Salmonella serotype prediction using the GalaxyTrakr SeqSero2 workflow v1

Salmonella serotypes are defined by two surface structures, O antigen and two H antigens. Traditional serotype determination is performed with the Salmonella serological somatic (O) and flagellar (H) tests and paired with biochemical confirmation. More than 2,600 Salmonella serotypes have been described in the White-Kauffmann-Le Minor scheme. Molecular methods for serotype determination have been developed based on genes responsible for serotype antigens. These genes are encoded in the rfb gene cluster, fliC, and fljB. SeqSero2 is a bioinformatic pipeline that uses whole genome sequence (WGS) data from pure-culture isolates to perform in silico analysis to determine the antigenic formula, including somatic (O) antigens and both flagellar (H) antigens. This provides continuity with the well-established scheme for phenotypic Salmonella serotypes. PURPOSE: This document outlines the steps required to run SeqSero2 v1.1.1 on a collection of isolates in the GalaxyTrakr environment. This is performed by utilizing a custom workflow called “SeqSero2 v1.1.1 collection workflow” and downloading the resulting table. SCOPE: This protocol covers the following tasks: 1. set up an account in GalaxyTrakr 2. Create a new history/workspace 3. Upload data 4. Execute the SeqSero2 workflow 5. Download the results

The modulatory effects of alfalfa polysaccharide on intestinal microbiota and systemic health of Salmonella serotype (ser.) Enteritidis-challenged broilers

Salmonella serotype (ser.) Enteritidis infection in broilers is a main foodborne illness that substantially threatens food security. This study aimed to examine the effects of a novel polysaccharide isolated from alfalfa (APS) on the intestinal microbiome and systemic health of S. ser. Enteritidis-infected broilers. The results indicated that broilers receiving the APS-supplemented diet had the improved (P < 0.05) growth performance and gut health than those fed no APS-supplemented diet. Supplementation with APS enhanced (P < 0.05) the richness of gut beneficial microbes such as Bacteroidetes, Barnesiella, Parabacteroides, Butyricimonas, and Prevotellaceae, while decreased (P < 0.05) the abundance of facultative anaerobic bacteria including Proteobacteria, Actinobacteria, Ruminococcaceae, Lachnospiraceae, and Burkholderiaceae in the S. ser. Enteritidis-infected broilers. The Bacteroides and Odoribacter were identified as the two core microbes across all treatments and combined with their syntrophic microbes formed the hub in co-occurrence networks linking microbiome structure to performance of broilers. Taken together, dietary APS supplementation improved the systemic health of broilers by reshaping the intestinal microbiome regardless of whether S. ser. Enteritidis infection was present. Therefore, APS can be employed as a potential functional additives to inhibit the S. ser. Enteritidis and enhance the food safety in poultry farming.

Occurrence of Salmonella in the Cattle Production in France

Salmonella is among the most common foodborne pathogens worldwide, and can lead to acute gastroenteritis. Along with poultry, cattle production is recognized as an important source of human infection. Salmonella transmission from cattle to humans can occur through the environment, or through close contact with sick animals or their derived products. This study aimed to investigate the intestinal carriage of Salmonella spp. within French cattle production. A total of 959 cattle intestinal samples, from one of the largest French slaughterhouses, were analyzed. Isolated strains were genotyped by pulsed field gel electrophoresis (PFGE), and a sub-selection was taken by whole genome sequencing (WGS). Twenty-nine samples were positive for Salmonella spp., yielding an estimated prevalence of 3% in cattle production. Eight different Salmonella serotypes were found: Montevideo was the most prevalent (34%), followed by Mbandaka (24%) and Anatum (14%). PFGE genotyping allowed the clustering of Salmonella isolates according to their serotype. Within the clusters, some isolates presented 100% similarity. To investigate potential epidemiological links between them, WGS and core genome multilocus sequence typing (cgMLST) were used, revealing identical profiles between isolates originating from different areas and/or different animal breeds. This investigation provides new insights on Salmonella serotype epidemiology in cattle production in France.

Prevalence of Enteric Fever Pathogens Isolated from Blood Culture at a Tertiary Care Centre

