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.

Sero-detection of Coxiella burnetii infection in cattle, sheep and goats in selected regions of Nepal.

Coxiella burnetii, a Gram-negative bacterium is a zoonotic agent causing coxiellosis in animals. Small ruminants and cattle are the primary reservoirs for human infection. This study was aimed to estimate the sero-prevalence of C. burnetii in the ruminants of the selected region in Nepal. Field visits were carried out at four sites in different geographical regions of Nepal. A total of 522 sera samples were collected from 118 sheep, 242 goats and 162 cattle with the history of abortion, anoestrus and infertility. Sera were tested for the presence of antibodies against C. burnetii using a commercially available ready-to-use ELISA test kit. The overall true sero-prevalence was 1.89% (95% CI: 0.33-3.45), the prevalence ranged between 4.35% and 23.21% in goats. Sero-prevalence in goat was higher than that of cattle and sheep which ascertained that total freedom from coxiellosis cannot be confirmed in Nepal. This could complement the impacts of other infectious causes of the infertility in the farm animals as well as the public health of the farming households.

ONE Health Approach to Address Zoonotic Brucellosis: A Spatiotemporal Associations Study Between Animals and Humans.

Background: Brucellosis is one of the most significant zoonosis over the world, threatening both veterinary and human public health. However, few studies were focused on nationwide animal brucellosis and made association with human brucellosis. Methodology and Principal Findings: We conducted a bilingual literature search on Brucella or brucellosis in China on the two largest databases (China National Knowledge Infrastructure and PubMed) and conducted a systematic review. A total of 1,383 Chinese and 81 English publications, published between 1958 and 2018 were identified. From them, 357 publications presenting 692 datasets were subjected to the meta-analysis. The overall prevalence rate is 1.70% (95% CI: 1.66-1.74), with a declining (until the late 1990s) and rising trend (starting the early 2000s). Interestingly, the animal with highest prevalence rate is canine (8.35%, 95% CI: 7.21-9.50), and lowest in cattle (1.22%, 95% CI: 1.17-1.28). The prevalence of Brucella in animals was unequally distributed among the 24 examined regions in China. Conclusions: Brucellosis is a reemerging disease for both humans and animals in China. The observed data suggests that dogs and yaks are the leading reservoirs for Brucella, and the provinces with highest prevalence rates in animals are Hubei, Sichuan, Inner Mongolia, Fujian, and Guizhou. Accordingly targeted intervention policy should be implemented to break the Brucella transmission chain between animals and humans in China.

Corrigendum: Antibiotic Resistance in Salmonella Typhimurium Isolates Recovered From the Food Chain Through National Antimicrobial Resistance Monitoring System Between 1996 and 2016.

[This corrects the article DOI: 10.3389/fmicb.2019.00985.].

Persistent Asymptomatic Human Infections by Salmonella enterica Serovar Newport in China.

Salmonella enterica serovar Newport (S Newport) infections are gradually on the rise in China from the last decade. For humans' infections, S Newport has been ranked among the top five serovars responsible for persistent infections, globally. A total of 290 S. Newport strains with their relevant clinical metadata were analyzed, and the strains were subjected to whole-genome sequence analysis. Among these, 62.4% (n = 181) were from diarrheic patients and 28.9% (n = 84) were from asymptomatic individuals (including adults and youngsters) while 8.6% (n = 25) were from cases of persistent diarrhea in infants (28%, n = 7) and toddlers (72%, n = 18). The association between the sequence types (STs) and the variations in the clinical presentation was statistically significant (P = 0.0432), with ST46 causing diarrhea or representing asymptomatic patients and ST31 or ST68 causing persistent diarrhea. Genomic analysis revealed that the highest proportion of the isolates (98.5%, n = 279), primarily from patients with or without diarrhea rather than from asymptomatic individuals, carried antimicrobial resistance determinants corresponding to the aminoglycosides and beta-lactams, highlighting the need for cautionary usage of antimicrobials in such patients. These findings also suggest that cases of nontyphoidal Salmonella infection with symptoms of acute diarrhea or persistent diarrhea caused by S Newport should be handled with caution, due to the high chance of development of an antimicrobial resistance phenotype that might lead to therapeutic failures. Together, S Newport ST31 and ST46, which have the highest frequency of carriage of multidrug resistance, are potentially responsible for antimicrobial-resistant diarrhea/persistent diarrhea in infants and children, while adult humans are more likely to be (asymptomatic) carriers of the S Newport strains.IMPORTANCE Human infections caused by Salmonella Newport generally lead to gastrointestinal diseases. These infections are normally self-limiting; however, in certain cases, broad-spectrum antimicrobials are prescribed for the treatment. The Chinese National Foodborne Disease Surveillance Network has reported a gradual increase in the incidence of multidrug-resistant S Newport infections in humans. After careful evaluation of the dynamic relationship among the clinical findings, the age group, and the genomic sequence data, it was found that young patients represented the major group with persistent diarrhea, whereas adults were either asymptomatic or diarrheic. Furthermore, all these strains contained multiple acquired antimicrobial resistance determinants, which limited the use of antimicrobials for human patients of all age groups. This analysis of the laboratory-confirmed cases, coupled with genetic analysis of the corresponding pathogen, revealed that antimicrobial treatment of persistent infections by S Newport in infants and toddlers, and in asymptomatic or diarrheic adults, may not be successful. If the antimicrobials must be prescribed at all, they must be used with caution because of the presence of multiple acquired antimicrobial resistance determinants in such strains.

