Evolución de los serotipos causantes de enfermedad neumocócica invasiva aislados durante 2008-2022 en un Hospital Público Madrileño de nivel dos, en relación con su inclusión en diferentes vacunas conjugadas / Evolution of the serotypes causing invasive pneumococcal disease along 2008-2022 in a Level 2 Public Hospital of the Madrid Region, in relation to their inclusion in different conjugate vaccines

Introducción. El uso de vacunas conjugadas frente a Streptococcus pneumoniae ocasiona cambios en la epidemio logía de la Enfermedad Neumocócica Invasiva (ENI). El objetivo de este estudio fue analizar la evolución de los serotipos de S. pneumoniae aislados en el Hospital Universitario de Getafe entre 2008 y 2022. Material y métodos. Se estudiaron 313 cepas de S. pneu moniae. El serotipado se realizó mediante el test de aglutina ción por látex (Pneumotest-latex) y la reacción de Quellung. Además, se determinó la concentración mínima inhibitoria (CMI) frente a penicilina, eritromicina y levofloxacino por el método de gradiente de concentración (E-test) según los cri terios de corte EUCAST. Resultados. Los serotipos más frecuentes en todo el pe riodo de estudio fueron 8, 3, 19A, 1, 11A y 22F correspondien do con el 46,6 % de los aislados. Durante los años 2008-2012, los serotipos 3, 1, 19A, 7F, 6C y 11A supusieron en conjunto el 53,6% de los aislamientos. Entre 2013 y 2017 los serotipos 3, 8, 12F, 19A, 22F y 19F representaron el 51% de los aislados. Entre 2018-2022 los serotipos 8, 3, 11A, 15A, 4 y 6C incluyeron al 55,5% de los casos. En total, 5 cepas (1,6%) se mostraron resistentes a penicilina, 64 (20,4%) resistentes a eritromicina y 11 (3,5%) resistentes a levofloxacino. Los niveles de CMI50 y CMI90 frente a los tres antibióticos se mantuvieron estables a lo largo del tiempo. Conclusiones. El uso de vacunas conjugadas condicionó un descenso de los serotipos cubiertos junto con un aumento de los no vacunales. Los patrones de sensibilidad a eritromicina y levofloxacino se mantuvieron relativamente estables. La re sistencia a penicilina fue muy baja, no encontrándose este tipo de cepas resistentes en el último periodo de estudio (AU)

Introduction. The use of conjugate vaccines against Streptococcus pneumoniae originates changes in the invasive pneumococcal disease (IPD). The aim of this study was to in vestigate the evolution of S. pneumoniae serotypes isolated in the Hospital Universitario de Getafe between 2008 and 2022. Material and Methods. 313 of S. pneumoniae strains were studied. Serotyping was carried out by latex agglutina tion (Pneumotest-latex) and the Quellung reaction. In addi tion, the minimal inhibitory concentration (MIC) was deter mined against penicillin, erythromycin and levofloxacin by the concentration gradient method (E-test) according the EUCAST breakpoints. Results. The most frequent serotypes throughout the study period were 8, 3, 19A, 1, 11A and 22F corresponding to 46.6% of the isolates. Along 2008-2012 the serotypes 3, 1, 19A, 7F, 6C and 11A represented altogether 53.6% of the isolates. Between 2013 and 2017 the serotypes 3, 8, 12F, 19A, 22F and 19F grouped 51% of the isolates. During 2018-2022 the serotypes 8, 3, 11A, 15A, 4 and 6C included the 55.5% of the cases. In total 5 strains (1.6%) were penicillin resistant, 64 (20.4%) erythromycin resistant and 11 (3.5%) levofloxacin re sistant. The MIC50 and MIC90 levels maintained stables along the time. Conclusion. The conjugate vaccines use with different se rotype coverage conditioned a decrease of the vaccine-includ ed and an increase of non-covered. Despite these changes, the global antimicrobial susceptibility patterns to erythromycin and levofloxacin maintained relatively stables. The resistance a penicillin was low, not finding this type of resistant strains in the last study period (AU)

Identifying Children Likely to Benefit From Antibiotics for Acute Sinusitis: A Randomized Clinical Trial.

Importance: The large overlap between symptoms of acute sinusitis and viral upper respiratory tract infection suggests that certain subgroups of children being diagnosed with acute sinusitis, and subsequently treated with antibiotics, derive little benefit from antibiotic use. Objective: To assess if antibiotic therapy could be appropriately withheld in prespecified subgroups. Design, Setting, and Participants: Randomized clinical trial including 515 children aged 2 to 11 years diagnosed with acute sinusitis based on clinical criteria. The trial was conducted between February 2016 and April 2022 at primary care offices affiliated with 6 US institutions and was designed to evaluate whether symptom burden differed in subgroups defined by nasopharyngeal Streptococcus pneumoniae, Haemophilus influenzae, or Moraxella catarrhalis on bacterial culture and by the presence of colored nasal discharge. Interventions: Oral amoxicillin (90 mg/kg/d) and clavulanate (6.4 mg/kg/d) (n = 254) or placebo (n = 256) for 10 days. Main Outcomes and Measures: The primary outcome was symptom burden based on daily symptom scores on a validated scale (range, 0-40) during the 10 days after diagnosis. Secondary outcomes included treatment failure, adverse events including clinically significant diarrhea, and resource use by families. Results: Most of the 510 included children were aged 2 to 5 years (64%), male (54%), White (52%), and not Hispanic (89%). The mean symptom scores were significantly lower in children in the amoxicillin and clavulanate group (9.04 [95% CI, 8.71 to 9.37]) compared with those in the placebo group (10.60 [95% CI, 10.27 to 10.93]) (between-group difference, -1.69 [95% CI, -2.07 to -1.31]). The length of time to symptom resolution was significantly lower for children in the antibiotic group (7.0 days) than in the placebo group (9.0 days) (P = .003). Children without nasopharyngeal pathogens detected did not benefit from antibiotic treatment as much as those with pathogens detected; the between-group difference in mean symptom scores was -0.88 (95% CI, -1.63 to -0.12) in those without pathogens detected compared with -1.95 (95% CI, -2.40 to -1.51) in those with pathogens detected. Efficacy did not differ significantly according to whether colored nasal discharge was present (the between-group difference was -1.62 [95% CI, -2.09 to -1.16] for colored nasal discharge vs -1.70 [95% CI, -2.38 to -1.03] for clear nasal discharge; P = .52 for the interaction between treatment group and the presence of colored nasal discharge). Conclusions: In children with acute sinusitis, antibiotic treatment had minimal benefit for those without nasopharyngeal bacterial pathogens on presentation, and its effects did not depend on the color of nasal discharge. Testing for specific bacteria on presentation may represent a strategy to reduce antibiotic use in this condition. Trial Registration: ClinicalTrials.gov Identifier: NCT02554383.

