Comparison of tracheal aspirate and bronchoalveolar lavage samples in the microbiological diagnosis of lower respiratory tract infection in pediatric patients.

2022

2405-2410

05/2022

1099-0496

BACKGROUND: Bacterial cultures from tracheal aspirates (TA) and bronchoalveolar lavage (BAL) specimens can be used to assess patients with artificial airways for lower respiratory tract infections (LRTI). TA collection may be advantageous in situations of limited resources or critical illness. Literature comparing these diagnostic modalities in pediatric populations is scarce.

METHODS: Single-center, retrospective analysis of 52 pediatric patients with an artificial airway undergoing evaluation for LRTI. All patients had a TA specimen collected for semiquantitative Gram stain and culture followed by BAL within 48 h. Microbiologic diagnosis of LRTI was defined as a BAL sample with >25% neutrophils and growth of >10 colony-forming units/ml of one or more bacterial species. The test characteristics of TA were compared with these BAL results as the reference standard. Concordance in microorganism identification was also assessed.

RESULTS: Overall, 24 patients (47%) met criteria for LRTI using BAL as the diagnostic standard. TA samples positive for an isolated organism had poor sensitivity for acute LRTI when compared with BAL, regardless of semiquantitative white blood cell (WBC) count by Gram stain. Using a TA diagnostic threshold of organism growth and at least "moderate" WBC yielded a specificity of 93%. Positive predictive value was highest when an organism was identified by TA. Negative predictive value was >70% for TA samples with no WBC by semiquantitative analysis, with or without growth of an organism. Complete concordance of cultured species was 58% for all patients, with a higher rate seen among those with endotracheal tubes.

CONCLUSIONS: The role of cultures obtained by TA remains limited for the diagnosis of acute LRTI as demonstrated by the poor correlation to BAL results within our cohort. Optimal strategies for diagnosing LRTI across patient populations and airway types remain elusive.

10.1002/ppul.26049

Pediatr Pulmonol

35781810

SARS-CoV-2 variants associated with vaccine breakthrough in the Delaware Valley through summer 2021.

2021

2021 Oct 20

<p>The severe acute respiratory coronavirus-2 (SARS-CoV-2) is the cause of the global outbreak of COVID-19. Evidence suggests that the virus is evolving to allow efficient spread through the human population, including vaccinated individuals. Here we report a study of viral variants from surveillance of the Delaware Valley, including the city of Philadelphia, and variants infecting vaccinated subjects. We sequenced and analyzed complete viral genomes from 2621 surveillance samples from March 2020 to September 2021 and compared them to genome sequences from 159 vaccine breakthroughs. In the early spring of 2020, all detected variants were of the B.1 and closely related lineages. A mixture of lineages followed, notably including B.1.243 followed by B.1.1.7 (alpha), with other lineages present at lower levels. Later isolations were dominated by B.1.617.2 (delta) and other delta lineages; delta was the exclusive variant present by the last time sampled. To investigate whether any variants appeared preferentially in vaccine breakthroughs, we devised a model based on Bayesian autoregressive moving average logistic multinomial regression to allow rigorous comparison. This revealed that B.1.617.2 (delta) showed three-fold enrichment in vaccine breakthrough cases (odds ratio of 3; 95% credible interval 0.89-11). Viral point substitutions could also be associated with vaccine breakthroughs, notably the N501Y substitution found in the alpha, beta and gamma variants (odds ratio 2.04; 95% credible interval of 1.25-3.18). This study thus provides a detailed picture of viral evolution in the Delaware Valley and a geographically matched analysis of vaccine breakthroughs; it also introduces a rigorous statistical approach to interrogating enrichment of viral variants.</p>

<p><strong>Importance: </strong>SARS-CoV-2 vaccination is highly effective at reducing viral infection, hospitalization and death. However, vaccine breakthrough infections have been widely observed, raising the question of whether particular viral variants or viral mutations are associated with breakthrough. Here we report analysis of 2621 surveillance isolates from xsxpeople diagnosed with COVID-19 in the Delaware Valley in South Eastern Pennsylvania, allowing rigorous comparison to 159 vaccine breakthrough case specimens. Our best estimate is a three-fold enrichment for some lineages of delta among breakthroughs, and enrichment of a notable spike substitution, N501Y. We introduce statistical methods that should be widely useful for evaluating vaccine breakthroughs and other viral phenotypes.</p>

10.1101/2021.10.18.21264623

medRxiv

34704098

SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021.

