What’s in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B

Connor, Thomas R.; Owen, Siân V.; Langridge, Gemma C.; Connell, Samuel; Nair, Satheesh; Reuter, Sandra; Dallman, Timothy J.; Corander, Jukka; Tabing, Kristine C.; Hello, Simon Le; Fookes, María; Doublet, Benoît; Zhou, Zhemin; Feltwell, Theresa; Ellington, Matthew J.; Herrera, Silvia; Gilmour, Matthew W.; Cloeckaert, Axel; Achtman, Mark; Parkhill, Julian; Wain, John; Pinna, Elizabeth de; Weill, François‐Xavier; Peters, Tansy; Thomson, Nicholas R.

doi:10.1128/mbio.00527-16

Cited by 33 publications

(61 citation statements)

References 42 publications

(53 reference statements)

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“…Unfortunately, preliminary tests showed that the SPAB_01124 marker was not able to specifically identify all the S. Paratyphi B tested. This result was not surprising with regards to the heterogeneous genomic background of this serotype, illustrated by the 10 PGs described by Connor et al ( 2016 ). Our investigations on the SPAB_01124 marker showed that it was absent in some of our S. Paratyphi B genomes and in the S. Paratyphi B genome ERR403703 belonging to the PG10.…”

Section: Discussionsupporting

confidence: 59%

“…The WGS data were subsequently analyzed with Gegenees which is a software for comparative analysis of microbial WGS data, allowing to define genomic signatures unique for specified target groups. The contigs were exported to Gegenees (version 2.2.1; downloaded from http://www.gegenees.org ; Agren et al 2012 ) on a Linux platform with 16 S. Paratyphi B genomes (including 15 from Connor et al ( 2016 )) belonging to different PGs (two of each PG when possible) (Table 1 ) and 44 other genomes belonging to other frequent serotypes (Table 2 ), all publicly available on NCBI. The complete genomes mentioned in Tables 1 and 2 are annotated genomes which are preferably used as reference genomes.…”

Section: Methodsmentioning

confidence: 99%

“…The MLST technique was, however, not able to cluster all the Paratyphi B strains in one closely related group, as the Paratyphi B population is polyphyletic and a large heterogeneity of genotypes exists inside this serotype. Later, Connor et al ( 2016 ) described the genomic variation in the Paratyphi B group after analysis of a large amount of whole genome sequencing (WGS) data (191 strains sequenced), giving the first high-resolution view of this serotype. They were able to cluster the analyzed strains into phylogenetic groups (PGs) numbered from 1 to 10.…”

Section: Introductionmentioning

confidence: 99%

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Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java

Gand

Mattheus

Saltykova

et al. 2019

Appl Microbiol Biotechnol

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Discriminating between d -tartrate fermenting and non-fermenting strains of Salmonella enterica subsp. enterica serotype Paratyphi B is of major importance as these two variants have different pathogenic profiles. While d -tartrate non-fermenting S. Paratyphi B isolates are the causative agent of typhoid-like fever, d -tartrate fermenting isolates (also called variant Java) of the same serotype trigger the less dangerous gastroenteritis. The determination of S. Paratyphi B variants requires a time-consuming process and complex biochemical tests. Therefore, a quadruplex real-time PCR method, based on the allelic discrimination of molecular markers selected from the scientific literature and from whole genome sequencing data produced in-house, was developed in this study, to be applied to Salmonella isolates. This method was validated with the analysis of 178 S. Paratyphi B ( d -tartrate fermenting and non-fermenting) and other serotypes reaching an accuracy, compared with the classical methods, of 98% for serotyping by slide agglutination and 100% for replacement of the biochemical test. The developed real-time PCR permits to save time and to obtain an accurate identification of a S. Paratyphi B serotype and its d -tartrate fermenting profile, which is needed in routine laboratories for fast and efficient diagnostics. Electronic supplementary material The online version of this article (10.1007/s00253-019-09854-4) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 59%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java

Gand

Mattheus

Saltykova

et al. 2019

Appl Microbiol Biotechnol

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“…Noticeably, this approach offers the highest genomic resolution possible and discriminatory power for even highly genetically close strains, which is lacking in conventional subtyping methods. In the last 5 years or so, the number of sequenced Salmonella genomes has been growing exponentially, largely due to the implementation of high-throughput genomic sequencing by the FDA (145), PulseNet International (146), the Wellcome Trust Sanger Centre (147), and Public Health England (148). As a result, WGS-based analysis is becoming the method of choice by public health laboratories for bacterial pathogen characterization and subtyping for epidemiological studies.…”

