Serotype Surveillance Research Articles

420. Immunization Impact on Serotype Distribution of Invasive Pneumococcal Disease - Playing the Serotype Whack-A-Mole!

Abstract Background Implementation of 7-valent pneumococcal vaccine (PCV7) resulted in significant reduction of invasive pneumococcal disease (IPD) followed by a subsequent increase in IPD by non-vaccine (n-Vac) serotypes (ser) (19A, 7F, 3) with increased severity and antimicrobial resistance. Approved following immunogenicity data, 13-valent PCV (PCV13) adoption reduced IPD again. Surveillance was strongly recommended by the CDC. We present 13 years of countywide (Orange County, CA) surveillance of IPD and serotypes. Serotype distribution of IPD by Year Methods Prospective (1/2010 - 12/2023) countywide study of patients < 18 years old with culture proven IPD. Demographic, clinical course and immunization data were collected. Serotyping was by Quelung method. Antibiotic susceptibilities were obtained. Results During the study period 261 patients were identified; 42% female, median age 3.7 years, 52% < 5 years old. IPD rate per 10,000 decreased by 70% (0.408 – > 0.123) from 2010 - 2014 and increased steadily from 2015 to 2019 (peaking at 0.403). As COVID19 pandemic social distancing measures were adopted, IPD rate decreased by 86% (0.057 in 2021); it has since rapidly increased again (0.285) after lifting social distancing measures. Ser was known for 86%; 15B and 22F were the most common nVac ser seen (8% and10% respectively). Ser distributions by year are seen in Figure 1. Table 1 shows the distribution of IPD with immunization status and where the pneumonias and meningitis occurred. Pneumonia (102 [39%]) remains the most common IPD (30% with empyema); we saw a rise of meningitis cases after 2018, 1 was ser3, 13 were n-Vac ser and 3 unknown. IPD attributed mortality occurred in 8 (3%) patients; 4 were due to PCV13 ser. Penicillin resistance (meningitis) increased from 21% to 31%; penicillin non-susceptible (MIC >1) remained unchanged. New 15 and 20 valent ser include 12% and 19% of emerging n-Vac serotypes. Conclusion Similar to PCV-7, PCV-13 implementation resulted in an initial significant decrease in IPD, mainly due to 5 of the 6 additional ser included in PCV-13, ser 3 was not significantly affected. This was followed by resurgence of IPD, mainly to n-VAC serotypes. Of our IPD since 2010, 65% are from ser now included in 20-valent PCV. IPD attributable mortality remains high. Active surveillance following higher valent PCVs remains important. Disclosures All Authors: No reported disclosures

Detection of dengue virus serotype 4 in Panama after 23 years without circulation.

Panama is a country with endemic Dengue virus (DENV) transmission since its reintroduction in 1993. The four serotypes have circulated in the country and the region of the Americas, however, DENV-4 confirmed autochthonous cases have not been identified since 2000, despite its circulation in neighboring countries. Here, we report DENV-4 detection in Panama in the last four-month period of 2023 with co-circulation of the other serotypes, this was associated with a peak of dengue cases during the dry season even though most dengue outbreaks are described in the rainy season. Complete genomes of DENV-4 allowed us to determine that cases were caused by DENV-4 genotype IIb, the same genotype as 23 years ago, with high similarity to DENV-4 sequences circulating in Nicaragua and El Salvador during 2023. This report shows the importance of maintaining serotype and genotype surveillance for early detection of new variants circulating in the country.

Potential Performance of Two New RT-PCR and RT-qPCR Methods for Multiplex Detection of Dengue Virus Serotypes 1-4 and Chikungunya Virus in Mosquitoes.

Mosquitoes of the genus Aedes are the most important arthropod disease vector. Dengue virus (DENV) and Chikungunya virus (CHIKV) are the main arboviruses distributed throughout the world. Based on entomo-virological surveillance, appropriate public health strategies can be adopted to contain cases and control outbreaks. This study aims to show the potential performance of two new molecular methods for detecting DENV serotypes and CHIKV in mosquitoes. Mosquitoes were collected in urban and sylvatic areas of Bobo-Dioulasso, Burkina Faso, between July and August 2023. DENV and CHIKV were screened using new multiplex RT-PCR and RT-qPCR methods. A total of 2150 mosquitoes were trapped, consisting of 976 Aedes (959 Ae. aegypti, 6 Ae. furcifer, and 11 Ae. vittatus) and 1174 Culex sp. These were grouped into 39 pools, with each pool containing a maximum of 30 mosquitoes. Molecular screening revealed that 7.7% (3/39) of the pools were positive for DENV. Specifically, DENV-1 was detected in one pool (1/3), and DENV-3 was found in two pools (2/3). All pools tested negative for CHIKV. The overall minimum infection rate (MIR) of DENV in this study was 3.07 (95% CI: 2.24-19.86). This study shows the usefulness of our new molecular tools for the surveillance of DENV serotypes and CHIKV.

