scholarly journals Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry

2021 ◽  
Vol 9 (3) ◽  
pp. 608
Author(s):  
Dustin A. Therrien ◽  
Kranti Konganti ◽  
Jason J. Gill ◽  
Brian W. Davis ◽  
Andrew E. Hillhouse ◽  
...  
Keyword(s):  
Food Safety ◽  
Food Industry ◽  
Sequence Data ◽  
Bacterial Species ◽  
Genetic Alterations ◽  
Whole Genome ◽  
Genome Sequences ◽  
Widespread Application ◽  
Sequencing Platform ◽  
E Coli

In 2013, the U.S. Department of Agriculture Food Safety and Inspection Service (USDA-FSIS) began transitioning to whole genome sequencing (WGS) for foodborne disease outbreak- and recall-associated isolate identification of select bacterial species. While WGS offers greater precision, certain hurdles must be overcome before widespread application within the food industry is plausible. Challenges include diversity of sequencing platform outputs and lack of standardized bioinformatics workflows for data analyses. We sequenced DNA from USDA-FSIS approved, non-pathogenic E. coli surrogates and a derivative group of rifampicin-resistant mutants (rifR) via both Oxford Nanopore MinION and Illumina MiSeq platforms to generate and annotate complete genomes. Genome sequences from each clone were assembled separately so long-read, short-read, and combined sequence assemblies could be directly compared. The combined sequence data approach provides more accurate completed genomes. The genomes from these isolates were verified to lack functional key E. coli elements commonly associated with pathogenesis. Genetic alterations known to confer rifR were also identified. As the food industry adopts WGS within its food safety programs, these data provide completed genomes for commonly used surrogate strains, with a direct comparison of sequence platforms and assembly strategies relevant to research/testing workflows applicable for both processors and regulators.

scholarly journals Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2: TABLE 1 

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Yasuhiro Uchimura ◽  
Madeleine Wyss ◽  
Sandrine Brugiroux ◽  
Julien P. Limenitakis ◽  
Bärbel Stecher ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Bacterial Species ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
Sequencing Platform ◽  
Germ Free

We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species.

scholarly journals Comparison of whole genome sequences of three Bacillus cereus strains reveals the food safety risks of Apostichopus japonicus in China

2021 ◽  
Vol 20 ◽  
pp. 100649
Author(s):  
Xiaoran Zhao ◽  
Ruijun Li ◽  
Huifeng Dang ◽  
Luo Wang ◽  
Songzhe Fu ◽  
...  
Keyword(s):  
Food Safety ◽  
Bacillus Cereus ◽  
Apostichopus Japonicus ◽  
Whole Genome ◽  
Genome Sequences ◽  
Safety Risks

scholarly journals Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

2021 ◽  
Author(s):  
Viola Kurm ◽  
Ilse Houwers ◽  
Claudia E. Coipan ◽  
Peter Bonants ◽  
Cees Waalwijk ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
In Silico ◽  
Species Complex ◽  
Sequence Data ◽  
In Silico Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

scholarly journals Whole-Genome Draft Sequences of Nine Asymptomatic Escherichia coli Bacteriuria Isolates from Diabetic Patients

2018 ◽  
Vol 6 (2) ◽  
Author(s):  
Christoph Stork ◽  
Beáta Kovács ◽  
Eva Trost ◽  
Tamás Kovács ◽  
György Schneider ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract Infection ◽  
Asymptomatic Bacteriuria ◽  
Diabetic Patients ◽  
Whole Genome ◽  
Genome Sequences ◽  
Disease Response ◽  
Symptomatic Urinary Tract Infection ◽  
E Coli ◽  
Genome Draft

ABSTRACT Escherichia coli can colonize the urinary bladder without causing a disease response in the host. This asymptomatic bacteriuria (ABU) can protect against recurrent symptomatic urinary tract infection by virulent bacteria. Here, we report the whole-genome sequences of nine E. coli ABU isolates from diabetic patients.

scholarly journals High-Quality Whole-Genome Sequences for 77 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing

2018 ◽  
Vol 6 (19) ◽  
Author(s):  
Pooja N. Patel ◽  
Rebecca L. Lindsey ◽  
Lisley Garcia-Toledo ◽  
Lori A. Rowe ◽  
Dhwani Batra ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Foodborne Pathogen ◽  
Severe Illness ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
High Quality ◽  
Content Type ◽  
Sequencing Platform

