone evolved from ST-1504 by recombination.All tested strains were penicillin-susceptible (MIC <0.06 μg/mL). The ST-13578 clone was identified almost exclusively (99%) in the Jewish population and was mainly distributed in 3/7 Israeli districts. The outbreak is still ongoing, although declining since 2017.Conclusions: To the best of our knowledge, this is the first widespread Sp2 outbreak since PCV13 introduction worldwide, caused by the emerging ST-13578 clone.

Declines in Pediatric Bacterial Meningitis in the Republic of Benin Following Introduction of Pneumococcal Conjugate Vaccine: Epidemiological and Etiological Findings, 2011-2016

BACKGROUND

Pediatric bacterial meningitis (PBM) remains an important cause of disease in children in Africa. We describe findings from sentinel site bacterial meningitis surveillance in children <5 years of age in the Republic of Benin, 2011-2016.

METHODS

Cerebrospinal fluid (CSF) was collected from children admitted to Parakou, Natitingou, and Tanguieta sentinel hospitals with suspected meningitis. Identification of Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Neisseria meningitidis (meningococcus) was performed by rapid diagnostic tests, microbiological culture, and/or polymerase chain reaction; where possible, serotyping/grouping was performed.

RESULTS

A total of 10 919 suspected cases of meningitis were admitted to the sentinel hospitals. Most patients were 0-11 months old (4863 [44.5%]) and there were 542 (5.0%) in-hospital deaths. Overall, 4168 CSF samples were screened for pathogens and a total of 194 (4.7%) PBM cases were confirmed, predominantly caused by pneumococcus (98 [50.5%]). Following pneumococcal conjugate vaccine (PCV) introduction in 2011, annual suspected meningitis cases and deaths (case fatality rate) progressively declined from 2534 to 1359 and from 164 (6.5%) to 14 (1.0%) in 2012 and 2016, respectively (P < .001). Additionally, there was a gradual decline in the proportion of meningitis cases caused by pneumococcus, from 77.3% (17/22) in 2011 to 32.4% (11/34) in 2016 (odds ratio, 7.11 [95% confidence interval, 2.08-24.30]). Haemophilus influenzae meningitis fluctuated over the surveillance period and was the predominant pathogen (16/34 [47.1%]) by 2016.

CONCLUSIONS

The observed decrease in pneumococcal meningitis after PCV introduction may be indicative of changing patterns of PBM etiology in Benin. Maintaining vigilant and effective surveillance is critical for understanding these changes and their wider public health implications.

Upsurge of Conjugate Vaccine Serotype 4 Invasive Pneumococcal Disease Clusters Among Adults Experiencing Homelessness in California, Colorado, and New Mexico

After 7-valent pneumococcal conjugate vaccine introduction in the United States in 2000, invasive pneumococcal disease (IPD) due to serotype 4 greatly decreased in children and adults. Starting in 2013, serotype 4 IPD incidence increased among adults within 3 of 10 Active Bacterial Core surveillance sites. Of 325 serotype 4 cases among adults in 2010-2018, 36% were persons experiencing homelessness (PEH); incidence of serotype 4 IPD among PEH was 100-300 times higher than in the general population within these 3 areas. Genome sequencing for isolates recovered 2015-2018 (n = 246), revealed that increases in serotype 4 IPD were driven by lineages ST10172, ST244, and ST695. Within each lineage, clusters of near-identical isolates indicated close temporal relatedness. Increases in serotype 4 IPD were limited to Colorado, California, and New Mexico, with highest increases among PEH, who were at increased risk for exposure to and infections caused by these strains.

Risk for Invasive Streptococcal Infections among Adults Experiencing Homelessness, Anchorage, Alaska, USA, 2002-2015

The risk for invasive streptococcal infection has not been clearly quantified among persons experiencing homelessness (PEH). We compared the incidence of detected cases of invasive group A Streptococcus infection, group B Streptococcus infection, and Streptococcus pneumoniae (pneumococcal) infection among PEH with that among the general population in Anchorage, Alaska, USA, during 2002–2015. We used data from the Centers for Disease Control and Prevention’s Arctic Investigations Program surveillance system, the US Census, and the Anchorage Point-in-Time count (a yearly census of PEH). We detected a disproportionately high incidence of invasive streptococcal disease in Anchorage among PEH. Compared with the general population, PEH were 53.3 times as likely to have invasive group A Streptococcus infection, 6.9 times as likely to have invasive group B Streptococcus infection, and 36.3 times as likely to have invasive pneumococcal infection. Infection control in shelters, pneumococcal vaccination, and infection monitoring could help protect the health of this vulnerable group.