Capsular typing of Streptococcus pneumoniae isolated from clinical specimens in Gauhati Medical College and hospital, Assam, India.

PURPOSE: Streptococcus pneumoniae is an important human respiratory tract pathogen causing pneumococcal diseases in majority of children and adults. The capsule is a significant virulence factor of Pneumococci which determines the bacterial serotype and is the component used for synthesis of pneumococcal vaccines. This cross-sectional study aimed to isolate Streptococcus pneumoniae from clinical samples and determine the occurrence of its circulating serotypes in Assam, North East India. MATERIALS AND METHODS: A total of 80 clinical samples were collected from June 2019 to May 2020 from patients clinically suspected from pneumococcal infection and also included samples routinely sent to bacteriology laboratory. Isolation and identification of S. pneumoniae was performed using conventional culture and molecular methods. Antibiotic susceptibility patterns were monitored. Capsular serotyping was performed using PCR of cpsA gene followed by DNA sequencing. RESULTS: Majority of the cases suspected of pneumococcal infection belong to the paediatric group aged less than 5 years. Out of 80 samples, 10 (12.50%) were found to be positive by PCR of recP gene. Culture was positive in 80% (8/10) of the total positives. Co-trimoxazole resistance was seen in 33.33% of the isolate from sputum. Serotypes 6A, 6B, 6C and 19F were detected in our region, out of which 6C is a non-vaccine serotype. CONCLUSION: Continued surveillance is needed to monitor trends in non-vaccine serotypes that may emerge as highly associated with antibiotic resistance. Also, the need to continuous monitoring of the antibiotic susceptibility of S. pneumoniae in North eastern parts of India is of outmost importance.

Neumonía asociada a ventilación mecánica en pacientes con neumonía grave por SARS-CoV-2 / Ventilation associated pneumonia in patients with severe SARS-CoV-2 pneumonia

Introducción: Los pacientes con COVID-19 pueden evolucionar hacia una falla respiratoria aguda grave y requerir ventilación mecánica invasiva (VMI). La complicación más frecuente en estos pacientes es la neumonía asociada a ventilación mecánica (NAVM), con incidencias reportadas más altas que en la época pre-COVID. El objetivo de este estudio es reportar la incidencia, tasa de incidencia y microbiología de la NAVM en pacientes en VMI con COVID-19. Métodos: Se incluyeron a todos los pacientes con neumonía grave y PCR (+) para SARS-CoV-2 que ingresaron y requirieron VMI entre marzo y julio del 2021 en el Instituto Nacional del Tórax (INT). Se recolectaron datos demográficos, clínicos y de laboratorio de la ficha electrónica. Se registraron y caracterizaron los casos de neumonía asociado a la ventilación mecánica. Resultados: Se incluyeron 112 pacientes de los cuales el 42,8% presentó NAVM, con una tasa de incidencia de 28,8/1.000 días de VMI. Los microorganismos aislados más frecuentes fueron Klebsiella pneumoniae (29,6%), Staphylococcus aureus (21,8%) y Pseudomonas aeruginosa (12,5%). Los pacientes que cursaron NAVM estuvieron casi el doble de tiempo en VMI, pero sin presentar aumento de la mortalidad. Conclusión: La NAVM es una complicación frecuente en los pacientes con neumonía grave asociada a COVID-19. La microbiología de estas entidades no ha cambiado respecto a la era pre-pandémica. Estos resultados cobran relevancia en el inicio y suspensión de antibióticos en este grupo de pacientes.

Introduction: Patients with COVID-19 can progress to severe acute respiratory failure and require invasive mechanical ventilation (IMV). The most frequent complication in these patients is ventilator-associated pneumonia (VAP), with higher reported incidences than in the pre-COVID era. The objective of this study is to report the prevalence, incidence rate and microbiology of VAP in patients on IMV with COVID-19. Methods: Patients with severe pneumonia and PCR (+) for SARS-CoV-2 who were admitted to IMV between march and july 2021 at the Instituto Nacional del Tórax (Chile) were included. Demographic, clinical and laboratory data from electronic records were collected. Cases of pneumonia associated with mechanical ventilation were recorded and characterized. Results: 112 patients were included, 42.8% of them presented VAP with an incidence rate of 28.8/1,000 IMV days. The most frequent isolated microorganisms were Klebsiella pneumoniae (29.6%), Staphylococcus aureus (21.8%) and Pseudomonas aeruginosa (12.5%). Patients who underwent VAP spent almost twice as long on IMV, although they had not increase in mortality. Conclusion: VAP is a common complication in patients with severe pneumonia associated with COVID-19. The microbiology of these entities has not changed from the pre-pandemic era. These results become relevant in the initiation and suspension of antibiotics in this group of patients.

