Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing DOI Creative Commons
Leonardo de Oliveira Martins, Andrew J. Page, Alison E. Mather

et al.

NAR Genomics and Bioinformatics, Journal Year: 2019, Volume and Issue: 2(1)

Published: Nov. 14, 2019

Abstract DNA barcoding through the use of amplified regions ribosomal operon, such as 16S gene, is a routine method to gain an overview microbial taxonomic diversity within sample without need isolate and culture microbes present. However, bacterial cells usually have multiple copies this choosing ‘wrong’ copy could provide misleading species classification. While presents less problem for well-characterized organisms with large sequence databases interrogate, it significant challenge lesser known unknown number diversity. Using entire length which encompasses 16S, 23S, 5S internal transcribed spacer regions, should greater resolution but has not been well explored. Here, we publicly available reference genomes explore theoretical boundaries when using concatenated genes full-length operons, made possible by development uptake long-read sequencing technologies. We quantify issues both choice operon in phylogenetic context demonstrate that longer improve signal while maintaining accuracy.

Language: Английский

Seamless, rapid, and accurate analyses of outbreak genomic data using splitk-mer analysis DOI Creative Commons
Romain Derelle, Johanna von Wachsmann, Tommi Mäklin

et al.

Genome Research, Journal Year: 2024, Volume and Issue: 34(10), P. 1661 - 1673

Published: Oct. 1, 2024

Sequence variation observed in populations of pathogens can be used for important public health and evolutionary genomic analyses, especially outbreak analysis transmission reconstruction. Identifying this is typically achieved by aligning sequence reads to a reference genome, but approach susceptible biases requires careful filtering called genotypes. There need tools that process growing volume bacterial genome data, providing rapid results, remain simple so they without highly trained bioinformaticians, expensive data analysis, long-term storage processing large files. Here we describe split

Language: Английский

Citations

7
Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates DOI Creative Commons
Rebecca A. Gladstone, Stephanie W. Lo, Richard Goater

et al.

Microbial Genomics, Journal Year: 2020, Volume and Issue: 6(5)

Published: May 1, 2020

Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global disease. We provide interactive bioinformatic outputs to explore such topics, aiming increase dissemination genomic the wider community, without need for specialist training. prepared 12 country-specific phylogenetic snapshots, international snapshots 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, present them in Microreact. Gene presence absence Roary, recombination profiles derived from Gubbins are presented Phandango each GPSC. Temporal signal was assessed GPSC BactDating. examples how resources be used. In our example use a snapshot we determined that serotype 14 observed nine unrelated genetic backgrounds South Africa. The GPSC9, which most isolates Africa were observed, highlights there three independent sub-clusters represented by African isolates. estimated GPSC9-dated tree established during 1980s. show plots allowed identification 20 kb spanning capsular polysaccharide locus within GPSC97. This consistent with switch 6A 19A have occured 1990s GPSC97-dated tree. Plots gene presence/absence genes ( tet , erm cat ) across GPSC23 phylogeny acquisition composite transposon. GPSC23-dated occurred between 1953 1975. Finally, demonstrate assignment GPSC31 17 externally generated 1 assemblies Utah via Pathogenwatch. Most clustered USA-specific clade recent ancestor 1958 1981. provided used data, test hypothesis generate new hypotheses. accessible GPSCs allows others contextualize own collections beyond data here.

Language: Английский

Citations

49
Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens DOI Open Access
Kirsten I. Bos, Denise Kühnert, Alexander Herbig

et al.

Annual Review of Microbiology, Journal Year: 2019, Volume and Issue: 73(1), P. 639 - 666

Published: July 8, 2019

The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions past ailments to dynamic interpretations population health that draw upon multiple perspectives. recent adoption high-throughput DNA sequencing led an expanded understanding pathogen presence, evolution, and ecology across globe. This genomic revolution identification disease-causing microbes both expected unexpected contexts, while also providing for characterization pathogens previously believed be unattainable by available methods. In this review we explore development DNA-based research, specialized methods tools have emerged authenticate past, unique challenges persist molecular paleopathology. We offer guidelines mitigate impact these challenges, which will allow more reliable data rapidly evolving field investigation.

Language: Английский

Citations

45
Strain Differences in Bloodstream and Skin Infection: Methicillin-Resistant Staphylococcus aureus Isolated in 2018–2021 in a Single Health System DOI Creative Commons
Katrina S. Hofstetter, Natasia F. Jacko, Margot J. Shumaker

et al.