Molecular characterization of predominant Streptococcus pneumoniae serotypes causing invasive infections in Canada: the SAVE study, 2011-15

Objectives

This study characterized the 11 most predominant serotypes of invasive Streptococcus pneumoniae infections collected by the annual SAVE study in Canada, between 2011 and 2015.

Methods

A subset of the 11 most predominant serotypes (7F, 19A, 22F, 3, 12F, 11A, 9N, 8, 33F, 15A and 6C) collected by the SAVE study was analysed using PFGE and MLST, as well as PCR to identify pilus-encoding genes. WGS analyses were performed on a subset of the above isolates plus a random selection of background strains.

Results

Of the predominant serotypes analysed, 7F, 33F and 19A were obtained more commonly from children <6 years of age, whereas 15A, 6C, 22F and 11A were more common in adults >65 years of age. Pneumococcal pilus PI-1 was identified in antimicrobial-susceptible serotype 15A (61/212) and <10% of 6C isolates (16/188). PI-2 was found in serotype 7F (683/701) and two-thirds of 11A isolates (162/241). Only serotype 19A-ST320 possessed both pili. Molecular and phylogenetic analyses identified serotypes 19A, 15A, 6C, 9N and 33F as highly diverse, whereas 7F, 22F and 11A demonstrated clonality. Antimicrobial resistance determinants were common within diverse serotypes, and usually similar within a clonal complex.

Conclusions

Despite successful use of conjugate vaccines, S. pneumoniae remains a highly diverse organism in Canada. Several predominant serotypes, both antimicrobial susceptible and MDR, have demonstrated rapid clonal expansion or an increase in diversity. As S. pneumoniae continues to evolve in Canada, WGS will be a necessary component in the ongoing surveillance of antimicrobial-resistant and expanding clones.

Using pneumococcal carriage studies to monitor vaccine impact in low- and middle-income countries

Pneumococcal disease is a leading cause of childhood mortality, globally. The pneumococcal conjugate vaccine (PCV) has been introduced to many countries worldwide. However there are few studies evaluating PCV impacts in low- and middle-income countries (LMIC) because measuring the impact of PCV on pneumococcal disease in LMICs is challenging. We review the role of pneumococcal carriage studies for the evaluation of PCVs in LMICs and discuss optimal methods for conducting these studies. Fifteen carriage studies from 13 LMICs quantified the effects of PCV on carriage, and identified replacement carriage serotypes in the post-PCV era. Ten studies reported on the indirect effects of PCV on carriage. Results can be used to inform cost-effectiveness evaluations, guide policy decisions on dosing and product, and monitor equity in program implementation. Critically, we highlight gaps in our understanding of serotype replacement disease in LMICs and identify priorities for research to address this gap.

Homelessness in Adults with Invasive Pneumococcal Disease (IPD) in Calgary, Canada

Background

Homelessness is uncommon but is frequently a characteristic in adults with invasive pneumococcal disease (IPD). In Calgary, homeless persons comprise approximately 0.2% of the population. We evaluated the relationship of homelessness and IPD in Calgary.

Methods

Demographic, clinical, and microbiologic data were collected by the Calgary Streptococcus pneumoniae Epidemiology Research (CASPER) team through prospective, population-based surveillance of all IPD cases. Here, we report on cases in adults (≥18 years) from 2000 to 2016.

Results

Of 1729 IPD cases, 321 (18.8%) occurred in homeless persons. Compared with nonhomeless persons, homeless persons were younger, more often male, smokers, alcohol abusers, illegal drug users, and had a primary diagnosis of pneumonia. In multivariable models of outcomes, homeless persons had lower odds of being admitted to the ICU (odds ratio [OR], 0.7; P = .02) and lower odds of death (OR, 0.6; P = .146). IPD caused by serotypes 4, 5, or 8, which have caused outbreaks in Calgary, was more common in homeless persons (54.4% vs 21.0%; P < .001). In addition, regardless of homeless status, persons with IPD caused by serotypes 4, 5, or 8 had lower odds of ICU admission and mortality (OR, 0.7; P = .017; and OR, 0.4; P = .004; respectively).

