Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella

Tang, Silin; Orsi, Renato H.; Luo, Hao; Ge, Chongtao; Zhang, Guangtao; Baker, R. C.; Stevenson, Abigail E.; Wiedmann, Martin

doi:10.3389/fmicb.2019.01591

Cited by 72 publications

(69 citation statements)

References 176 publications

(298 reference statements)

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“…Even though many serotypes may contribute to human illness, the 20 most prevalent serotypes account for almost 70 % of the reported human cases in the USA according to a Centers for Disease Control and Prevention (CDC) report [5]. Serotyping is a useful and efficient way to subtype NTS infections, but it has low discriminatory power for differentiating between similar isolates belonging to the same serovar, which limits its use for epidemiological purposes, including tracing sources of infections [6]. Therefore, over the years, multiple molecular methods, such as pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and whole-genome sequencing (WGS), have been developed and increasingly applied to subtype Salmonella strains accurately, as reviewed by Tang et al .…”

Section: Introductionmentioning

confidence: 99%

Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA

et al. 2020

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Serotyping has traditionally been used for subtyping of non-typhoidal Salmonella (NTS) isolates. However, its discriminatory power is limited, which impairs its use for epidemiological investigations of source attribution. Whole-genome sequencing (WGS) analysis allows more accurate subtyping of strains. However, because of the relative newness and cost of routine WGS, large-scale studies involving NTS WGS are still rare. We aimed to revisit the big picture of subtyping NTS with a public health impact by using traditional serotyping (i.e. reaction between antisera and surface antigens) and comparing the results with those obtained using WGS. For this purpose, we analysed 18 282 sequences of isolates belonging to 37 serotypes with a public health impact that were recovered in the USA between 2006 and 2017 from multiple sources, and were available at the National Center for Biotechnology Information (NCBI). Phylogenetic trees were reconstructed for each serotype using the core genome for the identification of genetic subpopulations. We demonstrated that WGS-based subtyping allows better identification of sources potentially linked with human infection and emerging subpopulations, along with providing information on the risk of dissemination of plasmids and acquired antimicrobial resistance genes (AARGs). In addition, by reconstructing a phylogenetic tree with representative isolates from all serotypes (n=370), we demonstrated genetic variability within and between serotypes, which formed monophyletic, polyphyletic and paraphyletic clades. Moreover, we found (in the entire data set) an increased detection rate for AARGs linked to key antimicrobials (such as quinolones and extended-spectrum cephalosporins) over time. The outputs of this large-scale analysis reveal new insights into the genetic diversity within and between serotypes; the polyphyly and paraphyly of certain serotypes may suggest that the subtyping of NTS to serotypes may not be sufficient. Moreover, the results and the methods presented here, leading to differentiation between genetic subpopulations based on their potential risk to public health, as well as narrowing down the possible sources of these infections, may be used as a baseline for subtyping of future NTS infections and help efforts to mitigate and prevent infections in the USA and globally.

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Section: Introductionmentioning

confidence: 99%

Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA

et al. 2020

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“…There is an increasing array of methods to characterize microorganisms from whole genome sequencing to traditional culturing strategies (Chiou et al, 2015;Ibrahim and Morin, 2018). For Salmonella, a common foodborne pathogen that can cause disease in humans, the characterization must allow tracking of the contamination source by using appropriate subtyping tools (Tang et al, 2019). The "gold standard" classifying subtle differences between salmonella strains is based on the Kauffmann-White nomenclature (Grimont and Weill, 2007), representing a traditional phenotyping method that is logistically challenging, as it requires the use of more than 150 specific antisera and well-trained personnel to interpret the results (Diep et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…The typical symptom is abdominal pain and is diagnosed as gastroenteritis, with severe infections becoming life threatening. Food safety incidents and recalls continue in recent years, mostly associated with processed products (Pillai and Ricke, 2002;Maciorowski et al, 2004;Park et al, 2008;Hanning et al, 2009), and other food commodities (e.g., meat products, eggs, and vegetables) (Greig and Ravel, 2009;Wu et al, 2017;Ricke et al, 2018;Tang et al, 2019). These occurrences necessitate accurate and relatively rapid subtyping tools for identifying the original source of contamination (Olaimat and Holley, 2012;Barco et al, 2013;Shi et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Differential Biophysical Behaviors of Closely Related Strains of Salmonella

Liu

Hayes

2020

Front. Microbiol.

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Salmonella is an important pathogen and is a worldwide threat to food safety and public health. Surveillance of serotypes and fundamental biological and biochemical studies are supported by a wide variety of established and emerging bioanalytical techniques. These include classic serotyping based on the Kauffmann-White nomenclature and the emerging whole genome sequencing strategy. Another emerging strategy is native whole cell biophysical characterization which has yet to be applied to Salmonella. However, this technique has been shown to provide high resolution differentiation of serotypes with several other paired strains of other microbes and pathogens. To demonstrate that biophysical characterization might be useful for Salmonella serotyping, the closely related strains sv. Cubana and sv. Poona were chosen for study. These two serovars were subjected to biophysical measurements on a dielectrophoresisbased microfluidic device that generated full differentiation of the unlabeled and native cells. They were differentiated by the ratio of electrophoretic (EP) to dielectrophoretic (DEP) mobilities. This differentiation factor is 2.7 ± 0.3 × 10 10 V/m 2 for sv. Cubana, versus 2.2 ± 0.3 × 10 10 V/m 2 for sv. Poona. This work shows for the first time the differentiation, concentration, and characterization of the Salmonella serotypes by exploiting their biophysical properties. It may lead to a less expensive and more decentralized new tool and method for microbiologists, complimenting and working in parallel with other characterization methods.

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“…Among the loci that can be used for such an analysis, CRISPR have been quite popular for typing a number of other pathogenic bacteria, including Yersinia pestis and Salmonella (Tang et al , 2019). This is exemplified in the M. tuberculosis complex with the implementation and continued use of spoligotyping.…”

Section: Discussionmentioning

confidence: 99%

RapidMycobacterium tuberculosisspoligotyping from uncorrected long reads using Galru

Page¹,

Alikhan²,

Strinden³

et al. 2020

Preprint

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Spoligotyping of Mycobacterium tuberculosis provides a subspecies classification of this major human pathogen. Spoligotypes can be predicted from short read genome sequencing data; however, no methods exist for long read sequence data such as from Nanopore or PacBio. We present a novel software package Galru, which can rapidly detect the spoligotype of a Mycobacterium tuberculosis sample from as little as a single uncorrected long read. It allows for near real-time spoligotyping from long read data as it is being sequenced, giving rapid sample typing. We compare it to the existing state of the art software and find it performs identically to the results obtained from short read sequencing data. Galru is freely available from https://github.com/quadram-institute-bioscience/galru under the GPLv3 open source licence.

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Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella

Cited by 72 publications

References 176 publications

Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA

Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA

Differential Biophysical Behaviors of Closely Related Strains of Salmonella

RapidMycobacterium tuberculosisspoligotyping from uncorrected long reads using Galru

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