CRISPR Typing and Antibiotic Resistance Correlates with Polyphyletic Distribution in Human Isolates of Salmonella Kentucky

Megaplasmid Dissemination in Multidrug-Resistant Salmonella Serotypes from Backyard and Commercial Broiler Production Systems in the Southeastern United States

Over the past decade, there has been a rise in U.S. backyard poultry ownership, raising concern for residential area antimicrobial-resistant (AMR) Salmonella contamination. This study aims to lay the groundwork to better understand the persistence of AMR Salmonella in residential broiler production systems and make comparisons with commercial systems. Ten backyard and 10 commercial farms were sampled at three time points across bird production. Both fecal (n = 10) and environmental (soil, n = 5, litter/compost, n = 5, feeder, and waterer swabs, n = 6) samples were collected at each visit on days 10, 31, and 52 of production for backyard farms and days 10, 24, and 38 of production for commercial farms. AMR Salmonella was characterized phenotypically by broth microdilution and genotypically by whole-genome sequencing. Overall, Salmonella was more prevalent in commercial farm samples (52.31%) over backyard farms (19.10%). Kentucky (sequence type (ST) 152) was the most common serotype found in both backyard and commercial farms. Multidrug-resistant (MDR, resistance to ≥3 or more antimicrobial classes) isolates were found in both production systems, while ciprofloxacin- and nalidixic acid-resistant and intermediate isolates were more prevalent in commercial (33%) than backyard samples (1%). Plasmids that have been associated with MDR were found in Kentucky and Infantis isolates, particularly IncFIB(K)_1_Kpn3 megaplasmid (Infantis). Our study emphasizes the need to understand the selection pressures in disseminating megaplasmids in MDR Salmonella in distinct broiler production systems.

Salmonella enterica serotypes isolated for the first time in laying hens, and their susceptibility to antibiotics

In this study, a total of 323 drag swab samples were taken from laying hen fresh feces from 3 different provinces (Kırklareli, Edirne, and Tekirdağ), which are located in the European part of Türkiye. According to the ISO 6579: 2002 method, 17.3% of the samples were found positive for Salmonella. Obtained 56 Salmonella isolates were serotyped by slide agglutination using antisera according to Kauffmann White Le Minor Scheme. Sixteen serotypes of Salmonella were identified as S. Typhimurium (28.6%), S. Kentucky (17.9%), S. Abony (16.1%), S. Infantis (8.9%), S. Enteritidis (5.4%), S. Anatum (3.6%), S. Saintpaul (3.6%), S. Szentes (1.8%), S. Dibra (1.8%), S. Fallowfield (1.8%), S. Kimuenza (1.8%), S. Escanaba (1.8%), S. Nagoya (1.8%), S. Mbandaka (1.8%), S. Agona (1.8%), and Salmonella II 17: e, n, x, z15: 1,6 (1.8%). Isolations of S. Kimuenza, S. Escanaba, and S. Nagoya from laying hens are reported for the first time in Türkiye. The isolations of S. Dibra, S. Fallowfield, S. Szentes, and Salmonella II 17: e, n, x, z15: 1,6 from laying hens are the first report in the world. A total of 56 Salmonella isolates were tested for susceptibility to amoxicillin-clavulanic acid, cefepime, azithromycin, cefoxitin, and trimethoprim/sulfamethoxazole by the disk diffusion method. While 10% of S. Kentucky isolates were resistant to ofloxacin, and S. Kimuenza was only resistant to chloramphenicol.

Poultry production as the main reservoir of ciprofloxacin- and tigecycline-resistant extended-spectrum β-lactamase (ESBL)-producing Salmonella enterica serovar Kentucky ST198.2-2 causing human infections in China

Salmonella enterica serovar Kentucky (S. Kentucky) has been regarded as a common serotype causing human nontyphoidal salmonellosis, frequently associated with the consumption of contaminated poultry products. Recently, multidrug-resistant (MDR) S. Kentucky ST198 with strong resistance to cefotaxime, ciprofloxacin, and tigecycline has emerged and been frequently detected in both poultry and humans in Europe and Asia. In this study, whole-genome sequencing (WGS) analysis divided 327 S. Kentucky ST198 isolates into two clades, of which ST198.2 is more prevalent than ST198.1 worldwide. We further compared the genomic characteristics of 70 ST198 isolates from animals and humans during 2019-2022 plus previously reported 38 isolates from 2013 to 2019 in China. One hundred five of the 108 isolates were ST198.2, which could be differentiated into two subclades. ST198.2-1 was prevalent in isolates during 2013-2019, while ST198.2-2 has increased to be the predominant subclade in isolates since 2019. CRISPR typing can differentiate the clade ST198.1 isolates from clade ST198.2 ones but cannot differentiate the two subclade isolates. The acquisition of a large multi-drug resistant region in ST198.2-2 enhanced bacterial resistance to β-lactam, aminoglycoside, amphenicol, and fosfomycin. In addition, compared with the extended-spectrum β-lactamase (ESBL)-encoding gene blaCTX-M-14b in ST198.2-1, co-existence of blaCTX-M-55 and blaTEM-1B was detected in most of the ST198.2-2 isolates. The emergence of ciprofloxacin- and tigecycline-resistant ESBL-producing S. Kentucky ST198.2-2 strains highlight the necessity for Salmonella surveillance. It is imperative to implement more effective measures to prevent and control transmission of these strains from poultry to humans. IMPORTANCE Salmonella enterica serovar Kentucky (S. Kentucky) can cause human infections through consumption of contaminated food of animal origin, and the emergence of multidrug-resistant (MDR) ST198-S. Kentucky strains are of concern for human and animal health. Based on whole-genome sequencing (WGS) analysis, this study revealed that the clade ST198.2-2 S. Kentucky has increased to the predominant group in both chickens and humans in China since 2019, which is different to previous studies of the prevalent ST198.2-1 S. Kentucky before 2019. Acquirement of a multidrug resistance region (MRR) makes the ST198.2-2 S. Kentucky to be extensively drug-resistant (XDR) isolate compared with ST198.2-1 S. Kentucky. Besides, the ST198.2-2 S. Kentucky was mainly detected in chickens (chicken meat, intestinal contents, and slaughterhouse) and humans, indicating chicken is the main reservoir for these XDR S. Kentucky isolates. Therefore, it is necessary to implement continuous Salmonella surveillance and effective measures, such as the development of phages and novel antibiotics/compounds, to prevent the transmission of XDR ST198.2-2 S. Kentucky from chickens to humans across China.

