Staphylococcus aureus and also for skin and soft tissue infection (SSTI). However, whether LA-S. aureus nasal carriage is associated with increased risk of SSTI remains unclear. We aimed to examine S. aureus nasal carriage and recent (≤3 months prior to enrollment) SSTI symptoms among industrial hog operation (IHO) workers and their household contacts. IHO workers and their household contacts provided a nasal swab and responded to a questionnaire assessing self-reported personal and occupational exposures and recent SSTI symptoms. Nasal swabs were analyzed for S. aureus, including methicillin-resistant S. aureus (MRSA), multidrug-resistant-S. aureus (MDRSA), absence of scn (livestock association), and spa type. S. aureus with at least one indicator of LA was observed among 19% of 103 IHO workers and 6% of 80 household members. Prevalence of recent SSTI was 6% among IHO workers and 11% among 54 minor household members (0/26 adult household members reported SSTI). Among IHO workers, nasal carriers of MDRSA and scn-negative S. aureus were 8.8  and 5.1  times as likely to report recent SSTI as non-carriers, respectively. In one household, both an IHO worker and child reported recent SSTI and carried the same S. aureus spa type (t4976) intranasally. Prevalence of scn-negative S. aureus  was elevated among IHO workers who reported never versus always wearing a face mask at work. Although few SSTI were reported, this study of IHO workers and their household contacts is the first to characterize a relation between nasal carriage of antibiotic-resistant LA-S. aureus and SSTI. The direction and temporality of this relation and IHO workers’ use of face masks to prevent nasal carriage of these bacteria warrant further investigation.Swine production work is a risk factor for nasal carriage of livestock-associated (LA-)  Staphylococcus aureus have emerged globally among food-producing animals, as well as among people who have contact with food-producing animals [S. aureus, which include methicillin-resistant (MRSA) and multidrug-resistant S. aureus (MDRSA) strains, are commonly referred to as livestock-associated (LA-) S. aureus. LA-S. aureus may spread from animals to humans through direct contact and through contact with animal dander, particles from decomposing waste [S. aureus has increased among individuals without livestock exposure in several European Union countries, suggesting that human-to-human transmission may now be occurring in the community, albeit at a lower rate than typical community-associated S. aureus CCs [Over the past decade, animal-adapted strains of antibiotic-resistant  animals . These Sng waste , and aerng waste . Clonal ng waste ,5 and thng waste ,7. Nasalreus CCs –10.S. aureus nasal carriage among individuals occupationally-exposed to livestock [-S. aureus nasal carriage is a risk factor for skin and soft tissue infection (SSTI). Nasal carriage of hospital and community-associated S. aureus, which occurs among 20–40% of the general United States population, is an established risk factor for infection in the clinical setting [S. aureus appear to differ from hospital and community-associated strains in that they typically lack genetic factors associated with human infection, including Panton-Valentine leukocidin- (PVL-) encoding genes, enterotoxin-producing genes, and human immune evasion complex  genes [S. aureus CCs [S. aureus infections present as SSTI, which are of concern to IHO workers who can experience lacerations, abrasions, and other skin injuries through their daily work activities [S. aureus nasal carriage and SSTI are difficult to investigate through studies in clinical settings because many livestock workers lack regular access to medical care [S. aureus is not typically conducted for clinical SSTI cases [S. aureus exposure and associated infections among livestock workers and their household and community contacts.Despite high prevalence of LA-ivestock  and incrivestock ,11, it r setting . Howevern) genes –15. Theireus CCs ,17. Mosttivities ,19. AssoTI cases ,22. To dTI cases ,23,24. ITI cases , could hS. aureus among industrial hog operation (IHO) workers and their household members in North Carolina and estimated associations with self-reported SSTI symptoms. Using data from the baseline enrollment visit of a four-month repeated-measures study of S. aureus nasal carriage, we examined: (a) baseline prevalence and distribution of S. aureus nasal carriage patterns; (b) associations between S. aureus nasal carriage patterns and reports of recent (in the three months prior to the baseline visit) SSTI symptoms; and (c) associations between S. aureus nasal carriage patterns and IHO work exposures.In the present study, we assessed nasal carriage of LA-Data were collected between October 2013 and February 2014 by community organizers from the Rural Empowerment Association for Community Help (REACH) with researchers from the Johns Hopkins Bloomberg School of Public Health (JHSPH) and the Gillings School of Global Public Health at the University of North Carolina at Chapel Hill (UNC). Community organizers recruited volunteer livestock workers who fit the following inclusion criteria: currently worked at an industrial hog operation (IHO), resided in North Carolina, could speak English or Spanish, and were at least 18 years of age. Only individuals employed in production of live pigs were considered IHO workers for the purposes of this study; individuals employed in other types of food animal production or meat processing  were not included in the study. Up to three individuals living in the same household as an IHO worker were eligible to participate if they were at least seven years old and spoke English or Spanish. Because enrolled participants were encouraged to refer IHO workers in their social networks to participate, it was not possible to determine the total number of IHO workers who learned about this study, or the percent who were not interested in contacting community organizers for further information about participating. Before participating, adults provided written informed consent. Written parental permission and informed assent were collected for participants seven to 17 years of age (hereafter referred to as “minors”). The JHSPH Institutional Review Board (IRB) approved this study (IRB00004608). The UNC Non-Biomedical IRB approved reliance on the JHSPH IRB.S. aureus, and symptoms of SSTI and doctor-diagnosed S. aureus infection during the three months prior to the enrollment session. Participants also provided a self-collected BBL CultureSwab  from both of their anterior nares, under supervision and using illustrated diagrams and verbal instruction. Nasal swabs were self-collected rather than collected by investigators based on prior experience in a repeated-measures S. aureus nasal carriage study in which participants demonstrated consistent and repeatable nasal swabbing technique [Each participant attended a baseline enrollment session at the REACH office or in a community meeting space . Each enrollment session lasted between 2–3 hours. Participants responded to a baseline questionnaire which assessed demographic information, household characteristics, work