Poultry Science Volume 99, Issue 12, December 2020, Antimicrobial resistance and related gene analysis of Salmonella from egg and chicken sources by whole-genome sequencing. Introduction Salmonella has always been a serious threat to global public health.
In the United States, Salmonella caused approximately 1.2 million illnesses and 450 deaths annually; and about 1 million of these illnesses were due to contaminated foods (Centers for Disease Control and Prevention (CDC), 2019; Scallan et al., 2011). It was estimated that Salmonella serotypes Enteritidis, Typhimurium, and Heidelberg caused about 50% of the foodborne salmonellosis outbreaks in the United States and were frequently isolated from eggs and egg products, chicken meats, chicken ovaries, and feces (Schoeni et al., 1995; Chittick et al., 2006; Gast et al., 2017).
In the past 20 yr, the increasing resistance to medically important antimicrobial agents in Salmonella has been widely reported (Su et al., 2004). CDC EID - JULY 2020 - Linking Epidemiology and Whole-Genome Sequencing to Investigate Salmonella Outbreak, Massachusetts, USA, 2018. Disclaimer: Early release articles are not considered as final versions.
Any changes will be reflected in the online version in the month the article is officially released. Author affiliations: Massachusetts Department of Public Health, Boston, Massachusetts, USA Nontyphoidal salmonellae are among the most ubiquitous pathogens associated with foodborne illness worldwide (1). Salmonellosis detection is of public health value because of the ease with which the pathogen is transmitted (2), increased pathogen antimicrobial drug resistance (3), and high morbidity rates (4). FOOD SAFETY NEWS 28/05/20 WGS aided detection of parallel Salmonella outbreaks in Germany. Whole genome sequencing helped identify concurrent outbreaks of a rare Salmonella serotype in Germany in 2017, according to a study.
Whole genome sequencing (WGS) of Salmonella Kottbus isolates revealed three co-circulating clusters in the country between June and August 2017. A total of 69 infections were identified in 13 German states. Median age was 55 years with a range of 0 to 91 and 55 percent were female. Salmonella Kottbus is a rare serotype with usually three to four reports of patients per month. Researchers investigated the outbreak with WGS and a case-control study. Large outbreak linked to ham Thirty-six patients belonged to the largest outbreak cluster, called cluster 1. Of all interviewed confirmed patients, 82 percent of infections could be explained by raw smoked ham. One patient from the U.K. with symptom onset in May 2017 without travel history had handled and consumed raw pork. Two cases reported eating the eggs raw or soft-boiled. FRONT. MICROBIOL. 17/04/20 A New Whole Genome Culture-Independent Diagnostic Test (WG-CIDT) for Rapid Detection of Salmonella in Lettuce. Introduction Consumption of fresh fruits and vegetables is increasingly linked with outbreaks of foodborne illnesses, and the bacterial pathogen Salmonella is one of the most commonly incriminated causes (Centers for Disease Control and Prevention, 2005; Lynch et al., 2009; Kozak et al., 2013).
Human foodborne Salmonella infection is consistently one of the most burdensome of all microbial food safety hazards due to a combination of high disease prevalence and relatively high rates of hospitalization and deaths of exposed people (Batz et al., 2011; Thomas et al., 2015). Prevalence of foodborne salmonellosis has remained high throughout the world, with an estimated global mortality rate of 155,000 individuals due to non-typhoidal salmonellosis (95% Confidence Interval: 39,000 – 303,000 deaths; Majowicz et al., 2010).
As a foodborne pathogen, Salmonella displays a number of attributes which makes it a suitable model foodborne contaminant for evaluating a new approach to food safety. FRONT. MICROBIOL. 17/04/20 A New Whole Genome Culture-Independent Diagnostic Test (WG-CIDT) for Rapid Detection of Salmonella in Lettuce. FRONT. VET. SCI. 18/12/19 Identification of Genetic Features for Attenuation of Two Salmonella Enteritidis Vaccine Strains and Differentiation of These From Wildtype Isolates Using Whole Genome Sequencing. Introduction Salmonella Enteritidis is a leading cause of salmonellosis worldwide (1) and more than 80% of investigated outbreaks in Europe have been associated with the consumption of inadequately cooked eggs or foods containing uncooked eggs ( (2).
Over the last few decades the Colindale phage typing (PT) scheme has played a central role in epidemiological studies of S. Enteritidis while there are limitations regarding Pulsed-field Gel Electrophoresis (PFGE) and Multilocus Variable-Number Tandem Repeat Analysis (MLVA) methods and “neither PFGE nor MLVA could distinguish all of the S. Enteritidis PT30 from various sources,” for example (3–5).
Recent phylogenetic studies based on whole genome sequencing (WGS) have revealed the presence of two separate clonal lineages of S. Whole genome sequencing (WGS) has been applied as an epidemiological tool for outbreak investigations as it provides high resolution for comparing genomes (12). Materials and Methods Bacterial Isolates Table 1. Results. VIROLOGY JOURNAL 23/03/17 Mosquito-borne Inkoo virus in northern Sweden - isolation and whole genome sequencing.
Study area This study was conducted between June and September 2015, in selected areas of Västerbotten County, northern Sweden, see Fig. 1.
Three sites were selected in the Umeå area by the virtue of their close proximity to the inlet of the Gulf of Bothnia and the mouth of Umeå River containing many natural bird habitats. The geographic coordinates for the three sites (1, 2 and 3) in Umeå were: N 63° 44,925’ E 020° 17,718’; N 63° 45,661’ E 020° 18,458’) and N 63° 45,086’ E 020° 20,764’ respectively. Although the climate is subarctic, the area experiences fairly warm summers, which provide a conducive environment for diverse mosquito species to thrive. In addition, Umeå is the largest city in northern part of Sweden with about 120,000 inhabitants, and serves as the port where ferry lines connect to Vaasa city in Finland.