Genomic and phenotypic characterization of Salmonella enterica serovar Kentucky

Non-typhoidal Salmonella are extremely diverse and different serovars can exhibit varied phenotypes, including host adaptation and the ability to cause clinical illness in animals and humans. In the USA, Salmonella enterica serovar Kentucky is infrequently found to cause human illness, despite being the top serovar isolated from broiler chickens. Conversely, in Europe, this serovar falls in the top 10 serovars linked to human salmonellosis. Serovar Kentucky is polyphyletic and has two lineages, Kentucky-I and Kentucky-II; isolates belonging to Kentucky-I are frequently isolated from poultry in the USA, while Kentucky-II isolates tend to be associated with human illness. In this study, we analysed whole-genome sequences and associated metadata deposited in public databases between 2017 and 2021 by federal agencies to determine serovar Kentucky incidence across different animal and human sources. Of 5151 genomes, 90.3 % were from isolates that came from broilers, while 5.9 % were from humans and 3.0 % were from cattle. Kentucky-I isolates were associated with broilers, while isolates belonging to Kentucky-II and a new lineage, Kentucky-III, were more commonly associated with cattle and humans. Very few serovar Kentucky isolates were associated with turkey and swine sources. Phylogenetic analyses showed that Kentucky-III genomes were more closely related to Kentucky-I, and this was confirmed by CRISPR-typing and multilocus sequence typing (MLST). In a macrophage assay, serovar Kentucky-II isolates were able to replicate over eight times better than Kentucky-I isolates. Analysis of virulence factors showed unique patterns across these three groups, and these differences may be linked to their association with different hosts.

Comparison of Phenotype Nutritional Profiles and Phosphate Metabolism Genes in Four Serovars of Salmonella enterica from Water Sources

The surveillance of foods for Salmonella is hindered by bias in common enrichment media where serovars implicated in human illness are outgrown by less virulent serovars. We examined four Salmonella serovars, two common in human illness (Enteritidis and Typhimurium) and two that often dominate enrichments (Give and Kentucky), for factors that might influence culture bias. The four serovars had similar growth kinetics in Tryptic Soy Broth and Buffered Peptone Water. Phenotype microarray analysis with 950 chemical substrates to assess nutrient utilization and stress resistance revealed phenotype differences between serovars. Strains of S. Enteritidis had better utilization of plant-derived sugars such as xylose, mannitol, rhamnose, and fructose, while S. Typhimurium strains were able to metabolize tagatose. Strains of S. Kentucky used more compounds as phosphorus sources and grew better with inorganic phosphate as the sole phosphorus source. The sequences of nine genes involved in phosphate metabolism were compared, and there were differences between serovars in the catalytic ATP-binding domain of the histidine kinase phoR. Analysis of the predicted PhoR amino acid sequences from additional Salmonella genomes indicated a conservation of sequences each within the Typhimurium, Give, and Enteritidis serovars. However, three different PhoR versions were observed in S. Kentucky.

Combined Quantification and Deep Serotyping for Salmonella Risk Profiling in Broiler Flocks

Despite a reduction of Salmonella contamination on final poultry products, the level of human salmonellosis cases attributed to poultry has remained unchanged over the last few years. There needs to be improved effort to target serovars which may survive antimicrobial interventions and cause illness, as well as to focus on lessening the amount of contamination entering the processing plant. Advances in molecular enumeration approaches allow for the rapid detection and quantification of Salmonella in pre- and postharvest samples, which can be combined with deep serotyping to properly assess the risk affiliated with a poultry flock. In this study, we collected a total of 160 boot sock samples from 20 broiler farms across four different integrators with different antibiotic management programs. Overall, Salmonella was found in 85% (68/80) of the houses, with each farm having at least one Salmonella-positive house. The average Salmonella quantity across all four complexes was 3.6 log10 CFU/sample. Eleven different serovars were identified through deep serotyping, including all three key performance indicators (KPIs; serovars Enteritidis, Infantis, and Typhimurium) defined by the U.S. Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS). There were eight multidrug resistant isolates identified in this study, and seven which were serovar Infantis. We generated risk scores for each flock based on the presence or absence of KPIs, the relative abundance of each serovar as calculated with CRISPR-SeroSeq (serotyping by sequencing the clustered regularly interspaced palindromic repeats), and the quantity of Salmonella organisms detected. The work presented here provides a framework to develop directed processing approaches and highlights the limitations of conventional Salmonella sampling and culturing methods. IMPORTANCE Nearly one in five foodborne Salmonella illnesses are derived from chicken, making it the largest single food category to cause salmonellosis and indicating a need for effective pathogen mitigation. Although industry has successfully reduced Salmonella incidence in poultry products, there has not been a concurrent reduction in human salmonellosis linked to chicken consumption. New efforts are focused on improved control at preharvest, which requires improved Salmonella surveillance. Here, we present a high-resolution surveillance approach that combines quantity and identity of Salmonella in broiler flocks prior to processing which will further support improved Salmonella controls in poultry. We developed a framework for this approach, indicating that it is possible and important to harness deep serotyping and molecular enumeration to inform on-farm management practices and to minimize risk of cross-contamination between flocks at processing. Additionally, this framework could be adapted to Salmonella surveillance in other food animal production systems.

Application of a CRISPR Sequence-Based Method for a Large-Scale Assessment of Salmonella Serovars in Ontario Poultry Production Environments