[The study of microbiota in patients with bullous lesions of the oral mucosa]. / Izuchenie mikrobioty slizistoi obolochki rta u patsientov s bulleznymi porazheniyami.

THE AIM OF THE STUDY: The study by the method of tissue polymerase chain reaction of the species composition of the microbiota of lesions of the oral mucosa in patients with bullous lesions. MATERIAL AND METHODS: Biopsy specimens of the oral mucosa of 51 patients were studied by the polymerase chain reaction method, of which 14 patients with pemphigus vulgaris, 17 patients with pemphigoid bullosa, and 20 patients with the bullous form of ruber lichen planus. 4 types of microorganisms have been identified - Fusobacterium, Streptococcus pneumoniae, Candida albicans, Ureaplasma spp. and viruses - Human Papillomavirus 16, Epstein-Barr virus and Citomegalovirus. RESULTS: In the study of the microbiota of bullous lesions, associations of microorganisms and viruses were established in a significant number of cases. Associations of Str.pneumoniae and C. albicans were quite common in patients with pemphigus vulgaris in 26.3%, pemphigoid bullosa in 20.0%, and in patients with the bullous form of ruber lichen planus in 14.3% of cases. In patients with pemphigus vulgaris, the association of Str.pneumoniae, C. albicans and EBV was noted in 31.6% of cases. In patients with the bullous form of ruber lichen planus in a high percentage of cases (28.6%), the associations of Str. pneumoniae, EBV and CMV. CONCLUSION: Identification at earlier stages of management of patients with bullous lesions Str. pneumoniae, Candida albicans, and Fusobacterium associated with herpes viruses should be regarded as one of the triggering mechanisms of an autoimmune conflict, which subsequently causes a specific clinical picture of these diseases.

Fatal Pediatric Streptococcal Infection: A Clinico-Pathological Study.

PURPOSE AND CONTEXT: Streptococcal Infection (SI) is an important cause of pediatric death in children, yet limited reports exist on autopsy findings in fatal SI cases. METHOD: Case records (1997-2019) of SI with no pre-existing risk factors were reviewed and selected. Their clinical and pathological findings in the autopsy reports were analyzed. RESULTS: In our cohort of 38 cases based on bacterial culture results, SI was most commonly caused by Streptococcus pneumoniae (SPn; 45%) and Streptococcus pyogenes (SPy; 37%). 92% of decedents had some prodromal symptoms prior to terminal presentation. The clinical course was often rapid, with 89% found unresponsive, suddenly collapsing, or dying within 24 hours of hospital admission. 64% of deaths were attributed to sepsis, more frequently diagnosed in the SPy group than in the SPn group (71% vs 48%). Pneumonia was found in both SPn and SPy groups, whereas meningitis was exclusively associated with SPn. CONCLUSION: Our study shows fatal SI is most commonly caused by either SPn or SPy, both of which are frequently associated with prodromal symptoms, rapid terminal clinical course, and evidence of sepsis. Postmortem diagnosis of sepsis is challenging and should be correlated with clinical features, bacterial culture results, and autopsy findings.

Pneumococcal meningitis in adults in 2014-2018 after introduction of pediatric 13-valent pneumococcal conjugate vaccine in Japan.

We assessed the impact of the pediatric 13-valent pneumococcal conjugate vaccine (PCV13) on pneumococcal meningitis in adults in Japan in 2014-2018 by comparing epidemiological characteristics of adults with invasive pneumococcal disease with (n = 222) and without (n = 1258) meningitis. The annual incidence of pneumococcal meningitis in 2016-2018 was 0.20-0.26 cases/100,000 population. Age (p < 0.001) and case fatality rate (p = 0.003) were significantly lower in patients with meningitis than in those without meningitis. The odds of developing meningitis were higher in asplenic/hyposplenic or splenectomized patients (adjusted odds ratio [aOR] 2.29, 95% CI 1.27-4.14), for serotypes 10A (aOR 3.26, 95% CI 2.10-5.06) or 23A (aOR 3.91, 95% CI 2.47-6.19), but lower for those aged ≥ 65 years (aOR 0.59, 95% CI 0.44-0.81). PCV13 had an indirect effect on nonmeningitis, but its impact on meningitis was limited because of an increase in non-PCV13 serotypes. Of meningitis isolates, 78 (35.1%) and 3 (1.4%) were penicillin G- or ceftriaxone-resistant, respectively. We also confirmed an association of the pbp1bA641C mutation with meningitis (aOR 2.92, 95% CI 1.51-5.65).

Comparison of pneumococcal colonization density among healthy children and children with respiratory symptoms using real time PCR (RT-PCR).

