scholarly journals A whole-genome screen identifies Salmonella enterica serovar Typhi genes involved in fluoroquinolone susceptibility

2020 ◽  
Vol 75 (9) ◽  
pp. 2516-2525
Author(s):  
A Keith Turner ◽  
Sabine E Eckert ◽  
Daniel J Turner ◽  
Muhammud Yasir ◽  
Mark A Webber ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Insertion Site ◽  
Whole Genome ◽  
Genome Screen ◽  
Polysaccharide Biosynthesis ◽  
Salmonella Enterica Serovar Typhi ◽  
Transposon Insertion ◽  
Associated Functions ◽  
The Impact ◽  
Insertion Mutations

Abstract Objectives A whole-genome screen at sub-gene resolution was performed to identify candidate loci that contribute to enhanced or diminished ciprofloxacin susceptibility in Salmonella enterica serovar Typhi. Methods A pool of over 1 million transposon insertion mutants of an S. Typhi Ty2 derivative were grown in a sub-MIC concentration of ciprofloxacin, or without ciprofloxacin. Transposon-directed insertion site sequencing (TraDIS) identified relative differences between the mutants that grew following the ciprofloxacin treatment compared with the untreated mutant pool, thereby indicating which mutations contribute to gain or loss of ciprofloxacin susceptibility. Results Approximately 88% of the S. Typhi strain’s 4895 annotated genes were assayed, and at least 116 were identified as contributing to gain or loss of ciprofloxacin susceptibility. Many of the identified genes are known to influence susceptibility to ciprofloxacin, thereby providing method validation. Genes were identified that were not known previously to be involved in susceptibility, and some of these had no previously known phenotype. Susceptibility to ciprofloxacin was enhanced by insertion mutations in genes coding for efflux, other surface-associated functions, DNA repair and expression regulation, including phoP, barA and marA. Insertion mutations that diminished susceptibility were predominantly in genes coding for surface polysaccharide biosynthesis and regulatory genes, including slyA, emrR, envZ and cpxR. Conclusions A genomics approach has identified novel contributors to gain or loss of ciprofloxacin susceptibility in S. Typhi, expanding our understanding of the impact of fluoroquinolones on bacteria and of mechanisms that may contribute to resistance. The data also demonstrate the power of the TraDIS technology for antibacterial research.

scholarly journals Draft Genome Sequence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Strain from a Returned Traveler from Pakistan

2020 ◽  
Vol 9 (31) ◽  
Author(s):  
Samantha Hao ◽  
Tess Veuthey ◽  
Saharai Caldera ◽  
Paula Hayakawa Serpa ◽  
Barbara Haller ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genome Sequence ◽  
Salmonella Enterica ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome ◽  
Drug Resistant ◽  
Content Type ◽  
Salmonella Enterica Serovar Typhi ◽  
Extensively Drug Resistant

ABSTRACT We report a draft genome sequence of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi isolated from a returned traveler from Pakistan who developed sepsis. Whole-genome sequencing revealed relatedness to a previously reported outbreak in Pakistan and identified the blaCTX-M-15 and qnrS resistance genes.

scholarly journals Whole Genome Sequencing Analysis of Salmonella enterica Serovar Typhi: History and Current Approaches

2021 ◽  
Vol 9 (10) ◽  
pp. 2155
Author(s):  
Wan Ratmaazila Wan Makhtar ◽  
Izwan Bharudin ◽  
Nurul Hidayah Samsulrizal ◽  
Nik Yusnoraini Yusof
Keyword(s):  
Infectious Diseases ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Point Of Care ◽  
Genomic Research ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Significant Information ◽  
Salmonella Enterica Serovar Typhi

In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. In this review we discuss the findings of Salmonella enterica serovar Typhi genomes, publicly accessible from the initial complete genome to the recent update of Salmonella enterica serovar Typhi genomes, which has greatly improved Salmonella enterica serovar Typhi and other pathogen genomic research. Significant information on genetic changes, evolution, antimicrobial resistance, virulence, pathogenesis, and investigation from the genome sequencing of S. Typhi is also addressed. This review will gather information on the variation of the Salmonella enterica serovar Typhi genomes and hopefully facilitate our understanding of their genome evolution, dynamics of adaptation, and pathogenesis for the development of the typhoid point-of-care diagnostics, medications, and vaccines.