Accurate detection of all Salmonella serovars present in a sample is important in surveillance programs. Current detection protocols are limited to detection of a predominant serovar, missing identification of less abundant serovars in a sample. An alternative method, called CRISPR-SeroSeq, serotyping by sequencing of amplified CRISPR spacers, was employed to detect multiple serovars in a sample without the need of culture isolation. The CRISPR-SeroSeq method successfully detected 34 most frequently reported Salmonella serovars in pure cultures and target serovars at 104 CFU/mL in 27 Salmonella-negative environmental enrichment samples post-spiked with one of 15 different serovars, plus 2 additional serovars at 1 log CFU/mL higher abundance. When the method was applied to 442 naturally contaminated environmental samples collected from 192 poultry farms, 25 different serovars were detected from 430 of the samples. In 73.1% of the samples, 2 to 7 serovars were detected, with Salmonella Kiambu (55.7%), Salmonella Infantis (48.4%), Salmonella Kentucky (27.1%), Salmonella Livingstone (26.6%), and Salmonella Mbandaka/Montevideo (23.4%) being the most prevalent on the farms. Single isolates from 384 samples were also analyzed using a traditional serotyping method, and the same serovar identified by culture was detected by CRISPR-SeroSeq in 96.1% (369/384) of samples, with the former missing detection of additional and sometimes critical serovars. The surveillance data obtained via CRISPR-SeroSeq revealed a significant emergence of Salmonella Kiambu and Salmonella Rissen on poultry farms in Ontario. The results highlight the effectiveness of the CRISPR-SeroSeq approach in detecting multiple Salmonella serovars in poultry environmental samples under applied conditions, providing updated surveillance information on Salmonella serovars on poultry farms in Ontario. IMPORTANCE The CRISPR-SeroSeq method represents an alternative molecular tool to the traditional culture-based serotyping method that can detect multiple Salmonella serovars in a sample and provide rapid serovar results without the need of selective enrichment and culture isolation. The evaluation results can facilitate implementation of the method in routine Salmonella surveillance on poultry farms and in outbreak investigations. The application of the method can increase the accuracy of current serovar prevalence information. The results highlight the effectiveness of the validated method and the need for monitoring Salmonella serovars in poultry environments to improve current surveillance programs. The updated surveillance data provide timely information on emergence of different Salmonella serovars on poultry farms in Ontario and support on-farm risk assessment and risk management of Salmonella.

Comprehensive Assessment of Subtyping Methods for Improved Surveillance of Foodborne Salmonella

High-resolution and efficient typing for the bacterial pathogen is essential for tracking the sources, detecting or diagnosing variants, and conducting a risk assessment. However, a systematic in-field investigation of Salmonella along the food chain has not been documented. This study assessed 12 typing methods, such as antimicrobial-resistance (AMR) gene profile typing, Core Genome Multilocus Sequence Typing (cgMLST), and CRISPR multi-virulence locus sequence typing (CRISPR-MVLST), to evaluate their effectiveness for use in routine monitoring of foodborne Salmonella transmission along the poultry production chain. During 2015-16, a total of 1,064 samples were collected from poultry production chain, starting from breeding farms and slaughterhouses to the markets of Zhejiang province in China. A total of 61 consecutive unique Salmonella isolates recovered from these samples were selected for genome sequencing and further comparative typing analysis. Traditional typing methods, including serotyping, AMR phenotype-based typing, as well as modern genotyping approaches, were evaluated and compared by their discrimination index (DI). The results showed that the serotyping method identified nine serovars. The gold standard cgMLST method indicated only 18 different types (DI = 0.8541), while the CRISPR-MVLST method detected 30 types (DI = 0.9628), with a higher DI than all examined medium-resolution WGS-based genotyping methods. We demonstrate that the CRISPR-MVLST might be used as a tool with high discriminatory power, comparable ease of use, ability of tracking the source of Salmonella strains along the food chain and indication of genetic features especially virulence genes. The available methods with different purposes and laboratory expertise were also illustrated to assist in rational implementation. IMPORTANCE In public health field, high-resolution and efficient typing of the bacterial pathogen is essential, considering source-tracking and risk assessment are fundamental issues. Currently, there are no recommendations for applying molecular characterization methods for Salmonella along the food chain, and a systematic in-field investigation comparing subtyping methods in the context of routine surveillance was partially addressed. Using 1,064 samples along a poultry production chain with a considerable level of Salmonella contamination, we collected representative isolates for genome sequencing and comparative analysis by using 12 typing techniques, particularly with whole-genome sequence (WGS) based methods and a recently invented CRISPR multi-virulence locus sequence typing (CRISPR-MVLST) method. CRISPR-MVLST is identified as a tool with higher discriminatory power compared with medium-resolution WGS-based typing methods, comparable ease of use and proven ability of tracking Salmonella isolates. Besides, we also offer recommendations for rational choice of subtyping methods to assist in better implementation schemes.

Prevalence and whole-genome sequencing analysis of Salmonella reveal its spread along the duck production chain

Salmonella is the most important foodborne pathogen in poultry production systems and can infect humans via consumption of contaminated food. Ducks, an important waterfowl widely raised in China, are also a vehicle that transmits Salmonella through the food supply chain. In this study, 701 samples were collected from each production stage of the duck production chain. Salmonella was isolated and identified, and the isolates were tested for drug sensitivity and molecular typing based on whole genome sequencing (WGS) to explore the prevalence of Salmonella in the duck production chain. Altogether, a total of 180 Salmonella isolates (25.7%) were obtained from the duck production chain, 82 (35.7%) isolates were from hatchery samples, followed by 64 (29.2%) from market samples, 17 (23.6%) from farm samples, and 17 (9.4%) from slaughterhouse samples. All isolates were divided into 9 serotypes, among which S. Typhimurium, S. Anatum, and S. Enteritidis were the dominant serotypes. The S. Typhimurium was distributed in various production stages in the duck production chain. Among the 16 antibiotics, selected 60 isolates were only resistant to NAL, indicating that resistance of Salmonella in the duck production chain was low. WGS phylogenetic relationship results based on core-genome SNPs showed that S. Typhimurium can spread across geographic regions and along between different stages of the duck production chain, eventually reaching the market where it is a potential threat to consumer health. This study explored the prevalence of Salmonella in the duck production chain which will provide data support for proposing some interventions to control Salmonella.

Research progress on antibiotic resistance of Salmonella

Antibiotic abuse results in various antibiotic resistance among a number of foodborne bacteria, posing a severe threat to food safety. Antibiotic resistance genes are commonly detected in foodborne pathogens, which has sparked much interest in finding solutions to these issues. Various strategies against these drug-resistant pathogens have been studied, including new antibiotics and phages. Recently, a powerful tool has been introduced in the fight against drug-resistant pathogens, namely, clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) system aggregated by a prokaryotic defense mechanism. This review summarized the mechanism of antibiotic resistance in Salmonella and resistance to common antibiotics, analysed the relationship between Salmonella CRISPR-Cas and antibiotic resistance, discussed the changes in antibiotic resistance on the structure and function of CRISPR-Cas, and finally predicted the mechanism of CRISPR-Cas intervention in Salmonella antibiotic resistance. In the future, CRISPR-Cas is expected to become an important tool to reduce the threat of antibiotic-resistant pathogens in food safety.