Conclusions

Homelessness is overrepresented in IPD cases in Calgary, despite most homeless persons having fewer risk factors than the overall population of persons with IPD. Most cases are caused by serotypes in both the 23-valent polysaccharide vaccine and the 13-valent conjugate vaccine. Thus, enhanced efforts are needed to deliver both vaccines to this vulnerable population.

Clonal spread of serotype 12F ST4846 Streptococcus pneumoniae

Introduction. In 2016-2017, there was an increase in the number of paediatric invasive pneumococcal disease (IPD) cases caused by Streptococcus pneumoniae serotype 12F in Chiba Prefecture, Japan. Serotype 12F is one of the major causative serotypes of IPD following the introduction of pneumococcal conjugate vaccine 13 (PCV13), and outbreaks of IPD caused by serotype 12F have recently been reported in several countries.Aim. Our goal here was to clarify the relationship among local outbreak strains and the outbreak strains in other countries, and for this we analysed clinical isolates of S. pneumoniae serotype 12F using several genetic identification methods.Methodology. All reported IPD cases caused by serotype 12F were reviewed and bacterial strains were collected and analysed. We also analysed S. pneumoniae serotype 12F strains isolated from other time periods, geographical areas, cases of adult IPD and respiratory specimens as control strains. Multi-locus sequence typing, PFGE and multi-locus variable number tandem repeat analysis (MLVA) were conducted on all isolates.Results. All 26 S. pneumoniae serotype 12F isolates, including control strains, belonged to a single sequence type (ST4846) that was the specific ST in Japan. All tested strains demonstrated five MLVA patterns and two PFGE patterns.Conclusion. We determined that the 2016-2017 outbreak of IPD in Chiba Prefecture was caused by clonally related isolates of serotype 12F. The continuous monitoring of IPD caused by serotype 12F is important for evaluating the impact of re-emerging pneumococcal serotypes following the PCV13 introduction era, and MLVA could be a useful tool for identification of outbreak strains.

Impact of the pediatric 13-valent pneumococcal conjugate vaccine on serotype distribution and clinical characteristics of pneumococcal pneumonia in adults: The Japan Pneumococcal Vaccine Effectiveness Study (J-PAVE)

BACKGROUND

The pediatric 13-valent pneumococcal conjugate vaccine (PCV13) was included in the pediatric immunization programme in Japan in late 2013. The impact of vaccination on the serotype distribution and clinical characteristics of pneumococcal pneumonia has not been described.

METHODS

The first phase of this multicentre prospective study was conducted at community-based hospitals in Japan from 2011 to 2014. The second phase was conducted from 2016 to 2017. Pneumococcal isolates and clinical data were collected from patients with community-acquired pneumonia who were ≥15 years of age. Patients were classified by pneumococcal serotype to PCV13 serotype, 23-valent pneumococcal polysaccharide vaccine (PPV23) non-PCV13 serotype, and non-vaccine serotype.

RESULTS

A total of 484 patients were enrolled, 241 in the first phase and 243 in the second. The proportion of PCV13 serotypes decreased from 53% to 33% (p < 0.001), whereas PPV23 non-PCV13 serotypes did not change (p = 0.754). PCV13 serotypes were associated with increased risk of elevated blood urea nitrogen (adjusted odds ratio 2.49; 95% confidence interval: 1.49-4.16) and hospitalization (adjusted odds ratio 1.74; 95% confidence interval: 1.02-2.95). These associations were not observed in patients with PPV23 non-PCV13 serotypes.

CONCLUSIONS

The occurrence of pneumococcal pneumonia caused by vaccine-covered serotypes dramatically decreased following the introduction of pediatric PCV13. The PCV13 serotypes were associated with pneumonia severity.