Serotype distribution of invasive pneumococcal disease from countries of the WHO Africa, Americas, Eastern Mediterranean, South-East Asia, and Western Pacific regions: a systematic literature review from 2010 to 2021.

Most publications on invasive pneumococcal disease (IPD) serotype distribution are from about 20 countries (Australia, Canada, China, European Union members, Japan, New Zealand, South Korea, and USA). Here, we reviewed the literature among underrepresented countries in the Americas (AMRO), Africa (AFRO), Eastern Mediterranean (EMRO), South-East Asia (SEARO), and Western Pacific (WPRO) WHO regions. We performed a systematic review of the most recent IPD serotype surveillance publications (from 01/01/2010 to 31/12/2021, Medline/Embase) in those WHO regions. Selection criteria were delineated by contemporality, within-country geographical scope, and number of samples. Reported serotype distributions for each country were stratified by age group, pneumococcal conjugate vaccine (PCV) serotype category (considering undifferentiated serotypes), and PCV program period (pre-PCV, intermediate, or PCVhv [higher valency PCV formulation]). Pre-PCV period pooled data estimated PCV serotype category distribution by age group across WHO regions, while for the PCVhv period, country-level dataset tables were prepared. Of 2,793 publications screened, 107 were included (58 pediatric, 11 adult, 37 all ages, and one comprising every age group). One-third of eligible countries (51/135) published serotype distribution, ranging from 30 to 43% by WHO region. Considering number of samples per WHO region, a few countries prevailed: AMRO (Brazil), AFRO (South Africa, Malawi, and Burkina Faso), and WPRO (Taiwan). In the pre-PCV period, PCV13 formulation serotypes predominated: ranging from 74 to 85% in children and 58-86% in adults in the different WHO regions. The PCVhv period represented half of the most recent IPD surveillance by countries (26/51). Undifferentiated serotypes represented >20% of IPD from most countries (34/51). Ubiquity of undifferentiated serotypes among the publications could constrain estimates of PCV program impact and of serotype coverage for newer PCVhv formulations; consequently, we recommend that countries favor techniques that identify serotypes specifically and, rather than reporting PCV formulation serotype distributions, provide serotype results individually. The protocol has been prospectively registered at PROSPERO, identifier: CRD42021278501. https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=278501.

Surveillance of pneumococcal serotypes in adults hospitalised with acute lower respiratory tract infection in Bristol, UK

IntroductionPneumococcus remains a major cause of adult lower respiratory tract infections (LRTI). Few data exist on the relative contribution of serotypes included in pneumococcal vaccines to community-acquired pneumonia (CAP) and non-pneumonic (NP) LRTI. We measured the burden of all and vaccine-serotype pneumococcal respiratory infection following SARS-CoV-2 emergence to inform evidence-based vaccination policy. MethodsA prospective cohort study at two Bristol hospitals (UK) including all adults age ≥ 18-years hospitalised with acute lower respiratory tract disease (aLRTD) from Nov2021–Nov2022. LRTI patients were classified as: a) radiographically-confirmed CAP (CAP+/RAD+), b) clinically-diagnosed CAP without radiological confirmation (CAP+/RAD−), or c) NP-LRTI. Pneumococcus was identified by blood culture, BinaxNOW™and serotype-specific urine antigen detection assays (UAD). ResultsOf 12,083 aLRTD admissions, 10,026 had LRTI and 2,445 provided urine: 1,097 CAP + RAD+; 207 CAP + RAD−; and 1,141 NP-LRTI. Median age was 71.1y (IQR57.9–80.2) and Charlson comorbidity index = 4 (IQR2-5); 2.7 % of patients required intensive care, and 4.4 % died within 30-days of hospitalisation. Pneumococcus was detected in 280/2445 (11.5 %) participants. Among adults aged ≥ 65y and 18-64y, 12.9 % (198/1534) and 9.0 % (82/911), respectively, tested pneumococcus positive. We identified pneumococcus in 165/1097 (15.0 %) CAP + RAD+, 23/207 (11.1 %) CAP + RAD−, and 92/1141 (8.1 %) NP-LRTI cases. Of the 280 pneumococcal cases, 102 (36.4 %) were due to serotypes included in PCV13 + 6C, 115 (41.7 %) in PCV15 + 6C, 210 (75.0 %) in PCV20 + 6C/15C and 228 (81.4 %) in PPV23 + 15C. The most frequently identified serotypes were 8 (n = 78; 27.9 % of all pneumococcus), 7F (n = 25; 8.9 %), and 3 (n = 24; 8.6 %). DiscussionAmong adults hospitalised with respiratory infection, pneumococcus is an important pathogen across all subgroups, including CAP+/RAD- and NP-LRTI. Despite 20-years of PPV23 use in adults ≥ 65-years and herd protection due to 17-years of PCV use in infants, vaccine-serotype pneumococcal disease still causes a significant proportion of LRTI adult hospitalizations. Direct adult vaccination with high-valency PCVs may reduce pneumococcal disease burden.