2022

e0378821

2022 Feb 08

2150-7511

<p>The severe acute respiratory coronavirus-2 (SARS-CoV-2) is the cause of the global outbreak of COVID-19. Evidence suggests that the virus is evolving to allow efficient spread through the human population, including vaccinated individuals. Here, we report a study of viral variants from surveillance of the Delaware Valley, including the city of Philadelphia, and variants infecting vaccinated subjects. We sequenced and analyzed complete viral genomes from 2621 surveillance samples from March 2020 to September 2021 and compared them to genome sequences from 159 vaccine breakthroughs. In the early spring of 2020, all detected variants were of the B.1 and closely related lineages. A mixture of lineages followed, notably including B.1.243 followed by B.1.1.7 (alpha), with other lineages present at lower levels. Later isolations were dominated by B.1.617.2 (delta) and other delta lineages; delta was the exclusive variant present by the last time sampled. To investigate whether any variants appeared preferentially in vaccine breakthroughs, we devised a model based on Bayesian autoregressive moving average logistic multinomial regression to allow rigorous comparison. This revealed that B.1.617.2 (delta) showed 3-fold enrichment in vaccine breakthrough cases (odds ratio of 3; 95% credible interval 0.89-11). Viral point substitutions could also be associated with vaccine breakthroughs, notably the N501Y substitution found in the alpha, beta and gamma variants (odds ratio 2.04; 95% credible interval of1.25-3.18). This study thus overviews viral evolution and vaccine breakthroughs in the Delaware Valley and introduces a rigorous statistical approach to interrogating enrichment of breakthrough variants against a changing background. SARS-CoV-2 vaccination is highly effective at reducing viral infection, hospitalization and death. However, vaccine breakthrough infections have been widely observed, raising the question of whether particular viral variants or viral mutations are associated with breakthrough. Here, we report analysis of 2621 surveillance isolates from people diagnosed with COVID-19 in the Delaware Valley in southeastern Pennsylvania, allowing rigorous comparison to 159 vaccine breakthrough case specimens. Our best estimate is a 3-fold enrichment for some lineages of delta among breakthroughs, and enrichment of a notable spike substitution, N501Y. We introduce statistical methods that should be widely useful for evaluating vaccine breakthroughs and other viral phenotypes.</p>

10.1128/mbio.03788-21

mBio

34704098

Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus Associated with Bacteremia and Monocyte Evasion, Rio de Janeiro, Brazil.

2021

2825-2835

2021

1080-6059

<p>We typed 600 methicillin-resistant Staphylococcus aureus (MRSA) isolates collected in 51 hospitals in the Rio de Janeiro, Brazil, metropolitan area during 2014-2017. We found that multiple new clonal complex (CC) 5 sequence types had replaced previously dominant MRSA lineages in hospitals. Whole-genome analysis of 208 isolates revealed an emerging sublineage of multidrug-resistant MRSA, sequence type 105, staphylococcal cassette chromosome mec II, spa t002, which we designated the Rio de Janeiro (RdJ) clone. Using molecular clock analysis, we hypothesized that this lineage began to expand in the Rio de Janeiro metropolitan area in 2009. Multivariate analysis supported an association between bloodstream infections and the CC5 lineage that includes the RdJ clone. Compared with other closely related isolates, representative isolates of the RdJ clone more effectively evaded immune function related to monocytic cells, as evidenced by decreased phagocytosis rate and increased numbers of viable unphagocytosed (free) bacteria after in vitro exposure to monocytes.</p>

10.3201/eid2711.210097

Emerg Infect Dis

34670645

Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates.

2021

ofab300

2021 Jul

2328-8957

<p>We report the genome of a B.1.1.7+E484K severe acute respiratory syndrome coronavirus 2 from Southeastern Pennsylvania and compare it with all high-coverage B.1.1.7+E484K genomes (n = 235) available. Analyses showed the existence of at least 4 distinct clades of this variant circulating in the United States and the possibility of at least 59 independent acquisitions of the E484K mutation.</p>

10.1093/ofid/ofab300

Open Forum Infect Dis

34254040

Early pandemic molecular diversity of SARS-CoV-2 in children.

2021

2021 Feb 19

<p><strong>Background: </strong>In the US, community circulation of the SARS-CoV-2 virus likely began in February 2020 after mostly travel-related cases. Children's Hospital of Philadelphia began testing on 3/9/2020 for pediatric and adult patients, and for all admitted patients on 4/1/2020, allowing an early glimpse into the local molecular epidemiology of the virus.</p>

<p><strong>Methods: </strong>We obtained 169 SARS-CoV-2 samples (83 from patients &lt;21 years old) from March through May and produced whole genome sequences. We used genotyping tools to track variants over time and to test for possible genotype associated clinical presentations and outcomes in children.</p>

<p><strong>Results: </strong>Our analysis uncovered 13 major lineages that changed in relative abundance as cases peaked in mid-April in Philadelphia. We detected at least 6 introductions of distinct viral variants into the population. As a group, children had more diverse virus genotypes than the adults tested. No strong differences in clinical variables were associated with genotypes.</p>

<p><strong>Conclusions: </strong>Whole genome analysis revealed unexpected diversity, and distinct circulating viral variants within the initial peak of cases in Philadelphia. Most introductions appeared to be local from nearby states. Although limited by sample size, we found no evidence that different genotypes had different clinical impacts in children in this study.</p>

<p><strong>Summary: </strong>Using sequencing and a novel technique for quantifying SARS-CoV-2 diversity, we investigated 169 SARS-CoV-2 genomes (83 &lt;21 years old). This analysis revealed unexpected diversity especially in children. No clear differences in clinical presentation were associated with the different virus lineages.</p>

10.1101/2021.02.17.21251960

medRxiv

33619507