Open Forum Infectious Diseases, Journal Year: 2024, Volume and Issue: 11(6)

Published: May 6, 2024

Abstract Staphylococcus aureus is a common cause of skin and soft-tissue infections (SSTIs) has become the most bloodstream (BSIs) in recent years, but whether strains causing these two clinical syndromes overlap not been studied adequately. USA300/500 (clonal complex [CC] 8–sequence type [ST] 8) USA100 (CC5-ST5) have dominated among methicillin-resistant S (MRSA) United States since early 2000s. We compared genomes unselected MRSA isolates from 131 SSTIs with those 145 BSIs at single US center overlapping periods 2018–2021. CC8 was more SSTIs, CC5 BSIs, consistent prior literature. Based on clustering threshold 15 single-nucleotide polymorphisms, we identified clusters limited to patients SSTI separate exclusively comprising BSIs. However, also eight that included least one BSI isolate. This suggests virulent are transmitted person locally healthcare setting or community lineages often capable both

Language: Английский

Citations

4
On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference DOI Creative Commons
Alexis Criscuolo

F1000Research, Journal Year: 2020, Volume and Issue: 9, P. 1309 - 1309

Published: Nov. 10, 2020

Recently developed MinHash-based techniques were proven successful in quickly estimating the level of similarity between large nucleotide sequences. This article discusses their usage and limitations practice to approximating uncorrected distances genomes, transforming these pairwise dissimilarities into proper evolutionary distances. It is notably shown that complex distance measures can be easily approximated using simple transformation formulae based on few parameters. therefore very useful for implementing fast yet accurate alignment-free phylogenetic reconstruction procedures from sets genomes. last point view assessed with a simulation study dedicated bioinformatics tool.

Language: Английский

Citations

32
Extensive sequence analysis: revealing genomic knowledge throughout various domains DOI
Abdul Razak Mohamed Sikkander, Suman Lata Tripathi,

G. Theivanathan

et al.

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 17 - 30

Published: Jan. 1, 2025

Language: Английский

Citations

0
The capsule and genetic background, rather than specific loci, strongly influence pneumococcal growth kinetics DOI Open Access
Chrispin Chaguza, Daan W. Arends, Stephanie W. Lo

et al.

Published: March 26, 2025

Bacterial growth characteristics intrinsic to each strain can impact and influence gene expression, antibiotic susceptibility, disease pathogenesis. However, little is known about specific genomic variations that these bacterial features. Here, we investigate the of Streptococcus pneumoniae genetics on its in vitr o features shed light genes may be important targets development vaccines therapeutics. We use statistical models estimate show they varied significantly across capsular serotypes lineages, strongly correlated with phylogeny, were highly heritable, highlighting a strong genetic basis. Despite this, genome-wide association studies revealed no loci statistically associated independently background, including those polysaccharide synthesis locus. Our findings serotype lineage, possibly combination loci, pneumococcal kinetics, which have implications

Language: Английский

Citations

0
The capsule and genetic background, rather than specific loci, strongly influence pneumococcal growth kinetics DOI Open Access
Chrispin Chaguza, Daan W. Arends, Stephanie W. Lo

et al.

Published: March 26, 2025

Bacterial growth characteristics intrinsic to each strain can impact and influence gene expression, antibiotic susceptibility, disease pathogenesis. However, little is known about specific genomic variations that these bacterial features. Here, we investigate the of Streptococcus pneumoniae genetics on its in vitr o features shed light genes may be important targets development vaccines therapeutics. We use statistical models estimate show they varied significantly across capsular serotypes lineages, strongly correlated with phylogeny, were highly heritable, highlighting a strong genetic basis. Despite this, genome-wide association studies revealed no loci statistically associated independently background, including those polysaccharide synthesis locus. Our findings serotype lineage, possibly combination loci, pneumococcal kinetics, which have implications

Language: Английский

Citations

0
Gracilibacillus pellucidus sp. nov., a moderately halophilic bacterium isolated from saline soil in Xinjiang province, China DOI

Zengqin Zhang,

Hui Wang, Mengli Xia

et al.

Antonie van Leeuwenhoek, Journal Year: 2025, Volume and Issue: 118(5)

Published: April 22, 2025

Language: Английский

Citations

0
Integrated population clustering and genomic epidemiology with PopPIPE DOI Creative Commons
M. McHugh, Samuel Horsfield, Johanna von Wachsmann

et al.

Microbial Genomics, Journal Year: 2025, Volume and Issue: 11(4)

Published: April 28, 2025

Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations and as an additional source of information when detecting possible transmission events. Due their variable gene content order, reference-free methods offer more sensitive detection genetic differences, especially among samples found in outbreaks. However, across longer distances, frequent recombination make calculation interpretation these differences challenging, requiring significant bioinformatic expertise manual intervention during the analysis process. Here, we present a Pop ulation PIPE line (PopPIPE) which combines rapid genome analyse genomes two scales, splitting whole subclusters plausible events within clusters. We use k-mer sketching split strains, followed by removal create alignments strains. first show that this approach creates high-quality on population-wide dataset Streptococcus pneumoniae . When applied nosocomial vancomycin-resistant Enterococcus faecium samples, PopPIPE finds clusters are epidemiologically than core or multilocus sequence typing (MLST) approaches. Our pipeline is reproducible, interactive visualizations easily reconfigured re-run new datasets. Therefore, provides user-friendly for analyses spanning species-wide clustering outbreak investigations.

Language: Английский

Citations

0