Emerging pneumococcal serotypes in Iraq: scope for improved vaccine development.

Pneumococcal disease is a global public health concern as it affects the young, aged and the immunocompromised. The development of pneumococcal vaccines and their incorporation in the immunization programs has helped to reduce the global burden of disease. However, serotype replacement and the emergence of non-vaccine serotypes as well as the persistence of a few vaccine serotypes underscores the need for development of new and effective vaccines against such pneumococcal serotypes. In the Middle East, places of religious mass gatherings are a hotspot for disease transmission in addition to the global risk factors. Therefore, the periodic surveillance of pneumococcal serotypes circulating in the region to determine the effectiveness of existing prevention strategies and develop improved vaccines is warranted. Currently, there is a lack of serotype prevalence data for Iraq due to inadequate surveillance in the region. Thus, this review aims to determine the pneumococcal serotypes circulating in Iraq which may help in the development and introduction of improved pneumococcal vaccines in the country.

Antimicrobial resistance in Streptococcus pneumoniae: a retrospective analysis of emerging trends in the United Arab Emirates from 2010 to 2021.

Although pneumococcal conjugate vaccines (PCV) have been effective in reducing the burden of Streptococcus pneumoniae infections, there is a paucity of data on the relationship with antimicrobial resistance (AMR) trends in the Arabian Gulf region. This study was carried out to assess S. pneumoniae resistance trends in the United Arab Emirates (UAE) where PCV-13 vaccination was introduced in 2011. Retrospective analysis of S. pneumoniae demographic and microbiological data collected as part of the national AMR surveillance program from 2010 to 2021 was carried out. A survey of reporting sites and hand searching of annual reports of local health authorities was carried out to identify data on S. pneumoniae serotypes as this is not included in the AMR surveillance database. From 2010 to 2021, 11,242 non-duplicate S. pneumoniae isolates were reported, increasing from 324 in 2010 to 1,115 in 2021. Factoring in annual increment in the number of surveillance sites, the number of isolates per site showed an upward trajectory from 2015 to 2018 and declined in 2020 with the onset of the pandemic. The majority of isolates (n/N = 5,751/11,242; 51.2%) were from respiratory tract specimens with 44.5% (n/N = 2,557/5,751) being nasal colonizers. Up to 11.9% (n/N = 1,337/11,242) were invasive pneumococcal disease (IPD) isolates obtained from sterile site specimens including blood (n = 1,262), cerebrospinal (n = 52), pleural (n = 19) and joint (n = 4) fluid; and were predominantly from pediatric patients. The downward trend for amoxicillin and for penicillin G at the non-meningitis and meningitis as well as oral penicillin breakpoints was statistically significant. In contrast, increasing trends of resistance were seen for levofloxacin, moxifloxacin, trimethoprim/sulfamethoxazole and erythromycin. IPD and non-IPD isolates showed similar demographic and AMR trends. None of the surveillance sites carried out S. pneumoniae serotyping and handsearching of annual reports did not yield this information. The increasing trend of pneumococcal disease and AMR with emergence of isolates with MDR phenotype despite is of concern. In the absence of S. pneumoniae serotyping the role of non-vaccine serotypes in driving this pattern remains unknown. There is an urgent need for serotype, genomic and AMR surveillance of S. pneumoniae isolates in the UAE.