BACKGROUND: Nasopharyngeal colonization is considered a necessary step in the initiation of pneumococcal diseases. Real time PCR (RT-PCR) is an alternative approach for the identification and quantification of pneumococci directly from samples. OBJECTIVES: To compare pneumococcal detection rates using culture-based method versus RT-PCR direct detection and to quantify pneumococcal colonization in two study cohorts (healthy children and hospitalized children with respiratory symptoms) using quantitation through RT-PCR. METHODOLOGY: A total of 101 nasopharyngeal swabs (NPS) from healthy children and 183 NPSs from hospitalized children with respiratory symptoms were included in the study. None of the children were vaccinated. All children were between 2 months to 2 years. In parallel to routine culture and identification, a RT-PCR assay targeting the lytA gene was done. RESULTS: Considering all 284 samples tested, colonization rate by conventional culture was 41.2% (n = 117) while positive colonization using RT-PCR was 43.7% (n = 124). The colonization rate detected by RT-PCR in the healthy cohort was 33.7% (n = 34) and it was 49.2% (n = 90) in the hospitalized cohort. It was 37.6% (n = 38) and 43.2% (n = 79) for the two cohorts by culture. The mean Cq value for the healthy cohort is 29.61 (SD 2.85) and 28.93 (SD 3.62) for the hospitalized cohort. With the standard curve obtained from amplifying a dilution series of control DNA, the mean amount of genomic DNA copy numbers detected in children with respiratory symptoms was log10 7.49 (SD 1.07) while it was log10 7.30 (SD 0.23) in healthy children and the difference was not statistically significant. CONCLUSIONS: The overall colonization rate was higher when detected using RT-PCR compared to culture. However, it was lower in the healthy group when detected with RT-PCR compared to culture. Even though there was a higher detection of pneumococcal colonization density in children with respiratory symptoms, this was not significantly higher unlike many previous studies. Therefore, the use of RT-PCR to detect pneumococcal colonization needs further evaluation with careful analysis of interpretation and confounders.

Association between household air pollution and nasopharyngeal pneumococcal carriage in Malawian infants (MSCAPE): a nested, prospective, observational study.

BACKGROUND: Household air pollution from solid fuels increases the risk of childhood pneumonia. Nasopharyngeal carriage of Streptococcus pneumoniae is a necessary step in the development of pneumococcal pneumonia. We aimed to assess the association between exposure to household air pollution and the prevalence and density of S pneumoniae carriage among children. METHODS: The Malawi Streptococcus pneumoniae Carriage and Air Pollution Exposure study was a nested, prospective, observational study of children participating in the cluster randomised controlled Cooking and Pneumonia Study (CAPS) in the Karonga Health and Demographic Surveillance System (HDSS) area in northern Malawi. CAPS compared the effects of a cleaner burning biomass-fuelled cookstove (intervention group) with traditional open-fire cooking (control group) on the incidence of pneumonia in children. Eligible children aged 6 weeks or 6 months (those recruited a 6 weeks were also followed up at age 6 months) were identified by the Karonga HDSS centre. Nasopharyngeal swabs were taken to detect S pneumoniae, and infant exposure to particulate matter with a diameter of ≤2·5 µm (PM2·5) exposure was assessed by use of a MicroPEM device. The primary outcome was the prevalence of nasopharyngeal S pneumoniae carriage in all children aged 6 months, assessed in all children with valid data on PM2·5. The effects of the intervention stoves (intention-to-treat analysis) and PM2·5 (adjusted exposure-response analysis) on the prevalence of S pneumoniae carriage were also assessed in the study children. FINDINGS: Between Nov 15, 2015, and Nov 2, 2017, 485 children were recruited (240 from the intervention group and 245 from the control group). Of all 450 children with available data at age 6 months, 387 (86% [95% CI 82-89]) were positive for S pneumoniae. Geometric mean PM2·5 exposure was 60·3 µg/m3 (95% CI 55·8-65·3) in S pneumoniae-positive children and 47·0 µg/m3 (38·3-57·7) in S pneumoniae-negative children (p=0·044). In the intention-to-treat analysis, a non-significant increase in the risk of S pneumoniae carriage was observed in intervention group children compared with control group children (odds ratio 1·36 [95% CI 0·95-1·94]; p=0·093). In the exposure-response analysis, a significant association between PM2·5 exposure and S pneumoniae carriage was observed; a one unit increase in decile of PM2·5 was found to significantly increase the risk of S pneumoniae carriage by 10% (1·10 [1·01-1·20]; p=0·035), after adjustment for age, sex, 13-valent pneumococcal conjugate vaccination status, season, current use of antibiotics, and MicroPEM run-time. INTERPRETATION: Despite the absence of effect from the intervention cookstove, household air pollution exposure was significantly associated with the prevalence of nasopharyngeal S pneumoniae carriage. These results provide empirical evidence for the potential mechanistic association between exposure to household air pollution and childhood pneumonia. FUNDING: Bill & Melinda Gates Foundation.

Childhood Invasive Bacterial Disease in Kathmandu, Nepal (2005-2013).

BACKGROUND: Invasive bacterial disease (IBD; including pneumonia, meningitis, sepsis) is a major cause of morbidity and mortality in children in low-income countries. METHODS: We analyzed data from a surveillance study of suspected community-acquired IBD in children <15 years of age in Kathmandu, Nepal, from 2005 to 2013 before introduction of pneumococcal conjugate vaccines (PCV). We detailed the serotype-specific distribution of invasive pneumococcal disease (IPD) and incorporated antigen and PCR testing of cerebrospinal fluid (CSF) from children with meningitis. RESULTS: Enhanced surveillance of IBD was undertaken during 2005-2006 and 2010-2013. During enhanced surveillance, a total of 7956 children were recruited of whom 7754 had blood or CSF culture results available for analysis, and 342 (4%) had a pathogen isolated. From 2007 to 2009, all 376 positive culture results were available, with 259 pathogens isolated (and 117 contaminants). Salmonella enterica serovar Typhi was the most prevalent pathogen isolated (167 cases, 28% of pathogens), followed by Streptococcus pneumoniae (98 cases, 16% pathogens). Approximately, 73% and 78% of pneumococcal serotypes were contained in 10-valent and 13-valent PCV, respectively. Most cases of invasive pneumococcal disease (IPD) were among children ≥5 years of age from 2008 onward. Antigen and PCR testing of CSF for pneumococci, Haemophilus influenzae type b and meningococci increased the number of these pathogens identified from 33 (culture) to 68 (culture/antigen/PCR testing). CONCLUSIONS: S. enterica serovar Typhi and S. pneumoniae accounted for 44% of pathogens isolated. Most pneumococcal isolates were of serotypes contained in PCVs. Antigen and PCR testing of CSF improves sensitivity for IBD pathogens.