Introduction: Typhoid fever and paratyphoid fever commonly called as enteric fever is a life-threatening illness caused by Salmonella serotype Typhi and Salmonella serotype Paratyphi, respectively. It is a major public health issue in underdeveloped and developing countries. The aim of the study is to find out the prevalence of enteric fever pathogens in blood culture of patients attending a tertiary care centre. Methods: A descriptive cross-sectional study was conducted in 3483 blood samples of patients attending a tertiary care centre, with the history and symptoms suspicious of enteric fever during one year period from mid-September 2019 to mid-September 2020 after ethical approval from the institutional review committee. Isolates were identified by standard microbiological methods and tested for in vitro antibiotic susceptibility by modified kirby-bauer disc diffusion method. The obtained data was entered and analyzed in WHONET 5.6 program, point estimate at 95% was calculated along with frequency and proportion for binary data. Results: In our study, enteric fever pathogens were isolated from 18 (0.51%) blood samples. Out of which, Salmonella Paratyphi A was isolated from 10 (8.19%) and Salmonella Typhi was isolated from 8 (6.55%) blood samples. Other serotypes were not isolated. Antimicrobial susceptibility test showed that salmonella species that was isolated were sensitive to most of the drugs. Conclusions: Prevalence of enteric fever pathogens was lesser compared to other studies. Varying degrees of antibiotic resistance among isolated enteric fever pathogens necessitates continuous surveillance of the susceptibility patterns. Prudent use of antimicrobials, active infection control practices and stringent antibiotic policy should be implemented to prevent emergence of antibiotic resistance and future outbreaks.

Endocarditis en válvula aórtica nativa por Salmonella serotype Choleraesuis

Se presenta el caso de un paciente con antecedente de Leucemia Mieloide Crónica (LMC) llevado a trasplante alogénico de precursores hematopoyéticos, en el día 10 postoperatorio refiere dificultad respiratoria y empeoramiento de clase funcional además de picos febriles de 38.9, al examen físico presencia de soplo holosistólico en focos de la base, realizan hemocultivos con reporte positivo de S. choleraesuis en 4 de 4, se toma ecocardiograma transesofágico donde se evidencia vegetación en válvula aórtica - valva semilunar posterior (no coronaria) de 12 mm filiforme sin condicionamiento de fracción de eyección -, por estabilidad clínica del paciente sin evidencia de compromiso hemodinámico se decide manejo médico con quinolonas por 4 semanas, logrando desaparición de la vegetación y del soplo a la semana de tratamiento médico y negativización de hemocultivos posteriores.

Biofilm Production Potential of Salmonella Serovars Isolated from Chickens in North West Province, South Africa

Bacterial biofilms have recently gained considerable interest in the food production and medical industries due to their ability to resist destruction by disinfectants and other antimicrobials. Biofilms are extracellular polymer matrices that may enhance the survival of pathogens even when exposed to environmental stress. The effect of incubation temperatures (25°C, 37°C, and 40°C) and Salmonella serotype on biofilm-forming potentials was evaluated. Previously typed Salmonella serotypes (55) isolated from the gut of chickens were accessed for biofilms formation using a standard assay. Salmonella Typhimurium ATCC 14028TM and Salmonella Enteritidis ATCC 13076TM (positive controls), Escherichia coli (internal control) and un-inoculated Luria Bertani (LB) broth (negative control) were used. The isolates formed no biofilm (11.86–13.56%), weak (11.86–45.76%), moderate (18.64–20.34%), strong biofilms (23.73–54.24%) across the various temperatures investigated. Serotypes, Salmonella Heidelberg and Salmonella Weltevreden were the strongest biofilm formers at temperatures (25°C, 37°C, and 40°C, respectively). The potential of a large proportion (80%) of Salmonella serotypes to form biofilms increased with increasing incubation temperatures but decreased at 40°C. Findings indicate that average temperature favours biofilm formation by Salmonella serotypes. However, the influence of incubation temperature on biofilm formation was greater when compared to serotype. A positive correlation exists between Salmonella biofilm formed at 25°C, 37°C and 40°C (p ≥ 0.01). The ability of Salmonella species to form biofilms at 25°C and 37°C suggests that these serotypes may present severe challenges to food-processing and hospital facilities.

Genomic Characterization of Salmonella Minnesota Clonal Lineages Associated with Poultry Production in Brazil

Salmonella serotype Minnesota has been increasingly detected in Brazilian poultry farms and food products (chicken meat, eggs) in recent years. In addition, S. Minnesota isolates from poultry are generally resistant to several antibiotics and persistent in farm environments. The present study aimed to assess phylogenomic diversity of S. Minnesota isolates from the poultry production chain in Brazil. In total, 107 worldwide S. Minnesota whole genomes (including 12 from Brazil) were analyzed using a comparative approach. Phylogenetic analysis demonstrated two clades more related to poultry production in Brazil: S. Minnesota poultry lineages I and II (SM-PLI and SM-PLII). Phylodynamic analysis demonstrated that SM-PLI had a common ancestor in 1915, while SM–PLII originated circa 1971. SM-PLII encompassed a higher number of isolates and presented a recent increase in effective population size (mainly from 2009 to 2012). Plasmids IncA/C2 and ColRNA, antimicrobial resistance genes (aph(3′)-Ia, blaCMY-2, qnrB19, sul2, and tet(A)) and mainly a virulence genetic cluster (including the yersiniabactin operon) were detected in isolates from SM-PLI and/or SM-PLII. This study demonstrates the dissemination of two distinct S. Minnesota lineages with high resistance to antibiotics and important virulence genetic clusters in Brazilian poultry farms.