activities, risk factors for exposure to echnique . Self-coechnique ,26–28. PS. aureus were streaked on quadrants of a new CSA plate. If direct plating did not yield colonies with S. aureus morphology, swabs and remaining PBS were enriched overnight at 37°C in 10 mL Mueller-Hinton broth containing 6.5% NaCl. A loopful (~10 μL) of Mueller-Hinton broth was streaked onto both Baird Parker and CSA plates to increase sensitivity of detection [S. aureus on either media were then streaked on quadrants of a new CSA plate. In total, presumptive S. aureus colonies were isolated within two to four days of nasal swab collection. Presumptive colonies were archived at -80°C in brain heart infusion broth with 15% (w/v) glycerol.Baseline swabs were transported to UNC at 4°C within 12 hours of collection. A trip blank was included with each shipment to confirm lack of contamination during transport. Within three days of arrival, each swab was clipped into one ml of phosphate-buffered saline and vortexed for 60 seconds. One hundred μL of this eluate was plate spread on CHROMagar™ Staph aureus  (CSA) while the remaining eluate and swab were refrigerated at 4°C. After incubation at 37°C for 24 hours, at least two colonies with morphology characteristic of etection , and incet al. [spa, scn, mecA, and mecC genes [spa and mecC, while a clinical MRSA isolate was used as an extraction and PCR control for spa, scn, and mecA. Sterile water was used as a negative control. PCR products were visualized on 2% agarose gels stained with ethidium bromide. Colonies positive for spa, a S. aureus-specific gene, were classified as S. aureus. Singleplex PCR was used to evaluate the presence of pvl-encoding genes among all S. aureus isolates [A crude DNA extraction was performed on each isolate using a protocol adapted from Reischl et al. . MultiplcC genes . Strain isolates .spa typing using the Ridom StaphType software and the Ridom SpaServer (http://spa.ridom.de/index.shtml) [S. aureus CCs, including CC398 and CC9, are traditionally inferred through multi-locus sequence typing (MLST), which we did not perform. However, spa types associated with CC398 and CC9 have been described by other studies in which both MLST and spa typing were performed [spa type, the literature, and the Ridom SpaServer, as others have done [All isolates were characterized by x.shtml) . S. aureerformed ,34,35. Tave done ,36.S. aureus-positive nasal swab was assessed for susceptibility to a panel of antibiotics . Hereafter, we refer to this outcome as “recent SSTI.”We created the main infection outcome variable, “any symptoms of S. aureus nasal carriage between workers and household members. For analyses in which prevalence of S. aureus nasal carriage was evaluated as an outcome, results for adult and minor household members were combined for sample size considerations. We calculated the prevalence of nasal carriage of S. aureus, MRSA, and MDRSA among workers and their household members, including livestock-associated classifications of the above.We compared the distributions of potential individual  and household risk factors  for S. aureus nasal carriage outcomes, S. aureus nasal carriage outcomes and recent SSTI, and occupational exposures and S. aureus nasal carriage outcomes. We used generalized estimating equations with an exchangeable correlation matrix to account for the non-independence of observations within-household [We used log-binomial regression models to estimate crude prevalence ratios (PR) and 95% confidence intervals (CI) for associations between participant type (worker versus household member) and ousehold . IndividS. aureus were uncommon among IHO workers and adult household members . Among minors, recently playing contact sports (36%) and using a gym or workout facility (55%) were more common, but using antibiotics was uncommon (6%) , 26 adult household members (14%), and 54 minor children (30%) completed a baseline questionnaire and provided a baseline nasal swab . All butmon (6%) .In total, the 183 participants comprised 81 households . Most hoS. aureus at baseline and MRSA was observed in only one worker (S. aureus carried by IHO workers exhibited a larger diversity of antibiotic resistance patterns (10 distinct patterns observed) than S. aureus carried by their household members (five patterns observed) (Forty-five of 103 workers (44%) and 31 of 80 household members (39%) carried e worker . Twenty-e worker . S. aurebserved) .scn-negative S. aureus , tetracycline-resistant S. aureus , tetracycline-resistant MDRSA , and scn-negative, tetracycline-resistant S. aureus  among workers compared to household members (S. aureus CC9 was only observed among workers (9/103) but putative S. aureus CC398, including CC398 with additional indicators of livestock association, was observed among both workers and their household members ,  members . Putativ members . We did S. aureus infection. Six of 80 household members (8%) reported recent SSTI, and all of these household members were minors   reported recent SSTI . Three I54; 11%) . Three mS. aureus  and MDRSA  ; associations between recent SSTI and nasal carriage of S. aureus and tetracycline-resistant S. aureus were positive but not statistically significant   intranasnificant .S. aureus isolates recovered from the anterior nares of workers and minors who reported recent SSTI are described in S. aureus nasal carriage positive and carried the same S. aureus spa type (t4976), although the minor’s isolate was tetracycline-susceptible , and tetracycline-resistant S. aureus  was observed among workers who reported never wearing a face mask versus those who reported always wearing a face mask at work  . Almost  at work . Examina at work .S. aureus was associated with recent symptoms of SSTI. Among IHO workers specifically, we observed positive associations between nasal carriage of each S. aureus-related outcome we examined  and recent SSTI. Only associations with MDRSA and scn-negative S. aureus were statistically significant; however, the direction and similar magnitude of these associations indicates that nasal carriage may be associated with SSTI outcomes in this study population. Overall, the twelve participants who reported recent SSTI included two IHO worker-minor pairs; one of these worker-minor pairs reported that a doctor had confirmed their SSTI symptoms as a S. aureus infection. This is one of the first reports in the United States of an association between nasal carriage of livestock-associated S. aureus and SSTI among individuals with frequent and intensive exposure to industrial hog production, as well as of SSTI prevalence among their minor child household members. This finding warrants further investigation to assess the directionality of the relation between S. aureus nasal carriage and SSTI in this population.In this study population of IHO workers and their household contacts, we found that nasal carriage of et al. observed an incidence of 6.6 cases/1,000 person-months [et al. in several ways. First, Wardyn et al. only examined farm owners and operators, for whom exposure to animals and the confinement barn environment may be less intensive than for hired laborers whose job tasks primarily involve