Regional Salmonella Differences in United States Broiler Production from 2016 to 2020 and the Contribution of Multiserovar Populations to Salmonella Surveillance

Poultry remains a considerable source of foodborne salmonellosis despite significant reduction of Salmonella incidence during processing. There are multiple entry points for Salmonella during production that can lead to contamination during slaughter, and it is important to distinguish the serovars present between the different stages to enact appropriate controls. National Salmonella data from the U.S. Department of Agriculture-Food Safety Inspection Service (USDA-FSIS) monitoring of poultry processing was analyzed from 2016 to 2020. The overall Salmonella incidence at processing in broiler carcasses and intact parts (parts) decreased from 9.00 to 6.57% over this period. The incidence in parts was higher (11.15%) than in carcasses (4.78%). Regional differences include higher proportions of serovars Infantis and Typhimurium in the Atlantic and higher proportion of serovar Schwarzengrund in the Southeast. For Georgia, the largest broiler-producing state, USDA-FSIS data were compared to Salmonella monitoring data from breeder flocks over the same period, revealing serovar Kentucky as the major serovar in breeders (67.91%) during production but not at processing, suggesting that it is more effectively removed during antimicrobial interventions. CRISPR-SeroSeq was performed on breeder samples collected between 2020 and 2021 to explain the incongruence between pre- and postharvest and showed that 32% of samples contain multiple serovars, with up to 11 serovars found in a single flock. High-resolution sequencing identifies serovar patterns at the population level and can provide insight to develop targeted controls. The work presented may apply to other food production systems where Salmonella is a concern, since it overcomes limitations associated with conventional culture. IMPORTANCE Salmonella is a leading cause of bacterial foodborne illness in the United States, with poultry as a significant Salmonella reservoir. We show the relative decrease in Salmonella over a 5-year period from 2016 to 2020 in processed chicken parts and highlight regional differences with respect to the prevalence of clinically important Salmonella serovars. Our results show that the discrepancy between Salmonella serovars found in pre- and postharvest poultry during surveillance are due in part by the limited detection depth offered by traditional culture techniques. Despite the reduction of Salmonella at processing, the number of human salmonellosis cases has remained stable, which may be attributed to differences in virulence among serovars and their associated risk. When monitoring for Salmonella, it is imperative to identify all serovars present to appropriately assess public health risk and to implement the most effective Salmonella controls.

Relationship between CRISPR sequence type and antimicrobial resistance in avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) is a primary cause of extraintestinal disease and respiratory infections in chickens; therefore, various antimicrobials applied via mass medication in farms to control APEC in Korea. In this study, we analyzed the relationship between CRISPR sequence type and antimicrobial resistance (AMR) in APEC isolates. Based on spacer distribution, a total of 103 CRISPR-positive APEC isolates were classified into 25 E. coli sequence types (ESTs), largely into two clusters that were correlated with phylogenetic groups: isolates appearing to have CRISPR 1 and/or 2 (93.2 %) and those having CRISPR 3 and 4 (6.8 %). Moreover, ESTs were divided into three AMR pattern-based groups: cephems-resistant group, non-cephems-resistant group, and antimicrobial sensitive group. There were significant differences among the groups (p < 0.05). Sixteen of the 25 ESTs had a significantly higher distribution of multidrug-resistant (MDR) isolates than the other ESTs (p < 0.05), and the ratio of MDR isolates was significantly higher than that of non-MDR isolates in the CRISPR 1 and 2 arrays (p < 0.05). A total of 9 protospacers were identified with protospacer, with protospacer 1 in CRISPR 1 being the most prevalent among the isolates (41.7 %). The protospacers of CRISPR 1 and 2 loci were associated with protection against external invaders such as bacteriophage or endogenous gene regulation. However, each protospacer of the CRISPR 3 and 4 loci originated from genes associated with AMR plasmids. These results indicate that CRISPR sequence type can improve AMR bacteria and enhance strategies for tackling the complexity of AMR in bacterial pathogens.

Differences in biofilm formation of Salmonella serovars on two surfaces under two temperature conditions

AIMS

Salmonella is extremely diverse, with >2500 serovars that are genetically and phenotypically diverse. The aim of this study was to build a collection of Salmonella isolates that are genetically diverse and to evaluate their ability to form biofilm under different conditions relevant to a processing environment.

METHODS AND RESULTS

Twenty Salmonella isolates representative of 10 serovars were subtyped using Clustered regularly interspaced short palindromic repeats (CRISPR)-typing to assess the genetic diversity between isolates of each serovar. Biofilm formation of the isolates on both plastic and stainless-steel surfaces at 25 and 15°C was assessed. At 25°C, 8/20 isolates each produced strong and moderate biofilm on plastic surface compared to stainless-steel (3/20 and 13/20 respectively). At 15°C, 5/20 produced strong biofilm on plastic surface and none on stainless-steel. Several isolates produced weak biofilm on plastic (11/20) and stainless-steel (16/20) surfaces. Serovar Schwarzengrund consistently produced strong biofilm while serovars Heidelberg and Newport produced weak biofilm.

CONCLUSION

These results suggest that Salmonellae differ in their attachment depending on the surface and temperature conditions encountered, which may influence persistence in the processing environment.

SIGNIFICANCE AND IMPACT OF STUDY

These differences in biofilm formation could provide useful information for mitigation of Salmonella in processing environments.

Genomic diversity and resistome profiles of Salmonella enterica subsp. enterica serovar Kentucky isolated from food and animal sources in Ireland

Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from poultry, dairy and beef cattle, the environment and people with clinical salmonellosis globally. However, the sources of this serovar and its diversity and antimicrobial resistance capacities remain poorly described in many regions. To further understand the genetic diversity and antimicrobial sensitivity patterns among S. Kentucky strains isolated from non-human sources in Ireland, we sequenced and analysed the genomes of 61 isolates collected from avian, bovine, canine, ovine, piscine, porcine, environmental and vegetation sources between 2000 and 2016. The majority of isolates (n = 57, 93%) were sequence type (ST) 314, while only three isolates were ST198 and one was ST152. Several isolates were multidrug-resistant (MDR) and 14 carried at least one acquired antimicrobial resistance gene. When compared to a database of publicly available ST314, four distinct clades were identified (clades I-IV), with the majority of isolates from Ireland clustering together in Clade I. Two of the three ST198 isolates were characteristic of those originating outside of the Americas (Clade ST198.2), while one was distantly clustered with isolates from South and North America (Clade ST198.1). The genomes of the two clade ST198.2 isolates encoded Salmonella Genomic Island 1 (SGI1), were multidrug-resistant and encoded polymorphisms in the DNA gyrase (gyrA) and DNA topoisomerase (parC) known to confer resistance to fluoroquinolones. The single ST152 isolate was from raw beef, clustered with isolates from food and bovine sources in North America and was pan-susceptible. Results of this study indicate that most S. Kentucky isolates from non-human sources in Ireland are closely related ST314 and only a few isolates are antimicrobial-resistant. This study also demonstrates the presence of multidrug-resistant ST198 in food sources in Ireland.

