High-Quality Complete and Draft Genome Sequences for Three
            <i>Escherichia</i>
            spp. and Three
            <i>Shigella</i>
            spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping

Schroeder, Max R.; Juieng, Phalasy; Batra, Dhwani; Knipe, Kristen; Rowe, Lori A.; Sheth, Mili; Smith, P. B.; Garcia-Toledo, Lisley; Loparev, Vladimir N.; Lindsey, Rebecca L.

doi:10.1128/genomea.01384-17

Cited by 8 publications

(8 citation statements)

References 4 publications

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“…Heat stabilization treatment prior to DNA isolation did not appear to affect sequence reads obtained from next-generation sequencing from the Pac-Bio (Supplemental File 2) or Illumina (Supplemental File 3) platforms, and combined data were used to complete genomes. 12 DNA isolated after heat stabilization treatment was also compatible with multiplex PCR (Supplemental Figure S1) and real-time PCR (Supplemental Figure S2). The PFGE banding patterns were virtually identical when comparing patterns obtained for untreated control and heat stabilization treated bacterial suspensions (Supplemental Figure S3).…”

Section: Resultsmentioning

confidence: 99%

“…Bacterial strains used in this study included 6 Escherichia strains, E. albertii 2014C-4356, E. coli 2011C-4315, E. coli 2012C-4431, E. coli D181, Shigella dysenteriae BU53M1, S. flexneri 94-3007, S. flexneri 71-2783, 12 Clostridium cadaveris isolated from the spleen of a cow, and 26 additional species listed in Table 1. Work was performed in a BSL-2 laboratory within a Class II biological safety cabinet.…”

Section: Methodsmentioning

confidence: 99%

“…Bacterial strains used in this study included 6 Escherichia 12 Clostridium cadaveris isolated from the spleen of a cow, and 26 additional species listed in Table 1. Work was performed in a BSL-2 laboratory within a Class II biological safety cabinet.…”

Section: Bacterial Strains Media and Growth Conditionsmentioning

confidence: 99%

“…DNA templates, libraries, and sequence reactions, data analysis, and genomic assemblies were performed as described previously. 12…”

Section: Dna Sequencingmentioning

confidence: 99%

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Rapid Inactivation of Non-Endospore-Forming Bacterial Pathogens by Heat Stabilization is Compatible with Downstream Next-Generation Sequencing

Schroeder

Loparev

2019

Appl Biosaf.

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Introduction: Heat stabilization treatment preserves the in vivo state of biological samples by rapidly inactivating enzymes that cause degradation of proteins and nucleic acids. Historically, proteomics studies used this technique as an alternative to chemical fixation. More recently, microbiologists discovered that heat stabilization treatment rapidly inactivates pathogens present in tissue samples and preserves deoxyribonucleic acid (DNA) in the tissue. However, these recent studies did not investigate the inactivation of high-density bacterial suspensions and the quality of bacterial DNA. Methods and Results: High-density suspensions of Escherichia coli (>109 cfu/mL) were completely inactivated by heat stabilization treatment using the Denator Stabilizor T1 instrument at 72°C and 95°C for 45 seconds. Using the heat stabilization instrument, a panel of 30 species, 20 Gram-negative and 10 non-endospore-forming Gram-positive species, were fully inactivated by treatment (95°C for 45 seconds). DNA was isolated from bacterial suspensions of Gram-negative bacteria, including E. albertii, E. coli, Shigella dysenteriae, and S. flexneri, following inactivation via heat stabilization treatment and without treatment. DNA isolated following heat stabilization treatment was fully compatible with all downstream molecular applications tested, including next-generation sequencing, pulsed-field gel electrophoresis, multiplex polymerase chain reaction (PCR), and real-time PCR. Conclusions and Discussion: Heat stabilization treatment of Gram-negative and non-endospore-forming Gram-positive pathogens completely inactivates high-density bacterial suspensions. This treatment is compatible with downstream DNA molecular assays, including next-generation sequencing, pulsed-field gel electrophoresis, and PCR. Inactivation by heat stabilization is a rapid process that may increase safety by decreasing risks for laboratory-associated infections and risks associated with transportation of infectious materials.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Bacterial Strains Media and Growth Conditionsmentioning

confidence: 99%

“…DNA templates, libraries, and sequence reactions, data analysis, and genomic assemblies were performed as described previously. 12…”