direct contact with livestock. Second, participants in Wardyn et al.’s study were primarily Caucasian (98.9%), while participants in this study were primarily Hispanic (89%). Hispanic livestock production workers are believed to significantly underreport occupational injuries compared to Caucasian workers [et al. ascertained S. aureus infections using prospectively-collected skin swabs, while we only assessed SSTI through participants’ recall of recent symptoms. Participants’ recall of SSTI symptoms may have included infections prior to the three months before enrollment, skin afflictions that were not related to a bacterial infection, and/or SSTIs with a bacterial etiology other than S. aureus. In order to minimize the possibility of reporting errors, we showed participants pictures of S. aureus SSTI  prior to asking them to report SSTI symptoms. In our study, any potential misclassification due to recall was non-differential with respect to S. aureus nasal carriage status since participants were blinded to their lab result at enrollment. However, whether recent SSTI preceded or was a consequence of participants’ S. aureus nasal carriage could not be investigated with our study design. Fourth, Wardyn et al. did not describe S. aureus nasal carriage status among individuals who reported SSTI. Thus, any association between antecedent S. aureus nasal carriage and SSTI in their study population is not known. The results presented here provide some of the first insights into the association between nasal carriage of S. aureus with multiple indicators of livestock association and prevalence of SSTI among IHO workers and their household contacts in the United States.Few studies have surveyed SSTI among individuals employed in livestock production. In this cross-sectional analysis, we observed a SSTI prevalence of 6.6% (12/183). A retrospective analysis of reported injuries among pork meatpacking and poultry processing workers from 2004–2009 determined average annual SSTI prevalence to be 33% and 12%, respectively . A crossn-months . The pre workers . Third, S. aureus present in participants' nares were the same strains responsible for recent SSTI. However, we observed associations between nasal carriage of S. aureus, MDRSA, and S. aureus with indicators of livestock association (absence of scn) and self-reported SSTI. Additionally, risk factors for community-associated and healthcare-associated antibiotic-resistant S. aureus infection  were uncommon among IHO workers and their household members. Some risk factors were more common among minors .Because we asked participants about SSTI during the three months prior to and including the enrollment session, we were unable to assess whether the S. aureus spa types observed among workers and household members. Fifty-nine of the 81 households enrolled in this study contained more than one study participant. Ten of these households contained at least two individuals who shared the same S. aureus spa type at baseline . One worker-household member pair shared a tetracycline-resistant spa type (t701) and one worker-worker pair shared a S. aureus spa type associated with CC9 (t337), which was also scn-negative. One worker-household member pair shared the same spa type (t4976), but only the worker carried S. aureus with an indicator of livestock association (tetracycline resistance).baseline . Seven oS. aureus spa type, we observed little evidence of household transmission of livestock-associated S. aureus. Other studies have detected S. aureus CC398 transmission between occupationally-exposed individuals (i.e. livestock veterinarians) and their household members [S. aureus in this study population because it does not occur, or because of limitations in our study design. First, we examined transmission events in the context of a cross-sectional analysis. Since transmission events may be infrequent [S. aureus isolate per nasal swab for spa type and indicators of livestock association. Since a portion (~7%) of S. aureus-colonized individuals carries multiple strain types simultaneously [spa types between household members. However, recent whole genome sequencing studies have demonstrated that shared spa types may not indicate true transmission events; both false positives and false negatives are possible [Although ten of 59 households contained participants who shared the same  members . We may frequent , a longianeously , it is ppossible ,47.S. aureus-related carriage outcomes. First, because we directly plated nasal swabs, our sensitivity to detect MRSA may have been lower than if we used an antibiotic-supplemented enrichment broth [S. aureus-colonized individuals carry multiple S. aureus strains simultaneously[S. aureus-related outcomes in this population. Third, we only assessed S. aureus nasal carriage to maximize participant acceptability. However, S. aureus colonization has been documented at additional body sites [S. aureus carriage by not swabbing other body sites. However, it is likely that such underestimation would have been non-differential with respect to the outcome , which could have had an attenuating influence on our PR (95% CI) estimates. Other common S. aureus body colonization sites of IHO workers  are more likely to be protected in the IHO environment than the anterior nares. Thus, the possibility that we greatly underestimated S. aureus body carriage is likely to be low. Fourth, IHO workers and their household members volunteered to participate in this study; participants were not randomly selected from an enumerated population (e.g. employee roster/records). Thus, it is unclear how generalizable our findings are to all livestock workers in North Carolina or the United States. Nevertheless, the potential for exposure to and infection with antibiotic-resistant S. aureus among the estimated 292,000 livestock workers employed in the United States in 2012 [There were several limitations to our assessment of nt broth . Howevernt broth , in whictaneously, as mentdy sites . It is p in 2012 –52 meritS. aureus and SSTI. In this study population, we observed that nasal carriage of S. aureus, including MDRSA, and scn-negative S. aureus, was more common among individuals who reported recent symptoms of SSTI. This association is in accordance with previously observed associations between S. aureus nasal carriage and infection in clinical settings [S. aureus  and SSTI. Because few cases of SSTI were reported, future studies should examine this association in a larger cohort and over time to assess its repeatability and directionality. Overall, this study adds to the growing body of evidence suggesting that individuals exposed to livestock-associated, antibiotic-resistant S. aureus, MRSA, and MDRSA via hog production work in the United States could be at risk for SSTI.Additional research is needed to establish the direction and temporality of the association between nasal carriage of livestock-associated, antibiotic-resistant settings , and proS1 Appendix(XLSX)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.S4 Table(DOCX)Click here for additional data file.S5 Table(DOCX)Click here for additional data file.S6 Table(DOCX)Click here for additional data file.


