Serotyping forms the basis of national and international surveillance networks for Salmonella, one of the most prevalent foodborne pathogens worldwide (1–3). Public health microbiology is currently being transformed by whole-genome sequencing (WGS), which opens the door to serotype determination using WGS data. SeqSero (www.denglab.info/SeqSero) is a novel Web-based tool for determining Salmonella serotypes using high-throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants ( rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing (i) raw reads from genomes of 308 Salmonella isolates of known serotype; (ii) raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and (iii) 354 other publicly available draft or complete Salmonella genomes. We also demonstrated Salmonella serotype determination from raw sequencing reads of fecal metagenomes from mice orally infected with this pathogen. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization.

Salmonella Serotype Determination Utilizing High-throughput Genome Sequencing Data

In April 2015, Public Health England implemented whole genome sequencing (WGS) as a routine typing tool for public health surveillance of Salmonella, adopting a multilocus sequence typing (MLST) approach as a replacement for traditional serotyping. The WGS derived sequence type (ST) was compared to the phenotypic serotype for 6,887 isolates of S. enterica subspecies I, and of these, 6,616 (96%) were concordant. Of the 4% (n = 271) of isolates of subspecies I exhibiting a mismatch, 119 were due to a process error in the laboratory, 26 were likely caused by the serotype designation in the MLST database being incorrect and 126 occurred when two different serovars belonged to the same ST. The population structure of S. enterica subspecies II-IV differs markedly from that of subspecies I and, based on current data, defining the serovar from the clonal complex may be less appropriate for the classification of this group. Novel sequence types that were not present in the MLST database were identified in 8.6% of the total number of samples tested (including S. enterica subspecies I-IV and S. bongori) and these 654 isolates belonged to 326 novel STs. For S. enterica subspecies I, WGS MLST derived serotyping is a high throughput, accurate, robust, reliable typing method, well suited to routine public health surveillance. The combined output of ST and serovar supports the maintenance of traditional serovar nomenclature while providing additional insight on the true phylogenetic relationship between isolates.

Identification of Salmonella for public health surveillance using whole genome sequencing.

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.

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

The food industry is facing a major transition regarding methods for confirmation, characterization, and subtyping of Salmonella Whole-genome sequencing (WGS) is rapidly becoming both the method of choice and the gold standard for Salmonella subtyping; however, routine use of WGS by the food industry is often not feasible due to cost constraints or the need for rapid results To facilitate selection of subtyping methods by the food industry, we present: (i) a comparison between classical serotyping and selected widely used molecular-based subtyping methods including pulsed-field gel electrophoresis, multilocus sequence typing, and WGS (including WGS-based serovar prediction) and (ii) a scoring system to evaluate and compare Salmonella subtyping assays This literature-based assessment supports the superior discriminatory power of WGS for source tracking and root cause elimination in food safety incident; however, circumstances in which use of other subtyping methods may be warranted were also identified This review provides practical guidance for the food industry and presents a starting point for further comparative evaluation of Salmonella characterization and subtyping methods

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Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella.

Acute diarrheal disease remains a major public health issue. Salmonella spp. infection is one of the leading causes of acute diarrheal disease despite the preventive measures implemented. The clinical picture of salmonellosis varies from a common gastroenteritis to enteric fevers which are life-threatening diseases requiring a prompt and correct antibiotic treatment. In this review we present recent salmonellosis outbreaks and point out that Salmonella infections continue to be an important health issue. Numerous outbreaks of Salmonella spp. have been reported worldwide in recent years, indicating that prevention and control programs need to be improved as well as the infectious diseases surveillance, all over the world.

Salmonella spp. infection - a continuous threat worldwide.

Salmonella is a diverse foodborne pathogen, which has more than 2600 recognized serovars. Classification of Salmonella isolates into serovars is essential for surveillance and epidemiological investigations; however, determination of Salmonella serovars, by traditional serotyping, has some important limitations (e.g. labor intensive, time consuming). To overcome these limitations, multiple methods have been investigated to develop molecular serotyping schemes. Currently, molecular methods to predict Salmonella serovars include (i) molecular subtyping methods (e.g. PFGE, MLST), (ii) classification using serovar-specific genomic markers and (iii) direct methods, which identify genes encoding antigens or biosynthesis of antigens used for serotyping. Here, we reviewed reported methodologies for Salmonella molecular serotyping and determined the "serovar-prediction accuracy", as the percentage of isolates for which the serovar was correctly classified by a given method. Serovar-prediction accuracy ranged from 0 to 100%, 51 to 100% and 33 to 100% for molecular subtyping, serovar-specific genomic markers and direct methods, respectively. Major limitations of available schemes are errors in predicting closely related serovars (e.g. Typhimurium and 4,5,12:i:-), and polyphyletic serovars (e.g. Newport, Saintpaul). The high diversity of Salmonella serovars represents a considerable challenge for molecular serotyping approaches. With the recent improvement in sequencing technologies, full genome sequencing could be developed into a promising molecular approach to serotype Salmonella.