High-Resolution Comparative Genomics of Salmonella Kentucky Aids Source Tracing and Detection of ST198 and ST152 Lineage-Specific Mutations

Non-typhoidal Salmonella (NTS) is a major cause of foodborne illness globally. Salmonella Kentucky is a polyphyletic NTS serovar comprised of two predominant multilocus sequence types (STs): ST152 and ST198. Epidemiological studies have revealed that ST152 is most prevalent in US poultry whereas ST198 is more prevalent in international poultry. Interestingly, ST152 is sporadically associated with human illness, whereas ST198 is more commonly associated with human disease. The goal of this study was to develop a better understanding of the epidemiology of ST198 and ST152 in WA State. We compared the antimicrobial resistance phenotypes and genetic relationship, using pulsed-field gel electrophoresis, of 26 clinical strains of S. Kentucky isolated in Washington State between 2004 and 2014, and 140 poultry-associated strains of S. Kentucky mostly recovered from the northwestern USA between 2004 and 2014. We also sequenced whole genomes of representative human clinical and poultry isolates from the northwestern USA. Genome sequences of these isolates were compared with a global database of S. Kentucky genomes representing 400 ST198 and 50 ST152 strains. The results of the phenotypic, genotypic, and case report data on food consumption and travel show that human infections caused by fluoroquinolone-resistant (FluR) S. Kentucky ST198 in WA State originated from outside of North America. In contrast, fluoroquinolone-susceptible (FluS) S. Kentucky ST198 and S. Kentucky ST152 infection have a likely domestic origin, with domestic cattle and poultry being the potential sources. We also identified lineage-specific non-synonymous single nucleotide polymorphisms (SNPs) that distinguish ST198 and ST152. These SNPs may provide good targets for further investigations on lineage-specific traits such as variation in virulence, metabolic adaptation to different environments, and potential for the development of intervention strategies to improve the safety of food.

Selective pre-enrichment method to lessen time needed to recover Salmonella from commercial poultry processing samples

Conventional Salmonella detection is time consuming, often employing a 24-h pre-enrichment step in buffered peptone water (BPW), followed by a 24-h selective enrichment in either Rappaport Vassiliadis (RV) or tetrathionate (TT) broths before streaking onto selective indicator agar. To reduce this time, we sought to optimize pre-enrichment for Salmonella recovery by evaluating the addition of selective chemicals to BPW. Duplicate samples each representative of 500 carcasses were collected by catching processing water drip under moving carcass shackle lines immediately after feather removal in each of nine commercial processing plants. Carcass drip samples were cultured under selective pre-enrichment conditions in parallel with BPW pre-enrichment followed by RV and TT selective enrichment. Addition of bile salts (1 g/L) and novobiocin (0.015 g/L) resulted in Salmonella recovery from 89% samples when plated directly after pre-enrichment compared to 67% recovery in non-selective BPW alone. Salmonella serovar identities were determined using CRISPR-SeroSeq. Overall, serovars matched between selective pre-enrichment and traditional enrichment methods. These data suggest that increasing the selectivity of Salmonella pre-enrichment step may lessen the need for a separate selective enrichment step thereby reducing time required for Salmonella isolation by 24 h.

Salmonella spp. prevalence and antimicrobial resistance in broiler chicken and turkey flocks in Canada from 2013 to 2018

Salmonella infections are a major human health concern. In the elderly and immunocompromised, infections can be life-threatening and may require antibiotic therapy. Where antibiotic therapy is required, antimicrobials of choice include fluoroquinolones and extended-spectrum cephalosporins (ESC). The aim of this study is to utilize data from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) to compare the prevalence of Salmonella serovars between broiler chicken and turkey flocks across Canada, and to gain an understanding of the prevalence of resistance to antimicrobials categorized as important to human health. There were 1,596 Salmonella isolates obtained from 514 broiler chicken flocks, and 659 Salmonella isolates obtained from 217 turkey flocks (2013-2018). All isolates were obtained from pooled faecal samples. Among broiler chicken flocks, the top three serovars were Kentucky (n = 573, 36%), Enteritidis (n = 314, 20%) and Heidelberg (n = 127, 8%). Resistance to ceftriaxone among Salmonella ser. Kentucky decreased from 27% in 2013 to 22% in 2018. There was no resistance among Salmonella ser. Enteritidis reported until 2018 when one isolate from British Columbia was resistant to ampicillin, streptomycin, sulphisoxazole and tetracycline. Salmonella ser. Heidelberg resistance to ceftriaxone decreased from 19% in 2013 to 14% in 2018. Among turkey flocks the top three serovars were Uganda (n = 109, 16.5%), Hadar (n = 85, 12%) and Muenchen (n = 66, 10%). No isolates of Salmonella ser. Uganda or Salmonella ser. Muenchen were resistant to any β-lactams. Salmonella ser. Hadar (34/81, 42%) exhibited resistance to ampicillin. There was no resistance to quinolones among turkey isolates. Emerging resistance among Salmonella ser. Enteritidis, and resistance to β-lactams and fluoroquinolones among Salmonella ser. Kentucky from broilers are cause for concern as these classes of antimicrobials are important for treatment of salmonellosis.

Salmonella Genomics and Population Analyses Reveal High Inter- and Intraserovar Diversity in Freshwater