Yersinia enterocolitica is the causative agent of yersiniosis, a zoonotic disease of growing epidemiological importance with significant consequences for public health. This pathogenic species has been intensively studied for many years. Six biotypes  and more than 70 serotypes of Y. enterocolitica have been identified to date. The biotypes of Y. enterocolitica are divided according to their pathogenic properties: the non-pathogenic biotype 1A, weakly pathogenic biotypes 2–5, and the highly pathogenic biotype 1B. Due to the complex pathogenesis of yersiniosis, further research is needed to expand our knowledge of the molecular mechanisms involved in the infection process and the clinical course of the disease. Many factors, both plasmid and chromosomal, significantly influence these processes. The aim of this study was to present the most important virulence markers of Y. enterocolitica and their role during infection. Yersinia belonging to the Enterobacteriaceae family consists of 18 species, of which only three, Yersinia pestis, Yersinia enterocolitica, and Yersinia pseudotuberculosis, are pathogenic for humans and animals [Y. enterocolitica is one of the most important foodborne zoonotic diseases in Europe [Y. enterocolitica have been identified to date [Y. enterocolitica are divided regarding their pathogenic properties: the non-pathogenic biotype 1A, weakly pathogenic biotypes 2–5, and the highly pathogenic biotype 1B [Y enterocolitica infections are influenced by several structures, both plasmid and chromosomal, referred to as virulence markers or virulence determinants [The genus n Europe . This pa to date . The biootype 1B . Y enterYersinia virulence (pYV) with a size of 64–75 kb is the most known and important virulence marker of Y. enterocolitica [Y. enterocolitica strains harboring pYV also carry the chromosomal high pathogenicity island (HPI) associated with the iron acquisition system (yersiniabactin) which facilitates the uptake and utilization of iron by Y. enterocolitica, and promotes their growth under iron-limiting conditions [Y. enterocolitica are located within the pYV, such as yadA encoding the Yersinia adhesin (YadA), or the yop virulon encoding Yersinia outer membrane proteins (Yops) [Y. enterocolitica strains based on plasmid markers alone can produce false negative results, due to a spontaneous loss of pYV by bacteria caused by, for example, prolonged strain storage, frequent passaging or temperatures higher than 37 °C [ail, invA, myfA, and yst genes, which encode the production of Ail (attachment-invasion locus) protein, primary internalization factor invasin InvA, mucoid Yersiniae factor MyfA and Yst (Yersinia-stable toxin) enterotoxin, respectively, is more justified from the diagnostic point of view [The plasmid of colitica ,6. All bnditions . Severalan 37 °C . The sea of view . invA) are expressed below 30 °C, whereas plasmid-encoded virulence genes  are expressed at 37 °C [virF, encoding the transcriptional activator of the Yersinia virulence regulon. VirF, a DNA-binding protein of 30 kDa, belonging to the AraC family, is produced only at 37 °C, although other factors are also required to initiate the transcription of VirF target genes [yop and yadA genes [Yersinia modulator, YmoA, negatively regulates the transcription of virF and invA [invA expression [rovA; therefore, it acts as a global coordinator of surface virulence markers in Y. enterocolitica, which suggests that it can be an excellent target for new antimicrobial strategies [Physicochemical parameters, such as temperature, the concentration of calcium and iron ions, pH, and osmolarity also play a role during infection ,10,11,12et genes . VirF isdA genes . The Yerand invA ,16. Invapression . Chaperorategies . The mecY. enterocolitica and their role during infection.The aim of this study was to present the most important virulence markers of per os with contaminated water or food [Y. enterocolitica usually colonize palatine tonsils, where they multiply and reach further segments of the gastrointestinal tract. Before the pathogen can come into contact with enteric epithelial cells, bacteria have to penetrate the layer of gastrointestinal mucus which is secreted by goblet cells. Gastrointestinal mucus contains mucins which are responsible for its gel-like properties [Y. enterocolitica biotypes may adhere to human and rabbit mucin to a greater extent than 1A biotype strains which that do not possess pYV. Lipopolysaccharide (LPS) is encoded chromosomally, it is an integral component of the external cell membrane which forms complex structures with proteins and phospholipids, protects bacterial cells against bile, and complements system components [Y. enterocolitica cells, including cells that enter the intestinal lumen, contain smooth type (S) LPS that varies substantially in the chemical content of the polysaccharide fraction . At 37 °C, LPS is transformed to smooth-rough type (S-R) LPS, which contains less core fraction and O-specific polysaccharide [Bacteria most often enter the body  or food . In pigsoperties . Mantle operties  demonstrmponents . Free-liccharide ,22. LPS Y. enterocolitica infection [Y. enterocolitica penetrates microfold cells (M cells) and, subsequently, induces the destruction of Peyer’s patches. Autenrieth et al. [Y. enterocolitica infection, adjacent villi were dilated from lymphangiectasis, and transmigrating polymorphonuclear leucocytes were found within the epithelium. Interestingly, a pathogenic Y enterocolitica serotype 0:8 colonizes ileal Peyer’s patches about 1000 times more densely than surrounding epithelium of a comparable surface area [Y. enterocolitica are abdominal lymph nodes, where the microorganism multiplies and causes inflammatory changes and ulcerations, and from where it can invade internal organs [Follicle-associated epithelium (FAE) is the primary site of host–pathogen interactions in nfection . Y. enteh et al.  showed tace area . The FAEace area . The tarl organs . Escherichia coli, which could suggest that MyfA promotes the adhesion to enterocytes [Y. pestis [myfA gene encoding a fibrillar subunit of MyfA was found in