Serotype Typhimurium Research Articles

Antimicrobial resistance and related gene analysis of Salmonella from egg and chicken sources by whole-genome sequencing

Whole-genome sequencing (WGS) is a valuable tool in research on foodborne pathogens. In this study, a total of 143 isolates of Salmonella serotypes Enteritidis, Typhimurium, and Heidelberg sourced from eggs and chickens were analyzed for their antimicrobial resistance profiles using WGS data. The isolates carried high rate of genes resistant to aminoglycoside (70.63%), tetracycline (26.57%), fosfomycin (25.17%), sulfonamides (23.78%), and β-lactamases (15.38%); and aadA was the most frequently observed antimicrobial resistance gene (ARG). Antimicrobial resistance varies by Salmonella serotypes, with Salmonella enterica serovar Enteritidis (Salmonella ser. Enteritidis) isolates being highly resistant to aminoglycoside (particularly streptomycin); Salmonella ser. Typhimurium more resistant to aminoglycoside, tetracycline, and sulfonamides; and Salmonella ser. Heidelberg more resistant to aminoglycoside and fosfomycin. Salmonella ser. Typhimurium isolates presented more varieties of ARG than Salmonella ser. Enteritidis and Salmonella ser. Heidelberg. Our data showed that 5 isolates of Salmonella ser. Typhimurium and Salmonella ser. Heidelberg contained ARG resistant to ≥ 5 antimicrobials. In addition, 23 Salmonella isolates carried ARG resistant to 4 antimicrobials.

Vitamin A supplementation boosts control of antibiotic-resistant Salmonella infection in malnourished mice

Disseminated disease from non-typhoidal Salmonella enterica strains results in >20% mortality globally. Barriers to effective treatment include emerging multidrug resistance, antibiotic treatment failure, and risk factors such as malnutrition and related micronutrient deficiencies. Individuals in sub-Saharan Africa are disproportionately affected by non-typhoidal S. enterica bloodstream infections. To inform a clinical trial in people, we investigated vitamin A as a treatment in the context of antibiotic treatment failure in a mouse model of vitamin A deficiency. Vitamin A-deficient (VAD) mice exhibited higher systemic bacterial levels with a multidrug-resistant clinical isolate in comparison to mice on a control diet. Sex-specific differences in vitamin A deficiency and disseminated infection with S. enterica serotype Typhimurium (S. Typhimurium) were observed. VAD male mice had decreased weight gain compared to control male mice. Further, infected VAD male mice had significant weight loss and decreased survival during the course of infection. These differences were not apparent in female mice. In a model of disseminated S. Typhimurium infection and antibiotic treatment failure, we assessed the potential of two consecutive doses of vitamin A in alleviating infection in male and female mice on a VAD or control diet. We found that subtherapeutic antibiotic treatment synergized with vitamin A treatment in infected VAD male mice, significantly decreasing systemic bacterial levels, mitigating weight loss and improving survival. These results suggest that assessing vitamin A as a therapy during bacteremia in malnourished patients may lead to improved health outcomes in a subset of patients, especially in the context of antibiotic treatment failure.

Simultaneous removal of multidrug-resistant Salmonella enterica serotype typhimurium, antibiotics and antibiotic resistance genes from water by electrooxidation on a Magnéli phase Ti4O7 anode

Antibiotics and multidrug resistant bacteria are present extensively in different environmental matrices, and considered as contaminants of emerging concern. This study evaluated the feasibility and effectiveness of using electrooxidation (EO) with Magnéli phase Ti4O7 anode to simultaneously remove bacterial pathogens, antibiotics and antibacterial resistance genes (ARGs) from water. A model pathogen, multidrug-resistant Salmonella enterica serotype Typhimurium DT104, was completely deactivated with 6.2 log reduction in 15 min at the current density of 10.0 mA cm−2, while ARGs (i.e., TetG, floR and sul1), class 1 integron gene (intI1) and virulence genes (invA and spvC) that were contained in the pathogen were removed by as much as 99.65% to 99.94%. Model antibiotics, tetracycline (TC) and sulfadimethoxine (SDM), were degraded 97.95 % and 93.42 % in the same EO treatment system within 3 h. It was found that both direct electron transfer (DET) and OH-mediated oxidation played important roles in the removal of the ARGs during the EO process. EO may be a promising tool to control the spread of antibiotic resistence by removing pathogens, antibiotics and ARGs simultaneously.