Freshwater can support the survival of the enteric pathogen Salmonella, though temporal Salmonella diversity in a large watershed has not been assessed. At 28 locations within the Susquehanna River basin, 10-liter samples were assessed in spring and summer over 2 years. Salmonella prevalence was 49%, and increased river discharge was the main driver of Salmonella presence. The amplicon-based sequencing tool, CRISPR-SeroSeq, was used to determine serovar population diversity and detected 25 different Salmonella serovars, including up to 10 serovars from a single water sample. On average, there were three serovars per sample, and 80% of Salmonella-positive samples contained more than one serovar. Serovars Give, Typhimurium, Thompson, and Infantis were identified throughout the watershed and over multiple collections. Seasonal differences were evident: serovar Give was abundant in the spring, whereas serovar Infantis was more frequently identified in the summer. Eight of the ten serovars most commonly associated with human illness were detected in this study. Crucially, six of these serovars often existed in the background, where they were masked by a more abundant serovar(s) in a sample. Serovars Enteritidis and Typhimurium, especially, were masked in 71 and 78% of samples where they were detected, respectively. Whole-genome sequencing-based phylogeny demonstrated that strains within the same serovar collected throughout the watershed were also very diverse. The Susquehanna River basin is the largest system where Salmonella prevalence and serovar diversity have been temporally and spatially investigated, and this study reveals an extraordinary level of inter- and intraserovar diversity.IMPORTANCESalmonella is a leading cause of bacterial foodborne illness in the United States, and outbreaks linked to fresh produce are increasing. Understanding Salmonella ecology in freshwater is of importance, especially where irrigation practices or recreational use occur. As the third largest river in the United States east of the Mississippi, the Susquehanna River is the largest freshwater contributor to the Chesapeake Bay, and it is the largest river system where Salmonella diversity has been studied. Rainfall and subsequent high river discharge rates were the greatest indicators of Salmonella presence in the Susquehanna and its tributaries. Several Salmonella serovars were identified, including eight commonly associated with foodborne illness. Many clinically important serovars were present at a low frequency within individual samples and so could not be detected by conventional culture methods. The technologies employed here reveal an average of three serovars in a 10-liter sample of water and up to 10 serovars in a single sample.

Phylogeny of Salmonella enterica subspecies arizonae by whole-genome sequencing reveals high incidence of polyphyly and low phase 1 H antigen variability

Salmonella enterica subspecies arizonae is frequently associated with animal reservoirs, particularly reptiles, and can cause illness in some mammals, including humans. Using whole-genome sequencing data, core genome phylogenetic analyses were performed using 112 S. enterica subsp. arizonae isolates, representing 46 of 102 described serovars. Nearly one-third of these are polyphyletic, including two serovars that appear in four and five distinct evolutionary lineages. Subspecies arizonae has a monophasic H antigen. Among the 46 serovars investigated, only 8 phase 1 H antigens were identified, demonstrating high conservation for this antigen. Prophages and plasmids were found throughout this subspecies, including five novel prophages. Polyphyly was also reflected in prophage content, although some clade-specific enrichment for some phages was observed. IncFII(S) was the most frequent plasmid replicon identified and was found in a quarter of S. enterica subsp. arizonae genomes. Salmonella pathogenicity islands (SPIs) 1 and 2 are present across all Salmonella, including this subspecies, although effectors sipA, sptP and arvA in SPI-1 and sseG and ssaI in SPI-2 appear to be lost in this lineage. SPI-20, encoding a type VI secretion system, is exclusive to this subspecies and is well maintained in all genomes sampled. A number of fimbral operons were identified, including the sas operon that appears to be a synapomorphy for this subspecies, while others exhibited more clade-specific patterns. This work reveals evolutionary patterns in S. enterica subsp. arizonae that make this subspecies a unique lineage within this very diverse species.

CRISPR Typing of Salmonella Isolates

Polymerase chain reaction (PCR) and sequencing-based subtyping tools are useful for rapid analyses of Salmonella isolates. Here we describe the process of clustered regularly interspaced short palindromic repeat-multiple virulence locus sequence typing (CRISPR-MVLST) for Salmonella subtyping.

Incidence of Salmonella serovars isolated from commercial animal feed mills in the United States and serovar identification using CRISPR analysis

AIMS

In this study, we sought to determine the incidence and diversity of Salmonella in a broad collection of commercial animal feeds collected from animal feed mills across the United States over an 11-month period and utilize CRISPR analysis to identify individual serovars.

METHODS AND RESULTS

Over two independent trials, 387 feed samples from 135 different animal feed mills in the United States were screened for Salmonella. A total of 6·2% (24/387) of samples were contaminated with Salmonella, which is concordant with similar studies. Clustered regularly interspaced short palindromic repeats (CRISPR)-typing was used to serotype Salmonella isolates, and serovars Infantis and Tennessee were the most common.

CONCLUSIONS

Serogroups O:4 and O:7 were enriched in the feed samples, suggesting that these serogroups are better adapted to surviving in low moisture animal feeds. The study supports the utility of CRISPR to determine serovar type since most of the serovars identified in this study have been also isolated and identified in earlier studies using more classical serotyping methods.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work contributes to a growing body of literature concerning the Salmonella prevalence in animal feeds and highlights the need to effectively mitigate pathogens in livestock and poultry feed.

Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana

Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850 allelic differences). This study demonstrates the population structure of TN and global Salmonella ser. Javiana isolates, a clinically important Salmonella serovar and can provide guidance for phylogenetic cluster analyses for public health surveillance and response.

Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria

Salmonella is an important human pathogen and poultry products constitute an important source of human infections. This study investigated prevalence; identified serotypes based on whole genome sequence, described spatial distribution of Salmonella serotypes and predicted risk factors that could influence the prevalence of Salmonella infection in commercial poultry farms in Nigeria. A cross sectional approach was employed to collect 558 pooled shoe socks and dust samples from 165 commercial poultry farms in North West Nigeria. On-farm visitation questionnaires were administered to obtain information on farm management practices in order to assess risk factors for Salmonella prevalence. Salmonella was identified by culture, biotyping, serology and polymerase chain reaction (PCR). PCR confirmed isolates were paired-end Illumina- sequenced. Following de novo genome assembly, draft genomes were used to obtain serotypes by SeqSero2 and SISTR pipeline and sequence types by SISTR and Enterobase. Risk factor analysis was performed using the logit model. A farm prevalence of 47.9% (CI95 [40.3-55.5]) for Salmonella was observed, with a sample level prevalence of 15.9% (CI95 [12.9-18.9]). Twenty-three different serotypes were identified, with S. Kentucky and S. Isangi as the most prevalent (32.9% and 11%). Serotypes showed some geographic variation. Salmonella detection was strongly associated with disposal of poultry waste and with presence of other livestock on the farm. Salmonella was commonly detected on commercial poultry farms in North West Nigeria and S. Kentucky was found to be ubiquitous in the farms.

