Use of polymerase chain reaction to characterize the etiology of culture-negative empyema and parapneumonic effusion among Alaska Native children - 2018-2023.

We used polymerase chain reaction (PCR) to identify bacterial infections in culture-negative pleural fluid specimens from Alaska Native children hospitalized with empyema. PCR identified ≥1 organism in 11 (79%) of 14 specimens. Streptococcus pneumoniae serotype 3 was detected in six specimens; all six participants had received 13-valent pneumococcal conjugate vaccine.

Pneumococcal Carriage in Burkina Faso After 13-Valent Pneumococcal Conjugate Vaccine Introduction and Before a Schedule Change.

Background: In October 2013, Burkina Faso introduced 13-valent pneumococcal conjugate vaccine (PCV13) into the routine childhood immunization program using 3 primary doses with no booster. Previous pneumococcal carriage studies showed reductions in vaccine-type (VT) carriage in children aged <5 years but not in older age groups.

Methods: We conducted a cross-sectional, age-stratified pneumococcal carriage study among healthy persons aged ≥1 month in Bobo-Dioulasso in March 2020.

Recombinational exchange of M-fibril and T-pilus genes generates extensive cell surface diversity in the global group A population.

Among genes present in all group A streptococci (GAS), those encoding M-fibril and T-pilus proteins display the highest levels of sequence diversity, giving rise to the two primary serological typing schemes historically used to define strain. A new genotyping scheme for the pilin adhesin and backbone genes is developed and, when combined with typing, provides an account of the global GAS strain population. Cluster analysis based on nucleotide sequence similarity assigns most T-serotypes to discrete pilin backbone sequence clusters, yet the established T-types correspond to only half the clusters.

Diagnosis of Streptococcus pneumoniae infection using circulating antibody secreting cells.

Background: Streptococcus pneumoniae infections cause morbidity and mortality worldwide. A rapid, simple diagnostic method could reduce the time needed to introduce definitive therapy potentially improving patient outcomes.

Methods: We introduce two new methods for diagnosing S.

Triplex Direct Quantitative Polymerase Chain Reaction for the Identification of Streptococcus pneumoniae Serotypes.

The quantitative polymerase chain reaction (qPCR) method presented in this study allows the identification of pneumococcal capsular serotypes in cerebrospinal fluid without first performing DNA extraction. This testing approach, which saves time and resources, demonstrated similar sensitivity and a high level of agreement between cycle threshold values when it was compared side-by-side with the standard qPCR method with extracted DNA.

Pneumococcal Carriage in Burkina Faso After 13-Valent Pneumococcal Conjugate Vaccine Introduction: Results From 2 Cross-sectional Population-Based Surveys.

Background: Burkina Faso, a country in Africa's meningitis belt, introduced 13-valent pneumococcal conjugate vaccine (PCV13) in October 2013, with 3 primary doses given at 8, 12 and 16 weeks of age. To assess whether the new PCV13 program controlled pneumococcal carriage, we evaluated overall and serotype-specific colonization among children and adults during the first 3 years after introduction.

Methods: We conducted 2 population-based, cross-sectional, age-stratified surveys in 2015 and 2017 in the city of Bobo-Dioulasso.

Pneumococcal Disease Outbreak at a State Prison, Alabama, USA, September 1-October 10, 2018.

A pneumococcal disease outbreak caused by Streptococcus pneumoniae serotype 12F occurred in a state prison in Alabama, USA. Among 1,276 inmates, 40 cases were identified (3 confirmed, 2 probable, 35 suspected). Close living quarters, substance use, and underlying conditions likely contributed to disease risk.

Sequential Quadriplex Real-Time PCR for Identifying 20 Common Types of Group A .

We developed a sequential quadriplex real-time PCR-based method for rapid identification of 20 types commonly found in invasive group A (iGAS) strains recovered through the Centers for Disease Control and Prevention's Active Bacterial Core surveillance. Each real-time PCR assay showed high specificity and accurately identified the respective target type, including subtypes in the United States. Furthermore, this method is useful for rapid typing of GAS isolates and culture-negative specimens during outbreak investigations.

Genomic Surveillance of Strains Causing Invasive Disease, United States, 2016-2017.