Prevalence and Antimicrobial Resistance of Salmonella spp. From Irrigation Water in Two Major Sources in Jordan.

Irrigation water could be a direct source of pathogenic microorganisms that contaminates fresh produce and causes human diseases. In this study, we evaluated the prevalence of Salmonella spp. and its serotypes Typhimurium and Enteritidis, antimicrobial susceptibility and multidrug resistance (MDR) status, and seasonal variation, of Salmonella spp. in irrigation water of King Abdullah Canal (KAC) and Wadi Shueib (WS) in Jordan. The study results demonstrated that 32.2% (29/90) of irrigation water was contaminated with Salmonella spp. and the irrigation water of WS was found highly contaminated (62.1%) with Salmonella spp. compared to KAC (37.9%). In addition, higher prevalence of Salmonella were recorded in spring (33.3%) and summer (36.3%) seasons, compared to winter seasons. Among the contaminated irrigation water samples, prevalence of Salmonella Typhimurium serotype was found in (37.9%) (11/29) samples, while S. Enteritidis was absent. The most common antimicrobial resistance of Salmonella isolates was observed as tetracycline (11/29, 37.9%) and 6 (20.7%) Salmonella Typhimurium isolates were found multidrug resistance (MDR). Thus, this study results confirmed that the irrigation water was contaminated with pathogenic MDR Salmonella spp.

2-Aminobenzothiazoles Inhibit Virulence Gene Expression and Block Polymyxin Resistance in Salmonella enterica.

One promising strategy to combat antibiotic-resistant bacteria is to develop compounds that block bacterial defenses against antibacterial conditions produced by the innate immune system. Salmonella enterica, which causes food-borne gastroenteritis and typhoid fever, requires histidine kinases (HKs) to resist innate immune defenses such as cationic antimicrobial peptides (CAMPs). Herein, we report that 2-aminobenzothiazoles block histidine kinase-dependent phenotypes in Salmonella enterica serotype Typhimurium. We found that 2-aminobenzothiazoles inhibited growth under low Mg2+ , a stressful condition that requires histidine kinase-mediated responses, and decreased expression of the virulence genes pagC and pagK. Furthermore, we discovered that 2-aminobenzothiazoles weaken Salmonella's resistance to polymyxin B and polymyxin E, which are last-line antibiotics and models for host defense CAMPs. These findings raise the possibilities that 2-aminobenzothiazoles can block HK-mediated bacterial defenses and can be used in combination with polymyxins to treat infections caused by Salmonella.

Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State

Salmonella enterica serotype Typhimurium (S. Typhimurium) boasts a broad host range and can be transmitted between livestock and humans. While members of this serotype can acquire resistance to antimicrobials, the temporal dynamics of this acquisition is not well understood. Using New York State (NYS) and its dairy cattle farms as a model system, 87 S. Typhimurium strains isolated from 1999 to 2016 from either human clinical or bovine-associated sources in NYS were characterized using whole-genome sequencing. More than 91% of isolates were classified into one of four major lineages, two of which were largely susceptible to antimicrobials but showed sporadic antimicrobial resistance (AMR) gene acquisition, and two that were largely multidrug-resistant (MDR). All four lineages clustered by presence and absence of elements in the pan-genome. The two MDR lineages, one of which resembled S. Typhimurium DT104, were predicted to have emerged circa 1960 and 1972. The two largely susceptible lineages emerged earlier, but showcased sporadic AMR determinant acquisition largely after 1960, including acquisition of cephalosporin resistance-conferring genes after 1985. These results confine the majority of AMR acquisition events in NYS S. Typhimurium to the twentieth century, largely within the era of antibiotic usage.