Epidemiological and clinical features of invasive pneumococcal disease caused by serotype 12F in adults, Japan

Enhanced surveillance of invasive pneumococcal disease (IPD) in adults was conducted during April 2013–March 2018 in 10 of 47 prefectures in Japan, and a total of 1277 IPD patients were enrolled. An emergence of IPD caused by serotype 12F was identified during May 2015–March 2018 through this surveillance. 12F isolates were composed of four related sequence types. In total, 120 patients with 12F IPD were reported during this period. To characterize the clinical features of 12F IPD, the disease characteristics of these patients were compared with those of 1157 patients with non-12F IPD. Compared with the non-12F IPD patients, a significantly lower proportion of 12F IPD patients was aged 65 years or older (55% vs. 70%), vaccinated with 23-valent pneumococcal polysaccharide (4% vs. 14%), had comorbid illness (65% vs. 77%), or were immunocompromised (19% vs. 30%; all P < 0.05). No significant difference in the proportion of case fatalities was found between the two groups. The proportions of those aged 65 years or older (53% vs. 69%) and with bacteremic pneumonia (35% vs. 69%) were significantly lower in 17 patients who died from 12F IPD than in 205 patients who died from non-12F IPD (all P < 0.05). Differences in clinical features were similarly found between 12F IPD patients and patients in low- or intermediate-level invasive potential serogroups. Our data demonstrated that serotype 12F was associated with IPD in younger adults and a lower proportion of comorbid illness, including immunocompromised conditions, in adult IPD, suggesting the high invasive potential of the serotype 12F. In addition, patients who died from 12F IPD were younger and had proportionately more bacteremia without focus. These findings may provide new insight into the pathogenesis of IPD in adults caused by 12F serotype with a high invasive potential.

Emergence of Streptococcus pneumoniae Serotype 12F after Sequential Introduction of 7- and 13-Valent Vaccines, Israel

Israel implemented use of 7- and 13-valent pneumococcal vaccine in 2009 and 2010, respectively. We describe results of prospective, population-based, nationwide active surveillance of Streptococcus pneumoniae serotype 12F (Sp12F) invasive pneumococcal disease (IPD) dynamics in the 7 years after vaccine introduction. Of 4,573 IPD episodes during July 2009-June 2016, a total of 434 (9.5%) were caused by Sp12F. Sp12F IPD rates (cases/100,000 population) increased in children <5 years of age, from 1.44 in 2009-2010 to >3.9 since 2011-2012, followed by an increase in all ages. During 2011-2016, Sp12F was the most prevalent IPD serotype. Sp12F isolates were mostly penicillin nonsusceptible (MIC >0.06 µg/mL; MIC₅₀ = 0.12) and predominantly of sequence type 3774), a clone exclusively found in Israel (constituting ≈90% of isolates in 2000-2009). The sharp increase, long duration, and predominance of Sp12F IPD after vaccine implementation reflect a single clone expansion and may represent more than a transient outbreak.

Outbreak of invasive Streptococcus pneumoniae among an inner-city population in Victoria, British Columbia, 2016-2017

Background

Invasive pneumococcal disease (IPD) is a significant cause of morbidity and mortality; however, outbreaks of IPD are relatively rare. Homelessness and substance use are known risk factors for IPD and have been associated with several outbreaks in Canada, despite national recommendations for routine childhood and targeted adult pneumococcal vaccination.

Objectives

To describe the epidemiology and public health challenges related to an outbreak of novel serotype 4 IPD in a homeless and unstably housed population in Victoria, British Columbia during the autumn and winter of 2016-2017.

Results

Prospective, enhanced surveillance was initiated for laboratory confirmed cases reported to public health, including variables recording housing status and substance use. Thirty-three cases of serotype 4 IPD within the Victoria area were reported to public health between August 1, 2016 and September 1, 2017. Compared with other serotypes, these cases were more likely to be middle-aged, homeless or unstably housed, and to have a recent history of substance use. A targeted pneumococcal vaccination campaign was initiated in collaboration with external community organizations; however, these initiatives were challenged by incomplete data and staffing constraints.

Conclusion

This report illustrates an outbreak of serotype 4 IPD among an inner-city population with multiple risk factors, including homelessness, unstable housing and substance use. Given the challenges controlling the outbreak, outreach capacity and pneumococcal vaccination coverage is needed among this marginalized population.

Streptococcus pneumoniae outbreaks and implications for transmission and control: a systematic review

BACKGROUND

Streptococcus pneumoniae is capable of causing multiple infectious syndromes and occasionally causes outbreaks. The objective of this review is to update prior outbreak reviews, identify control measures, and comment on transmission.

METHODS

We conducted a review of published S. pneumoniae outbreaks, defined as at least two linked cases of S. pneumoniae.