Global Burden of Colistin-Resistant Bacteria: Mobilized Colistin Resistance Genes Study (1980-2018).

Colistin is considered to be an antimicrobial of last-resort for the treatment of multidrug-resistant Gram-negative bacterial infections. The recent global dissemination of mobilized colistin resistance (mcr) genes is an urgent public health threat. An accurate estimate of the global prevalence of mcr genes, their reservoirs and the potential pathways for human transmission are required to implement control and prevention strategies, yet such data are lacking. Publications from four English (PubMed, Scopus, the Cochrane Database of Systematic Reviews and Web of Science) and two Chinese (CNKI and WANFANG) databases published between 18 November 2015 and 30 December 2018 were identified. In this systematic review and meta-analysis, the prevalence of mcr genes in bacteria isolated from humans, animals, the environment and food products were investigated. A total of 974 publications were identified. 202 observational studies were included in the systematic review and 71 in the meta-analysis. mcr genes were reported from 47 countries across six continents and the overall average prevalence was 4.7% (0.1-9.3%). China reported the highest number of mcr-positive strains. Pathogenic Escherichia coli (54%), isolated from animals (52%) and harboring an IncI2 plasmid (34%) were the bacteria with highest prevalence of mcr genes. The estimated prevalence of mcr-1 pathogenic E. coli was higher in food-animals than in humans and food products, which suggests a role for foodborne transmission. This study provides a comprehensive assessment of prevalence of the mcr gene by source, organism, genotype and type of plasmid.

Characterization of Salmonella Dublin isolated from bovine and human hosts.

BACKGROUND: Salmonella enterica subsp. enterica serovar Dublin (S. Dublin), a cattle adapted serovar causes enteritis, and systemic disease in bovines. The invasive index of this serovar far exceeds that of the other serovars and human infections often present as fatal or highly resistant infections. In this, observational study, phenotypic properties of human and bovine-derived isolates of S. Dublin along with antibiogram of common antimicrobials were evaluated. The multiplex PCR confirmed isolates were genotyped using 7-gene legacy MLST. MIC assay was done by broth microdilution method. Previously published protocols were used to assess the motility, biofilm formation and morphotype. Vi antigen was agglutinated using commercial antiserum. Caenorhabditis elegans infection model was used to evaluate the virulence potiential. Phenotyping experiments were done in duplicates while virulence assay was done in triplicates. Whole-genome sequencing was used to predict the genes responsible for acquired resistance and a genotype-phenotype comparison was made. RESULTS: We evaluated 96 bovine and 10 human isolates in this study. All the isolates belonged to ST10 in eBG53 and were negative for Vi-antigen. The swarming motility, biofilm formation and morphotype were variable in the isolates of both groups. Resistance to sulfamethoxazole, ampicillin, chloramphenicol, tetracycline was > 90% in animal isolates whereas resistance to sulfamethoxazole was > 70% in human isolates. MDR was also higher in animal isolates. Human isolates were significantly (P < 0.0001) more virulent than animal isolates on C. elegans infection model. The genomic comparison based on the core SNPs showed a high degree of homogeneity between the isolates. The carriage of IncA/C2 plasmid was seen as a typical feature of isolates from the bovine hosts. CONCLUSION: Human isolates showed more diversity in the phenotypic assays. Animal isolates showed a higher degree of antimicrobial resistance with greater MDR but human isolates formed more biofilm and had greater swarming motility as well as increased virulence to the nematode C. elegans. The carriage of IncA/C2 plasmid could contribute to the distinguishing feature of the bovine isolates. The tandem use of genotypic-phenotypic assays improves the understanding of diversity and differential behaviour of the same serovar from unrelated host sources.