Conserved CRISPR arrays in Salmonella enterica serovar Infantis can serve as qPCR targets to detect Infantis in mixed serovar populations

Salmonellosis is a leading bacterial cause of foodborne illness, and numerous Salmonella enterica serovars have been responsible for foodborne outbreaks. In the United States outbreaks are often linked to poultry and poultry-related products. The prevalence of Salmonella serovar Infantis has been increasing in poultry processing facilities over the past few years and in 2018 was identified as the causative agent for a large multistate outbreak linked to raw chicken. CRISPR-typing is a subtyping approach based on PCR and the sequencing of two Salmonella loci, CRISPR1 and CRISPR2. CRISPR-typing was used to interrogate 138 recent (2018-2019) isolates and genomes of ser. Infantis. Results show that the CRISPR elements are remarkably conserved in this serovar. The most conserved spacers, and those also unique to ser. Infantis, were used as targets to develop a ser. Infantis-specific qPCR assay. This assay was able to detect ser. Infantis in mixed serovar cultures of Salmonella, down to 0·1% of the population, highlighting the utility of this molecular approach in improving surveillance sensitivity for this important food safety pathogen. SIGNIFICANCE AND IMPACT OF THE STUDY: The incidence of human salmonellosis cases caused by Salmonella enterica serovar Infantis (ser. Infantis) has been increasing, as has its prevalence in broiler chickens, which are a frequent reservoir of Salmonella. A cluster of ser. Infantis genetically linked to an outbreak strain have been identified in numerous processing facilities. A qPCR assay targeting CRISPR elements that are unique to ser. Infantis has been developed and can detect this serovar directly from mixed cultures. This assay is sensitive enough to reveal ser. Infantis within a mixed Salmonella population where it constitutes only 0·1% of the population. The rapid nature of qPCR lends this assay to high-throughput screening of poultry samples to detect this important pathogen.

Ciprofloxacin-Resistant Salmonella enterica Serovar Kentucky ST198 in Broiler Chicken Supply Chain and Patients, China, 2010-2016

Salmonella enterica serovar Kentucky (S. Kentucky) sequence type 198 has emerged as a global zoonotic pathogen. We explored Salmonella enterica serovar Kentucky ST198 samples from the broiler chicken supply chain and patients between 2010 and 2016. Here, we collected 180 S. Kentucky isolates from clinical cases and the poultry supply chain. We performed XbaI pulsed-field gel electrophoresis and multilocus sequence typing. We assessed mutations in the quinolone resistance-determining regions and screened for the presence of the Salmonella genomic island 1 (SGI1). We determined that 63 (35.0%) of the 180 isolates were S. Kentucky ST198. Chinese strains of S. Kentucky ST198 have a high transmission of ciprofloxacin resistance (38/63, 60.3%) and a high risk of multidrug resistance. The quinolone resistance of the S. Kentucky ST198 strain found in China may be due to mutations in its quinolone resistance-determining region. Our study firstly revealed that ciprofloxacin-resistant S. Kentucky ST198 strains can undergo cross-host transmission, thereby causing a serious foodborne public health problem in China.

CRISPR-cas3 of Salmonella Upregulates Bacterial Biofilm Formation and Virulence to Host Cells by Targeting Quorum-Sensing Systems

Salmonella is recognized as one of the most common microbial pathogens worldwide. The bacterium contains the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems, providing adaptive immunity against invading foreign nucleic acids. Previous studies suggested that certain bacteria employ the Cas proteins of CRISPR-Cas systems to target their own genes, which also alters the virulence during invasion of mammals. However, whether CRISPR-Cas systems in Salmonella have similar functions during bacterial invasion of host cells remains unknown. Here, we systematically analyzed the genes that are regulated by Cas3 in a type I-E CRISPR-Cas system and the virulence changes due to the deletion of cas3 in Salmonella enterica serovar Enteritidis. Compared to the cas3 gene wild-type (cas3 WT) Salmonella strain, cas3 deletion upregulated the lsrFGBE genes in lsr (luxS regulated) operon related to quorum sensing (QS) and downregulated biofilm-forming-related genes and Salmonella pathogenicity island 1 (SPI-1) genes related to the type three secretion system (T3SS). Consistently, the biofilm formation ability was downregulated in the cas3 deletion mutant (Δcas3). The bacterial invasive and intracellular capacity of Δcas3 to host cells was also reduced, thereby increasing the survival of infected host cells and live chickens. By the transcriptome-wide screen (RNA-Seq), we found that the cas3 gene impacts a series of genes related to QS, the flagellum, and SPI-1-T3SS system, thereby altering the virulence phenotypes. As QS SPI-1-T3SS and CRISPR-Cas systems are widely distributed in the bacteria kingdom, our findings extend our understanding of virulence regulation and pathogenicity in mammalian hosts for Salmonella and potentially other bacteria.

Population Analyses Reveal Preenrichment Method and Selective Enrichment Media Affect Salmonella Serovars Detected on Broiler Carcasses

Poultry is a major Salmonella reservoir, but conventional culture-based methods typically identify the most abundant serovars while those less abundant remain undetected. Choice of enrichment procedure also introduces bias, and for broiler carcasses, a 1-min rinse before preenrichment is insufficient to release all Salmonella present. The inability to assess serovar diversity means that serovars more often associated with human illness may be masked by more abundant Salmonella. CRISPR-SeroSeq (serotyping by sequencing clustered regularly interspaced short palindromic repeats), an amplicon-based, next-generation sequencing tool, allows detection of multiple serovars and maps the relative serovar frequencies in a sample. To address the preceding limitations, CRISPR-SeroSeq was used on broiler carcasses collected prechilled at a commercial plant. Standard carcass rinse aliquot preenrichments and whole carcass preenrichments that were enriched in Rappaport-Vassiliadis (RV) and tetrathionate (TT) broths were compared. On average, five serovars were observed per carcass, including nine on one carcass. CRISPR-SeroSeq detected serovars comprising as little as 0.005% of the population. CRISPR-SeroSeq data matched (28 of 32) standard culture analysis for abundant serovars. Salmonella serovars Kentucky, Typhimurium, and Schwarzengrund were found on each carcass. Overall, serovar diversity was higher in whole carcass preenrichments that were enriched in RV (P < 0.05). Serovar Schwarzengrund was present at higher frequencies in whole carcass preenrichments compared with rinse aliquot preenrichments (t test, P < 0.05), suggesting it adheres more strongly to the carcass. Salmonella serovar Enteritidis was enriched eightfold more in TT than in RV, and serovars Schwarzengrund and Reading were preferentially enriched in RV. Comparison of preenriched and enriched samples suggests that selective enrichment in RV or TT was inhibitory to some serovars. This article addresses limitations of Salmonella surveillance protocols and provides information related to Salmonella population dynamics.