RESULTS

A total of 98 articles (86 respiratory; 8 conjunctivitis; 2 otitis media; 1 surgical site; 1 multiple), detailing 94 unique outbreaks occurring between 1916 to 2017 were identified. Reported serotypes included 1, 2, 3, 4, 5, 7F, 8, 12F, 14, 20, and 23F, and serogroups 6, 9, 15, 19, 22. The median attack rate for pneumococcal outbreaks was 7.0% (Interquartile range: 2.4%, 13%). The median case-fatality ratio was 12.9% (interquartile range: 0%, 29.2%). Age groups most affected by outbreaks were older adults (60.3%) and young adults (34.2%). Outbreaks occurred in crowded settings, such as universities/schools/daycares, military barracks, hospital wards, and long-term care facilities. Of outbreaks that assessed vaccination coverage, low initial vaccination or revaccination coverage was common. Most (73.1%) of reported outbreaks reported non-susceptibility to at least one antibiotic, with non-susceptibility to penicillin (56.0%) and erythromycin (52.6%) being common. Evidence suggests transmission in outbreaks can occur through multiple modes, including carriers, infected individuals, or medical devices. Several cases developed disease shortly after exposure (< 72 h). Respiratory outbreaks used infection prevention (55.6%), prophylactic vaccination (63.5%), and prophylactic antibiotics (50.5%) to prevent future cases. PPSV23 covered all reported outbreak serotypes. PCV13 covered 10 of 16 serotypes. For conjunctival outbreaks, only infection prevention strategies were used.

CONCLUSIONS

To prevent the initial occurrence of respiratory outbreaks, vaccination and revaccination is likely the best preventive measure. Once an outbreak occurs, vaccination and infection-prevention strategies should be utilized. Antibiotic prophylaxis may be considered for high-risk exposed individuals, but development of antibiotic resistance during outbreaks has been reported. The short period between initial exposure and development of disease indicates that pneumococcal colonization is not a prerequisite for pneumococcal respiratory infection.

The relative invasive disease potential of Streptococcus pneumoniae among children after PCV introduction: A systematic review and meta-analysis

OBJECTIVES

Burden of pneumococcal disease depends on the prevalence and invasive disease potential of serotypes. We aimed to estimate the invasive disease potential of serotypes in children under 5 years of age by combining data from different settings with routine immunisation with pneumococcal conjugate vaccines (PCV).

METHODS

We conducted a systematic review, supplemented by unpublished data, to identify data on the frequency of pneumococcal serotypes in carriage and invasive pneumococcal disease (IPD). We estimated the invasive disease potential of serotypes as the ratio of IPD in relation to carriage (odds ratio and 95%CI) compared with 19A (reference serotype) by meta-analysis. We report results based on a random effects model for children aged 0-23, 24-29, and 0-59 months and by invasive clinical syndromes.

RESULTS

In comparison with 19A, serotypes 1, 7F, and 12F had a significantly higher invasive disease potential in children aged 0-23 and 0-59 months for all IPD and clinical syndromes (OR > 5). Several non-vaccine types (NVTs) (6C, 15A, 15BC, 16F, 23B, in these two age groups) had a lower invasive disease potential than 19A (OR 0.1-0.3). NVTs 8, 12F, 24F, and 33F were at the upper end of the invasiveness spectrum.

CONCLUSIONS

There is substantial variation among pneumococcal serotypes in their potential to cause IPD and disease presentation, which is influenced by age and time after PCV introduction. Surveillance of IPD and carriage is critical to understand the expected effectiveness of current PCVs (in the longer term) and guide the development of future vaccines.

Long-term trends in invasive pneumococcal disease in Manitoba, Canada

Invasive pneumococcal disease (IPD) remains a significant public health problem in Manitoba, Canada although publically-funded pneumococcal conjugate (PCV7 and PCV13) and polysaccharide (PPV23) vaccination programs exist. We analyzed routine surveillance and administrative health data to examine trends in IPD rates as these vaccines were introduced. Data on all individuals with a laboratory-confirmed diagnosis of IPD between 2001 and 2014 were obtained from the provincial Communicable Diseases Surveillance database and linked with Manitoba's provincial immunization registry and physician and hospital databases. We calculated IPD incidence rates overall, by serotype and for different population subgroups defined by socio-demographic and clinical (e.g., chronic diseases, immune status) characteristics. Annual IPD incidence (95%CI) was 8.6 (8.2-9.1)/100,000 people during the study period (n = 1092), and rates were higher in recent years and in regions with predominately indigenous populations. Reduction in the incidence of serotypes included in PCV7 have been offset by rising rates of PCV13-only serotypes in children, and more recently by rising rates of PPV-only serotypes and non-vaccine serotypes among young children and older adults (≥ 65 years). Rates were 3 times higher in those with a chronic disease and highest (> 175-fold) among alcoholics, organ-transplant, and chronic kidney failure patients. The case fatality rate was 12.0% within 30 d of diagnosis. Despite the introduction of several vaccination programs, overall rates of IPD have not declined in Manitoba in the last decade, due to increase in incidence of non-PCV7 serotypes. A disproportionately high burden of disease impacts indigenous communities and people with chronic disease.