Multiplex polymerase chain reaction detection of Streptococcus pneumoniae and Haemophilus influenzae and their antibiotic resistance in patients with community-acquired pneumonia from southwest Iran.

BACKGROUND: This study aimed to evaluate the occurrence of Streptococcus pneumoniae and Haemophilus influenzae in sputum of patients with community-acquired pneumonia (CAP) using culture and multiplex polymerase chain reaction (M-PCR) methods and to survey the antibiotic resistance patterns of aforesaid isolates. RESULT: In total, 23.9 % (n = 22/92) of sputum samples showed positive results in the culture method. S. pneumoniae and H. influenzae were isolated from 15 (16.3 %) and 7 (7.6%) samples, respectively. Using M-PCR, 44 (47.8 %) samples were positive for S. pneumoniae and H. influenzae. Of these, S. pneumoniae and H. influenzae were detected in 33 (35.8%) and 11 (11.9%) of the sputum samples, respectively. The sensitivity, specificity, and accuracy rates of PCR in detection of S. pneumoniae in comparison with culture method were 100, 76.6, and 83.6%, respectively. While, the sensitivity, specificity, and accuracy rates of PCR in detection of H. influenzae in comparison with culture method were 100, 95.3, and 95.8%, respectively. Out of 11 isolates of H. influenzae, two strains confirmed as H. influenzae type b (Hib) and 3 isolates were type f. However, 6 isolates were non-typable. The co-trimoxazole and amoxicillin/clavulanate were the less effective antibiotics against S. pneumonia and H. influenzae, respectively. Ceftriaxone with 13.3% resistance rates was the most effective antibiotic against S. pneumoniae, while, clarithromycin, ceftriaxone, and gentamicin with resistance rates of 28.6% for each one were the most effective chemicals against H. influenzae isolates. CONCLUSION: In this study, the prevalence of S. pneumoniae was more than H. influenzae using culture and M-PCR methods. The M-PCR provided better efficiency in detecting the bacterial agents in CAP patients compared to culture method. This method can improve the early detection of pathogens contributed to CAP. The drug resistant S. pneumoniae and H. influenzae indicated the need to develop a codified monitoring program to prevent further spread of these strains.

Antimicrobial Resistance in Pneumococcal Carriage Isolates from Children under 2 Years of Age in Rural Pakistan.

Antimicrobial resistance is an emerging public health concern. Ten-valent pneumococcal vaccine (PCV10) was introduced in Pakistan's Expanded Program on Immunization (EPI) in 2012 as a 3 + 0 schedule without catchup. From 2014 to 2018, children <2 years were randomly selected in two rural union councils of Matiari, Pakistan. Nasopharyngeal swabs were collected using standard WHO guidelines by trained staff and processed at Infectious Disease Research Laboratory at The Aga Khan University, Karachi using culture on sheep blood agar and Multiplex PCR methods described by CDC, USA. Pneumococcal isolates were identified by optochin sensitivity and bile solubility tests. Isolates were then tested for antimicrobial susceptibility by standard Kirby-Bauer disk-diffusion method on Mueller-Hinton Agar (MHA) with 5% sheep blood agar as per Clinical & Laboratory Standards Institute (CLSI) recommendations. Of 3140 children enrolled, pneumococcal isolates were detected in 2370 (75%). Vaccine coverage improved from 41% to 68.4%. Out of the 2370 isolates, 88.4%, 37.6% and 25% were resistant to cotrimoxazole, tetracycline and erythromycin, respectively. There was no resistance to penicillin, ceftriaxone, and vancomycin. For erythromycin, resistance increased from 20% in 2014/15 to 30.8% in 2017/18 and for tetracycline it increased from 34.9% to 41.8% both of which were explained by an increase in prevalence of serotype 19A. Pneumococcal isolates were susceptible to penicillin, ceftriaxone, and vancomycin. They were largely resistant to cotrimoxazole and tetracycline. There was an increase in erythromycin and tetracycline resistance attributed to increasing prevalence of serotype 19A. Pneumococcal isolates from carriage and invasive disease should be closely monitored for antimicrobial susceptibility. IMPORTANCE Antimicrobial resistance is an emerging public health concern particularly in low- and middle-income countries where there is poor regulation and easy availability of antibiotics. This is the first study from Pakistan to report antimicrobial resistance patterns of pneumococcus after vaccine introduction in the community. Pakistan was the first South-Asian country to introduce PCV10 in its Expanded Program on Immunization (EPI) in 2012 as a 3 + 0 schedule without catchup. In this study, we describe the PCV10 impact on antimicrobial resistance patterns of pneumococcal nasopharyngeal carriage in children younger than 2 years of age in a rural district in Pakistan after the introduction of the vaccine.

Serotypes and Clonal Composition of Streptococcus pneumoniae Isolates Causing IPD in Children and Adults in Catalonia before 2013 to 2015 and after 2017 to 2019 Systematic Introduction of PCV13.