Prevalence of Salmonella serotypes S. Enteritidis and S. Typhimurium in poultry and poultry products

AbstractSalmonella continues to be a major food safety and public health threat. In the present study, Salmonella enterica subsp. enterica serotypes Enteritidis (SE) and Typhimurium (ST) were isolated from poultry and characterized for virulence, antimicrobial susceptibility, and biofilm formation. Prevalence of Salmonella serotypes in poultry was 3.35%; predominant serotypes isolated were S. Enteritidis (68.1%) and S. Typhimurium (31.8%). Source‐wise, Salmonella were isolated from retail market chicken meat (4.8%), live chicken at farm (2.5%), and table eggs (2.1%). Salmonella isolates produced invA gene of 284 bp (100%), spvR gene of 310 bp (77.27%), spvC gene of 571 bp (22.72%), and stn gene of 260 bp (100%) as virulence/ pathogenicity determinants. Salmonella isolates exhibited resistance to common antimicrobials; 72.7% isolates showed multiple resistance (≥3 antimicrobial class), highest resistance was observed for polymyxin‐B (81.8%) followed by nalidixic acid (72.7%), colistin (59.1%), ampicillin/tetracyline (45.5%), ampicillin + sulbactam (40.9%), cefodroxil (18.2%), streptomycin (9.1%), and cefazidine/ceftriaxone‐tazobactam (4.5%). Multiple antimicrobial resistance (MAR) index of poultry Salmonella isolates ranged from 0.11 to 0.35; wherein, 59.1% isolates showed MAR of >0.2. About 81.8% Salmonella isolates produced biofilm and were categorized as strong (13.6%), moderate (45.4%), and weak (22.7%) biofilm producers. Occurrence of antimicrobial resistant virulent Salmonella strains in poultry requires implementation of suitable strategies so as to protect the public health.

Constructing conjugate vaccine against Salmonella Typhimurium using lipid-A free lipopolysaccharide

BackgroundSalmonella enterica serotype Typhimurium is a nontyphoidal and common foodborne pathogen that causes serious threat to humans. There is no licensed vaccine to prevent the nontyphoid bacterial infection caused by S. Typhimurium.MethodsTo develop conjugate vaccines, the bacterial lipid-A free lipopolysaccharide (LFPS) is prepared as the immunogen and used to synthesize the LFPS–linker–protein conjugates 6a–9b. The designed bifunctional linkers 1–5 comprising either an o-phenylenediamine or amine moiety are specifically attached to the exposed 3-deoxy-D-manno-octulosonic acid (Kdo), an α-ketoacid saccharide of LFPS, via condensation reaction or decarboxylative amidation. In addition to bovine serum albumin and ovalbumin, the S. Typhimurium flagellin (FliC) is also used as a self-adjuvanting protein carrier.ResultsThe synthesized conjugate vaccines are characterized by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and fast performance liquid chromatography (FPLC), and their contents of polysaccharides and protein are determined by phenol–sulfuric acid assay and bicinchoninic acid assay, respectively. Enzyme-linked immunosorbent assay (ELISA) shows that immunization of mouse with the LFPS–linker–protein vaccines at a dosage of 2.5 μg is sufficient to elicit serum immunoglobulin G (IgG) specific to S. Typhimurium lipopolysaccharide (LPS). The straight-chain amide linkers in conjugates 7a–9b do not interfere with the desired immune response. Vaccines 7a and 7b derived from either unfractionated LFPS or the high-mass portion show equal efficacy in induction of IgG antibodies. The challenge experiments are performed by oral gavage of S. Typhimurium pathogen, and vaccine 7c having FliC as the self-adjuvanting protein carrier exhibits a high vaccine efficacy of 74% with 80% mice survival rate at day 28 post the pathogen challenge.ConclusionsThis study demonstrates that lipid-A free lipopolysaccharide prepared from Gram-negative bacteria is an appropriate immunogen, in which the exposed Kdo is connected to bifunctional linkers to form conjugate vaccines. The decarboxylative amidation of Kdo is a novel and useful method to construct a relatively robust and low immunogenic straight-chain amide linkage. The vaccine efficacy is enhanced by using bacterial flagellin as the self-adjuvanting carrier protein.Graphical abstract

High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya.