Y. enterocolitica strains of bioserotype 4/O:3 isolated from clinical cases of yersiniosis [Y. enterocolitica biotype 1A strains isolated from patients with diarrhea [One of the most intriguing factors, MyfA, plays an important role at the beginning of infection . MyfA clerocytes . MyfA is. pestis . The myfsiniosis . It was diarrhea . Accordidiarrhea , Myf fibyadA, invA, and ail, are mainly involved in the processes of adhesion and invasion [yadA, located extrachromosomally on pYV. YadA is a member of the trimeric autotransporter adhesin (TAA) family, and it forms fibrous, lollipop-like structures on the cell surface that mediate binding to human epithelial cells (HEp-2), as well as microvilli that constitute the intestinal brush border [Y. enterocolitica infections, such as reactive arthritis [Yersinia in three-dimensional collagen gels [The proteins encoded by three genes, invasion . YadA (ph border . YadA birthritis . YadA sugen gels . Leo et gen gels  examinedgen gels . Y. enterocolitica strains with serum glycoprotein vitronectin (Vn), which acts as an inhibitory regulator of the terminal complement complex. According to these authors, YadA-mediated Vn binding is caused by the “uptake region” of the protein’s N-terminus, and it promotes the adhesion of selected Y. enterocolitica strains. This “uptake region”, similar to the “uptake region” of Y. pseudotuberculosis YadA, was defined as a crucial for the high-affinity binding of Vn [YadA also elicits an inflammatory response in epithelial cells by inducing the production of interleukin-8 (IL-8), which is mediated by mitogen-activated protein kinase (MAPK), and by contributing to the intestinal inflammatory cascade . Additiong of Vn . It is wYersinia. They observed that hfq mutants exhibited decreased translocation of proteins into host cells by the type III secretion system (T3SS), consistent with decreased YadA production [yadA promoter region, which suggests that expression is inhibited by a direct mechanism. They identified yadA as a new member of the OmpR regulon, and postulated that OmpR negatively regulates yadA, and that the downregulation of YadA could increase the survival of Y. enterocolitica by preventing bacterial binding to host cells, which promotes further spread to deeper tissues. To summarize, YadA seems to be the most important single contributor to the virulence of Y. enterocolitica, in particular, because it acts not only as an adhesin, but also as an invasin to facilitate the penetration of host cells [Y. enterocolitica to evade complement-mediated clearance in the human host. Kinetic killing tests, which were conducted by Biedzka-Sarek et al. [The production of YadA is promoted by the RNA chaperone Hfq, a widely conserved protein that stabilizes sRNAs, facilitates sRNA–mRNA pairing, and modulates the degradation of target RNAs . Accordioduction . They asoduction  demonstrst cells . YadA alst cells  showed tk et al. , revealeY. enterocolitica infection, InvA is required for effective bacteria translocation into M cells and Peyer’s patches colonization [invA chromosomal gene [Y. enterocolitica to epithelial cells. The above is known as the “zipper” invasion mechanism, and internalization allows the delivery of Yops to host cells [Some studies showed that in an early phase of nization . The 987mal gene . The β-bmal gene . InvA bist cells .Y. enterocolitica begins with a direct interaction between InvA and any of the five types of β1 integrins  on the surface of target epithelial cells [1 integrins on host cells [1 integrins rapidly induces IL-18 mRNA expression, which could suggest that integrins provide the first signal for inflammasome activation [Yersinia InvA leads to the recruitment of phagocytes and tissue disruption. Wiedemann et al. [1 integrins, InvA induces phagocytosis of nonopsonized Y. enterocolitica by activating actin polymerization. Y. enterocolitica resists macrophage killing, becomes sequestered inside these cells, and the invasin-triggered recruitment of macrophages creates replicative niches for Y. enterocolitica and enables the pathogen to avoid exposure to the host’s immune system [The penetration of M cells by al cells . InvA bist cells . Accordist cells , the invtivation . After btivation . Accorditivation , the infn et al.  demonstre system . Accordie system , InvA alY. enterocolitica is dependent on the growth phase and, according to recent research, on serotype. Uliczka et al. [invA promoter region in Y. enterocolitica serotype O:3. However, Pepe et al. [invA expression. invA is expressed maximally at 26 °C and neutral pH, and is only poorly expressed at 37 °C and neutral pH; however, a decrease in pH increases invA expression at 37 °C. The expression of InvA in response to environmental signals is regulated by several proteins, and genetic studies have revealed the complex nature of this regulatory process [InvA expression is regulated mostly by RovA. Single substitution of amino acid P98S increases the thermostability of RovA, leading to higher expression of InvA in serotype O:3 [invA expression regardless of the presence of histone-like nucleoid structuring (H-NS) protein, however, in general, the thermoregulation of invA gene transcription in Y. enterocolitica is controlled by three regulatory proteins: RovA, H-NS, and YmoA [yaxA and yaxB genes [InvA synthesis in a et al.  observede et al.  demonstr process . InvA extype O:3 . Admittetype O:3  demonstrand YmoA . RovA alxB genes . Wagner xB genes  found thxB genes .Y. enterocolitica. During the logarithmic phase of growth, Ail is synthesized at 30 °C; although in the stationary phase, the ail gene is only expressed at 37 °C [Y. enterocolitica [Y. enterocolitica by binding C4bp, a complement component, which inactivates C3 convertase and destabilizes the formation of active attack complexes on the bacterial membrane [ail mutant of Y. enterocolitica and the expression of the ail gene in E. coli, and observed that Ail increased serum resistance 100-fold. O-group LPS side chains sugars could mask the Ail receptor-binding regions, thereby weakening its serum resisting properties, but the loss of O-group sugars