Antibiotic Resistance Profiles of Salmonella Recovered From Finishing Pigs and Slaughter Facilities in Henan, China.

With the increase in commercial pig farming, there is a simultaneous increase in the use of antibiotics for prophylaxis as well as therapeutics in China. In this study, we evaluated the prevalence and resistance diversity of salmonellae isolated from feces of asymptomatic, live and slaughtered pigs. We analyzed 1,732 pig fecal samples collected over 8 months, at Henan province of China. The salmonellae were isolated and identified by PCR. They were serotyped using commercial antisera and assayed for the MIC of 16 antibiotics by broth microdilution method. The average prevalence of Salmonella was 19.4% (95% CI: 17.6-21.4). Large farms (herd size ≥1,000) were found to have a higher prevalence as compared to the small- and medium-scale farms (p < 0.0001). The prevalence of salmonellae in samples collected from the farms [11.77% (95% CI: 10.1-13.6)] and from the slaughterhouse [45.23% (95% CI: 40.3-50.30)] was statistically different (p < 0.0001). Uncommon serovars of Salmonella such as Agama and common serovars such as Derby and Typhimurium were isolated. High resistance (>80%) was recorded toward ciprofloxacin (100%), tetracycline (99.4%), doxycycline (97%), sulfamethoxazole (85.8%), ampicillin (81.6%), and amoxicillin (80.4%). Multidrug resistance (MDR) to four, five, and seven classes of antibiotics was recorded to be approximately 25% in the most prevalent serovar like Derby. We conclude that the presence of alarmingly high resistance, toward the critical antibiotics such as fluoroquinolones and beta-lactams, in large swine farms in China, should draw public attention. These results highlight the need for continued antibiotic stewardship programs for judicious use of critical antibiotics in animal health as well as for producing safe pork.

Antibiotic Resistance in Salmonella Typhimurium Isolates Recovered From the Food Chain Through National Antimicrobial Resistance Monitoring System Between 1996 and 2016.

Salmonella is a major foodborne pathogen which causes widespread contamination and infection worldwide. Salmonella Typhimurium is one of the leading serovars responsible for human and animal salmonellosis, globally. The increasing rate of antibiotic resistance in Salmonella Typhimurium poses a significant global concern, and an improved understanding of the distribution of antibiotic resistance patterns in Salmonella Typhimurium is essential for choosing the suitable antibiotic for the treatment of infections. To evaluate the roles of animal and human in antibiotic resistance dissemination, this study aims to categorize 11,447 S. Typhimurium strains obtained across the food-chain, including food animals, retail meats and humans for 21 years in the United States by analyzing minimum inhibitory concentrations (MICs) values for 27 antibiotics. Random Forest Algorithm and Hierarchical Clustering statistics were used to group the strains according to their minimum inhibitory concentration values. Classification and Regression Tree analysis was used to identify the best classifier for human- and animal-populations' isolates. We found the persistent population or multi-drug resistant strains of S. Typhimurium across the four time periods (1996∼2000, 2001∼2005, 2006∼2010, 2011∼2016). Importantly, we also detected that there was more diversity in the MIC patterns among S. Typhimurium strains isolated between 2011 and 2016, which suggests significant emergence of diversified multi-drug resistant strains. The most frequently observed (43%) antibiotic resistance patterns found in S. Typhimurium were tetra-resistant pattern ASSuT (ampicillin, streptomycin, sulfonamides, and tetracycline) and the penta-resistant pattern ACSSuT (ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline). Animals (mainly swine and bovine) are the major source for these two frequently found antibiotic resistance patterns. The occurrence of antibiotic resistant strains from humans and chicken is alarming. Strains were mostly susceptible to fluoroquinolones. Together, this study helped in understanding the expansion of dynamics of antibiotic resistance of S. Typhimurium and recommended fluoroquinolones as a possible treatment options against S. Typhimurium infection.