Pneumococcal conjugate vaccines in pediatrics, its impact on Public Health

Streptococcus pneumoniae (also known as pneumococcus) is part of the natural bacterial flora of the nasal and pharyngeal mucosa, colonizes mainly the nasopharynx, and causes this carriage to precede pneumococcal disease, thus becoming the main source of propagation among people, especially in children. Since 1983, when the first 23-component anti-pneumococcal vaccine was authorized, different conjugated vaccines have been developed according to the circulating serotypes that cause invasive pneumococcal diseases (IPD), reducing the incidence and mortality of these diseases considerably. In November 2021, a group of experts held a virtual meeting to update and analyze the impact that pneumococcal vaccines have generated on the countries' public health, especially during the COVID-19 pandemic. The recommendations that emerged included the need to look for alternatives in serotype-independent vaccines after the introduction of pneumococcal conjugate vaccines (PCV) in the national immunization schedules, as well as to strengthen the surveillance of serotypes, focusing on those not included in the current vaccines. The objective of this report is to communicate the conclusions of the group of experts that in November 2021 analyzed the impact of pneumococcal vaccines on public health in the countries, in order to generate recommendations applicable in Latin America.

Multiplex PCR to Streptococcus pneumoniae serotype identification directly in cerebrospinal fluid samples.

Streptococcus pneumoniae causes invasive diseases of significant public health concern, such as meningitis. The culture of cerebrospinal fluid (CSF) samples, the standard technique for meningitis diagnoses, is not always positive. Consequently, meaningful information about the etiological agent is lost, which can compromise effective epidemiological surveillance and the improvement of immunization policies. This study aims to standardize a method to genotype pneumococcus in the CSF samples which could mitigate the absence of isolated strains, and also evaluate the prediction of this assay. We applied eight multiplex PCR (mPCR) assays to CSF samples paired with the Quellung reaction applied to the isolated strains. We also compared different master mix kits in the mPCR. Moreover, a retrospective study was conducted with CSF samples considered pneumococcus positive due to the presence of the lytA gene. Results showed that genotyping by the mPCR correlated 100% with the Quellung reaction, and genotyping was dependent on the master mix applied. In the retrospective study (2014-2020), 73.4% were successfully genotyped. The analyses of the receiver operating characteristic curve showed that the cycle threshold (Ct value) around 30 for the lytA gene had a 75% positive chance of successful genotyping, whereas with a Ct value > 35, the chance was 12.5%. Finally, we observed that genotype 19A was prevalent in the period (12%), information unknown until now due to the lack of isolated strains. Therefore, the mPCR of CSF samples can efficiently predict S. pneumoniae serotypes, especially in the absence of isolated strains, which can be a great tool for pneumococcal serotype surveillance.

Invasive pneumococcal infections in France: Changes from 2009 to 2021 in antibiotic resistance and serotype distribution of Streptococcus pneumoniae based on data from the French Regional Pneumococcal Observatories network

ObjectiveThe 23 French Regional Pneumococcal Observatories (ORPs) analyzed antibiotic resistance and serotypes of Streptococcus pneumoniae strains isolated from invasive infections in France over a 12-year period. MethodsBetween 2009 and 2021, the ORPs analyzed 19,319 strains, including 1,965 in children and 17,354 in adults. Strains were assessed for their resistance to penicillin G, amoxicillin and cefotaxime. Serotypes were identified in collaboration with the National Reference Centre. ResultsDuring this period, the number of strains collected yearly decreased significantly. The decrease was particularly pronounced up until 2013, especially in children (-61.0%). However, penicillin non-susceptible strains (PNSPs) increased in children (24.7% in 2009 vs 45.0% in 2021, p < 0.0001) and in adults (27.1% in 2009 vs 31.3% in 2021, p < 0.05), as well as resistance (I + R) to amoxicillin (children: 12.5% in 2009 vs 19.4% in 2021, p < 0.05; adults: 13.4% in 2009 vs 14.5% in 2021, NS) and resistance (I + R) to cefotaxime (children: 8.0% in 2009 vs 13.1% in 2021, p < 0.05; adults: 7.1% in 2009 vs 11.9% in 2021, p < 0.0001). All in all, the proportion of strains belonging to serotypes present in the PCV13 vaccine has fallen sharply, from 64.8% in 2009 to 23.6 % in 2021. At the same time, serotypes such as 8, 10A, 11A, 15B/C and 9N, not included in PCV13, were increasing. ConclusionDuring the study period, data collected by the network highlighted an increase of invasive PNSPs in children and non-vaccine serotypes. Surveillance of resistance and serotypes remains instrumental, particularly to monitor the evolution of vaccine efficacy.