Invasive Non-typhoidal Salmonella (iNTS) disease is a major public health challenge, especially in Sub-Saharan Africa (SSA). In Kenya, mortality rates are high (20–25%) unless prompt treatment is instituted. The most common serotypes are Salmonella enterica serotype Typhimurium (S. Typhimurium) and Salmonella enterica serotype Enteritidis (S. Enteritidis). In a 5 year case-control study in children residing in the Mukuru informal settlement in Nairobi, Kenya, a total of 4201 blood cultures from suspected iNTS cases and 6326 fecal samples from age-matched controls were studied. From the laboratory cultures we obtained a total of 133 S. Typhimurium isolates of which 83(62.4%) came from cases (53 blood and 30 fecal) and 50(37.6%) from controls (fecal). A total of 120 S. Enteritidis consisted of 70(58.3%) from cases (43 blood and 27 fecal) and 50(41.7%) from controls (fecal).The S. Typhimurium population fell into two distinct ST19 lineages constituting 36.1%, as well as ST313 lineage I (27.8%) and ST313 lineage II (36.1%) isolates. The S. Enteritidis isolates fell into the global epidemic lineage (46.6%), the Central/Eastern African lineage (30.5%), a novel Kenyan-specific lineage (12.2%) and a phylogenetically outlier lineage (10.7%). Detailed phylogenetic analysis revealed a high level of relatedness between NTS from blood and stool originating from cases and controls, indicating a common source pool. Multidrug resistance was common throughout, with 8.5% of such isolates resistant to extended spectrum beta lactams. The high rate of asymptomatic carriage in the population is a concern for transmission to vulnerable individuals and this group could be targeted for vaccination if an iNTS vaccine becomes available.

Metabolomics profiling and antibacterial activity of fermented ginger paste extends the shelf life of chicken meat

Fermented ginger paste is a traditional condiment in South East Asia used to marinate meat to extend the shelf life and improve the taste. The present study aimed to determine the metabolomics profile of fermented ginger and the effects on the shelf life of chicken meat. Sterilised chicken meat slices were marinated using the fermented and fresh ginger paste and incubated at 8 °C to determine the effects on the microbial growth. The bioactive metabolites were identified using 1H NMR based analysis. The results demonstrated that fermentation significantly (p˂0.05) increased the antibacterial activity of the ginger paste against Salmonella enterica serotype Typhimurium (97%), Listeria monocytogenes (97%) and Staphylococcus aureus (100%), with the microbial load significantly (p < 0.05) reducing to 4.0 and 4.5 Log10 CFU g−1 in the chicken meat slices marinated in fermented ginger. Fermented ginger paste significantly reduced the pH value, moisture content and water activity of chicken meat slices after the incubation for 2 days at 8 °C. A total of 25 metabolites were identified in the fermented ginger paste. These results revealed the potential application of fermented ginger paste to enhance the safety of chicken meat via reducing the microbial load.

Prevalence, serotypes, and antimicrobial resistance of Salmonella isolates from patients with diarrhea in Shenzhen, China

BackgroundSalmonella is one of the main causative agents of diarrhea which results in substantial disease burden. To determine the prevalence, serotype distribution, and antimicrobial resistance profiles of clinical Salmonella isolates in Shenzhen, a 6-year surveillance study was conducted.ResultsA total of 297 (5.7%) Salmonella strains were isolated from stool samples from 5239 patients. Among the 42 serotypes identified, serotype Typhimurium was the most common one which represented 39.7% of the isolates (118), followed by serotype Enteritidis (71, 23.9%), London (12, 4.0%), 4, 5, 12: i: - (11, 3.7%), and Senftenberg (8, 2.7%). A high frequency of resistance was found in ampicillin (70.6%), piperacillin (64.5%), tetracycline (63.5%), and streptomycin (54.3%). Resistance to ampicillin and tetracycline was observed in 95.3% of S. Typhimurium isolates; and nalidixic acid in 93.1% of S. Enteritidis isolates. Resistance to 5 or more antimicrobial agents was found in 78.8% of S. Typhimurium and 69.0% of S. Enteritidis isolates. A decreased susceptibility to ciprofloxacin and levofloxacin was associated with amino acid alteration in gyrA gene. Point mutations without amino acid changes were seen in gyrB, parC, and parE genes.ConclusionsA broad range of serotypes are responsible for Salmonellosis in Shenzhen, with Enteritidis and Typhimurium being the most common serotypes. The high level of antibiotic resistance is of public health significance and ongoing monitoring combined with rational use of antibiotics are recommended. Point mutations in gyrA gene might play an important role in the resistance to fluoroquinolones.