Impact of pneumococcal conjugate vaccines on pneumococcal meningitis cases in France between 2001 and 2014: a time series analysis

BACKGROUND

Pneumococcal meningitis (PM) is a major invasive pneumococcal disease. Two pneumococcal conjugate vaccines (PCVs) have been introduced in France: PCV7 was recommended in 2003 and replaced in 2010 by PCV13, which has six additional serotypes. The impact of introducing those vaccines on the evolution of PM case numbers and serotype distributions in France from 2001 to 2014 is assessed herein.

METHODS

Data on 5166 Streptococcus pneumoniae strains isolated from cerebrospinal fluid between 2001 and 2014 in the 22 regions of France were obtained from the National Reference Center for Pneumococci. The effects of the different vaccination campaigns were estimated using time series analyses through autoregressive moving-average models with exogenous variables ("flu-like" syndromes incidence) and intervention functions. Intervention functions used 11 dummy variables representing each post vaccine epidemiological period. The evolution of serotype distributions was assessed for the entire population and the two most exposed age groups (<5 and > 64 years old).

RESULTS

For the first time since PCV7 introduction in 2003, total PM cases decreased significantly after starting PCV13 use: -7.1 (95% CI, -10.85 to -3.35) cases per month during 2013-2014, and was confirmed in children < 5 years old (-3.5; 95% CI, -4.81 to -2.13) and adults > 64 years old (-2.0; 95% CI, -3.36 to -0.57). During 2012-2014, different non-vaccine serotypes emerged: 12F, 24F in the entire population and children, 6C in the elderly; serotypes 3 and 19F persisted in the entire population.

CONCLUSIONS

Unlike other European countries, the total PM cases in France declined only after introduction of PCV13. This suggests that vaccine pressure alone does not explain pneumococcal epidemiological changes and that other factors could play a role. Serotype distribution had changed substantially compared to the pre-vaccine era, as in other European countries, but very differently from the US. A highly reactive surveillance system is thus necessary not only to monitor evolutions due to vaccine pressure and to verify the local serotypic appropriateness of new higher-valent pneumococcal vaccines, but also to recognise and prevent unexpected changes due to other internal or external factors.

Association of serotype with respiratory presentations of pneumococcal infection, Ontario, Canada, 2003-2011

BACKGROUND

Pneumococcal disease burden is difficult to quantify due to limited data regarding non-bacteremic disease. We assessed serotype-specific differences in pneumococcal disease presentations in adults in Toronto, Canada.

METHODS

From 2003 to 2011, population-based surveillance for invasive pneumococcal disease was conducted and respiratory pneumococcal isolates collected in Metropolitan Toronto/Peel Region, Canada. Episodes of care were classified into disease categories.

RESULTS

Of 3105 eligible cases of IPD, 2060 cases were bacteremic pneumonia, and 1045 bacteremia without pneumonia. Of 2751 eligible respiratory cases, 1542 (56.0%) were non-bacteremic pneumonia (NBPP), 467 (17.0%) were other acute respiratory infection (oARI), and 742 (27.0%) were isolates representing colonization. Serotypes 3 (11.3%), 19A (8.4%) and 22F (6.2%) were the most common; serotypes 1,5, and 8 were rare. Serotypes 4, 14, 7F, 9V, 12F, 14, 19A and 6C were over-represented in bacteremic disease, and serotypes 3, 6A, 11A, 19F, 23A, 23F, 35B, 35F were more common in NBPP. The proportion of cases due to PCV7 serotypes declined from 48.7% to 8.7% in bacteremic pneumonia, from 35.3% to 10.9% in NBPP, from 34.2% to 7.5% in oARI, and from 38.7% to 12.2% in colonizing isolates. In 2010-2011, PCV13 serotypes accounted for 62.6% of isolates associated with bacteremic pneumonia, 42.0% of bacteremia without pneumonia, 41.1% of NBPP, 25.7% of oARI, and 32.9% of colonizing isolates.