714. Increase in Multidrug-resistant Salmonella Serotype I 4,[5],12:i:- Infections Linked to Pork—United States, 2009–2018

Background Salmonella enterica I 4,[5],12:i:- is the 5th most common serotype causing clinical Salmonella infections in the United States. A strain with resistance to ampicillin, streptomycin, sulfamethoxazole, and tetracycline (ASSuT) has been linked to swine production in Europe and the United States. We reviewed U.S. surveillance data to describe clinical infections with antibiotic-resistant I 4,[5],12:i:-. Methods We reviewed data from CDC’s National Antimicrobial Resistance Monitoring System (NARMS) from 2009–2018 to describe trends. We analyzed whole-genome sequence data in PulseNet, the molecular surveillance network for foodborne illness in the United States, from 2015–2018 to distinguish between strains of I 4,[5],12:i:- using core-genome multilocus sequence typing, and identified antibiotic resistance determinants (ARDs). We reviewed data from the Foodborne Disease Outbreak Surveillance System to identify foods associated with outbreaks during 2009–2018. Results From 2009–2013 to 2014–2018, I 4,[5],12:i:- increased as a proportion of nontyphoidal Salmonella isolates in NARMS from 4.3% to 5.0% (P=0.006), while I 4,[5],12:i:- resistant to ASSuT increased from 1.1% to 2.6% (P&lt; 0.001). Of the 3,056 sequenced I 4,[5],12:i:- isolates in PulseNet, 2,105 (69%) were in a clade within 0–108 alleles of each other (ASSuT clade). Within this clade, 77% of isolates had ARDs conferring resistance to ASSuT, compared with 3% outside the clade. Isolates in the clade were also more likely than those outside the clade to have ARDs conferring decreased susceptibility to ciprofloxacin (13.1% vs. 5.2%, P&lt; 0.001) and resistance to ceftriaxone (5.4% vs. 2.3%, P&lt; 0.001). Among I 4,[5],12:i:- outbreaks with a single food source, those related to the ASSuT clade were more often linked to pork (10/15 [67%] vs. 1/5 [20%], P=0.07). Conclusion The increase in I 4,[5],12:i:- infections during 2009–2018 was likely driven by a clade of which most members had resistance to ASSuT, and many had decreased susceptibility to antibiotics used for empiric treatment. The association of this strain with outbreaks linked to pork suggests that measures to decrease carriage of Salmonella and selection for this strain in swine could prevent clinical infections with multidrug resistant Salmonella I 4,[5],12:i-. Disclosures All Authors: No reported disclosures

132. Emergence and Spread of Multidrug-resistant salmonella Serotype Infantis Infections in the United States, 2003–2018

Background Infantis re-emerged as a leading Salmonella serotype when a multidrug-resistant (MDR) strain with a rare extended spectrum β-lactamase (ESBL) blaCTX-M-65 gene emerged among returned travelers from Peru in 2012 and then spread domestically. This strain has been isolated from chickens at slaughter and retail, and humans in outbreaks traced to chicken. We reviewed national surveillance data to determine incidence trends and antibiotic resistance among Infantis infections. Methods We reviewed data from 2003–2018 from the Foodborne Diseases Active Surveillance Network to determine the incidence and epidemiology of infections in 10 sites under surveillance; PulseNet to determine pulsed-field gel electrophoresis (PFGE) patterns; and National Antimicrobial Resistance Monitoring System (NARMS) to determine antimicrobial susceptibility testing (AST) results and resistance genes of isolates identified by whole genome sequencing (WGS). We defined MDR Infantis as having ceftriaxone resistance by AST and either the blaCTX-M-65 gene or one of 18 PFGE patterns linked to that gene by WGS. Results The 2,154 patients with Infantis infection had a median age of 36 years and 57% were female; 86% had isolates from stool, 9% from urine, and 3% from blood. Only 10% reported foreign travel and 27% were hospitalized. The incidence of infections began increasing in 2010 and by 2017–2018 was 2-fold higher than the average during 2003–2009. During 2003–2018, 856 (88%) of 970 NARMS isolates had PFGE or WGS data; 48 isolates were MDR Infantis, and in addition to ceftriaxone and ampicillin resistance (by definition), all 48 were resistant to 3 or more antibiotic classes, 94% had decreased susceptibility to ciprofloxacin, and 67% were resistant to cotrimoxazole. During 2012–2016, 2% of isolates were MDR Infantis; this increased to 17% during 2017–2018 (Figure). Conclusion During the past decade, the incidence of Infantis infections markedly increased. This was likely driven by the emergence of an ESBL-producing strain that was initially associated with travel, and is now mostly domestically acquired and associated with consuming chicken. MDR Infantis now accounts for 1 in 5 Infantis infections. Public health strategies to reduce Salmonella contamination of chicken could help prevent these infections. Disclosures All Authors: No reported disclosures