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) is an enteric foodborne pathogen that can cause mild to severe illness. Here, we report the availability of high-quality whole-genome sequences for 77 STEC strains generated using the PacBio sequencing platform.

scholarly journals Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection

2019 ◽  
Vol 20 (S15) ◽  
Author(s):  
Jinhong Shi ◽  
Yan Yan ◽  
Matthew G. Links ◽  
Longhai Li ◽  
Jo-Anne R. Dillon ◽  
...  
Keyword(s):  
Feature Selection ◽  
Antimicrobial Resistance ◽  
Genome Sequence ◽  
Sequence Data ◽  
Bacterial Species ◽  
Clinical Diagnostics ◽  
New Drugs ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data

Abstract Background Antimicrobial resistance (AMR) is a major threat to global public health because it makes standard treatments ineffective and contributes to the spread of infections. It is important to understand AMR’s biological mechanisms for the development of new drugs and more rapid and accurate clinical diagnostics. The increasing availability of whole-genome SNP (single nucleotide polymorphism) information, obtained from whole-genome sequence data, along with AMR profiles provides an opportunity to use feature selection in machine learning to find AMR-associated mutations. This work describes the use of a supervised feature selection approach using deep neural networks to detect AMR-associated genetic factors from whole-genome SNP data. Results The proposed method, DNP-AAP (deep neural pursuit – average activation potential), was tested on a Neisseria gonorrhoeae dataset with paired whole-genome sequence data and resistance profiles to five commonly used antibiotics including penicillin, tetracycline, azithromycin, ciprofloxacin, and cefixime. The results show that DNP-AAP can effectively identify known AMR-associated genes in N. gonorrhoeae, and also provide a list of candidate genomic features (SNPs) that might lead to the discovery of novel AMR determinants. Logistic regression classifiers were built with the identified SNPs and the prediction AUCs (area under the curve) for penicillin, tetracycline, azithromycin, ciprofloxacin, and cefixime were 0.974, 0.969, 0.949, 0.994, and 0.976, respectively. Conclusions DNP-AAP can effectively identify known AMR-associated genes in N. gonorrhoeae. It also provides a list of candidate genes and intergenic regions that might lead to novel AMR factor discovery. More generally, DNP-AAP can be applied to AMR analysis of any bacterial species with genomic variants and phenotype data. It can serve as a useful screening tool for microbiologists to generate genetic candidates for further lab experiments.

scholarly journals Coagulase-Negative Staphylococci Pathogenomics

2019 ◽  
Vol 20 (5) ◽  
pp. 1215 ◽  
Author(s):  
Xavier Argemi ◽  
Yves Hansmann ◽  
Kevin Prola ◽  
Gilles Prévost
Keyword(s):  
Staphylococcus Aureus ◽  
Virulence Factors ◽  
Molecular Basis ◽  
Sequence Data ◽  
Commensal Bacteria ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Coagulase Negative Staphylococci ◽  
Major Pathogens

Coagulase-negative Staphylococci (CoNS) are skin commensal bacteria. Besides their role in maintaining homeostasis, CoNS have emerged as major pathogens in nosocomial settings. Several studies have investigated the molecular basis for this emergence and identified multiple putative virulence factors with regards to Staphylococcus aureus pathogenicity. In the last decade, numerous CoNS whole-genome sequences have been released, leading to the identification of numerous putative virulence factors. Koch’s postulates and the molecular rendition of these postulates, established by Stanley Falkow in 1988, do not explain the microbial pathogenicity of CoNS. However, whole-genome sequence data has shed new light on CoNS pathogenicity. In this review, we analyzed the contribution of genomics in defining CoNS virulence, focusing on the most frequent and pathogenic CoNS species: S. epidermidis, S. haemolyticus, S. saprophyticus, S. capitis, and S. lugdunensis.

scholarly journals Coexistence of Fosfomycin and Colistin Resistance in Klebsiella pneumoniae : Whole-Genome Shotgun Sequencing

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Balaji Veeraraghavan ◽  
Susmitha K. Perumalla ◽  
Naveen Kumar Devanga Ragupathi ◽  
Agila Kumari Pragasam ◽  
Dhiviya Prabaa Muthuirulandi Sethuvel ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Sequence Data ◽  
Draft Genome ◽  
Shotgun Sequencing ◽  
Whole Genome ◽  
Colistin Resistance ◽  
Genome Sequences ◽  
Major Threat ◽  
Carbapenem Resistant ◽  
Whole Genome Shotgun Sequencing