The goal of this study was to investigate the distribution of serotypes and clonal composition of Streptococcus pneumoniae isolates causing invasive pneumococcal disease (IPD) in Catalonia, before and after systematic introduction of PCV13. Pneumococcal strains isolated from normally sterile sites obtained from patients of all ages with IPD received between 2013 and 2019 from 25 health centers of Catalonia were included. Two study periods were defined: presystematic vaccination period (2013 and 2015) and systematic vaccination period (SVP) (2017 to 2019). A total of 2,303 isolates were analyzed. In the SVP, there was a significant decrease in the incidence of IPD cases in children 5 to 17 years old (relative risk [RR] 0.61; 95% confidence interval [CI] 0.38 to 0.99), while there was a significant increase in the incidence of IPD cases in 18- to 64-year-old adults (RR 1.33; 95% CI 1.16 to 1.52) and adults over 65 years old (RR 1.23; 95% CI 1.09 to 1.38). Serotype 8 was the major emerging serotype in all age groups except in 5- to 17-year-old children. In children younger than 5 years old, the main serotypes in SVP were 24F, 15A, and 3, while in adults older than 65 years they were serotypes 3, 8, and 12F. A significant decrease in the proportions of clonal complexes CC156, CC191, and ST306 and an increase in those of CC180, CC53, and CC404 were observed. A steady decrease in the incidence of IPD caused by PCV13 serotypes indicates the importance and impact of systematic vaccination. The increase of non-PCV13 serotypes highlights the need to expand serotype coverage in future vaccines and rethink vaccination programs for older adults. IMPORTANCE We found that with the incorporation of the PCV13 vaccine, the numbers of IPD cases caused by serotypes included in this vaccine decreased in all of the age groups. Still, there was an unforeseen increase of the serotypes not included in this vaccine causing IPD, especially in the >65-year-old group. Moreover, a significant increase of serotype 3 included in the vaccine has been observed; this event has been reported by other researchers. These facts call for the incorporation of more serotypes in future vaccines and a more thorough surveillance of the dynamics of this microorganism.

Molecular surveillance of pneumococcal carriage following completion of immunization with the 13-valent pneumococcal conjugate vaccine administered in a 3 + 1 schedule.

In a cross-sectional study, with the use of molecular methods, we aimed to gain insight into oropharyngeal pneumococcal colonization over time in 1212 Greek children recruited in general pediatric settings throughout the country; they were fully vaccinated with PCV13 (3 + 1 schedule). A single sample was obtained from each child at a time interval of 26 days to 70 months after administration of the 4th (booster) PCV13 dose; sampling time was divided into six time intervals. Carriage of Streptococcus pneumoniae was detected by real-time PCR targeting the lytA gene and isolates were serotyped by singleplex real-time PCR assays. Multiple control procedures to avoid false-positive results were applied. We showed an overall S. pneumoniae carriage rate of 48.6%. Serotyping identified typeable isolates in 82% of the total lytA-positive samples. Non-PCV13 serotypes represented 83.8% of total isolates when excluding serogroups with mixed PCV13 and non-PCV13 serotypes. In multivariate analysis daycare/school attendance emerged as the main contributing factor. Notably, serotypes 19A and 3 were the only two PCV13 serotypes the colonization rate of which increased over time (χ2 for trend P < 0.001 and P = 0.012, respectively). The application of the SP2020 gene on lytA-positive serotyped samples showed pneumococcal colonization in 97% of cases, and the overall colonization profile over time closely resembled that of the lytA gene. With the provisions of the methodological approach and age group of our study, the use of the oropharynx emerges as a reliable alternative to the nasopharynx in estimating pneumococcal carriage in epidemiological studies.

Rapid Diagnostic Tests to Guide Case Management of and Improve Antibiotic Stewardship for Pediatric Acute Respiratory Illnesses in Resource-Constrained Settings: a Prospective Cohort Study in Southwestern Uganda.

Pediatric acute respiratory illness (ARI) is one of the most common reasons for evaluation at peripheral health centers in sub-Saharan Africa and is frequently managed based on clinical syndrome alone. Although most ARI episodes are likely caused by self-limited viral infections, the majority are treated with antibiotics. This overuse contributes to the development of antimicrobial resistance. To evaluate the preliminary feasibility and potential impact of adding pathogen-specific and clinical biomarker diagnostic testing to existing clinical management algorithms, we conducted a prospective, observational cohort study of 225 children presenting with malaria-negative, febrile ARI to the outpatient department of a semi-urban peripheral health facility in southwestern Uganda from October 2019 to January 2020. In addition to routine clinical evaluation, we performed influenza and Streptococcus pneumoniae antigen testing and measured levels of C-reactive protein, procalcitonin, and lactate in the clinic's laboratory, and conducted a follow-up assessment by phone 7 days later. Almost one-fifth of participants (40/225) tested positive for influenza. Clinical biomarker measurements were low with C-reactive protein of >40 mg/L in only 11% (13/222) of participants and procalcitonin >0.25 ng/mL in only 13% (16/125). All but two children received antibiotic treatment; only 3% (7/225) were admitted. At follow-up, 59% (118/201) of caregivers reported at least one persistent symptom, but fever had resolved for all children. Positive influenza testing was associated with persistent symptoms. In summary, we demonstrate that simple, rapid pathogen-specific testing and biomarker measurement are possible in resource-limited settings and could improve syndromic management and, in turn, antibiotic stewardship. IMPORTANCE Globally, respiratory illness is one of the most common reasons that children seek care. It is often treated inappropriately with antibiotics, which can drive the development of antibiotic resistance. In resource-rich settings, testing for specific pathogens or measurement of clinical biomarkers, such as procalcitonin and C-reactive protein, is often employed to help determine which children should receive antibiotics. However, there are limited data on the use of these tests in resource-constrained, outpatient contexts in sub-Saharan Africa. We enrolled children with respiratory illness presenting to a clinic in southwestern Uganda and performed testing for influenza, Streptococcus pneumoniae, C-reactive protein, and procalcitonin on-site. Almost all children received antibiotics. We demonstrate that employing clinical algorithms that include influenza and clinical biomarker testing could significantly decrease antibiotic prescriptions. Our study therefore provides preliminary data to support the feasibility and potential utility of diagnostics to improve management of respiratory illness in resource-constrained settings.