CONCLUSIONS

Serotype distributions differ significantly in different presentations of pneumococcal disease. Herd protection due to PCV7 has changed serotype distribution, but PCV13 serotypes remain important in all categories of disease.

Invasive disease potential of pneumococci before and after the 13-valent pneumococcal conjugate vaccine implementation in children

BACKGROUND

Changes in serotype distribution have been induced after pneumococcal conjugate vaccines (PCV) implementation, and non-vaccine serotypes are now circulating. Among these latter serotypes, we aimed to distinguish those with high invasive disease potential before (2008-2009) and after PCV13 implementation (2012-2013).

METHODS

Invasive pneumococcal disease (IPD) serotypes isolated from children 6 to 24 months were compared with nasopharyngeal-colonizing serotypes in healthy children. To assess the invasive potential of a given serotype, odds ratios (ORs) were calculated. For each serotype, OR >1 indicated increased probability of association with IPD and OR <1 decreased probability.

RESULTS

In 2008/2009 and 2012/2013, 355 pneumococci were isolated from 1212 healthy children and from 569 IPD, including 166 meningitis, 114 pneumonia, and 289 other IPDs. In period 1, serotypes 7F, 3, 1, 24F, and 19A showed highly significant invasive disease potential whereas in period 2, only serotype 24F was associated with a significant high OR (6.6 [95% CI 2.6; 16.2]). Of note, for serotype 12F, OR could not be calculated because of no carrier recorded, however, if there had been a single 12F carrier, the OR would be among the highest, in period 2, 15.7 [95% 3.4; 73.0]). Only two serotypes appeared negatively associated with IPD, 11A and 23B in the period 2 as compared with nine in period 1. In the second period, pneumococcal penicillin non-susceptible isolates were mostly represented by serotypes 19A, 15A, 19F, 35B and 24F both in carriers and IPD. Only one strain was resistant to penicillin with MIC=4 μg/ml (serotype 19A) during the first period.

CONCLUSION

In children <2 years old, compared to the previous period, the number of serotypes having a high disease potential decreased after PCV13 implementation, only two non-vaccine serotypes, 24F and 12F, had high invasive disease potential.

Comparison of the epidemiology of laboratory-confirmed influenza A and influenza B cases in Manitoba, Canada

Background

Despite the public health significance of annual influenza outbreaks, the literature comparing the epidemiology of influenza A and B infections is limited and dated and may not reflect recent trends. In Canada, the relative contribution of influenza A and B to the burden of morbidity is not well understood. We examined rates of laboratory-confirmed cases of influenza A and B (LCI-A and LCI-B) in the Canadian province of Manitoba between 1993 and 2008 and compared cases of the two types in terms of socio-demographic and clinical characteristics.

Methods

Laboratory-confirmed cases of influenza A and B in Manitoba between 1993 and 2008 were identified from the Cadham Provincial Laboratory (CPL) Database and linked to de-identified provincial administrative health records. Crude and age-adjusted incidence rates of LCI-A and LCI-B were calculated. Demographic characteristics, health status, health service use, and vaccination history were compared by influenza type.

Results

Over the study period, 1,404 of LCI-A and 445 cases of LCI-B were diagnosed, corresponding to an annual age-standardized rate of 7.2 (95% CI: 6.5-7.9) for LCI-A and 2.2 (CI: 1.5 – 3.0) per 100,000 person-years for LCI-B. Annual rates fluctuated widely but there was less variation in the LCI-B rates. For LCI-A, but not LCI-B, incidence was inversely related to household income. Older age, urban residence and past hospitalization were associated with increased detection of LCI-A whereas receipt of the influenza vaccine was associated with decreased LCI-A detection. Once socio-demographic variables were controlled, having a pre-existing chronic disease or immune suppression was not related to influenza type.

Conclusion

Influenza A and B affected different segments of the population. Older age was associated with increased LCI-A detection, but not with pre-existing chronic diseases. This information may be useful to public health professionals in planning and evaluating new and existing seasonal influenza vaccines.