Salmonella enterica serovar Kentucky recovered from human clinical cases in Maryland, USA (2011-2015)

Salmonella Kentucky is among the most frequently isolated S. enterica serovars from food animals in the United States. Recent research on isolates recovered from these animals suggests there may be geographic and host specificity signatures associated with S. Kentucky strains. However, the sources and genomic features of human clinical S. Kentucky isolated in the United States remain poorly described. To investigate the characteristics of clinical S. Kentucky and the possible sources of these infections, the genomes of all S. Kentucky isolates recovered from human clinical cases in the State of Maryland between 2011 and 2015 (n = 12) were sequenced and compared to a database of 525 previously sequenced S. Kentucky genomes representing 12 sequence types (ST) collected from multiple sources on several continents. Of the 12 human clinical S. Kentucky isolates from Maryland, nine were ST198, two were ST152, and one was ST314. Forty-one per cent of isolates were recovered from patients reporting recent international travel and 58% of isolates encoded genomic characteristics similar to those originating outside of the United States. Of the five isolates not associated with international travel, three encoded antibiotic resistance genes conferring resistance to tetracycline or aminoglycosides, while two others only encoded the cryptic aac(6')-Iaa gene. Five isolates recovered from individuals with international travel histories (ST198) and two for which travel was not recorded (ST198) encoded genes conferring resistance to between 4 and 7 classes of antibiotics. Seven ST198 genomes encoded the Salmonella Genomic Island 1 and substitutions in the gyrA and parC genes known to confer resistance to ciprofloxacin. Case report data on food consumption and travel were, for the most part, consistent with the inferred S. Kentucky phylogeny. Results of this study indicate that the majority of S. Kentucky infections in Maryland are caused by ST198 which may originate outside of North America.

Frequent human-poultry interactions and low prevalence of Salmonella in backyard chicken flocks in Massachusetts

The backyard chicken (BYC) movement in the USA has increased human contact with poultry and subsequently, human contact with the pathogen Salmonella. However, to date, there have been few studies assessing prevalence of Salmonella in backyard flocks, despite the known public health risk this zoonotic bacterium poses. The objective of this study was to characterize human-BYC interactions and assess the prevalence of Salmonella among BYC flocks. We interviewed 50 BYC owners using a structured questionnaire to determine flock and household characteristics that facilitate contact with BYC and that may be associated with Salmonella in the BYC environment. Composite faecal material, cloacal swabs and dust samples from 53 flocks housed on 50 residential properties in the Greater Boston, Massachusetts area were tested for Salmonella using standard culture techniques and confirmed using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometer. Microbroth dilution and whole genome sequencing were used to determine phenotypic and genotypic resistance profiles, respectively, and sequence results were used to determine multilocus sequencing type. No owners self-reported a diagnosis of salmonellosis in the household. Over 75% of a subset of owners reported that they and their children consider BYC pets. This perception is evident in how owners reported interacting with their birds. Salmonella enterica subspecies enterica serotype Kentucky ST152 (serogroup C)-a strain not commonly associated with human infection-was confirmed in one flock, or 2% of tested flocks, and demonstrated resistance to tetracycline and streptomycin. We detected Salmonella at low prevalence in BYC. Further study of the health effects of exposure to zoonotic gastrointestinal pathogens such as Salmonella among families with BYC is warranted.

High-Resolution Identification of Multiple Salmonella Serovars in a Single Sample by Using CRISPR-SeroSeq

Salmonella enterica is represented by >2,600 serovars that can differ in routes of transmission, host colonization, and in resistance to antimicrobials. S. enterica is the leading bacterial cause of foodborne illness in the United States, with well-established detection methodology. Current surveillance protocols rely on the characterization of a few colonies to represent an entire sample; thus, minority serovars remain undetected. Salmonella contains two CRISPR loci, CRISPR1 and CRISPR2, and the spacer contents of these can be considered serovar specific. We exploited this property to develop an amplicon-based and multiplexed sequencing approach, CRISPR-SeroSeq (serotyping by sequencing of the CRISPR loci), to identify multiple serovars present in a single sample. Using mixed genomic DNA from two Salmonella serovars, we were able to confidently detect a serovar that constituted 0.01% of the sample. Poultry is a major reservoir of Salmonella spp., including serovars that are frequently associated with human illness, as well as those that are not. Numerous studies have examined the prevalence and diversity of Salmonella spp. in poultry, though these studies were limited to culture-based approaches and therefore only identified abundant serovars. CRISPR-SeroSeq was used to investigate samples from broiler houses and a processing facility. Ninety-one percent of samples harbored multiple serovars, and there was one sample in which four different serovars were detected. In another sample, reads for the minority serovar comprised 0.003% of the total number of Salmonella spacer reads. The most abundant serovars identified were Salmonella enterica serovars Montevideo, Kentucky, Enteritidis, and Typhimurium. CRISPR-SeroSeq also differentiated between multiple strains of some serovars. This high resolution of serovar populations has the potential to be utilized as a powerful tool in the surveillance of Salmonella species.IMPORTANCESalmonella enterica is the leading bacterial cause of foodborne illness in the United States and is represented by over 2,600 distinct serovars. Some of these serovars are pathogenic in humans, while others are not. Current surveillance for this pathogen is limited by the detection of only the most abundant serovars, due to the culture-based approaches that are used. Thus, pathogenic serovars that are present in a minority remain undetected. By exploiting serovar-specific differences in the CRISPR arrays of Salmonella spp., we have developed a high-throughput sequencing tool to be able to identify multiple serovars in a single sample and tested this in multiple poultry samples. This novel approach allows differences in the dynamics of individual Salmonella serovars to be measured and can have a significant impact on understanding the ecology of this pathogen with respect to zoonotic risk and public health.

Prevalence of Group I Salmonella Kentucky in domestic food animals from Pennsylvania and overlap with human clinical CRISPR sequence types

Although infrequently associated with illness in humans, Salmonella enterica, subsp. enterica serovar Kentucky is the most common non-clinical, non-human serovar reported in the United States, being largely found in poultry and poultry products, as well as being associated with cattle. This serovar is polyphyletic and can be separated into two groups, Group I and II, based on CRISPR-typing analysis. In Salmonella Kentucky isolates from human clinical samples in Pennsylvania, both lineages are equally represented. The goal of this study was to determine whether both groups were also represented in domestic food animals in Pennsylvania. We analysed the CRISPR arrays from 67 Salmonella Kentucky isolates used PCR and sequencing of CRISPR arrays or analysis of whole genome sequences to analyse the CRISPR arrays and Across a collection of 67 Salmonella Kentucky isolates that includes those collected from farms, veterinary clinical samples as well as isolates from retail meats, we show that Group I Salmonella Kentucky are the exclusive lineage present. We reveal that the specific subtype of over a quarter of these animal isolates are also found to be responsible for causing human salmonellosis in the same region over the same time period.