Resistance to colistin is a major threat that limits therapeutic choices for treating carbapenem-resistant Klebsiella pneumoniae infections. Herein, we report the draft genome sequences of two colistin-resistant K. pneumoniae isolates (BA41763 and B6753). The sequence data indicate that BA41763 and B6753 contain genomes of ~5.9 and 5.7 Mb in size with several plasmids.

scholarly journals Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences

2016 ◽  
Vol 55 (2) ◽  
pp. 616-623 ◽  
Author(s):  
Marie A. Chattaway ◽  
Ulf Schaefer ◽  
Rediat Tewolde ◽  
Timothy J. Dallman ◽  
Claire Jenkins
Keyword(s):  
Escherichia Coli ◽  
Clonal Complex ◽  
Shigella Flexneri ◽  
Bacterial Species ◽  
Whole Genome ◽  
Content Type ◽  
E Coli ◽  
Shigella Species ◽  
Close Phylogenetic Relationship ◽  
Initial Identification

ABSTRACTEscherichia coliandShigellaspecies are closely related and genetically constitute the same species. Differentiating between these two pathogens and accurately identifying the four species ofShigellaare therefore challenging. The organism-specific bioinformatics whole-genome sequencing (WGS) typing pipelines at Public Health England are dependent on the initial identification of the bacterial species by use of a kmer-based approach. Of the 1,982Escherichia coliandShigellasp. isolates analyzed in this study, 1,957 (98.4%) had concordant results by both traditional biochemistry and serology (TB&S) and the kmer identification (ID) derived from the WGS data. Of the 25 mismatches identified, 10 were enteroinvasiveE. coliisolates that were misidentified asShigella flexneriorS. boydiiby the kmer ID, and 8 wereS. flexneriisolates misidentified by TB&S asS. boydiidue to nonfunctionalS. flexneriO antigen biosynthesis genes. Analysis of the population structure based on multilocus sequence typing (MLST) data derived from the WGS data showed that the remaining discrepant results belonged to clonal complex 288 (CC288), comprising bothS. boydiiandS. dysenteriaestrains. Mismatches between the TB&S and kmer ID results were explained by the close phylogenetic relationship between the two species and were resolved with reference to the MLST data.Shigellacan be differentiated fromE. coliand accurately identified to the species level by use of kmer comparisons and MLST. Analysis of the WGS data provided explanations for the discordant results between TB&S and WGS data, revealed the true phylogenetic relationships between different species ofShigella, and identified emerging pathoadapted lineages.

Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2742-2751 ◽  
Author(s):  
Henryk Urbanczyk ◽  
Yoshitoshi Ogura ◽  
Tetsuya Hayashi
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Draft Genome ◽  
Taxonomic Revision ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genome Sequence Data ◽  
The Family

Use of inadequate methods for classification of bacteria in the so-called Harveyi clade (family Vibrionaceae, Gammaproteobacteria) has led to incorrect assignment of strains and proliferation of synonymous species. In order to resolve taxonomic ambiguities within the Harveyi clade and to test usefulness of whole genome sequence data for classification of Vibrionaceae, draft genome sequences of 12 strains were determined and analysed. The sequencing included type strains of seven species: Vibrio sagamiensis NBRC 104589T, Vibrio azureus NBRC 104587T, Vibrio harveyi NBRC 15634T, Vibrio rotiferianus LMG 21460T, Vibrio campbellii NBRC 15631T, Vibrio jasicida LMG 25398T, and Vibrio owensii LMG 25443T. Draft genome sequences of strain LMG 25430, previously designated the type strain of [Vibrio communis], and two strains (MWB 21 and 090810c) from the ‘beijerinckii’ lineage were also determined. Whole genomes of two additional strains (ATCC 25919 and 200612B) that previously could not be assigned to any Harveyi clade species were also sequenced. Analysis of the genome sequence data revealed a clear case of synonymy between V. owensii and [V. communis], confirming an earlier proposal to synonymize both species. Both strains from the ‘beijerinckii’ lineage were classified as V. jasicida, while the strains ATCC 25919 and 200612B were classified as V. owensii and V. campbellii, respectively. We also found that two strains, AND4 and Ex25, are closely related to Harveyi clade bacteria, but could not be assigned to any species of the family Vibrionaceae. The use of whole genome sequence data for the taxonomic classification of the Harveyi clade bacteria and other members of the family Vibrionaceae is also discussed.

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