Classical swine fever virus C-strain with eight mutation sites shows enhanced cell adaptation and protects pigs from lethal challenge.

Control of classical swine fever (CSF) in developing countries is achieved by immunization with attenuated vaccines, such as the lapinized C-strain vaccine that has been widely used in China. However, C-strain has relatively low growth rate in cell cultures, thus affecting productivity of the vaccine for the industry. In this study, eight amino acid residues were mutated on the C-strain backbone, resulting in a cell-adapted strain Cmut8. The mutant strain exhibited rapid growth with titer of about 100 fold higher than its parental C-strain. The mutation sites located at structural proteins Erns and E2 contributed more to cell adaptation than those located in non-structural proteins. Sera collected from pigs inoculated with Cmut8 and C-strain at the same dose showed similar antibody levels and neutralization titers. Pigs inoculated with different doses of Cmut8 (low, medium and high) and with C-strain offered full protection against challenge with a virulent strain, shown as absence of fever and other symptoms, marginal low levels of viral load, and no obvious gross pathological changes in major organs. Unvaccinated control pigs challenged with the virulent strain showed high fever from day 2 post-challenge and apparent clinical symptoms with two deaths. Viral load were markedly elevated in these control pigs after challenge. The pigs inoculated with high dose of Cmut8 did not show fever or other typical CSF symptoms, and no apparent pathological changes were observed in major organs. Besides, the Cmut8 strain did not induce typical fever response in rabbits. These results demonstrate that the cell-adapted Cmut8 strain remains non-pathogenic to the weaned pigs, provides full protection and could be a good candidate vaccine strain for improved yield at lower cost.

E2 and Erns of classical swine fever virus C-strain play central roles in its adaptation to rabbits.

The classical swine fever virus (CSFV) C-strain has been used as a vaccine strain for over 60 years in China. A recent study has demonstrated that the E2 protein of C-strain plays a major role in its adaptation to rabbits. E2 protein in combination with either Erns or E1 confers rabbit adaptation for the C-strain, and the residues P108 and T109 in domain I of E2 are critical for rabbit adaptation. To further identify the contributions of the glycoproteins to rabbit adaptation, a series of C-strain-based chimeric viruses containing single or double glycoprotein substitutions of the Shimen strain were generated and inoculated into rabbits. Profiles of rectal temperature, viral RNA, E2 protein expression, and antibody responses were compared among the chimeric viruses. Replacement of Erns, E2, Erns-E2, or E1-E2 of the C-strain with the counterpart(s) of the Shimen strain led to decreased fever response, reduction of viral RNA and antibody responses in rabbits, as compared with their parental C-strain. The C-strain-based chimeric virus expressing the Shimen strain E1 exhibited typical fever response and viral RNA level similar to the C-strain. However, substitution of both Erns and E2 in the C-strain backbone abolished fever response, and the chimeric virus did not show adaptation in rabbits as demonstrated by lack of viral RNA and E2 protein expression in the spleen and weak antibody responses. These results indicate that Erns has partial contribution to adaptation of the C-strain in rabbits, and combination of E2 and Erns is essential for the C-strain to have adaptive replication in rabbits.

The potential role of tubeimosides in cancer prevention and treatment.

Natural compounds are important sources of anticancer drugs. Rhizoma Bolbostemmatis (Chinese name "Tu Bei Mu") is the dry tuber of Bolbostemma paniculatum (Maxim.) Franquet (Cucurbitaceae). It has long been widely used for treating various ailments including cancer in traditional Chinese medicine. Its major pharmacologically active components are the triterpenoid saponins tubeimosides (TBMs) including tubeimoside (TBM) I, II and III. Extensive researches have provided evidences of the anticancer activities of TBMs in different stages of carcinogenesis both in vitro and in vivo model. TBMs could inhibit cell growth and proliferation, induce cell differentiation, apoptosis, autophagy and, inhibit inflammation, and suppress angiogenesis, invasion and metastasis via various signaling pathways. They are effective in combination therapies, particularly at targeting drug-resistant cancer cells. This mini-review aims to summarize and analyze the current knowledge on the pre-clinical studies of anti-tumor effects, the underlying molecular mechanisms and discuss the prospects of the application of TBMs in cancer prevention and treatment. The potential of TBMs as pertinent candidates could be appropriately developed and designed into an efficacious anticancer drug.

Diversified sources for human infections by Salmonella enterica serovar newport.

Salmonella enterica Newport (S. Newport), with phylogenetic diversity feature, contributes to significant public health concerns. Our previous study suggested that S. Newport from multiple animal-borne routes, with distinct antibiotic resistant pattern, might transmit to human. However, their genetic information was lacking. As a complement to the earlier finding, we investigate the relationship between each other among the hosts, sources, genotype and antibiotic resistance in S. Newport. We used the multilocus sequence typing (MLST) in conjunction with minimum inhibitory concentration of 16 antibiotics of globally sampled 1842 S. Newport strains, including 282 newly contributed Chinese strains, to evaluate this association. Our analysis reveals that sequence types (STs) are significantly associated with different host sources, including livestock (ST45), birds (ST5), contaminated water and soil (ST118), reptiles (ST46) and seafood (ST31). Importantly, ST45 contained most of (344/553) the multi-drug resistance (MDR) strains, which were believed to be responsible for human MDR bacterial infections. Chinese isolates were detected to form two unique lineages of avian (ST808 group) and freshwater animal (ST2364 group) origin. Taken together, genotyping information of S. Newport could serve to improve Salmonella source-originated diagnostics and guide better selection of antibiotic therapy against Salmonella infections.

Dual flow immunochromatographic assay for rapid and simultaneous quantitative detection of ochratoxin A and zearalenone in corn, wheat, and feed samples.

A one-step dual flow immunochromatographic assay (DICGA), based on a competitive format, was developed for simultaneous quantification of ochratoxin A (OTA) and zearalenone (ZEN) in corn, wheat, and feed samples. The limit of detection for OTA was 0.32 ng/ml with a detection range of 0.53‒12.16 ng/ml, while for ZEN it was 0.58 ng/ml with a detection range of 1.06‒39.72 ng/ml. The recovery rates in corn, wheat, and feed samples ranged from 77.3% to 106.3% with the coefficient of variation lower than 15%. Naturally contaminated corn, wheat, and feed samples were analyzed using both DICGA and liquid chromatography-tandem mass spectrometry (LC-MS/MS) and the correlation between the two methods was evaluated using a regression analysis. The DICGA method shows great potential for simple, rapid, sensitive, and cost-effective quantitative detection of OTA and ZEN in food safety control.

Antibody Microarray Immunoassay for Simultaneous Quantification of Multiple Mycotoxins in Corn Samples.

We developed and tested a prototype of an antibody microarray immunoassay for simultaneous quantitative detection of four typical mycotoxins (aflatoxin B1, ochratoxin A, zearalenone, and fumonisin B1) in corn samples. The test kit consisted of a nitrocellulose membrane layered with immobilized monoclonal antibodies against mycotoxins. During the assay, the mycotoxin-protein conjugates were biotinylated. The signal detection was enhanced by a combination of the biotin-streptavidin system and enhanced chemiluminescence (ECL). This improved the sensitivity of the assay. Under the optimized conditions, four calibration curves with goodness of fit (R² > 0.98) were plotted. The results showed that the detection limits for aflatoxin B1, ochratoxin A, zearalenone, and fumonisin B1 were 0.21, 0.19, 0.09, and 0.24 ng/mL, with detection ranges of 0.47⁻55.69, 0.48⁻127.11, 0.22⁻31.36, and 0.56⁻92.57 ng/mL, respectively. The limit of detection (LOD) of this antibody microarray for aflatoxin B1, ochratoxin A, zearalenone, and fumonisin B1 in corn was 5.25, 4.75, 2.25, and 6 µg/kg, respectively. The recovery rates from the spiked samples were between 79.2% and 113.4%, with coefficient of variation <10%. The results of the analysis of commercial samples for mycotoxins using this new assay and the liquid chromatography-tandem mass spectrometry (LC-MS/MS) were comparable and in good agreement. This assay could also be modified for the simultaneous detection of other multiple mycotoxins, as well as low-weight analytes, hazardous to human health.