Pneumococcal meningitis in Greece: A retrospective serotype surveillance study in the post-PCV13 era (2010–2020)

BackgroundAs Greece is a country which has introduced the 13-valent pneumococcal conjugate vaccine (PCV13) both in the infant and in the adult immunization programs, the aim of the study was to investigate age-specific and serotype-specific trends of pneumococcal meningitis over an 11-year period (2010–2020). Materials and MethodsData are reported from pneumococcal meningitis cases [notified to the National Public Health Organization (NPHO)], with clinical samples and bacterial isolates sent for pneumococcal identification and serotyping at the National Meningitis Reference Laboratory (NMRL). Pneumococcal identification was performed directly on clinical samples or bacterial isolates by multiplex PCR (mPCR) assay, while serotyping was carried out by application of the Capsular Sequence Typing (CST) method with the combination of single tube PCR assays. ResultsA total of 427 pneumococcal meningitis cases were notified to the NPHO between 2010 and 2020. Among those, 405 (94.8%) were microbiologically confirmed, while samples from 273 patients were sent to the NMRL for identification and/or further typing. The annual notification rate peaked at 0.47/100,000 in 2016 and since then has been decreasing. The incidence was highest in infants and in older adults. Pneumococcal serotypes were identified in 260/273 (95.2%) cases, where clinical samples were sent to the NMRL. The most prevalent serotypes (≥5%) were 3, 19A, 23B, 15B/C, 11A/D, 23A, 22F. During the study period there has been a decrease of PCV13 serotypes combined with an increase of non-PCV13 serotypes (p = 0.0045). ConclusionsThis is the first study to report serotypes for pneumococcal meningitis across all ages in the post-PCV13 era in Greece. There is a need to enhance surveillance, by close monitoring of the emerging serotypes and the impact of vaccination programs. Higher-valency PCVs may help to improve the coverage of pneumococcal disease.

Impact of a Single-Tube PCR Assay for the Detection of Haemophilus influenzae Serotypes a, c, d, e and f on the Epidemiological Surveillance in Greece.

Background: The decrease in the rate of meningitis due to Haemophilus influenzae type b after vaccine introduction and a possible change in epidemiology of H. influenzae disease highlights the need for continuous serotype surveillance. Methods: A single-tube multiplex PCR assay for serotyping of H. influenzae was developed and deployed. Results: During 2003–2020, 108 meningitis cases due to H. influenzae were notified; 86 (80%) were confirmed and serotyped by molecular methods. The overall specificity and sensitivity of the assay were estimated (100% PPV and NPV respectively). The overall mean annual reported incidence for H. influenzae was 0.02, while for Hib and non-b meningitis equaled 0.02 and 0.03 per 100 000, respectively. Analysis by age group revealed that H. influenzae peaks in toddlers and children 0–4 years and in adults >45 years old. Among the serotyped cases, 39.8% were identified as Hib, 46.3% as NTHi, and 0.9% and 2.8% as serotypes a (Hia) and f (Hif)) respectively. Conclusions: Low incidence due to Hib was observed while non-typeable H. influenzae (NTHi) and serotypes Hia and Hif seem to emerge. The application of the current assay discloses the ongoing change of invasive H. influenzae disease trends during the Hib post-vaccine era.

Multicenter Surveillance of Capsular Serotypes, Virulence Genes, and Antimicrobial Susceptibilities of Klebsiella pneumoniae Causing Bacteremia in Taiwan, 2017-2019.

We conducted a longitudinal epidemiological surveillance of hypervirulent Klebsiella pneumoniae (hvKP) in Taiwan. Bacteremic KP isolates collected from 16 hospitals in Taiwan between 2017 and 2019 were collected, and the virulent serotypes (K1, K2, K20, K54, and K57), antimicrobial susceptibilities, and virulence genes of these isolates were investigated. During the 3-year period, 1,310 bacteremic KP isolates were collected, of which 27.5% belonged to virulent serotypes, including K1 (n = 162), K2 (n = 74), K57 (n = 56), K54 (n = 41), and K20 (n = 27). K1 was the most prevalent capsular serotype, with an annual prevalence of 11–15%, and was equally distributed across the four geographic areas. The prevalence of K2 declined significantly in 2019. According to wzi-K typing results, 87% of K1 isolates were classified as wzi-1. Among K2 isolates, wzi-72 (55.4%) and wzi-2 (41.9%) were the most common, whereas wzi-206 was the most prevalent (48.2%) among K57 isolates, followed by wzi-77 (25.0%). Wzi-115 accounted for 85.4% of the K54 isolates, whereas wzi-95 accounted for 92.6% of K20 isolates. rmpA was present in 99.4% of K1, 98.6% of K2, 89.3% of K57, 78.0% of K54, and 84.0% of K20 isolates. rmpA2 was present in 100% of K1 and 98.6% of K2 isolates but was only present in 64.3% of K57, 58.5% of K54, and 74.1% of K20 isolates. K1 remains the dominant hvKP serotype and is associated with most virulence genes in Taiwan. Further studies are required to elucidate the significance of other virulent serotypes.