A map showing the study areas where mosquitoes were sampled between June and September 2015 in Umeå and Lövånger, Västerbotten County, Sweden. PLOS 11/09/15 Whole Genome Sequence Analysis of Salmonella Enteritidis PT4 Outbreaks from a National Reference Laboratory’s Viewpoint. Introduction: In April and May 2014, two suspected egg-related outbreaks of Salmonella enterica subsp. enterica serovar Enteritidis (S.
Enteritidis) were investigated by the Belgian National Reference Laboratory of Foodborne Outbreaks. Both the suspected food and human isolates being available, and this for both outbreaks, made these the ideal case study for a retrospective whole genome sequencing (WGS) analysis with the goal to investigate the feasibility of this technology for outbreak investigation by a National Reference Laboratory or National Reference Centre without thorough bioinformatics expertise. Methods: The two outbreaks were originally investigated epidemiologically with a standard questionnaire and with serotyping, phage typing, multiple-locus variable-number of tandem repeats analysis (MLVA) and antimicrobial susceptibility testing as classical microbiological methods. Retrospectively, WGS of six outbreak isolates was done on an Illumina HiSeq. Introduction Methods Results. JOURNAL OF FOOD PROTECTION - 2005 - Growth of Salmonella Serovars, Escherichia coli O157:H7, and Staphylococcus aureus during Thawing of Whole Chicken and Retail Ground Beef Portions at 22 and 30 C.
FRONTIERS IN MICROBIOLOGY 27/03/18 Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal Salmonella enterica. Introduction Salmonella enterica subspecies enterica is responsible for 99% of salmonellosis cases in humans and animals, and can be further subdivided into the host-restricted typhoidal salmonellae and the more generalist non-typhoidal salmonellae (NTS) (Langridge et al., 2015; Wain et al., 2015).
As host-adapted or generalist organisms, NTS can be transferred from animals to humans causing zoonotic infections and therefore fall under the World Health Organization’s One Health approach. Globally, NTS were estimated to cause 93.8 million enteric infections resulting in 155,000 deaths annually (Majowicz et al., 2010), and in the United Kingdom they are the third most common cause of bacterial gastroenteritis (Tam et al., 2012). Although NTS symptoms are often limited to the gastrointestinal tract, invasive disease can occur, especially in high-risk groups such as immunocompromised patients and the elderly (Parry et al., 2013). FRONT. SUSTAIN. FOOD SYST 08/06/18 For the Safety of Fresh Produce: Regulatory Considerations for Canada on the Use of Whole Genome Sequencing to Subtype Salmonella. Introduction Eating a well-balanced diet integrating fruits and vegetables is known to alleviate the risks of developing several non-communicable diseases including heart-related conditions (Acheson and Williams, 1983; van't Veer et al., 2000; Lock et al., 2005; Wang et al., 2014; Rodriguez-Casado, 2016).
FDA 28/04/16 FDA NARMS Retail Meat Interim Report for Salmonella Shows Encouraging Early Trends Continue; Includes Whole Genome Sequencing Data for the First Time. May 4, 2016 — The U.S.
Food and Drug Administration has released a new interim report that measures antimicrobial resistance in Salmonella isolated from raw retail meat and poultry collected through the National Antimicrobial Resistance Monitoring System (NARMS). The 2014-2015 Retail Meat Interim Report contains data from January 2014 – June 2015. EUROSURVEILLANCE 23/04/15 A multi-country Salmonella Enteritidis phage type 14b outbreak associated with eggs from a German producer: ‘near real-time’ application of whole genome sequencing and food chain investigations, United Kingdom, May to September 2.
EUROSURVEILLANCE 07/12/17 Investigation using whole genome sequencing of a prolonged restaurant outbreak of Salmonella Typhimurium linked to the building drainage system, England, February 2015 to March 2016. EUROSURVEILLANCE 07/08/14 Au sommaire: A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012.
DTU NATIONAL FOOD INSTITUTE 14/01/15 The best way to determine salmonella type using whole genome sequencing. There is no single analytical method for whole genome sequencing data, which can be used universally to determine salmonella bacteria’s type. A PhD project at the National Food Institute, Technical University of Denmark has evaluated what methods are best suited for different purposes and developed an online analytical tool for use in determining various bacteria’s type. CDC EID - OCT 2017 - Investigation of Outbreaks of Salmonella enterica Serovar Typhimurium and Its Monophasic Variants Using Whole-Genome Sequencing, Denmark.
Author affiliations: Statens Serum Institut, Copenhagen, Denmark (P. Gymoese, G. Sørensen, E. CDC EID - AOUT 2014 - Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis. Author affiliations: Cornell University, Ithaca, New York, USA (H. den Bakker, M. Wiedmann); US Food and Drug Administration, College Park, Maryland, USA (M.W. Allard, E.W. Brown, E. Strain); New York State Department of Health/Wadsworth Center, Albany, New York, USA (D. Bopp, R. BIORXIV 27/06/18 Retrospective whole-genome sequencing analysis distinguished PFGE and drug resistance matched retail meat and clinical Salmonella isolates. EUROSURVEILLANCE 24/01/19 Whole genome sequencing of Salmonella Chester reveals geographically distinct clusters, Norway, 2000 to 2016. EUROSURVEILLANCE 23/04/15 A multi-country Salmonella Enteritidis phage type 14b outbreak associated with eggs from a German producer: ‘near real-time’ application of whole genome sequencing and food chain investigations, United Kingdom, May to September 2.
BMC INFECTIOUS DISEASE - 2017 - The invasome of Salmonella Dublin as revealed by whole genome sequencing. BMC GENOMICS 06/11/18 Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources.