Genomic Diversity, Antimicrobial Resistance, and Virulence Gene Profiles of Salmonella Serovar Kentucky Isolated from Humans, Food, and Animal Ceca Content Sources in the United States.

Salmonella serovar Kentucky is frequently isolated from chickens and dairy cattle, but recovery from humans is comparatively low based on the U.S. National Antimicrobial Resistance Monitoring System (NARMS) reports. We aimed to better describe the genetic diversity, antimicrobial resistance, and virulence determinants of Salmonella Kentucky isolates from humans, food animal ceca, retail meat and poultry products, imported foods and food products, and other samples. We analyzed the genomes of 774 Salmonella Kentucky isolates and found that 63% (54/86) of human isolates were sequence type (ST)198, 33% (29/86) were ST152, and 3.5% (3/86) were ST314. Ninety-one percent (570/629) of cecal isolates and retail meat and poultry isolates were ST152 or ST152-like (one allele difference), and 9.2% (58/629) were ST198. Isolates from imported food were mostly ST198 (60%, 22/37) and ST314 (29.7%, 11/37). ST198 isolates clustered into two main lineages. Clade ST198.2 comprised almost entirely isolates from humans and imported foods, all containing triple mutations in the quinolone resistance-determining region (QRDR) that confer resistance to fluoroquinolones. Clade ST198.1 contained isolates from humans, ceca, retail meat and poultry products, and imported foods that largely lacked QRDR mutations. ST152 isolates from cattle had a lineage (Clade 2) distinct from ST152 isolates from chicken (Clade 4), and half of ST152 human isolates clustered within two other clades (Clades 1 and 3), largely distinct from Clades 2 and 4. Although clinical illness associated with Salmonella Kentucky is low, ST198 appears to account for most human infections in the Unites States but is uncommon among ceca of domestic food animals and retail meat and poultry products. These findings, combined with human exposure data, suggest that fluoroquinolone-resistant ST198 infections may be linked to the consumption of food products that are imported or consumed while traveling. We also found unique differences in the composition of virulence genes and antimicrobial resistance genes among the clades, which may provide clues to the host specificity and pathogenicity of Salmonella Kentucky lineages.

Prevalence of Antimicrobial Resistance in Select Bacteria From Retail Seafood-United States, 2019.

In 2019, the United States National Antimicrobial Resistance Monitoring System (NARMS) surveyed raw salmon, shrimp, and tilapia from retail grocery outlets in eight states to assess the prevalence of bacterial contamination and antimicrobial resistance (AMR) in the isolates. Prevalence of the targeted bacterial genera ranged among the commodities: Salmonella (0%-0.4%), Aeromonas (19%-26%), Vibrio (7%-43%), Pseudomonas aeruginosa (0.8%-2.3%), Staphylococcus (23%-30%), and Enterococcus (39%-66%). Shrimp had the highest odds (OR: 2.8, CI: 2.0-3.9) of being contaminated with at least one species of these bacteria, as were seafood sourced from Asia vs. North America (OR: 2.7; CI: 1.8-4.7) and Latin America and the Caribbean vs. North America (OR: 1.6; CI: 1.1-2.3) and seafood sold at the counter vs. sold frozen (OR: 2.1; CI: 1.6-2.9). Isolates exhibited pan-susceptibility (Salmonella and P. aeruginosa) or low prevalence of resistance (<10%) to most antimicrobials tested, with few exceptions. Seafood marketed as farm-raised had lower odds of contamination with antimicrobial resistant bacteria compared to wild-caught seafood (OR: 0.4, CI: 0.2-0.7). Antimicrobial resistance genes (ARGs) were detected for various classes of medically important antimicrobials. Clinically relevant ARGs included carbapenemases (bla IMI-2, bla NDM-1) and extended spectrum ß-lactamases (ESBLs; bla CTX-M-55). This population-scale study of AMR in seafood sold in the United States provided the basis for NARMS seafood monitoring, which began in 2020.

Assessing the effectiveness of performance standards for Salmonella contamination of chicken parts.

The United States Department of Agriculture's Food Safety and Inspection Service implemented Salmonella performance standards for establishments producing chicken parts in 2016. The standards were chosen based on the assumption that a 30 % reduction in the occurrence of Salmonella-contaminated chicken parts samples (i.e., legs, breasts or wings) would result following implementation of the performance standard program. The derivation of the performance standards was based on data collected prior to the implementation of the standards and in the intervening years, so overall changes in the Salmonella contamination of this product can be assessed. This study presents a historical review of changes in Salmonella contamination on chicken parts as these changes relate to the performance standard. The analysis demonstrates that the reduction in Salmonella contaminated chicken parts samples was more than 75 %, so the FSIS risk assessment significantly underestimated the actual reduction in Salmonella contamination. An analysis of chicken parts samples collected at retail demonstrates reductions of a similar magnitude. Changes in the characteristics of Salmonella contamination that are potentially relevant to the occurrence or severity of human illness, such as seasonal changes in contamination, the composition of serotypes and changes in antimicrobial resistance, are also assessed. Small but significant seasonal increases in contamination were observed, with the peaks occurring in late winter rather than the more traditional late summer peak. Rapid changes in both the five most common serotypes and antimicrobial resistance patterns were also observed.

A National Antimicrobial Resistance Monitoring System Survey of Antimicrobial-Resistant Foodborne Bacteria Isolated from Retail Veal in the United States.

ABSTRACT: Little is known about the prevalence of antimicrobial-resistant (AMR) bacteria in veal meat in the United States. We estimated the prevalence of bacterial contamination and AMR in various veal meats collected during the 2018 U.S. National Antimicrobial Resistance Monitoring System (NARMS) survey of retail outlets in nine states and compared the prevalence with the frequency of AMR bacteria from other cattle sources sampled for NARMS. In addition, we identified genes associated with resistance to medically important antimicrobials and gleaned other genetic details about the resistant organisms. The prevalence of Campylobacter, Salmonella, Escherichia coli, and Enterococcus in veal meats collected from grocery stores in nine states was 0% (0 of 358), 0.6% (2 of 358), 21.1% (49 of 232), and 53.5% (121 of 226), respectively, with ground veal posing the highest risk for contamination. Both Salmonella isolates were resistant to at least one antimicrobial agent as were 65.3% (32 of 49) of E. coli and 73.6% (89 of 121) of Enterococcus isolates. Individual drug and multiple drug resistance levels were significantly higher (P < 0.05) in E. coli and Enterococcus from retail veal than in dairy cattle ceca and retail ground beef samples from 2018 NARMS data. Whole genome sequencing was conducted on select E. coli and Salmonella from veal. Cephalosporin resistance (blaCMY and blaCTX-M), macrolide resistance (mph), and plasmid-mediated quinolone resistance (qnr) genes and gyrA mutations were found. We also identified heavy metal resistance genes ter, ars, mer, fieF, and gol and disinfectant resistance genes qac and emrE. An stx1a-containing E. coli was also found. Sequence types were highly varied among the nine E. coli isolates that were sequenced. Several plasmid types were identified in E. coli and Salmonella, with the majority (9 of 11) of isolates containing IncF. This study illustrates that veal meat is a carrier of AMR bacteria.

Antimicrobial resistance in non-Typhoidal Salmonella from retail poultry meat by antibiotic usage-related production claims - United States, 2008-2017.

Antimicrobial resistance (AMR) in non-typhoidal Salmonella from poultry is a public health concern. Injudicious use of antibiotics in humans and agriculture fuels the emergence of resistance. The objective of this study was to characterize the prevalence, antibiotic susceptibility profiles and genetic resistance mechanisms of Salmonella isolated from US retail poultry meat samples with and without antibiotic-related claims. We reviewed data from 46,937 poultry meat samples collected from 2008 to 2017 through the FDA NARMS retail meat program. Antibiotic usage claims on the poultry packaging were used to categorize the sample as 'conventionally raised' or 'reduced or no antibiotic use'. The results show that the prevalence of Salmonella in conventional poultry samples (8.6%) was higher than reduced or no antibiotic use poultry samples (5.1%). The odds of resistance to three or more antimicrobial classes (multi-drug resistant) were 2.61 times higher for Salmonella isolates from conventional samples, compared to isolates from reduced antibiotic use samples. The frequency of the aminoglycoside resistance gene, strB, and the beta-lactam resistant gene, blaCMY-2, were higher in isolates from conventional meat. This study suggests that conventionally raised poultry meat was more likely to be contaminated with multi-drug resistant Salmonella, and those Salmonella are more likely to carry genes for antibiotics resistance.

Comparative history of Campylobacter contamination on chicken meat and campylobacteriosis cases in the United States: 1994-2018.

In many countries campylobacteriosis ranks as one of the most frequently reported foodborne illnesses and poultry is the commodity that is most often associated with these illnesses. Nevertheless, efforts to reduce the occurrence of pathogen contamination on poultry are often more focused on Salmonella. While some control measures are pathogen specific, such as pre-harvest vaccination for Salmonella, improvements in sanitary dressing and interventions applied during the slaughter process can be effective against all forms of microbial contamination. To investigate the potential effectiveness of these non-specific pathogen reduction strategies in the United States, it is helpful to assess if, and by how much, Campylobacter contamination of chicken meat has changed across time. This study assesses change considering data collected in both slaughter and retail establishments and comparing observed trends in contamination with trends in human surveillance data. The results support the assertion that substantial reductions in Campylobacter contamination of chicken meat in the late 1990s and early 2000s contributed to a reduction in the human case rate of campylobacteriosis. Further reductions in chicken meat contamination between 2013 and 2018 are more difficult to associate with trends in human illnesses, with one contributing factor being the inclusion of culture independent diagnostic test results in the official case counts during that time. Other contributing factors are discussed.

The Western United States has Greater Antibiotic Resistance Among Salmonella Recovered from Intestinal Cecal Samples of Food Animals.

As part of the National Antimicrobial Resistance Monitoring System (NARMS) activities, the United States Department of Agriculture (USDA) Food Safety Inspection Service (FSIS) collected cecal samples from food animal slaughter facilities throughout the country between 2014 and 2018. Of the 26,780 cecal samples from cattle, swine, chicken and turkey , 6,350 (23.71%) tested positive for Salmonella . NARMS tested Salmonella for susceptibility to aminoglycosides, folate pathway inhibitors, macrolides, phenicols, quinolones, beta lactams, and tetracyclines. Using the regional subdivisions defined in the USDA Office of Investigation, we used chi-square test to assess potential association between the region from which the samples were collected and both Salmonella prevalence and susceptibility. The results show a significant association between region and Salmonella prevalence, when accounting for source and establishment size, with the southeast region having the highest probability of finding Salmonella . However, the western region had the highest resistance probability across all antimicrobial classes except for macrolides, which showed no regional association. This association between region and resistance was strongest among isolates from cattle. Analysis of whole-genome sequencing data indicated that a significantly higher prevalence of Salmonella Newport in cattle in the western region (accounting for 9.52% of cattle isolates, compared to 3.44% in other regions) may account for the greater resistance to multiple drug classes. Approximately 90% of Salmonella Newport in the west exhibited the MDR-AmpC phenotype encoded by aph(3'')-Ib/aph(6)-Id , bla CMY-2 , floR , sul2 , and tetA. . Thus, differences in resistance across regions may be due to geographical differences in the prevalence of specific Salmonella serotypes and their accompanying resistance genes.

Changes in Salmonella Contamination in Meat and Poultry Since the Introduction of the Pathogen Reduction and Hazard Analysis and Critical Control Point Rule.

ABSTRACT: In 1996, the Food Safety and Inspection Service (FSIS) published its pathogen reduction and hazard analysis and critical control point (PR-HACCP) rule. The intention of this program was to reduce microbial contamination on meat, poultry, and egg products. The program was implemented in stages between January 1998 and January 2000, with sampling for Escherichia coli O157:H7 and/or Salmonella in large production establishments beginning in 1998. As the PR-HACCP program begins its third decade, it is reasonable to question whether there have been reductions in the frequency of pathogen-contaminated meat and poultry products reaching consumers. This study summarizes the results for over 650,000 samples collected by FSIS between 2000 and 2018 in slaughter and processing establishments across the United States and compares these results to the roughly 100,000 retail samples collected by the U.S. Food and Drug Administration between 2002 and 2017. The data demonstrate that there has been an overall reduction in the occurrence of Salmonella on meat and poultry products, but the direction and magnitude of change has not been consistent over time or across commodities. Although the available data do not support the identification of causal factors for the observed changes, a historical review of the timing of various factors and policy decisions generates potential hypotheses for the observed changes.

Northeastern U.S. Salmonella Strains from Retail Meat Are More Prevalent and More Resistant to Antimicrobials.