Development of a Magnetic Nanoparticles-Based Screen-Printed Electrodes (MNPs-SPEs) Biosensor for the Quantification of Ochratoxin A in Cereal and Feed Samples.

A rapid and sensitive electrochemical biosensor based on magnetic nanoparticles and screen-printed electrodes (MNPs-SPEs sensor) was developed for the detection of ochratoxin A (OTA) in cereal and feed samples. Different types of magnetic nanoparticles-based ELISA (MNPs-ELISA) were optimized, and the signal detection, as well as sensitivity, was enhanced by the combined use of screen-printed electrodes (SPEs). Under the optimized conditions, the calibration curve of the MNPs-SPEs sensor was y = 0.3372x + 0.8324 (R² = 0.9805). The linear range of detection and the detection limit were 0.01⁻0.82 ng/mL and 0.007 ng/mL, respectively. In addition, 50% inhibition (IC50) was detectable at 0.10 ng/mL. The limit of detection (LOD) of this MNPs-SPEs sensor in cereal and feed samples was 0.28 µg/kg. The recovery rates in spiked samples were between 78.7% and 113.5%, and the relative standard deviations (RSDs) were 3.6⁻9.8%, with the coefficient of variation lower than 15%. Parallel analysis of commercial samples (corn, wheat, and feedstuff) showed a good correlation between MNPs-SPEs sensor and liquid chromatography tandem mass spectrometry (LC/MS-MS). This new method provides a rapid, highly sensitive, and less time-consuming method to determine levels of ochratoxin A in cereal and feedstuff samples.

Retracted: Antibiotic Resistance in Salmonella Enteritidis Isolates Recovered from Chicken, Chicken Breast, and Humans Through National Antimicrobial Resistance Monitoring System Between 1996 and 2014.

The online e-pub version of the article entitled, Antibiotic Resistance in Salmonella Enteritidis Isolates Recovered from Chicken, Chicken Breast, and Humans Through National Antimicrobial Resistance Monitoring System Between 1996 and 2014" by Paudyal N, Pan H, Li X. Fang W. Yue M., Foodborne Pathog Dis [Epub ahead of print]; DOI: 10.1089/fpd.2017.2402 is being officially retracted from Foodborne Pathogens and Disease (FPD) due to a significant number of errors in reporting and miscalculations of the National Antimicrobial Resistance Monitoring System (NARMS) datasets reported in the paper. Authors evaluated NARMS data, which are in the public domain, and analyzed a subset of NARMS data to address questions about a specific serotype of Salmonella in humans and chicken meat. Authors analyzed Salmonella Enteritidis isolates from humans, chicken and retail chicken meat, with their minimum inhibitory concentrations (MICs) to a range of commonly used antibiotics in the US collected over a period of 1996-2014 by NARMS, to segregate isolates based on their MIC value for a certain antimicrobial and evaluate their relationship along the foodborne transmission pathway. NARMS has data on more than 185,000 isolates that can be downloaded in an accessible format. To help make these large data sets more accessible, the NARMS teams continue to develop new tools to enable users to explore them according to their own interests. As a public health surveillance system, the goal is continuous improvement and open, transparent data sharing. The NARMS partners believe this is the best way to foster a collaborative effort to combat antibiotic resistance. After the online-ahead-of-print version of the paper, which used a subset of NARMS data, was published, a significant concern was brought to the attention of the Editor-in-Chief of FPD indicating that the article contained several significant errors which could potentially lead to a misunderstanding of the resistance situation in the United States. Of particular import is with regard to the authors of the paper reversing the poultry and human resistance data found in Figure 2, which displays the overall antimicrobial resistance data and is a central element of the article. The authors correctly state it in the text, but the figure is incorrect. Additionally, there appeared to be an accidental omission of a reference to a published article which shows a strong association between quinolone-resistant Salmonella Enteritidis infections in humans and international travel (O'Donnell et al., 2014) This appears to be a critical oversight given that the intention of the study was to analyze the NARMS data to help understand the dynamics of Salmonella transmission. The authors of the published article were notified of this communication by the Editor of FPD and were provided an opportunity to respond, which they quickly did. The corresponding author, Dr. Min Yue, agreed that after he and his team reanalyzed the data, there were indeed errors in the published paper and supplied revised versions of Figure 2 and supplemental Figure 3, as well as providing a significantly revised version of the manuscript, based upon the criticisms levied against the published paper. After giving the revised manuscript and figures very careful consideration, and after significant probing of his own, the Editor of FPD determined that the significantly revised manuscript, coupled with the multiple errors presented in the figures, is simply far too weighty for a correction statement to be issued, and determined a full retraction of the published article was warranted. It is important to note that there is no indication whatsoever that the errors or miscalculations were intentional, and that Dr. Yue and his team quickly and honestly replied to the concerns raised about their work. However, in the interest of upholding the proper protocols of peer review, and in accurate and truthful reporting in the scientific literature, the Editor of Foodborne Pathogens and Diseases is issuing this full and formal retraction of the article.