Genesis of Antibiotic Resistance (AR) LXX: Mechanism(s) of heterogeneity due to Fickle vaccine campaign prodded selection of epitope pool confer vaccine resistance consequent AR Pandemic (ARP) ‐ An Episodic selection pressure provoked Bottle neck event driven genetic drift in gene flow

The precise evolutionary mechanisms underlying vaccination campaign followed by serotype surveillance, serotype (Antigenic) multiplicity, serotype(Antigenic) variation, serotype conversion, serotype replacement, serotype diversity, and ultimate vaccine break potential and their role in vaccine resistance is not well understood at present. It is known that vaccination does not protect a host against all known serotypes of the target pathogen while it is known that all hosts do not generate an identical immune response (PMCID: PMC6304978 / PMID: 30559199; PMID: 28356449 / PMCID: PMC5378080 ). For example, Yersinia ruckeri, the causative agent of enteric red mouth disease, was known to have two biotypes, a motile type with a flagellum [biotype 1(Bt1)] and a non-motile type that lacks a flagellum (Bt2) (J Fish Dis. 1989;12:357–365). An outbreak in vaccinated populations implied that the vaccine resistance could have been caused by Bt2 (PMID: 18236630). The flagellin, a defining difference between Bt1 and Bt2, (PMID: 26719024), was attributed to conferring vaccine resistance against Yersinia ruckeri. On the contrary, it was shown that bacterial isolates differ in their ability to cause disease in vaccinated hosts, regardless of the presence of a flagellum. Here we present a plausible evolutionary mechanism(s) for the evolution of novel serotypes, antigenic loss, antigenic drift and life-history modifications, pathogen adaptation which will eventually undermine existing and next-generation vaccines directed at a multitude of epitopes of a target pathogen. It is suggested that subsequent to the vaccination campaign, the pathogenic potential of the target epitope(s) of a given pathogen is subjected to natural selection process altering the pattern of distribution of antigenic variants by either one or more process: directional selection favoring the antigenic variants at the extreme either genotype of dominant or recessive traits, disruptive selection favoring the antigenic variants at both ends dominant/recessive traits, and stabilizing selection favoring the elimination of extreme variants either dominant or recessive from the pool of epitopes and preserving the intermediate variants mounting the resistance to any given type of vaccination protocol (p497 – 498: ISBN: 978 013 518 8743. Pearson, NY .2020). Persisters (PMID: 20528688; PMID: 28529326; PMID: 29857815; PMID: 30414937; PMID: 30082460; PMID: 31036343) subjected to vaccine exposure and evolutionary selection pressure would acquire adaptive evolution endowed with unpredictable fluctuation of antigenic variation from one generation to next generation (Genetic Drift), forming a totally new genotype and phenotype variation (Founder effect) with altered “gene flow” impeding the prophylactic efficacy of vaccines. Taken together, the aforesaid mechanisms suggested to play a pivotal role in the processes of hyper mutation-induced affinity maturation of epitope(s) pool of persisters conferring vaccine resistance.

The impact of childhood pneumococcal conjugate vaccine immunisation on all-cause pneumonia admissions in Hong Kong: A 14-year population-based interrupted time series analysis

BackgroundNine years after the introduction of pneumococcal conjugate vaccine (PCV) in the United States, Hong Kong (HK) introduced the vaccine to its universal childhood immunisation programme in 2009. We aimed to assess the impact of childhood PCV immunisation on all-cause pneumonia (ACP) admissions among the overall population of HK. MethodsIn this population-based interrupted time series analysis, we used territory-wide population-representative electronic health records in HK to evaluate the vaccine impact. We identified hospitalised patients with a diagnosis of pneumonia from any cause between 2004 and 2017. We applied segmented Poisson regression to assess the gradual change in the monthly incidence of ACP admissions between pre- and post-vaccination periods. Negative outcome control, subgroup and sensitivity analyses were used to test the robustness of the main analysis. FindingsOver the 14-year study period, a total of 587,607 ACP episodes were identified among 357,950 patients. The monthly age-standardised incidence of ACP fluctuated between 33.42 and 87.44 per 100,000-persons. There was a marginal decreasing trend in pneumonia admissions after PCV introduction among overall population (incidence rate ratio [IRR]: 0·9965, 95% confidence interval [CI]: 0·9932–0·9998), and older adults (≥65 years, IRR: 0·9928, 95% CI: 0·9904–0·9953) but not in younger age groups. InterpretationThere was a marginally declining trend of overall ACP admissions in HK up to eight years after childhood PCV introduction. The significance disappeared when fitting sensitivity analyses. The results indicate the complexities of using non-specific endpoints for measuring vaccine effect and the necessity of enhancing serotype surveillance systems for replacement monitoring. FundingHealth and Medical Research Fund, Food and Health Bureau of the Government of Hong Kong (Reference number: 18171272).