Pneumococcal Carriage Among Indigenous Kichwa Children From the Ecuadorian Andes After the 10-Valent Pneumococcal Vaccine Introduction.

BACKGROUND: We assessed nasopharyngeal pneumococcal carriage in Andean Kichwa children, the largest Amerindian indigenous population in the Ecuadorian Andes. All children in our study had been vaccinated with the 10-valent pneumococcal vaccine (PCV10). METHODS: Nasopharyngeal swabs from 63 families, 100 children <10 years old including 38 children under 5 years and 63 adult caregivers, from 5 different communities, were cultivated for Streptococcus pneumoniae and isolates were serotyped and antibiotic susceptibility testing was performed. RESULTS: Respectively, 67% of the 38 children under 5 years old, 49% of the 62 children between 6 and 10 years old and 16% of the 100 adults were colonized with S. pneumoniae. Of these, 30.9% carried a vaccine serotype, 5.4% a serotype shared by the PCV10/13-valent pneumococcal vaccine (PCV13) vaccine and 25.5% a PCV13 serotype or PCV13 vaccine-related serotype, with 19A (10.9%) and 6C (10.9%) as the most prominent. Drug susceptibility testing revealed that 46% of the S. pneumoniae strains were susceptible to 6 tested antibiotics. However, 20.3% of the strains were multidrug-resistant or extensively drug-resistant strains, including 82% of the vaccine (-related) serotype 19A and 6C strains. CONCLUSIONS: Kichwa children, vaccinated with PCV10, were highly colonized with pneumococci and should be considered a high-risk group for pneumococcal disease. Twenty-five percent of the colonizing S. pneumoniae strains were PCV13-only vaccine-targeted serotypes, and in addition to that, most were multidrug-resistant or extensively drug-resistant strains. The vaccine benefits for this population possibly will significantly increase with the introduction of PCV13.

Genomic surveillance of invasive Streptococcus pneumoniae isolates in the period pre-PCV10 and post-PCV10 introduction in Brazil.

In 2010, Brazil introduced the 10-valent pneumococcal conjugate vaccine (PCV10) into the national children's immunization programme. This study describes the genetic characteristics of invasive Streptococcus pneumoniae isolates before and after PCV10 introduction. A subset of 466 [pre-PCV10 (2008-2009): n=232, post-PCV10 (2012-2013): n=234;<5 years old: n=310, ≥5 years old: n=156] pneumococcal isolates, collected through national laboratory surveillance, were whole-genome sequenced (WGS) to determine serotype, pilus locus, antimicrobial resistance and genetic lineages. Following PCV10 introduction, in the <5 years age group, non-vaccine serotypes (NVT) serotype 3 and serotype 19A were the most frequent, and serotypes 12F, 8 and 9 N in the ≥5 years old group. The study identified 65 Global Pneumococcal Sequence Clusters (GPSCs): 49 (88 %) were GPSCs previously described and 16 (12 %) were Brazilian clusters. In total, 36 GPSCs (55 %) were NVT lineages, 18 (28 %) vaccine serotypes (VT) and 11 (17 %) were both VT and NVT lineages. In both sampling periods, the most frequent lineage was GPSC6 (CC156, serotypes 14/9V). In the <5 years old group, a decrease in penicillin (P=0.0123) and cotrimoxazole (P<0.0001) resistance and an increase in tetracycline (P=0.019) were observed. Penicillin nonsusceptibility was predicted in 40 % of the isolates; 127 PBP combinations were identified (51 predicted MIC≥0.125 mg l-1); cotrimoxazole (folA and/or folP alterations), macrolide (mef and/or ermB) and tetracycline (tetM, tetO or tetS/M) resistance were predicted in 63, 13 and 21.6 % of pneumococci studied, respectively. The main lineages associated with multidrug resistance in the post-PCV10 period were composed of NVT, GPSC1 (CC320, serotype 19A), and GPSC47 (ST386, serotype 6C). The study provides a baseline for future comparisons and identified important NVT lineages in the post-PCV10 period in Brazil.

Neumonía necrotizante: experiencia en el Hospital Roberto del Río período 2014 a 2020 / Necrotizing pneumonia: experience at the Roberto del Río Hospital from 2014 to 2020

La neumonía necrotizante se refiere a la necrosis del parénquima pulmonar producto de una infección. Existe escasa literatura nacional sobre esta complicación. OBJETIVO: Caracterizar a los pacientes que cursaron con neumonía necrotizante en el Hospital Roberto del Río entre los años 2014 y 2020. MÉTODO: Revisión retrospectiva y descriptiva. RESULTADOS: 22 pacientes. Promedio de edad 4 años 7 meses, 68% masculino, esta complicación correspondió a 1,3% de todos los casos de neumonía hospitalizados en ese periodo. Un 95,5% presentó fiebre y un 59% dificultad respiratoria y tos. La duración promedio de la hospitalización fue de 31 días y del tratamiento antibiótico de 30,3 días. El 63% de los pacientes requirió cirugía. En el laboratorio destaca la leucocitosis y proteína C reactiva elevados con 71,4% > a 90 mg/L (promedio: 211 mg/L) y 52,3% leucocitosis > 15.000 (promedio: 18.127). La ecografía torácica fue la imagen más frecuentemente utilizada (95,5%). Agentes identificados Streptococcus pneumoniae (40%) y Staphylococcus aureus (40%). Un 63,6% ingresó a UCI, 35,7% requirió ventilación mecánica invasiva, 35,7% recibió drogas vasoactivas, 9% requirió de soporte ECMO (Oxigenación por Membrana Extracorpórea) y 1 paciente falleció (4,5%). DISCUSIÓN: en nuestro estudio encontramos una baja incidencia de esta patología, un alto índice de gravedad y una evolución favorable en la gran mayoría de los casos.

