SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

Inouye, Michael; Dashnow, Harriet; Raven, Lesley; Schultz, Mark B.; Pope, Bernard J.; Tomita, Takehiro; Zobel, Justin; Holt, Kathryn E.

doi:10.1186/s13073-014-0090-6

Cited by 927 publications

(878 citation statements)

References 47 publications

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“…KpI lineages were defined based on patristic distances in the ML tree using RAMI (38), supported by a phylogeny-free approach using fineSTRUCTURE (39). STs were assigned to each genome according to the K. pneumoniae MLST database (13) by mapping to known alleles using SRST2 (68). Full details of all analyses are provided in SI Appendix, Supplementary Text.…”

Section: Methodsmentioning

confidence: 99%

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Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health

Holt

Wertheim

Zadoks

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

1,013

1,123

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Klebsiella pneumoniae is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. K. pneumoniae is ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure of K. pneumoniae, so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework for K. pneumoniae based on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting of K. pneumoniae into three distinct species, KpI (K. pneumoniae), KpII (K. quasipneumoniae), and KpIII (K. variicola). Further, for K. pneumoniae (KpI), the entity most frequently associated with human infection, we show the existence of >150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We show K. pneumoniae has a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasive K. pneumoniae infections; our data provide the whole-genome framework against which to track the emergence of such threats.

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Section: Methodsmentioning

confidence: 99%

“…A gene content matrix, indicating coverage of each gene in each genome, was generated by mapping to the annotated pangenome sequence. Read sets also were screened for known alleles of important genes using a read mapping approach with SRST2 (68). Gene databases analyzed were AMR alleles [ARG-Annot (70) Statistical Analyses.…”

Section: Methodsmentioning

confidence: 99%

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health

Holt

Wertheim

Zadoks

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

1,013

1,123

View full text Add to dashboard Cite

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“…Phenotypic data were mapped onto the maximum-likelihood tree using the plotTree. R script (https://github.com/katholt/plotTree; Inouye et al 2014).…”

Section: Estimating Population Structure and Phylogenymentioning

confidence: 99%

Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs

et al. 2017

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Chronic bacterial infections of the lung are the leading cause of morbidity and mortality in cystic fibrosis patients. Tracking bacterial evolution during chronic infections can provide insights into how host selection pressures-including immune responses and therapeutic interventions-shape bacterial genomes. We carried out genomic and phenotypic analyses of 215 serially collected Burkholderia cenocepacia isolates from 16 cystic fibrosis patients, spanning a period of 2-20 yr and a broad range of epidemic lineages. Systematic phenotypic tests identified longitudinal bacterial series that manifested progressive changes in liquid media growth, motility, biofilm formation, and acute insect virulence, but not in mucoidy. The results suggest that distinct lineages follow distinct evolutionary trajectories during lung infection. Pan-genome analysis identified 10,110 homologous gene clusters present only in a subset of strains, including genes restricted to different molecular types. Our phylogenetic analysis based on 2148 orthologous gene clusters from all isolates is consistent with patient-specific clades. This suggests that initial colonization of patients was likely by individual strains, followed by subsequent diversification. Evidence of clonal lineages shared by some patients was observed, suggesting inter-patient transmission. We observed recurrent gene losses in multiple independent longitudinal series, including complete loss of Chromosome III and deletions on other chromosomes. Recurrently observed loss-of-function mutations were associated with decreases in motility and biofilm formation. Together, our study provides the first comprehensive genome-phenome analyses of B. cenocepacia infection in cystic fibrosis lungs and serves as a valuable resource for understanding the genomic and phenotypic underpinnings of bacterial evolution.

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“…This results in WGS becoming a viable alternative to some traditional typing methods for 63 public health infectious disease surveillance. 64 65 MLST can be derived from WGS using de novo assembly/BLAST based (Larsen et al, 2012;Jolley & 66 Maiden 2013) and mapping based (Inouye et al, 2012(Inouye et al, , 2014 approaches. De novo assembly/BLAST 67 based approaches work by assembling short reads into longer contiguous sequences and then 68 comparing these contigs to a reference allele database using BLAST to assign a MLST type.…”

mentioning

confidence: 99%

“…De novo assembly/BLAST 67 based approaches work by assembling short reads into longer contiguous sequences and then 68 comparing these contigs to a reference allele database using BLAST to assign a MLST type. Mapping 69 based approaches align short reads to reference (allele) sequences representing all alleles from MLST 70 loci using mapping tools such as BWA (Inouye et al, 2012) or Bowtie2 (Inouye et al, 2014). (Inouye et al, 2012(Inouye et al, , 2014.…”

mentioning

confidence: 99%

MOST: A modified MLST typing tool based on short read sequencing

Tewolde

Dallman

Schaefer

et al. 2016

Preprint

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Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR)amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS). This paper reports the comparison of the reliability of MLST results derived from WGS data, comparing mapping and assembly-based approaches to conventional methods using 325 bacterial genomes of diverse species. The sensitivity of the two WGS based methods were further investigated with 26 mixed and 29 low coverage genomic data sets from Salmonella enteridis and Streptococcus pneumoniae. Of the 325 samples, 92.9% (n=302), 97.2% (n=316) and 99.7% (n=324) full MLST profiles were derived by the conventional method, assembly-and mapping-based approaches, respectively. The concordance between samples that were typed by conventional (92.9%) and both WGS methods was 100%. From the 55 mixed and low coverage genomes, 90.9% (n=50) and 67.3% (n=37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. In conclusion, deriving MLST from WGS data is more sensitive than the conventional method.When comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the mapping based approach described here derives quality metrics, which are difficult to determine quantitatively using conventional and WGS-assembly 42 (n=37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. 43 In conclusion, deriving MLST from WGS data is more sensitive than the conventional method. When 44 comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the 45 mapping based approach described here derives quality metrics, which are difficult to determine 46 quantitatively using conventional and WGS-assembly based approaches.

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SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

Cited by 927 publications

References 47 publications

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health

Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs

MOST: A modified MLST typing tool based on short read sequencing

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