Background: is a major cause of severe, invasive infections in humans. The bacterial pathogen harbors a wide array of virulence factors and exhibits high genomic diversity. Rapid changes of circulating strains in a community are common.

Evaluation of pneumococcal meningitis clusters in Burkina Faso and implications for potential reactive vaccination.

Background: To better understand how to prevent and respond to pneumococcal meningitis outbreaks in the meningitis belt, we retrospectively examined Burkina Faso's case-based meningitis surveillance data for pneumococcal meningitis clusters and assessed potential usefulness of response strategies.

Methods: Demographic and clinical information, and cerebrospinal fluid laboratory results for meningitis cases were collected through nationwide surveillance. Pneumococcal cases were confirmed by culture, polymerase chain reaction (PCR), or latex agglutination; strains were serotyped using PCR.

Expanded sequential quadriplex real-time polymerase chain reaction (PCR) for identifying pneumococcal serotypes, penicillin susceptibility, and resistance markers.

We expanded our current Centers for Disease Control and Prevention triplexed real-time polymerase chain reaction scheme identifying 11 individual serotypes and 10 serogroups to a quadriplex format identifying 34 individual serotypes and 13 small serogroups, 4 antibiotic resistance determinants, pilus targets, and penicillin susceptibility. Newly developed assays are specific for serotypes/serogroups, are sensitive (10 copies/reaction), and further discriminate larger serogroups into individual serotypes or smaller serogroups.

Analysis of Global Collection of Group A Genomes Reveals that the Majority Encode a Trio of M and M-Like Proteins.

The core Mga (multiple gene activator) regulon of group A (GAS) contains genes encoding proteins involved in adhesion and immune evasion. While all GAS genomes contain genes for Mga and C5a peptidase, the intervening genes encoding M and M-like proteins vary between strains. The genetic make-up of the Mga regulon of GAS was characterized by utilizing a collection of 1,688 GAS genomes that are representative of the global GAS population.

Impact of 13-Valent Pneumococcal Conjugate Vaccine on Pneumococcal Meningitis, Burkina Faso, 2016-2017.

Background: In 2013, Burkina Faso introduced 13-valent pneumococcal conjugate vaccine (PCV13) into the routine childhood immunization program, to be administered to children at 8, 12, and 16 weeks of age. We evaluated the impact of PCV13 on pneumococcal meningitis.

Methods: Using nationwide surveillance, we gathered demographic/clinical information and cerebrospinal fluid (CSF) results for meningitis cases.

Emergent Invasive Group A Streptococcus dysgalactiae subsp. equisimilis, United States, 2015-2018.

The term group A Streptococcus is considered synonymous for the species Streptococcus pyogenes. We describe an emergent invasive S. dysgalactiae subspecies equisimilis lineage that obtained the group A antigen through a single ancestral recombination event between a group C S.

Nasopharyngeal carriage of Streptococcus pneumoniae in children under 5 years of age before introduction of pneumococcal vaccine (PCV10) in urban and rural districts in Pakistan.

Background: Benefits of pneumococcal conjugate vaccine programs have been linked to the vaccine's ability to disrupt nasopharyngeal carriage and transmission. The 10-valent pneumococcal vaccine (PCV10) was included in the Expanded Program on Immunization (EPI) in Sindh, Pakistan in February 2013. This study was carried out immediately before PCV10 introduction to establish baseline pneumococcal carriage and prevalent serotypes in young children and to determine if carriage differed in urban and rural communities.

Continued occurrence of serotype 1 pneumococcal meningitis in two regions located in the meningitis belt in Ghana five years after introduction of 13-valent pneumococcal conjugate vaccine.

Background: Increases in pneumococcal meningitis were reported from Ghanaian regions that lie in the meningitis belt in 2016-2017, despite introduction of 13-valent pneumococcal conjugate vaccine (PCV13) in 2012 using a 3-dose schedule (6, 10, and 14 weeks). We describe pneumococcal meningitis epidemiology in the Ghanaian Northern and Upper West regions across two meningitis seasons.

Methods: Suspected meningitis cases were identified using World Health Organization standard definitions.

Early impact of 13-valent pneumococcal conjugate vaccine on pneumococcal meningitis-Burkina Faso, 2014-2015.

Objectives: We evaluate early impact of 13-valent pneumococcal conjugate vaccine (PCV13) on pneumococcal meningitis in Burkina Faso.