at 37 °C exposes Ail [Ail protein is yet another virulence marker which plays an important role during attachment and invasion processes. Due to its small size 17 kDa), Ail protein is easily masked by other surface structures, like the LPS, decreasing its biological efficiency . Ail hasat 37 °C . Ail medcolitica . Ail in colitica ,55. Ail colitica . It confmembrane  examinedoses Ail . Becauseoses Ail . In cont kDa, Ailail gene is an important virulence marker which is widely used as a target in molecular analyses of the pathogenicity of Y. enterocolitica strains [invA sequence, sequences homologous to the ail gene have been identified only in Y. enterocolitica strains that are epidemiologically associated with clinical yersiniosis in humans, however, they are now more often detected in the 1A biotype [ail gene of a biotype 1A Y. enterocolitica strain  differed from a biotype 1B Y. enterocolitica strain  in only one point mutation—transition G2008088T. This finding suggests that the pathogenicity of Y. enterocolitica cannot be reliably determined based on ail detection in simple PCR. Bancerz-Kisiel et al. [ail single nucleotide polymorphisms (SNPs) correlated with the biotypes of the tested Y. enterocolitica strains. According to these authors, the HRMA supported reliable discrimination of three genotypes and phylogenetic groups: 1A—non-pathogenic Y. enterocolitica strains, 1B—highly pathogenic Y. enterocolitica strains, and 2/4—weakly pathogenic Y. enterocolitica strains [ail-positive Y. enterocolitica strains.The  strains ,59,60. I biotype ,62,63,64Y. enterocolitica strains have developed resistance mechanisms, mainly with the involvement of effector Yops encoded by the yop virulon. The yop virulon has four components: a type III secretion system, T3SS, known as Ysc-Yops, translocator Yops , control element YopN, and effector Yops  [1 integrins [Antigen transcytosis across the FAE of Peyer’s patches by M cells is significant for invasion and induction of effective immune responses to mucosal antigens . BacteriP, YopT) . SelecteP, YopT) . The trantegrins .Y. enterocolitica strains lacking YopD are unable to induce cytotoxicity in macrophages. These properties were not inherent to YopD, but indirectly related to its role in the secretion of YopE and YopH into host cells [Yersinia: it enters the nucleus of host cells, but the mechanisms governing its nucleocytoplasmic shuttling and its intranuclear activities have not been explained to date [The T3SS transports Yops to the cytoplasm of host cells through a syringe-like system, formed mainly by YscF and translocator Yops ,68. YopBst cells . YopN, ast cells . Effectost cells . YopE hast cells . YopH prst cells . YopO inst cells , and Yopst cells . YopM is to date . YopP ha to date .Y. enterocolitica. Although leukocytes are the target of Yops injected by Y. enterocolitica, it remains unknown which adhesins and leukocyte receptors are required for Yops injection. Deuschle et al. [1 integrins in Yops injection into leukocytes. Based on the results of a β-lactamase reporter assay, they found that the adhesion of Y. enterocolitica through InvA or YadA is sufficient to promote Yops injection into leukocytes. Serum factors inhibit YadA-mediated, but not InvA-mediated Yops injection into B and T cells, and YadA-mediated Yops injection is shifted towards neutrophils and other myeloid cells [Y. enterocolitica virulence and Yops injection into leukocytes, whereas InvA is not required for virulence, and plays only a temporary and minor role in the injection of Yops in the early phase of infection [1 integrins are not required for YadA-mediated Yops injection into leukocytes, but they contribute to InvA-mediated Yops injection. Keller et al. [1 integrins, YadA mediates Yops injection by interacting with αV integrins, and unidentified cofactors expressed by epithelial cells, but not fibroblasts. They revealed that by indirectly binding to a broad range of ECM host cell receptors in different cell types, YadA is a versatile tool for Yops injection [The injection of Yops into host cells by T3SS is an important immune evasion mechanism of e et al.  investigid cells . The abonfection . Deuschlnfection  demonstrr et al.  reportednjection .Y. enterocolitica virulence. Yst is a polypeptide chain composed of a 30 amino acid C-terminal domain as the mature component of the toxin and an 18 amino acid N-terminal signal sequence that is cut off during transport through the cytoplasmic membrane [Y. enterocolitica strains of biotypes 1B and 2–5 produce the YstIA heat-stable enterotoxin [Y. enterocolitica [E. coli [Enterotoxin Yst is one of the significant factors determining membrane . Three tmembrane . Y. enteerotoxin ,81. Resecolitica ,83. Biotcolitica . YstII, colitica . YstIC c[E. coli .Y. enterocolitica strains isolated from humans with yersiniosis were capable of producing YstI, which implies that YstI plays a significant role in the etiology of diarrhea in yersiniosis. Researchers opposing the theory that YstI is the key determinant of diarrhea have pointed out that YstI is not produced at temperatures higher than 30 °C. However, Singh et al. [E. coli, which are manifested by the activation of guanylate cyclase, an increase in cyclic guanosine monophosphate (cGMP) levels in epithelial cells, and the accumulation of fluids in the intestinal lumen, which leads to diarrhea [yst-positive strains produce enterotoxins, which could imply the presence of “silent genes”. This can probably be attributed to the presence of the ymoA gene, which encodes the production of YmoA protein (8.1 kDa). The YmoA protein belongs to the growing family of Hha proteins, referred to as YmoA in Y. enterocolitica, and it is similar to the N-terminal, dimerized domains of H-NS proteins [ymoA inhibits the expression of the invA gene, and participates in VirF regulation [Pathogenic h et al.  demonstrdiarrhea ,86. Inteproteins ,88. In iproteins ,92,93,94gulation  and tempgulation .ymoA gene mutations on YstIA production was first postulated by Cornelis et al. [ymoA gene. Cornelis et al. [ymoA mutations unblock the silencing of the yst gene and stimulate YstI