Molecular methods for serovar determination of Salmonella

Field portable X-ray fluorescence (FP-XRF) has tremendous potential in geoenvironmental engineering as a qualitative assessment tool. Identification of the elevated concentrations of the selected elements (Cr, Cu, Mn, Ni, Pb, and Zn) in various geomaterials like soil-like-material (SLM), incinerated bottom ash (IBA), construction and demolition waste (CDW), zinc tailings (ZT) and fly ash (FA) was performed by FP-XRF and compared with the local soil–Delhi silt. Comparably higher concentrations (mg/kg) of Cr (401.0), Cu (499.0), Pb (532.0), Zn (608.0) in SLM, Cr (195.0), Cu (419.0), Ni (93.0), Pb (931.0), Zn (771.0) in IBA and Cr (195.0), Cu (4000.0), Pb (671.0), Zn (7122.0) in ZT were observed. CDW and FA showed similar concentrations range as in local soils. FP-XRF was also used in-situ on local soil at 11 sites to examine its ability to identify the elements with significant variations in concentrations. The results showed high variability in Cl and S concentration values across the 11 sites attributed to the changing moisture content and dissolved salts. The concentration range for the remaining elements were similar at all sites. The verification of the detected elements through visual inspection of the spectrum was also carried out.

Qualitative comparison of elemental concentration in soils and other geomaterials using FP-XRF

Aims - To study Vitamin D levels in sepsis, correlation of qSOFA score for assessing the severity of sepsis
and predicting outcomes in patients of sepsis.
Material And Methods - A cross sectional observational study was conducted at MLN Medical College, Prayagraj. A total of 140
patients were enrolled in the study after following inclusion and exclusion criteria's.
Result – In the study, it was found that, higher values of qSOFA scores were found in the non-survivors patients (34.7% vs. 2.9%).
Also higher value was associated with longer hospital stay and multiorgan dysfunction and ICU admission. In this study, it was
also seen that higher values of serum Vitamin D was seen in survivors (27.9 ± 9.7 ng/dL v/s 9.7 ± 4.7 ng/dL; P < 0.0001).Also
lower values were associated with longer hospital stay and multiorgan dysfunction and ICU admission.
Conclusion – In this study, it was seen that higher values of qSOFA predicted poor clinical outcomes for patients with sepsis.
Likewise, low S. Vitamin D levels were also associated with dismal clinical outcomes in sepsis.

Evaluation of serum vitamin d levels in sepsis, correlation with qsofa score and clinical outcome.

ABSTRACT Erythropoietic protoporphyria (EPP) presents with nonblistering photosensitivity. Hepatobiliary manifestations are seen in around 5% cases and include cholelithiasis, elevations in liver enzymes, progressive jaundice, and end-stage liver disease. The diagnosis is suspected based on clinical features and elevated erythrocyte metal-free protoporphyrin and confirmed by genetic analysis showing loss-of-function mutations in the ferrochelatase (FECH) gene. We present an adolescent boy who presented with jaundice and photosensitivity with the liver biopsy showing deposition of brown pigments within the canaliculi and hepatocytes. This pigment showed Maltese cross birefringence on polarizing microscopy and Medusa-head appearance on electron microscopy. Genetic analysis revealed loss-of-function mutations in FECH. Introduction of EPP is an inborn error of heme biosynthesis caused by mutations in FECH with a prevalence of 1:75,000 to 1:200,000. We present a case of a 16-year-old adolescent boy with photosensitivity, abdominal pain, and jaundice with protoporphyrin deposition in the liver who was ultimately diagnosed with EPP based on genetic analysis.

An Enigmatic Case of Jaundice and Photosensitivity in an Adolescent

Abstract: The objective of this study is to compare the combustion, emissions, and engine performance of two different modified fuels. The oxygenated nanoparticles (CeO2 and Al2O3) were homogeneously mixed into B20 with an ultra sonicator at a specific ratio of 50,100 ppm to explore the potential of nanoparticles as a flexible booster in physiochemical properties of biodiesel. The generated nanoparticle fuel samples are then put to the CRDI VCR engine at various loads (3,6,9,12 kg): B20+50 Al2O3, B20+100 Al2O3, B20+50 CeO2, B20+100 CeO2. The different nano fuel's engine capabilities, combustion, and emissions are then contrasted with biodiesel, diesel, and one another. Performance-wise, BTE was 11.39% higher and SFC was 13.74% lower than B20 for B20+ 50 Al2O3 at high load. The cylinder pressure and heat release rate for B20+50 Al2O3 are respectively 16.77% and 21.48% greater at full load than for B20. In terms of hazardous emissions, B20+50 Al2O3 reduced CO emissions by 15.06% compared to B20, while B20+50 CeO2 reduced HC emissions by 50% compared to diesel at peak load. Additionally, at engine peak loads, B20+50 CeO2 Reduces NOx by 18.29% compared to B20. The findings suggest using nano fuel as a diesel oil replacement fuel.

Pranjal Singh

Papers

Molecular methods for serovar determination of Salmonella

Qualitative comparison of elemental concentration in soils and other geomaterials using FP-XRF

Evaluation of serum vitamin d levels in sepsis, correlation with qsofa score and clinical outcome.

An Enigmatic Case of Jaundice and Photosensitivity in an Adolescent

Examining How the Addition of AL2O3 and CEO2 Nanoparticles to Used Cooking Oil May Affect Engine Operation, Combustion, and Emissions