Non-vaccine serotype pneumococcal carriage in healthy infants in South Africa following introduction of the 13-valent pneumococcal conjugate vaccine.

Pneumococcal carriage studies provide a baseline for measuring the impact of pneumococcal conjugate vaccines (PCVs). The advent of conjugate vaccines has led to reductions in vaccine serotypes (VTs) in pneumococcal carriage. However, increasing non-vaccine serotypes (NVTs) remain a significant concern, necessitating continued surveillance of serotypes in the 13-valent PCV vaccine (PCV13) era. To investigate pneumococcal carriage, serotype distribution and risk factors for pneumococcal colonisation among children presenting for routine immunisation at two clinics in Gauteng Province, South Africa (SA), 10 years after PCV introduction into the SA Expanded Programme on Immunisation (EPI-SA). Nasopharyngeal swabs were collected from 322 healthy children aged between 6 weeks and 5 years at two clinic centres in 2014 and 2016. Demographic data, risk factors for colonisation and vaccination details were recorded. The pneumococcal isolates were serotyped and tested for antimicrobial susceptibility. Pneumococci were isolated from 138/316 healthy children (43.7%) presenting for routine immunisation at two clinics. The median age was 8.3 months and the age range 1.4 months - 5 years. Carriage varied across the age groups: 6 - 14 weeks 35.5%, 9 months 27.5%, 18months 21.7%, and 5 years 15.2%. Risk factors significantly associated with pneumococcal colonisation included young age (9 - 18months (odds ratio OR 3.5; 95% confidence interval (CI) 1.9 - 5.9), type of dwelling (single room (OR 8.1; 95% CI 1.3 - 52.3) or informal dwelling (OR 2.4; 95% CI 1.2 - 4.5)) and Haemophilus influenzae carriage (OR 5.6; 95% CI 0.6 - 2.5). Of the 26 serotypes detected, 19F (10/121; 8.3%) was the most frequent. The most frequent NVTs were 23B (16/121; 13.2%), 15B/C (14/121; 11.6 %) and 35B (11/121; 8.2%). Children aged 9 months carried the highest proportion of NVTs (33/101; 32.7%). Penicillin non-susceptibility was observed in 20 NVT isolates (20/36; 55.6%) and 2 VT isolates (2/36; 5.6%). The pneumococcal carriage prevalence described in our study varied across the age groups and was lower compared with other African studies that looked at pneumococcal carriage post PCV. The study gave insight into the common NVTs encountered at two immunisation clinics in Gauteng. Given that pneumococcal carriage precedes disease, common colonisers such as 15B/C and 35B may be sufficiently prevalent in carriage for expansion to result in significant disease replacement.

Utility of a Multiplex Real-Time Polymerase Chain Reaction for Combined Detection and Serotyping of Dengue Virus in Paediatric Patients Hospitalised with Severe Dengue: A Report from Chennai

AbstractObjective: Molecular detection and serotyping are rapid, sensitive and accurate techniques for early diagnosis of paediatric dengue. The present study evaluates multiplex real-time polymerase chain reaction (PCR) for diagnosis of dengue virus in children hospitalised with severe dengue (SD) and attempts to establish an association of clinical severity with specific serotypes. Methods: Four hundred and eighty-five samples were received from hospitalised paediatric patients with suspected dengue from March 2019 to February 2020. Multiplex real time PCR was employed for diagnosis. An in-house real-time PCR that combined diagnosis and serotyping was established. Non-structural protein 1 (NS1) assay and real-time PCR were assessed for their accuracy in diagnosing severe paediatric dengue. Results: Three hundred and twenty-five (67%) patients were positive for dengue RNA by real-time PCR. All four serotypes were identified throughout the year; dengue serotype 2 (DEN-2) was predominant (61%) followed by DEN-3, 20%. Compared to the commonly used NS1 testing, multiplex real-time PCR showed greater sensitivity in diagnosing SD. Conclusions: Compared to NS1, multiplex real-time PCR is a rapid and accurate diagnostic test for children hospitalised with SD. DEN-2 was the predominant serotype in severe cases. Continued surveillance of serotypes should be carried out year-round in endemic areas.