Section: Salmonella Typing Using Next-generation Sequencingmentioning

confidence: 99%

Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae

2018

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SUMMARY The ability of pathogenic bacteria to affect higher organisms and cause disease is one of the most dramatic properties of microorganisms. Some pathogens can establish transient colonization only, but others are capable of infecting their host for many years or even for a lifetime. Long-term infection is called persistence, and this phenotype is fundamental for the biology of important human pathogens, including Helicobacter pylori, Mycobacterium tuberculosis, and Salmonella enterica. Both typhoidal and nontyphoidal serovars of the species Salmonella enterica can cause persistent infection in humans; however, as these two Salmonella groups cause clinically distinct diseases, the characteristics of their persistent infections in humans differ significantly. Here, following a general summary of Salmonella pathogenicity, host specificity, epidemiology, and laboratory diagnosis, I review the current knowledge about Salmonella persistence and discuss the relevant epidemiology of persistence (including carrier rate, duration of shedding, and host and pathogen risk factors), the host response to Salmonella persistence, Salmonella genes involved in this lifestyle, as well as genetic and phenotypic changes acquired during prolonged infection within the host. Additionally, I highlight differences between the persistence of typhoidal and nontyphoidal Salmonella strains in humans and summarize the current gaps and limitations in our understanding, diagnosis, and curing of persistent Salmonella infections.

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“…Paratyphi B (HG3) could be distinguished from S . Java (HG2) using two genes encoding Type III Secretion System (TTSS) effector proteins; sseJ and srfJ (10): with S . Paratyphi B possessing only srfJ but S .…”

Section: Introductionmentioning

confidence: 99%

A real-time PCR for the differentiation of typhoidal and non-typhoidal Salmonella

Nair

Patel

Hickey

et al. 2019

Preprint

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22Rapid and accurate differentiation of Salmonella spp. causing enteric fever from non-23 typhoidal Salmonella is essential for clinical management of cases, laboratory risk 24 management and implementation of public health measures. Current methods used 25 for confirmation of identification including biochemistry and serotyping as well as 26 whole genome sequencing analyses, takes several days. Here we report the 27 development and evaluation of a real-time PCR assay that can be performed directly 28 on crude DNA extracts from bacterial colonies, for the rapid identification of typhoidal 29 and non-typhoidal Salmonella. 30 This novel two-hour assay identifies the genus Salmonella by detecting the ttr gene, 31 encoding tetrathionate reductase, and defines typhoidal Salmonella by the detection 32 of S. Typhi and Paratyphi-specific gene combinations. PCR assay performance was 33 determined using 211 clinical cultures of Salmonella (114 non-typhoidal and 97 34 Typhoidal strains) and 7 clinical non-Salmonella cultures. In addition, the specificity 35 of the assay was evaluated in silico using a diverse in-house collection of 1882 36 Salmonella whole genome sequences. The real-time PCR results for 218 isolates 37 and the genomic analysis of the 1882 isolates produced 100% sensitivity and 100% 38 specificity (based on a 7 gene profile) for identifying typhoidal Salmonella compared 39 to the Salmonella whole genome sequening identification methods currently used at 40 Public Health England.41 This paper describes a robust real-time PCR assay for the rapid, accurate 42 identification of typhoidal and non-typhoidal Salmonella which will be invaluable for 43 the urgent screening of isolates from symptomatic individuals, the safe processing of 44 isolates in laboratories and for assisting the management of public health risks. 45 46 Salmonella are a diverse genus of gastrointestinal pathogens that cause a wide 47 spectrum of disease from self-limiting gastroenteritis (non-typhoidal salmonellae, 48 NTS) to systemic enteric fever (typhoidal salmonellae -Salmonella enterica serovar 49 Typhi, Paratyphi A, B and C). Salmonellosis is global but typhoidal Salmonella are 50 found mainly in sub-Saharan Africa and South Asia where enteric fever is endemic 51 (1); although the detailed local surveillance data from endemic regions remains poor 52(2). A current concern is the increase in bacteraemia (and focal infections) 53 associated with multi-drug resistant NTS infection in sub-Saharan Africa. In high 54 income countries such as the UK, invasive NTS infection is mainly confined to 55 immune-compromised hosts and so the major risks are local outbreaks of NTS 56 through poor food hygiene and typhoidal infections associated with travel to endemic 57 regions. 58 Diagnostic hospital microbiology laboratories make only a presumptive identification 59 of Salmonella spp.: they do not usually hold a sufficient range of specific antisera for 60 full identification and rapid identification systems, such as Matrix Assisted Laser 61 Desorption/I...

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What’s in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B

Cited by 33 publications

References 42 publications

Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java

Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java

Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae

A real-time PCR for the differentiation of typhoidal and non-typhoidal Salmonella

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