High genetic similarity between non-typhoidal Salmonella isolated from paired blood and stool samples of children in the Democratic Republic of the Congo.

BackgroundNon-typhoidal Salmonella (NTS) serotypes Typhimurium and Enteritidis are a major cause of bloodstream infections in children in sub-Saharan Africa but their reservoir is unknown. We compared pairs of NTS blood and stool isolates (with the same NTS serotype recovered in the same patient) for genetic similarity.MethodsBetween November 2013 and April 2017, hospital-admitted children (29 days to 14 years) with culture-confirmed NTS bloodstream infections were enrolled in a cross-sectional study at Kisantu Hospital, DR Congo. Stool cultures for Salmonella were performed on a subset of enrolled children, as well as on a control group of non-febrile hospital-admitted children. Pairs of blood and stool NTS isolates were assessed for genetic similarity by multiple-locus variable-number of tandem repeats (MLVA) and genomics analysis.ResultsA total of 299 children with NTS grown from blood cultures (Typhimurium 68.6%, Enteritidis 30.4%, other NTS 1.0%) had a stool sample processed; in 105 (35.1%) of them NTS was detected (Typhimurium 70.5%, Enteritidis 25.7%, other NTS 3.8%). A total of 87/105 (82.9%) pairs of blood and stool NTS isolates were observed (representing 29.1% of the 299 children). Among 1598 controls, the proportion of NTS stool excretion was 2.1% (p < 0.0001). MLVA types among paired isolates were identical in 82/87 (94.3%) pairs (27.4% of the 299 children; 61/66 (92.4%) in Typhimurium and 21/21 (100%) in Enteritidis pairs). Genomics analysis confirmed high genetic similarity within 41/43 (95.3%) pairs, showing a median SNP difference of 1 (range 0–77) and 1 (range 0–4) for Typhimurium and Enteritidis pairs respectively. Typhimurium and Enteritidis isolates belonged to sequence types ST313 lineage II and ST11 respectively.ConclusionNearly 30% of children with NTS bloodstream infection showed stool excretion of an NTS isolate with high genetic similarity, adding to the evidence of humans as a potential reservoir for NTS.

Survival behaviour of Salmonella enterica in fish and shrimp at different conditions of storage

Seafood contamination with Salmonella enterica is a public health concern. The objective of this study was to investigate the survivability of Salmonella enterica serotype Typhimurium in fish and shrimp subjected to chilled (1 ± 2 °C) and frozen storage (−18 ± 2 °C). Bombay duck fish (Harpadon nehereus) and shrimp (Parapenaeopsis stylifera) were surface inoculated with 8 and 4 log CFU/g levels of S. Typhimurium. Survivability was studied by surface plating method on Salmonella-specific selective agar at regular intervals. In fish and shrimp inoculated with 8 log CFU/g and stored at −18 °C, viable counts could be detected for up to 90 days. At lower inoculation level of 4 log CFU/g, Salmonella was viable up to 60 days in frozen fish, while in frozen shrimp the bacterium could survive for only 15 days. In fish and shrimp stored in ice for 15 days, Salmonella showed 1–2 log CFU/g reduction in counts irrespective of initial inoculation levels. The results of this study suggest that the survival behaviour of Salmonella is influenced by the seafood matrix, temperature of storage and the population density of the bacterium itself. Therefore, strict monitoring of handling and storage procedures is necessary to control the processes that foster the survival and multiplication of Salmonella in the seafood chain.