production. Mikulskis et al. [yst expression to a silent state, and other authors showed that yst gene presence is not always correlated with YstI production [ymoA gene fragments. Two point mutations in the non-coding region have been identified in some of the tested Y. enterocolitica strains, regardless of their enterotoxic properties [ymoA gene mutations influence ystA gene silencing was not confirmed.The possible effect of s et al. . They ids et al.  postulats et al.  also posoduction ,95. In toduction , no mutaoperties . Hence, Y. enterocolitica strains belonging to biotype 1A are commonly regarded as non-pathogenic; they are highly heterogeneous and include many O serogroups [Y. enterocolitica strains belonging to biotype 1A are regarded as avirulent and devoid of pYV, various forms of fimbriae have been observed in this biotype [Y. enterocolitica strains are much more resistant to macrophage killing and more likely to escape from host cells than nonclinical strains suggest that these properties may be responsible for virulence [ystB gene that encodes the production of homologous and biologically active enterotoxin YstIB. Rammamurthy et al. [Y. enterocolitica strains belonging to biotype 1A caused the accumulation of fluids in the intestines of suckling mice, which points to the toxigenic potential of the tested strains. Additionally, the minimum effective dose (MED) of purified YstIB enterotoxin (0.4 pmol) is much lower than an analogous dose of YstIA enterotoxin (7.6 pmol), which confirms its pathogenic potential [Y. enterocolitica strains belonged to biotype 1A [rogroups . Biotype biotype . Biotype biotype . They pe biotype . This su biotype . The pat biotype ,98. The irulence ,98. Althy et al.  showed totential . Accordiotential , biotypeotype 1A .The above suggests that pathogenicity cannot be reliably determined based on bioserotype classification alone.Yersinia enterocolitica are summarized in Major virulence markers of Yersinia enterocolitica is the causative agent of yersiniosis, a zoonotic disease of growing epidemiological importance with significant consequences for public health. Due to its complex pathogenesis, further research is needed to expand our knowledge of the molecular mechanisms involved in the infection process and the clinical course of the disease. Many factors, both plasmid and chromosomal, significantly influence these processes.


Giardia intestinalis is one of the most important zoonotic enteric parasites. As no information regarding prevalence and genotype of G. intestinalis in donkeys (Equus asinus) in China is available, 181 faecal samples from 48 donkeys from Jilin Province, from 104 from Shandong Province and from 29 from Liaoning Province were examined between May and December 2015.G. intestinalis-positive by nested amplification of the triosephosphate isomerase (tpi) gene. The prevalence in different regional groups varied from 10.42 to 18.27%. The prevalence in adult and young donkeys was 14.29 and 22.92%, respectively. Otherwise, the prevalence was 11.69% in summer and 18.27% in winter. However, no statistically significant differences were found in relation to region or age group. Sequence analysis of the tpi, glutamate dehydrogenase (gdh) and beta giardin (bg) loci identified 4, 1 and 3 subtypes of assemblage B, respectively. Moreover, four novel multilocus genotypes (MLGs novel-1 to novel-4) were identified in assemblage B.Twenty-eight (15.47%) out of 181 donkey samples were tested G. intestinalis in donkeys in China indicates that further studies of nation-wide molecular epidemiology and geographical distribution of Giardia in donkeys are warranted. Effective strategies should be implemented to control G. intestinalis infection in donkeys, other animals and humans.This first report of The online version of this article (doi:10.1186/s13071-016-1936-0) contains supplementary material, which is available to authorized users. Giardia intestinalis is the only species of Giardia which is found in human beings [G. intestinalis [Giardia cysts in contaminated food or water [8 cases of human giardiasis are reported world-wide per year, and the majority of them are reported in developing countries [G. intestinalis infections have been reported in humans and a variety of animal species [Equus asinus).n beings –4. It isn beings , 6. Eighstinalis . Of thesstinalis , but assstinalis . Diarrhestinalis  and tranor water ; approxi species –16, therGiardia intestinalis infection in horses has been reported in many countries around the world including China [Equus. It is an important edible animal species and used in Chinese traditional medicine, and is closely related to horses. Because they are maintained in a close association with their owners and veterinary personnel, donkeys are the important reservoirs for transmission of pathogens (such as Cryptosporidium hominis and Toxoplasma gondii) to humans and other animals [G. intestinalis, we conducted a study on the prevalence and genotypes of G. intestinalis in donkeys in Jilin, Liaoning and Shandong Provinces, China.ng China –21. The  animals , 23. To A total of 181 donkey faecal samples  were collected from three provinces, in northeastern and eastern China, between March and December 2015. Each of the fresh faecal samples was collected into sterile gloves separately after its defecation onto the ground, placed into box with ice and transported to the laboratory immediately. Genomic DNA was extracted directly from each faecal sample using the Stool DNA kit  according to the manufacturer’s instructions. Genomic DNA was stored at -20 °C until PCR amplification.G. intestinalis were determined by the nested PCR amplification of the triosephosphate isomerase (tpi) gene, beta giardin (bg) gene and glutamate dehydrogenase (gdh) genes as described by Zhao et al. [The prevalence and genotypes of o et al. . The pritpi, gdh and bg gene sequences of G. intestinalis available in GenBank using the BLAST (http://www.ncbi.nlm.nih.gov/BLAST/) and computer program Clustal X 1.83.Positive secondary PCR products were sequenced by Genscript Company . Bidirectional sequencing was used to confirm