ABSTRACT: Between 2002 and 2017, the National Antimicrobial Resistance Monitoring System (NARMS) recovered 5,803 Salmonella isolates from retail meat samples of chicken parts, ground turkey, pork chops, and ground beef collected in 21 states. NARMS tested these isolates for susceptibility to amoxicillin-clavulanic acid, ampicillin, azithromycin, cefoxitin, ceftiofur, ceftriaxone, chloramphenicol, gentamicin, nalidixic acid, streptomycin, tetracycline, trimethoprim-sulfamethoxazole (cotrimoxazole), sulfisoxazole, and ciprofloxacin. To evaluate possible geographic differences in the prevalence and distribution of antimicrobial-resistant Salmonella, we used a chi-square test of association. We used the U.S. Department of Agriculture Office of Investigation, Enforcement and Audit map for the regional subdivisions. A significant association was found between region, Salmonella prevalence, and Salmonella resistance to all tested antimicrobials except cotrimoxazole, streptomycin, ciprofloxacin, and azithromycin. The Northeast region was the most influential contributor to overall prevalence and resistance to most of the antimicrobials tested, and Salmonella Typhimurium was the serotype driving these associations. Although this work did not elucidate the reasons for differences in prevalence and antimicrobial resistance for Salmonella Typhimurium strains in the Northeast, lack of certain resistance mechanisms in Salmonella strains from other regions was ruled out by analysis of 484 sequences from the 485 isolates resistant to ampicillin, sulfonamides, and tetracycline.

Prevalence and Antimicrobial Resistance of Enterococci Isolated from Retail Meats in the United States, 2002 to 2014.

Bacteria of the genus Enterococcus are important human pathogens that are frequently resistant to a number of clinically important antibiotics. They are also used as markers of animal fecal contamination of human foods and are employed as sentinel organisms for tracking trends in resistance to antimicrobials with Gram-positive activity. As part of the National Antimicrobial Resistance Monitoring System (NARMS), we evaluated several retail meat commodities for the presence of enterococci from 2002 to 2014, and we found 92.0% to be contaminated. The majority of isolates were either Enterococcus faecalis (64.0%) or Enterococcus faecium (28.6%), and the antimicrobial resistance of each isolate was assessed by broth microdilution. The resistance prevalences for several drugs, including erythromycin and gentamicin, were significantly higher among poultry isolates, compared to retail beef or pork isolates. None of the isolates was resistant to the clinically important human drug vancomycin, only 1 isolate was resistant to linezolid, and resistance to tigecycline was below 1%. In contrast, a majority of both E. faecalis (67.5%) and E. faecium (53.7%) isolates were resistant to tetracycline. Overall, the robust NARMS testing system employed consistent sampling practices and methods throughout the testing period, with the only significant trend in resistance prevalence being decreased E. faecium resistance to penicillin. These data provide excellent baseline levels of resistance that can be used to measure future changes in resistance prevalence that may result from alterations in the use of antimicrobials in food animal production.IMPORTANCE Enterococci, including E. faecalis and E. faecium, are present in the guts of food-producing animals and are used as a measure of fecal contamination of meat. We used the large consistent sampling methods of NARMS to assess the prevalence of Enterococcus strains isolated from retail meats, and we found over 90% of meats to be contaminated with enterococci. We also assessed the resistance of the Enterococcus strains, commonly used as a measure of resistance to agents with Gram-positive activity, in foods. Resistance prevalence was over 25% for some antimicrobials and sample sources but was less than 1% for several of the most important therapeutic agents used in human medicine.

Retention of mothers and infants in the prevention of mother-to-child transmission of HIV programme is associated with individual and facility-level factors in Rwanda.