scholarly journals Transposon Insertion Site Sequencing of Providencia stuartii: Essential Genes, Fitness Factors for Catheter-Associated Urinary Tract Infection, and the Impact of Polymicrobial Infection on Fitness Requirements

mSphere ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Alexandra O. Johnson ◽  
Valerie Forsyth ◽  
Sara N. Smith ◽  
Brian S. Learman ◽  
Aimee L. Brauer ◽  
...  
Keyword(s):  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Insertion Site ◽  
Single Species ◽  
Polymicrobial Infection ◽  
Common Cause ◽  
Content Type ◽  
Transposon Insertion ◽  
Providencia Stuartii ◽  
The Impact

ABSTRACT Providencia stuartii is a common cause of polymicrobial catheter-associated urinary tract infection (CAUTI), and yet literature describing the molecular mechanisms of its pathogenesis is limited. To identify factors important for colonization during single-species infection and during polymicrobial infection with a common cocolonizer, Proteus mirabilis, we created a saturating library of ∼50,000 transposon mutants and conducted transposon insertion site sequencing (Tn-Seq) in a murine model of CAUTI. P. stuartii strain BE2467 carries 4,398 genes, 521 of which were identified as essential for growth in laboratory medium and therefore could not be assessed for contribution to infection. Using an input/output fold change cutoff value of 20 and P values of <0.05, 340 genes were identified as important for establishing single-species infection only and 63 genes as uniquely important for polymicrobial infection with P. mirabilis, and 168 genes contributed to both single-species and coinfection. Seven mutants were constructed for experimental validation of the primary screen that corresponded to flagella (fliC mutant), twin arginine translocation (tatC), an ATP-dependent protease (clpP), d-alanine-d-alanine ligase (ddlA), type 3 secretion (yscI and sopB), and type VI secretion (impJ). Infection-specific phenotypes validated 6/7 (86%) mutants during direct cochallenge with wild-type P. stuartii and 3/5 (60%) mutants during coinfection with P. mirabilis, for a combined validation rate of 9/12 (75%). Tn-Seq therefore successfully identified genes that contribute to fitness of P. stuartii within the urinary tract, determined the impact of coinfection on fitness requirements, and added to the identification of a collection of genes that may contribute to fitness of multiple urinary tract pathogens. IMPORTANCE Providencia stuartii is a common cause of polymicrobial catheter-associated urinary tract infections (CAUTIs), particularly during long-term catheterization. However, little is known regarding the pathogenesis of this organism. Using transposon insertion site sequencing (Tn-Seq), we performed a global assessment of P. stuartii fitness factors for CAUTI while simultaneously determining how coinfection with another pathogen alters fitness requirements. This approach provides four important contributions to the field: (i) the first global estimation of P. stuartii genes essential for growth in laboratory medium, (ii) identification of novel fitness factors for P. stuartii colonization of the catheterized urinary tract, (iii) identification of core fitness factors for both single-species and polymicrobial CAUTI, and (iv) assessment of conservation of fitness factors between common uropathogens. Genomewide assessment of the fitness requirements for common uropathogens during single-species and polymicrobial CAUTI thus elucidates complex interactions that contribute to disease severity and will uncover conserved targets for therapeutic intervention.

scholarly journals Insights from the Genome Sequence of a Salmonella enterica Serovar Typhi Strain Associated with a Sporadic Case of Typhoid Fever in Malaysia

2012 ◽  
Vol 194 (18) ◽  
pp. 5124-5125 ◽  
Author(s):  
Kien-Pong Yap ◽  
Cindy Shuan Ju Teh ◽  
Ramani Baddam ◽  
Lay-Ching Chai ◽  
Narender Kumar ◽  
...  
Keyword(s):  
Typhoid Fever ◽  
Genome Sequence ◽  
Salmonella Enterica ◽  
Evolutionary Dynamics ◽  
Sporadic Case ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Kuala Lumpur ◽  
Content Type ◽  
Salmonella Enterica Serovar Typhi

ABSTRACTSalmonella entericaserovar Typhi is the causative agent of typhoid fever, which causes nearly 21.7 million illnesses and 217,000 deaths globally. Herein, we describe the whole-genome sequence of theSalmonellaTyphi strain ST0208, isolated from a sporadic case of typhoid fever in Kuala Lumpur, Malaysia. The whole-genome sequence and comparative genomics allow an in-depth understanding of the genetic diversity, and its link to pathogenicity and evolutionary dynamics, of this highly clonal pathogen that is endemic to Malaysia.