Section: Dna Sequencingmentioning

confidence: 99%

See 2 more Smart Citations

Rapid Inactivation of Non-Endospore-Forming Bacterial Pathogens by Heat Stabilization is Compatible with Downstream Next-Generation Sequencing

Schroeder

Loparev

2019

Appl Biosaf.

Self Cite

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“…Each was identified in a different S. flexneri serotype (1c, Y, 7b and 4av), suggesting the dissemination of this MDR plasmid across multiple lineages. They were also identified across multiple continents [specifically in Australia, China, America (unpublished) and Malawi] [16][17][18]. This suggests the plasmid has been successfully horizontally transmitted between strains and spread intercontinentally.…”

Section: Impact Statementmentioning

confidence: 99%

Whole genome sequence analysis of Shigella from Malawi identifies fluoroquinolone resistance

et al. 2021

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Increasing antimicrobial resistance and limited alternative treatments have led to fluoroquinolone-resistant Shigella strain inclusion on the WHO global priority pathogens list. In this study we characterized multiple Shigella isolates from Malawi with whole genome sequence analysis, identifying the acquirable fluoroquinolone resistance determinant qnrS1.

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O-antigen biosynthesis gene clusters of Escherichia albertii: their diversity and similarity to Escherichia coli gene clusters and the development of an O-genotyping method

et al. 2019

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Escherichia albertii is a recently recognized human enteropathogen that is closely related to Escherichia coli . In many Gram-negative bacteria, including E. coli , O-antigen variation has long been used for the serotyping of strains. In E. albertii , while eight O-serotypes unique to this species have been identified, some strains have been shown to exhibit genetic or serological similarity to known E. coli / Shigella O-serotypes. However, the diversity of O-serotypes and O-antigen biosynthesis gene clusters (O-AGCs) of E. albertii remains to be systematically investigated. Here, we analysed the O-AGCs of 65 E. albertii strains and identified 40 E. albertii O-genotypes (EAOgs) (named EAOg1–EAOg40). Analyses of the 40 EAOgs revealed that as many as 20 EAOgs exhibited significant genetic and serological similarity to the O-AGCs of known E. coli / Shigella O-serotypes, and provided evidence for the inter-species horizontal gene transfer of O-AGCs between E. albertii and E. coli . Based on the sequence variation in the wzx gene among the 40 EAOgs, we developed a multiplex PCR-based O-genotyping system for E. albertii (EAO-genotyping PCR) and verified its usefulness by genotyping 278 E. albertii strains from various sources. Although 225 (80.9 %) of the 278 strains could be genotyped, 51 were not assigned to any of the 40 EAOgs, indicating that further analyses are required to better understand the diversity of O-AGCs in E. albertii and improve the EAO-genotyping PCR method. A phylogenetic view of E. albertii strains sequenced so far is also presented with the distribution of the 40 EAOgs, which provided multiple examples for the intra-species horizontal transfer of O-AGCs in E. albertii .

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High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping

Cited by 8 publications

References 4 publications

Rapid Inactivation of Non-Endospore-Forming Bacterial Pathogens by Heat Stabilization is Compatible with Downstream Next-Generation Sequencing

Rapid Inactivation of Non-Endospore-Forming Bacterial Pathogens by Heat Stabilization is Compatible with Downstream Next-Generation Sequencing

Whole genome sequence analysis of Shigella from Malawi identifies fluoroquinolone resistance

O-antigen biosynthesis gene clusters of Escherichia albertii: their diversity and similarity to Escherichia coli gene clusters and the development of an O-genotyping method

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