A Meta-Analysis of Major Foodborne Pathogens in Chinese Food Commodities Between 2006 and 2016.

Prevalence of pathogenic bacteria in food commodities in China have been reported in numerous publications over time. However, the results are scattered and varied. To calculate a robust point estimate with a higher statistical power, we applied meta-analytic approach for investigating the prevalence of common foodborne pathogens in major food items in China. Data, on prevalence of bacteria in various food commodities were extracted and analyzed from 361 (132 English and 229 Chinese) publications. Prevalence of eight most frequently reported pathogens on six broad food categories was used for pooled and subgroup meta-analysis by DerSimonian-Laird method in random-effects model. The estimated overall prevalence of pathogens in the foods was 8.5% (95% CI 8.2-8.7). The highest prevalence, irrespective of the pathogen type, was in the aquatic produce at 12.8% (12.0-13.5), while the least was in the vegetables at 3.0% (2.6-3.4). Among the pathogens, the most prevalent was Vibrio at 21.3% (19.6-23.1), whereas the least was pathogenic Escherichia coli at 4.3% (3.3-5.2). The major food pathogens in Chinese foods in decreasing order of prevalence were Vibrio parahaemolyticus, Campylobacter, Bacillus cereus, Staphylococcus aureus, Salmonella, Enterobacter, Listeria monocytogenes, and pathogenic E. coli. Presence of these organisms in foods equates the risk of microbiological food safety in China with other developed countries rather than the developing countries. This justifies the need of novel perspectives for formulating policies on microbiological food safety and risk mitigation.

Multiple Food-Animal-Borne Route in Transmission of Antibiotic-Resistant Salmonella Newport to Humans.

Characterization of transmission routes of Salmonella among various food-animal reservoirs and their antibiogram is crucial for appropriate intervention and medical treatment. Here, we analyzed 3728 Salmonella enterica serovar Newport (S. Newport) isolates collected from various food-animals, retail meats and humans in the United States between 1996 and 2015, based on their minimum inhibitory concentration (MIC) toward 27 antibiotics. Random Forest and Hierarchical Clustering statistic was used to group the isolates according to their MICs. Classification and Regression Tree (CART) analysis was used to identify the appropriate antibiotic and its cut-off value between human- and animal-population. Two distinct populations were revealed based on the MICs of individual strain by both methods, with the animal population having significantly higher MICs which correlates to antibiotic-resistance (AR) phenotype. Only ∼9.7% (267/2763) human isolates could be attributed to food-animal origins. Furthermore, the isolates of animal origin had less diverse antibiogram than human isolates (P < 0.001), suggesting multiple sources involved in human infections. CART identified trimethoprim-sulfamethoxazole to be the best classifier for differentiating the animal and human isolates. Additionally, two typical AR patterns, MDR-Amp and Tet-SDR dominant in bovine- or turkey-population, were identified, indicating that distinct food-animal sources could be involved in human infections. The AR analysis suggested fluoroquinolones (i.e., ciprofloxacin), but not extended-spectrum cephalosporins (i.e., ceftriaxone, cefoxitin), is the adaptive choice for empirical therapy. Antibiotic-resistant S. Newport from humans has multiple origins, with distinct food-animal-borne route contributing to a significant proportion of heterogeneous isolates.