OBJECTIVES: Investigate levels of retention at specified time periods along the prevention of mother-to-child transmission (PMTCT) cascade among mother-infant pairs as well as individual- and facility-level factors associated with retention. METHODS: A retrospective cohort of HIV-positive pregnant women and their infants attending five health centres from November 2010 to February 2012 in the Option B programme in Rwanda was established. Data were collected from several health registers and patient follow-up files. Additionally, informant interviews were conducted to ascertain health facility characteristics. Generalized estimating equation methods and modelling were utilized to estimate the number of mothers attending each antenatal care visit and assess factors associated with retention. RESULTS: Data from 457 pregnant women and 462 infants were collected at five different health centres (three urban and two rural facilities). Retention at 30 days after registration and retention at 6 weeks, 3, 6, 9 and 12 months post-delivery were analyzed. Based on an analytical sample of 348, we found that 58% of women and 81% of infants were retained in care within the same health facility at 12 months post-delivery, respectively. However, for mother-infant paired mothers, retention at 12 months was 74% and 79% for their infants. Loss to facility occurred early, with 26% to 33% being lost within 30 days post-registration. In a multivariable model retention was associated with being married, adjusted relative risk (ARR): 1.26, (95% confidence intervals: 1.11, 1.43); antiretroviral therapy eligible, ARR: 1.39, (1.12, 1.73) and CD4 count per 50 mm(3), ARR: 1.02, (1.01, 1.03). CONCLUSIONS: These findings demonstrate varying retention levels among mother-infant pairs along the PMTCT cascade in addition to potential determinants of retention to such programmes. Unmarried, apparently healthy, HIV-positive pregnant women need additional support for programme retention. With the significantly increased workload resulting from lifelong antiretroviral treatment for all HIV-positive pregnant women, strategies need to be developed to identify, provide support and trace these women at risk of loss to follow-up. This study provides further evidence for the need for such a targeted supportive approach.

A cluster analysis of tic symptoms in children and adults with Tourette syndrome: clinical correlates and treatment outcome.

Cluster analytic methods have examined the symptom presentation of chronic tic disorders (CTDs), with limited agreement across studies. The present study investigated patterns, clinical correlates, and treatment outcome of tic symptoms. 239 youth and adults with CTDs completed a battery of assessments at baseline to determine diagnoses, tic severity, and clinical characteristics. Participants were randomly assigned to receive either a comprehensive behavioral intervention for tics (CBIT) or psychoeducation and supportive therapy (PST). A cluster analysis was conducted on the baseline Yale Global Tic Severity Scale (YGTSS) symptom checklist to identify the constellations of tic symptoms. Four tic clusters were identified: Impulse Control and Complex Phonic Tics; Complex Motor Tics; Simple Head Motor/Vocal Tics; and Primarily Simple Motor Tics. Frequencies of tic symptoms showed few differences across youth and adults. Tic clusters had small associations with clinical characteristics and showed no associations to the presence of coexisting psychiatric conditions. Cluster membership scores did not predict treatment response to CBIT or tic severity reductions. Tic symptoms distinctly cluster with little difference across youth and adults, or coexisting conditions. This study, which is the first to examine tic clusters and response to treatment, suggested that tic symptom profiles respond equally well to CBIT. Clinical trials.gov. identifiers: NCT00218777; NCT00231985.

A LASSO-based approach to analyzing rare variants in genetic association studies.

Genetic markers with rare variants are spread out in the genome, making it necessary and difficult to consider them in genetic association studies. Consequently, wisely combining rare variants into "composite" markers may facilitate meaningful analyses. In this paper, we propose a novel approach of analyzing rare variant data by incorporating the least absolute shrinkage and selection operator technique. We applied this method to the Genetic Analysis Workshop 17 data, and our results suggest that this new approach is promising. In addition, we took advantage of having 200 phenotype replications and assessed the performance of our approach by means of repeated classification tree analyses. Our method and analyses were performed without knowledge of the underlying simulating model. Our method identified 38 markers (in 65 genes) that are significantly associated with the phenotype Affected and correctly identified two causal genes, SIRT1 and PDGFD.

Novel tree-based method to generate markers from rare variant data.

Existing methods for analyzing rare variant data focus on collapsing a group of rare variants into a single common variant; collapsing is based on an intuitive function of the rare variant genotype information, such as an indicator function or a weighted sum. It is more natural, however, to take into account the single-nucleotide polymorphism (SNP) interactions informed directly by the data. We propose a novel tree-based method that automatically detects SNP interactions and generates candidate markers from the original pool of rare variants. In addition, we utilize the advantage of having 200 phenotype replications in the Genetic Analysis Workshop 17 data to assess the candidate markers by means of repeated logistic regressions. This new approach shows potential in the rare variant analysis. We correctly identify the association between gene FLT1 and phenotype Affect, although there exist other false positives in our results. Our analyses are performed without knowledge of the underlying simulating model.