scholarly journals Salmonella enterica Serovar Typhi Induces Host Metabolic Reprogramming to Increase Glucose Availability for Intracellular Replication

2021 ◽  
Vol 22 (18) ◽  
pp. 10003
Author(s):  
Jingting Wang ◽  
Shuai Ma ◽  
Wanwu Li ◽  
Xinyue Wang ◽  
Di Huang ◽  
...  
Keyword(s):  
Glucose Uptake ◽  
Salmonella Enterica ◽  
Metabolic Reprogramming ◽  
Host Cells ◽  
Uptake System ◽  
Intracellular Replication ◽  
Glucose Content ◽  
Human Macrophages ◽  
Salmonella Enterica Serovar Typhi ◽  
The Impact

Salmonella enterica serovar Typhi (S. Typhi) is a human-limited intracellular pathogen and the cause of typhoid fever, a severe systemic disease. Pathogen–host interaction at the metabolic level affects the pathogenicity of intracellular pathogens, but it remains unclear how S. Typhi infection influences host metabolism for its own benefit. Herein, using metabolomics and transcriptomics analyses, combined with in vitro and in vivo infection assays, we investigated metabolic responses in human macrophages during S. Typhi infection, and the impact of these responses on S. Typhi intracellular replication and systemic pathogenicity. We observed increased glucose content, higher rates of glucose uptake and glycolysis, and decreased oxidative phosphorylation in S. Typhi-infected human primary macrophages. Replication in human macrophages and the bacterial burden in systemic organs of humanized mice were reduced by either the inhibition of host glucose uptake or a mutation of the bacterial glucose uptake system, indicating that S. Typhi utilizes host-derived glucose to enhance intracellular replication and virulence. Thus, S. Typhi promotes its pathogenicity by inducing metabolic changes in host macrophages and utilizing the glucose that subsequently accumulates as a nutrient for intracellular replication. Our findings provide the first metabolic signature of S. Typhi-infected host cells and identifies a new strategy utilized by S. Typhi for intracellular replication.

scholarly journals Importation of Extensively Drug-Resistant Salmonella enterica Serovar Typhi Cases in Ontario, Canada

2020 ◽  
Vol 64 (5) ◽  
Author(s):  
Alireza Eshaghi ◽  
Sandra Zittermann ◽  
Amrita Bharat ◽  
Michael R. Mulvey ◽  
Vanessa G. Allen ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Bloodstream Infections ◽  
Whole Genome ◽  
Drug Resistant ◽  
Outbreak Strain ◽  
Travel History ◽  
Content Type ◽  
Salmonella Enterica Serovar Typhi ◽  
Extensively Drug Resistant

ABSTRACT A strain of extensively drug-resistant (XDR) Salmonella enterica serovar Typhi has caused a large ongoing outbreak in Pakistan since 2016. In Ontario, Canada, 10 cases of mainly bloodstream infections (n = 9) were identified in patients who traveled to Pakistan. Whole-genome sequencing showed that Canadian cases were genetically related to the Pakistan outbreak strain. The appearance of XDR typhoid cases in Ontario prompted a provincial wide alert to physicians to recommend treatment with carbapenems or azithromycin in suspected typhoid cases with travel history to Pakistan.

scholarly journals Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells

2020 ◽  
Vol 375 (1795) ◽  
pp. 20190335 ◽  
Author(s):  
Wilson McKerrow ◽  
Zuojian Tang ◽  
Jared P. Steranka ◽  
Lindsay M. Payer ◽  
Jef D. Boeke ◽  
...  
Keyword(s):  
De Novo ◽  
Single Cells ◽  
Repetitive Sequences ◽  
Insertion Site ◽  
Restriction Enzyme Digestion ◽  
Whole Genome ◽  
Transposon Insertion ◽  
Genome Wide ◽  
A Genome ◽  
Wide Line