Necrotizing pneumonia refers to necrosis of lung parenchyma resulting from an infection. There is little national literature on this complication. OBJECTIVE: To characterize patients with necrotizing pneumonia at the Roberto del Río Children´s Hospital between 2014 to 2020. METHOD: Retrospective and descriptive review. RESULTS: A total of 22 patients, average age 4 years 7 months, male (68%). Average incidence 1.3% in 7 years; 95.5% had fever 59% had respiratory distress and cough. Average duration of hospitalization was 31 days and antibiotic treatment 30.3 days. A 63% of the patients had surgery. Leukocytosis and C-reactive protein (CRP) were elevated, 71.4% CRP > 90 mg /L (average: 211 mg /L) and 52.3% leukocytosis > 15.000 (average: 18.127). Chest ultrasound was used in 95.5%. Main agents identified were Streptococcus pneumoniae (40%) and Staphylococcus aureus (40%). A 63.6% of patients were admitted to ICU, 35.7% required invasive mechanical ventilation, 35.7% received vasoactive drugs, 9% required ECMO (Extracorporeal Membrane Oxygenation), and one patient died (4,5%). DISCUSSION: In our study we found a low incidence of this pathology, a high severity index an a favorable evolution in most cases.

Factors associated with severe sepsis in diarrheal adults and their outcome at an urban hospital, Bangladesh: A retrospective analysis.

BACKGROUND: To describe factors associated with severe sepsis in diarrheal adults and their outcomes and offender in blood and stool to understand their interplay as clinical features of sepsis and severe diarrhea often overlap. METHODS AND RESULTS: We used this retrospective chart analysis employing an unmatched case-control design to study critically ill diarrheal adults aged ≥18 years treated in ICU of Dhaka hospital, icddr,b between January 2011 to December 2015. Of 8,863 in-patient diarrheal adults, 350 having severe sepsis were cases and an equal number of randomly selected non-septic patients were the controls. Cases died significantly more (14.9% vs 4.6%, p = <0.001) than controls. 69% of the cases progressed to septic shock. In logistic regression analysis, steroid intake, ileus, acute kidney injury (AKI), metabolic acidosis, and hypocalcemia were significantly associated with severe sepsis in diarrheal adults (all, p<0.05). 12% of cases (40/335) had bacteremia. Streptococcus pneumoniae [9 (22.5%)] was the single most common pathogen and gram-negatives [27 (67.5%)] were prevailing as a group. CONCLUSION: Diarrheal adults who had ileus, AKI, metabolic acidosis, hypocalcemia, and also took steroids were found to have an association with severe sepsis. Strikingly, gram-negative were the predominant bacteria among the diarrheal adults having severe sepsis.

Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina.

Invasive disease caused by Streptococcus pneumoniae (IPD) is one of the leading causes of morbidity and mortality in young children worldwide. In Argentina, PCV13 was introduced into the childhood immunization programme nationwide in 2012 and PCV7 was available from 2000, but only in the private market. Since 1993 the National IPD Surveillance Programme, consisting of 150 hospitals, has conducted nationwide pneumococcal surveillance in Argentina in children under 6 years of age, as part of the SIREVA II-OPS network. A total of 1713 pneumococcal isolates characterized by serotype (Quellung) and antimicrobial resistance (agar dilution) to ten antibiotics, belonging to three study periods: pre-PCV7 era 1998-1999 (pre-PCV), before the introduction of PCV13 2010-2011 (PCV7) and after the introduction of PCV13 2012-2013 (PCV13), were available for inclusion. Fifty-four serotypes were identified in the entire collection and serotypes 14, 5 and 1 represented 50 % of the isolates. Resistance to penicillin was 34.9 %, cefotaxime 10.6 %, meropenem 4.9 %, cotrimoxazole 45 %, erythromycin 21.5 %, tetracycline 15.4 % and chloramphenicol 0.4 %. All the isolates were susceptible to levofloxacin, rifampin and vancomycin. Of 1713 isolates, 1061 (61.9 %) were non-susceptible to at least one antibiotic and 235(13.7 %) were multidrug resistant. A subset of 413 isolates was randomly selected and whole-genome sequenced as part of Global Pneumococcal Sequencing Project (GPS). The genome data was used to investigate the population structure of S. pneumoniae defining pneumococcal lineages using Global Pneumococcal Sequence Clusters (GPSCs), sequence types (STs) and clonal complexes (CCs), prevalent serotypes and their associated pneumococcal lineages and genomic inference of antimicrobial resistance. The collection showed a great diversity of strains. Among the 413 isolates, 73 known and 36 new STs were identified belonging to 38 CCs and 25 singletons, grouped into 52 GPSCs. Important changes were observed among vaccine types when pre-PCV and PCV13 periods were compared; a significant decrease in serotypes 14, 6B and 19F and a significant increase in 7F and 3. Among non-PCV13 types, serogroup 24 increased from 0 % in pre-PCV to 3.2 % in the PCV13 period. Our analysis showed that 66.1 % (273/413) of the isolates were predicted to be non-susceptible to at least one antibiotic and 11.9 % (49/413) were multidrug resistant. We found an agreement of 100 % when comparing the serotype determined by Quellung and WGS-based serotyping and 98.4 % of agreement in antimicrobial resistance. Continued surveillance of the pneumococcal population is needed to reveal the dynamics of pneumococcal isolates in Argentina in post-PCV13. This article contains data hosted by Microreact.