Antimicrobial Efficacy of Pelargonic Acid\xa0Micelles against Salmonella varies by Surfactant, Serotype and Stress Response

The antimicrobial properties of Pelargonic acid (PA), a component of tomatoes, makes it an attractive candidate as a food additive and sanitizer. The antimicrobial efficacy of PA emulsions generated using surfactants: Tween 80, Triton X100, Sodium Dodecyl Sulfate (SDS) and Quillaja Saponin was evaluated against Salmonella serotypes Newport, Oranienburg and Typhimurium. Micelle/dropletsize, and minimal inhibitory concentrations (MIC) were determined. Surfactant type and concentration significantly influenced the antimicrobial efficacy of PA (p < 0.05). Overall, Salmonella Newport was the most (p < 0.05) susceptible serotype to PA emulsions. PA emulsions generated with 1.00% SDS had the highest (p < 0.05) antimicrobial activity, with MIC of 7.82 mM against S. Newport and 15.62 mM against S. Oranienburg/S. Typhimurium, respectively. Addition of PA to Trypticase Soy Broth resulted in a decreased growth rate and an increased lag phase duration. Cells exposed to PA formed elongated filaments (>5 µm). Additionally, Salmonella serotypes Typhimurium and Newport also formed floccular biofilms. PA emulsions at a concentration of 31.25 mM generated using 1% SDS and 1% Quillaja saponin resulted in >6 log CFU/ml reduction in Salmonella population. Althought all PA emulsions evalauted inhibited Salmonella, morphological changes to this antimicrobial varied substantially among the Salmonella serotypes tested.

A Recombinase Polymerase Amplification and Lateral Flow Strip Combined Method That Detects Salmonella enterica Serotype Typhimurium With No Worry of Primer-Dependent Artifacts.

On-site detection demands are quickly increasing to control foodborne pathogenic bacteria along with the long food supply chains. Combining the isothermal recombinase polymerase amplification (RPA) with lateral flow strips (LFSs) is a promising molecular detection approach for the short reaction time, low isothermal condition, and simple and “instrument-free” procedure. However, the method comes with a non-negligible intrinsic risk of the primer-dependent artifacts. In this study, with an important foodborne pathogenic bacterium Salmonella enterica serotype Typhimurium (S. Typhimurium) as the model, system measures including the careful selection of primers targeting unique virulence genes, use of a probe in the RPA reaction, introducing base substitutions with specific guidelines in the primer and probe sequences, and analyzing and screening the primer–probe complex formation were taken to eliminate the primer-dependent artifacts. The measures were strictly tested for the efficacy, and the standardized method was able to specifically detect S. typhimurium within 30 min at 42°C without any interference of probe–primer signals. The established RPA-LFS method shared high sensitivity with the detection limit of 1 CFU/μl of unpurified culture. Our study provided practical measures for the prevention of false positive signals from primer–dimers or primer–probe complexes when using the RPA–LFS method in pathogen detections, and also established a readily applicable method for S. Typhimurium detection.

Phenotypic and genotypic characterization of non-typhoidal Salmonella isolated from a Brazilian pork production chain

Pork products are important sources of foodborne non-typhoidal Salmonella in Brazil where antibiotics are commonly used throughout the pork production process and this has the potential to selectively favor antibiotic-resistant strains. We characterized the genotypic and phenotypic diversity of S. enterica isolates (n = 41) that were isolated in Brazil. Isolates were collected from ten swine farms and one slaughterhouse. Whole-genome sequencing and in silico serotyping demonstrated that the S. enterica serovar Typhimurium was the most common serotype (n = 17), but eight additional servoars were identified. Isolates presented high similarity based on comparison of DNA sequences (minimum of 89.6%), and sequence variation grouped according to serotype. Eight multilocus sequence types were identified with ST19 being most common (n = 21). Several plasmids replicons were detected, with Col (RNAI) the most abundant (n = 30), followed by IncR (n = 22), IncI1 (n = 10) and IncA/C2 (n = 10). Minimum inhibitory concentration assays showed that the principle resistance phenotypes were for streptomycin (90.2%), tetracycline (87.8%), ampicillin (80.5%), chloramphenicol (70.7%) and ciprofloxacin (51.2%). Only two isolates were resistant to third-generation cephalosporins and no isolates were resistant to two tested carbapenems. Twenty-six unique antimicrobial-resistance genes were identified with blaTEM-1A and blaTEM-1B likely responsible for most beta-lactam resistance and floR responsible for most chloramphenicol resistance. Six strains were positive for mcr-1. At the time of collection, the sampled farms were adding ciprofloxacin to feed and this may have contributed to the high prevalence of resistance to this antibiotic. The high number of multidrug resistant Salmonella and the presence of multiple resistant genes and plasmids emphasize the diversity of Salmonella in the studied pork chain, specially from serotype Typhimurium.