Long interspersed element-1 (LINE-1, L1) sequences, which comprise about 17% of human genome, are the product of one of the most active types of mobile DNAs in modern humans. LINE-1 insertion alleles can cause inherited and de novo genetic diseases, and LINE-1-encoded proteins are highly expressed in some cancers. Genome-wide LINE-1 mapping in single cells could be useful for defining somatic and germline retrotransposition rates, and for enabling studies to characterize tumour heterogeneity, relate insertions to transcriptional and epigenetic effects at the cellular level, or describe cellular phylogenies in development. Our laboratories have reported a genome-wide LINE-1 insertion site mapping method for bulk DNA, named transposon insertion profiling by sequencing (TIPseq). There have been significant barriers applying LINE-1 mapping to single cells, owing to the chimeric artefacts and features of repetitive sequences. Here, we optimize a modified TIPseq protocol and show its utility for LINE-1 mapping in single lymphoblastoid cells. Results from single-cell TIPseq experiments compare well to known LINE-1 insertions found by whole-genome sequencing and TIPseq on bulk DNA. Among the several approaches we tested, whole-genome amplification by multiple displacement amplification followed by restriction enzyme digestion, vectorette ligation and LINE-1-targeted PCR had the best assay performance. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

scholarly journals Whole genome analysis and characterization of Salmonella enterica subsp. enterica serovar Typhimurium strain UPM 260 for mediated genetic manipulation

2020 ◽  
Author(s):  
Najwa Syahirah Roslan ◽  
Nurulfiza Mat Isa ◽  
Abdul Rahman Omar ◽  
Mohd. Hair Bejo ◽  
Aini Ideris
Keyword(s):  
Salmonella Enterica ◽  
Functional Characterization ◽  
Poultry Meat ◽  
Whole Genome Sequence ◽  
Health Concern ◽  
Type I ◽  
Whole Genome ◽  
Typhimurium Strain ◽  
Serovar Typhimurium ◽  
The Impact

Abstract Background Salmonella enterica serovar Typhimurium persists as one of the most frequent food-borne zoonoses, causing a major public health concern worldwide. Furthermore, Salmonella infection has a large economic impact. Globally, the main sources of infection for humans include the consumption of contaminated poultry meat and eggs. In animals however, Salmonella transmission usually occurs horizontally from infected birds and contaminated environments. Hence, to delve further on how the impact of this disease can be lessened, an epidemiological study needs to be performed. It is vital to determine the genomic sequences of microorganisms to understand their biology and functional characterization. Thus, we determined the whole-genome sequence and virulence profile of S. enterica serovar Typhimurium strain UPM 260 isolated from Perak, Malaysia. Whole genome sequencing (WGS) using paired-end sequencing generated 107 contigs with a total genome size of 4.9 Mbp and 52% G+C content. The contigs were annotated for phylogenetic and functional analysis. Results Through the analysis, it is revealed that the genome were resistant to a number of antimicrobial drug classes including aminoglycoside, fluoroquinolone, tetracycline and phenicol. Also found in UPM 260 genome were three intact prophages (Fels-1, Gifsy-2 and one unique prophage, mEp390). The genome housed four types of restriction-modification systems (RMS) and Type I-E subtype of CRISPR-Cas system. Two metal resistance operons (mer and cop) and six pathogenicity islands (SPIs) were also discovered in UPM 260 genome. The SPIs contributed mostly to the bacterial virulence properties since 1054 CDS were reported to be homologous to the virulence factors in the database VFDB. Conclusion This study benefits us specifically in the field of genome engineering where gene-based genetic manipulations can be applied in reducing the prevalence and pathogenicity in Salmonella.

scholarly journals Genomic Dissection of Travel-Associated Extended-Spectrum-Beta-Lactamase-Producing Salmonella enterica Serovar Typhi Isolates Originating from the Philippines: a One-Off Occurrence or a Threat to Effective Treatment of Typhoid Fever?

2014 ◽  
Vol 53 (2) ◽  
pp. 677-680 ◽  
Author(s):  
Rene S. Hendriksen ◽  
Pimlapas Leekitcharoenphon ◽  
Matthew Mikoleit ◽  
Jacob Dyring Jensen ◽  
Rolf Sommer Kaas ◽  
...  
Keyword(s):  
Typhoid Fever ◽  
Salmonella Enterica ◽  
The Philippines ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Content Type ◽  
Extended Spectrum Beta Lactamase ◽  
Salmonella Enterica Serovar Typhi ◽  
Extended Spectrum

One unreported case of extended-spectrum-beta-lactamase (ESBL)-producingSalmonella entericaserovar Typhi was identified, whole-genome sequence typed, among other analyses, and compared to other available genomes ofS. Typhi. The reported strain was similar to a previously published strain harboringblaSHV-12from the Philippines and likely part of an undetected outbreak, the first of ESBL-producingS. Typhi.

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