Methods: Nationwide surveillance gathered demographic/clinical information and cerebrospinal fluid (CSF) results for meningitis cases. Pneumococcal cases were confirmed by culture, polymerase chain reaction (PCR), or latex agglutination, and strains serotyped using PCR.

Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015.

Group A streptococci (GAS) are genetically diverse. Determination of strain features can reveal associations with disease and resistance and assist in vaccine formulation. We employed whole-genome sequence (WGS)-based characterization of 1,454 invasive GAS isolates recovered in 2015 by Active Bacterial Core Surveillance and performed conventional antimicrobial susceptibility testing.

Nationwide Trends in Bacterial Meningitis before the Introduction of 13-Valent Pneumococcal Conjugate Vaccine-Burkina Faso, 2011-2013.

Background: Following introduction of Haemophilus influenzae type b vaccine in 2006 and serogroup A meningococcal conjugate vaccine in 2010, Streptococcus pneumoniae (Sp) became the leading cause of bacterial meningitis in Burkina Faso. We describe bacterial meningitis epidemiology, focusing on pneumococcal meningitis, before 13-valent pneumococcal conjugate vaccine (PCV13) introduction in the pediatric routine immunization program in October 2013.

Methods: Nationwide population-based meningitis surveillance collects case-level demographic and clinical information and cerebrospinal fluid (CSF) laboratory results.

Species-specific real-time PCR assay for the detection of Streptococcus suis from clinical specimens.

A real-time polymerase chain reaction was developed to detect all known strains of Streptococcus suis. The assay was highly specific, and sensitivity was <10 copies/assay for S. suis detection from clinical samples.

Comparative analytical evaluation of the respiratory TaqMan Array Card with real-time PCR and commercial multi-pathogen assays.

In this study, a multicenter evaluation of the Life Technologies TaqMan(®) Array Card (TAC) with 21 custom viral and bacterial respiratory assays was performed on the Applied Biosystems ViiA™ 7 Real-Time PCR System. The goal of the study was to demonstrate the analytical performance of this platform when compared to identical individual pathogen specific laboratory developed tests (LDTs) designed at the Centers for Disease Control and Prevention (CDC), equivalent LDTs provided by state public health laboratories, or to three different commercial multi-respiratory panels. CDC and Association of Public Health Laboratories (APHL) LDTs had similar analytical sensitivities for viral pathogens, while several of the bacterial pathogen APHL LDTs demonstrated sensitivities one log higher than the corresponding CDC LDT.

vanG element insertions within a conserved chromosomal site conferring vancomycin resistance to Streptococcus agalactiae and Streptococcus anginosus.

Three vancomycin-resistant streptococcal strains carrying vanG elements (two invasive Streptococcus agalactiae isolates [GBS-NY and GBS-NM, both serotype II and multilocus sequence type 22] and one Streptococcus anginosus [Sa]) were examined. The 45,585-bp elements found within Sa and GBS-NY were nearly identical (together designated vanG-1) and shared near-identity over an ~15-kb overlap with a previously described vanG element from Enterococcus faecalis. Unexpectedly, vanG-1 shared much less homology with the 49,321-bp vanG-2 element from GBS-NM, with widely different levels (50% to 99%) of sequence identity shared among 44 related open reading frames.

Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection.

Identification of etiology remains a significant challenge in the diagnosis of infectious diseases, particularly in resource-poor settings. Viral, bacterial, and fungal pathogens, as well as parasites, play a role for many syndromes, and optimizing a single diagnostic system to detect a range of pathogens is challenging. The TaqMan Array Card (TAC) is a multiple-pathogen detection method that has previously been identified as a valuable technique for determining etiology of infections and holds promise for expanded use in clinical microbiology laboratories and surveillance studies.

Outbreak of bacterial meningitis among patients undergoing myelography at an outpatient radiology clinic.

Purpose: To investigate an outbreak of bacterial meningitis at an outpatient radiology clinic (clinic A) and to determine the source and implement measures to prevent additional infections.

Methods: A case was defined as bacterial meningitis in a patient undergoing myelography at clinic A from October 11 to 25, 2010. Patients who underwent myelography and other procedures at clinic A during that period were interviewed, medical records were reviewed, and infection prevention practices were assessed.