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation.

Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and bacteraemia worldwide, and a model organism for the study of host-pathogen interactions. Two S. Typhimurium strains (SL1344 and ATCC14028) are widely used to study host-pathogen interactions, yet genotypic variation results in strains with diverse host range, pathogenicity and risk to food safety. The population structure of diverse strains of S. Typhimurium revealed a major phylogroup of predominantly sequence type 19 (ST19) and a minor phylogroup of ST36. The major phylogroup had a population structure with two high order clades (α and β) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade β contained multiple subclades associated with wild avian species. The contrasting epidemiology of strains in clade α and β was reflected by the distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification. These observations were consistent with elevated anthropogenic selection of clade α lineages from adaptation to circulation in populations of domesticated livestock, and the predisposition of clade β lineages to undergo adaptation to an invasive lifestyle by a process of convergent evolution with of host adapted Salmonella serotypes. Gene flux was predominantly driven by acquisition and recombination of prophage and associated cargo genes, with only occasional loss of these elements. The acquisition of large chromosomally-encoded genetic islands was limited, but notably, a feature of two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) of clade α (SGI-1 and SGI-4).

Effect of soil type and temperature on survival of Salmonella enterica in poultry manure-amended soils.

The effects of soil type and temperature on the survival of a cocktail of five Salmonella enterica serotypes (Enteritidis, Infantis, Montevideo, Typhimurium and Zanzibar) in manure-amended soils under controlled laboratory conditions was assessed. Containers of clay loam or sandy soil, unaltered or amended with 2% (w/w) poultry manure, were inoculated with S. enterica (~5 log10 CFU per gram) and held at 5, 21 or 37°C for 6weeks. Statistical analysis of the persistence of S. enterica identified a significant three-way interaction between soil type, manure amendment and temperature. Clay loam soils and lower temperatures tended to support S. enterica persistence over 6weeks with only 1- and 2-log reductions respectively. In contrast, sand and higher temperatures resulted in a 4-log and either 3- to 4-log reductions respectively. Manure amendment had an overarching effect of reducing die-off of S. enterica in comparison with unamended soils. This study highlights that a large component of variation of the rate of S. enterica reduction in soils may be attributed to combinations of environmental factors, in particular, soil type and temperature. It further underscores the importance of risk management strategies and industry guidelines based on local data and that reflect the diversity of prevailing horticultural production environments. SIGNIFICANCE AND IMPACT OF THE STUDY: The persistence of Salmonella enterica in soil environments was shown to be significantly influenced by a range of individual and interacting environmental effects, including temperature, soil type and amendment addition. This indicates that current horticultural food safety management systems which employ a uniform prescribed exclusion period between application of manure and time of harvest may be unfit for purpose under certain conditions by either underestimating or overestimating pathogen die-off. These findings support exclusion periods that account for a range of environmental factors including temperature, soil type and growing region that may be more appropriate to manage microbiological risks associated with soil which has been amended with manure.

