Bordetella pertussis, a reemerging pathogen in pediatric respiratory infections. A study in Quito, Ecuador

Noguera, Saidy Vásconez; Jaramillo, Katherine; Zabala, Andrés; Villacís, José E

doi:10.1016/j.ram.2020.07.001

Cited by 3 publications

(2 citation statements)

References 30 publications

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“…These study showed a high prevalence in children under 2 months of age, followed by the 2-6 month group, indicating that this disease occurs in children who did not receive the vaccine yet and children with the incomplete vaccination scheme, as previously stated by other authors 15,18 . Similar to these results in Quito, Ecuador, it was found that the majority of positive cases of B. pertussis infections corresponded to infants belonging to the 0-3 months of age group, reaching a prevalence of 65% 19 . According to previous publications, in the age group of children under 3 months the rates of hospitalizations, complications and deaths are significantly higher and > 90% of all deaths associated with whooping cough occurred in infants who have not reached protection, since in most countries it begins at 2 months of age 12,20 .…”

Section: Discussionsupporting

confidence: 83%

Epidemiological characteristics of whooping cough in Paraguay (2005-2019)

León¹,

Kawabata²,

Nagai³

et al. 2022

Infect

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Objective: To describe the epidemiological characteristics of whooping cough in Paraguay. Methods: 5327 samples of children and adults of all ages with suspected whooping cough and their contacts were included in this study. 745 samples were processed per microbiological culture and 4582 samples per microbiological culture and PCR. Results: The overall frequency of cases and their laboratory-confirmed contacts was 9.1%. A total of 361 cases and 123 close case contacts were detected as positive. Positive cases were more common in the < 2 months (70.6%), followed by the 2-6 month (11.9%). Conclusion: In Paraguay it is a public health problem that mainly affects children under 2 months, who have not yet received the vaccine. Knowing the epidemiology of whooping cough or pertussis helps us to know the burden of the disease as well as to measure the effectiveness and impact of vaccines.

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Section: Discussionsupporting

confidence: 83%

Epidemiological characteristics of whooping cough in Paraguay (2005-2019)

León¹,

Kawabata²,

Nagai³

et al. 2022

Infect

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“…Seven of the nine unique FP could be explained by misannotations since they belonged to the same genus as the original species. For example, B. pertussis is a Gramnegative bacterium that causes whooping cough (Vásconez Noguera et al 2021) and belongs to the same genus as B. bronchiseptica, initially included in community A. In the case of B. vaginale, a Gram-positive bacterium that colonizes the vagina and contributes to the vaginal microbiome, studies have shown that bifidobacteria from vaginal and gut microbiomes are indistinguishable using comparative genomics (Freitas and Hill 2018).…”

Section: Discussionmentioning

confidence: 99%

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery

Rocha

Kasmanas

Toscan

et al. 2023

Preprint

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We hypothesize that sample evenness, sequencing depth and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample evenness, sequencing depth and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, whilst the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates the scientific community should their findings from MAG recovery, especially when asserting novel species or metabolic traits.

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Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery

Rocha,

Kasmanas,

Toscan

et al. 2024

PLoS Comput Biol

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We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.

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Bordetella pertussis, a reemerging pathogen in pediatric respiratory infections. A study in Quito, Ecuador

Cited by 3 publications

References 30 publications

Epidemiological characteristics of whooping cough in Paraguay (2005-2019)

Epidemiological characteristics of whooping cough in Paraguay (2005-2019)

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery

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