Differential Biophysical Behaviors of Closely Related Strains of Salmonella.

Salmonella is an important pathogen and is a world-wide threat to food safety and public health. Surveillance of serotypes and fundamental biological and biochemical studies are supported by a wide variety of established and emerging bioanalytical techniques. These include classic serotyping based on the Kauffmann–White nomenclature and the emerging whole genome sequencing strategy. Another emerging strategy is native whole cell biophysical characterization which has yet to be applied to Salmonella. However, this technique has been shown to provide high resolution differentiation of serotypes with several other paired strains of other microbes and pathogens. To demonstrate that biophysical characterization might be useful for Salmonella serotyping, the closely related strains sv. Cubana and sv. Poona were chosen for study. These two serovars were subjected to biophysical measurements on a dielectrophoresis-based microfluidic device that generated full differentiation of the unlabeled and native cells. They were differentiated by the ratio of electrophoretic (EP) to dielectrophoretic (DEP) mobilities. This differentiation factor is 2.7 ± 0.3 × 1010 V/m2 for sv. Cubana, versus 2.2 ± 0.3 × 1010 V/m2 for sv. Poona. This work shows for the first time the differentiation, concentration, and characterization of the Salmonella serotypes by exploiting their biophysical properties. It may lead to a less expensive and more decentralized new tool and method for microbiologists, complimenting and working in parallel with other characterization methods.

Pneumococcal serotype trends, surveillance and risk factors in UK adult pneumonia, 2013–18

BackgroundChanges over the last 5 years (2013–18) in the serotypes implicated in adult pneumococcal pneumonia and the patient groups associated with vaccine-type disease are largely unknown.MethodsWe conducted a population-based prospective...

2714. Streptococcus pneumoniae Nasopharyngeal Carriage in Canadian Adults Hospitalized with Community-Acquired Pneumonia from 2010 to 2017

Background Streptococcus pneumoniae can colonizes the human nasopharynx, and can cause life-threatening infections like community-acquired pneumonia (CAP) and invasive pneumococcal diseases (IPD). In Canada, the 13-valent conjugate vaccine (PCV13) was introduced in childhood immunization since 2010, with hopes that it would not only protect the vaccinated, but also confer indirect protection to adults through herd immunity. Given data on S. pneumoniae nasopharyngeal (NP) carriage in adults is scarce, this study reports on S. pneumoniae-positivity and serotype distribution in adult carriage from years 2010 to 2017.MethodsActive surveillance was performed in adults hospitalized with for CAP or IPD from December 2010 to 2017. For assessment of S. pneumoniae carriage, NP swabs were tested using lytA and cpsA real-time PCR. S. pneumoniae-positive NPs were subjected to serotyping using conventional and real-time multiplex PCRs.ResultsOverall, 6472 NP swabs were tested, and Spn was identified in 366 (5.7%). Of the 366 S. pneumoniae-positive NP swabs, a serotype was assigned in 355 (97.0%). From years 2010 to 2017, the proportion of S. pneumoniae-positive NP swabs declined from 8.9% to 4.3%. This was also reflected in the proportion of serotypeable results attributed to PCV13 serotypes, which also declined from 76.9% to 42.2%. The decline was primarily attributed to PCV13 serotypes 7F and 19A. PCV13 serotype 3 remained predominant throughout the study, as did non-PCV13 serotypes like 22F, 33F, and 11A. On the other hand, a proportional rise over time was noted for non-vaccine serotypes (from 15.4% to 31.1%). This was primarily attributed to serotypes 23A, 15A, and 35B.ConclusionMonitoring serotype trends is important to assess the impact of pneumococcal vaccines. While herd immunity from PCV13 childhood immunization was anticipated, few studies have assessed its impact on adult carriage. This study described Spn serotype distribution in adults over years 2010 to 2017, demonstrating not only a reduction of PCV13 serotypes over time, but a proportional rise in non-vaccine serotypes. These emerging serotypes may represent the emergence of serotype replacement. Ongoing serotype surveillance will be needed to compare S. pneumoniae carriage to serotypes associated with pneumococcal CAP and IPD.Disclosures All authors: No reported disclosures.