Supplementing neonatal Jersey calves with a blend of probiotic bacteria improves the pathophysiological response to an oral Salmonella enterica serotype Typhimurium challenge

The objectives of the current study were to determine the effects of supplementing a blend of probiotic bacteria (Provida Calf, MB Nutritional Sciences, Lubbock, TX) on the pathophysiological response to an oral Salmonella enterica serotype Typhimurium challenge in neonatal Jersey calves. Twenty-four Jersey bull calves within 24 h of birth were acquired from a local calf ranch, blocked by total serum protein and initial body weight, and randomly assigned to 1 of 3 treatments (n = 8). Calves were assigned to either (1) Control (CON); base milk replacer, (2) Control + Salmonella Typhimurium (CON+ST); base milk replacer and challenged with Salmonella Typhimurium on d 7; or (3) Provida Calf probiotics + Salmonella Typhimurium (PRO+ST); same milk replacer supplemented with a proprietary blend of Lactobacillus casei and Enterococcus faecium strains and challenged with Salmonella Typhimurium on d 7. The PRO+ST calves were supplemented for the first 3 d with 2 × 1010 cfu/d and then with 2 × 109 cfu/d for the remainder of the study. The CON+ST and PRO+ST calves were each challenged with approximately 5 × 106 cfu of Salmonella Typhimurium (ATCC# 14028), which was a mild challenge that did not cause scours in the calves. Peripheral blood samples were collected on d 0, 7, 10, 14, and 21 and analyzed for hematology; serum was collected and analyzed for haptoglobin, glucose, and urea N. Rectal temperatures were collected daily from d 6 to 21, when all calves were killed, so that persistent colonization of Salmonella Typhimurium and histomorphology of both the duodenum and ileum could be determined. Serum haptoglobin and urea N concentrations were increased among CON+ST on d 10. In contrast, the peak rectal temperature on d 10 in PRO+ST calves was 40.4°C, which was greater than that for CON and CON-ST (38.9°C and 39.7°C, respectively). The neutrophil percentage in peripheral circulation in PRO+ST calves was 55.4%, which was greater than that for CON and CON+ST (34.8 and 41.8%, respectively). Seven of the 8 PRO+ST calves had elevated neutrophil percentages on d 10 compared with d 7, whereas 4 of the 8 CON+ST calves had reduced neutrophil percentages on d 10 compared with d 7. Villus height-to-crypt depth ratios in the duodenum were greater among CON and PRO+ST calves, being 1.38, 0.84, and 1.43 for CON, CON+ST, and PRO+ST, respectively. In the ileum, the PRO+ST calves had greater villus height-to-crypt depth ratios than both the CON and CON+ST calves (1.64, 1.53, and 2.43 for CON, CON+ST, and PRO+ST, respectively). These data indicate that supplementing neonatal calves with the blend of probiotic bacteria used in the current study can influence the pathophysiological response to a mild enteric Salmonella Typhimurium challenge.

SipD and IpaD induce a cross-protection against Shigella and Salmonella infections.

Salmonella and Shigella species are food- and water-borne pathogens that are responsible for enteric infections in both humans and animals and are still the major cause of morbidity and mortality in the emerging countries. The existence of multiple Salmonella and Shigella serotypes as well as the emergence of strains resistant to antibiotics require the development of broadly protective therapies. Those bacteria utilize a Type III Secretion System (T3SS), necessary for their pathogenicity. The structural proteins composing the T3SS are common to all virulent Salmonella and Shigella spp., particularly the needle-tip proteins SipD (Salmonella) and IpaD (Shigella). We investigated the immunogenicity and protective efficacy of SipD and IpaD administered by intranasal and intragastric routes, in a mouse model of Salmonella enterica serotype Typhimurium (S. Typhimurium) intestinal challenge. Robust IgG (in all immunization routes) and IgA (in intranasal and oral immunization routes) antibody responses were induced against both proteins. Mice immunized with SipD or IpaD were protected against lethal intestinal challenge with S. Typhimurium or Shigella flexneri (100 Lethal Dose 50%). We have shown that SipD and IpaD are able to induce a cross-protection in a murine model of infection by Salmonella and Shigella. We provide the first demonstration that Salmonella and Shigella T3SS SipD and IpaD are promising antigens for the development of a cross-protective Salmonella-Shigella vaccine. These results open the way to the development of cross-protective therapeutic molecules.