the accuracy of the sequences. Sequences with mutations were considered as novel genotypes when confirmed from independent two PCR reactions on the same sample. To identify the assemblages and subtypes, nucleotide sequences were aligned with known reference G. intestinalis-infected donkeys and different variables including age, geographic origin and seasons were analyzed by Chi-square test using SPSS version 17.0  [P < 0.05. Odds ratios (ORs) and their 95% confidence intervals (CI) are also given.The relationship between prevalence of IL, USA) . The resG. intestinalis     out of 181 donkey samples were PCR-positive for G. intestinalis infection in donkeys was 15.47% , which was higher than that in horses in Xinjiang (1.5%) [G. intestinalis is more likely to be affected by climate (temperature and relative humidity) [G. intestinalis prevalence in different regions may be due to different local climatic conditions, as well as the detection methods, sampling time and sample sizes. Moreover, probably because of the smaller sample sizes, seasonal and age-related correlates previously found in cattle [The overall prevalence of g (1.5%) , Brazil g (1.5%) , foals ig (1.5%) . Previouumidity) , 27, so n cattle  and horsG. intestinalis in cattle [Budorcas taxicolor bedfordi) [Chinchilla lanigera) [G. intestinalis may be commonly occurring in China, and we should pay enough attention to. More importantly, assemblage B was also identified in raw urban wastewater in northern China [Assemblages A and B, responsible for the vast majority of human giardiasis , 28, andn cattle , have aln cattle . Howevern cattle , 28. In n cattle , horses n cattle , cattle n cattle , golden edfordi) , pet chianigera) , captiveanigera) , sheep [anigera)  and goatanigera) , suggestrn China . TherefoG. intestinalis genotypes have been recorded from a wide range of hosts worldwide [G. intestinalis infection [tpi, gdh and bg loci) has been developed and widely used for detection of G. intestinalis infection [G. intestinalis-positive samples were also genotyped based on bg and gdh loci. A total of 28 tpi, 22 bg and 16 gdh gene sequences were obtained, and analysis of these genes revealed only one assemblage (B); however, high genetic polymorphism was observed at these loci within this assemblage  was the most prevalent MLG, and responsible for 50% of all MLGs in the present study. These findings suggest a high genetic diversity of this prevalent genotype in donkeys in China, in agreement with previous conclusions that G. intestinalis isolates of the same assemblage may be grouped into distinct MLGs [Furthermore, 10 out of 28 positive isolates were successfully amplified at all three loci. These samples provided four novel MLGs in the assemblage B, namely MLGs novel-1 to novel-4 Table , Fig. 1.nct MLGs , 24.TablG. intestinalis infection in donkeys in China. Sequences analysis suggested that all the G. intestinalis isolates represented assemblage B, with four, one and three subtypes of assemblage B at the tpi gdh and bg loci, respectively. Moreover, four novel MLGs (MLGs novel-1 to novel-4) were identified within assemblage B. The results of the present study not only improve the information of the distribution of G. intestinalis genotypes in China, but also provide the foundation data for preventing and controlling G. intestinalis infection in donkeys, other animals and humans.The present study demonstrated the occurrence of


Arabidopsis thaliana.Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism http://www.biw.kuleuven.be/CSB/ARA-PEPs), a repository of putative peptides encoded by sORFs in the A. thaliana genome starting from in-house Tiling arrays, RNA-seq data and other publicly available datasets. ARA-PEPs currently lists 13,748 sORF-encoded peptides with transcriptional evidence. In addition to existing data, we have identified 100 novel transcriptionally active regions (TARs) that might encode 341 novel stress-induced peptides (SIPs). To aid in identification of bioactivity, we add functional annotation and sequence conservation to predicted peptides.To aid the functional annotation of these peptides, we have developed ARA-PEPs  contains supplementary material, which is available to authorized users. Arabidopsis thaliana is far from complete. To aid in annotation of peptide-encoding genes and deciphering their functions, dedicated resources to browse and access sORF-encoded peptides in A. thaliana would be very valuable. Several efforts have gone in this direction including Araport, a comprehensive information portal for plant biology research harbouring A. thaliana-related annotations and gene information [A. thaliana for annotated coding genes, ncRNA genes and sORFs [A. thaliana is currently lacking. Therefore, we have developed a webserver named ARA-PEPs to provide the research community with up-to-date information on putative peptides in A. thaliana, collected from publicly available datasets and predicted based on novel expression data.Recent advances in transcriptomics and proteomics have revealed a more complex transcriptome and proteome than formerly understood. In the past few years it has become increasingly clear that the short open reading frames (sORFs) embedded in intergenic regions, pseudogenes or non-coding RNAs (ncRNAs) can be directly translated into bioactive peptides . These pormation , the Araormation , and Hannd sORFs , 8. Howede novo transcriptome reconstruction methods such as Trinity or constructed based on RNA-seq alignments using TopHat-Cufflinks [A. thaliana. The relationship between TARs, SIPs and other annotated sORFs listed in ARA-PEPs database is illustrated in Fig. http://www.biw.kuleuven.be/CSB/ARA-PEPs. The interface is easy to use and allows the user to query peptides by name, peptide sequence, Tiling array expression level and chromosomal regions including chromosome number and position, presence of certain features such as signal sequences, transmembrane (TM) domains and the rates of synonymous (dS) and nonsynonymous (dN) substitutions per site (dN/dS) ratio of the entire ARA-PEPs dataset as well as Tiling array- and RNA-seq-identified expression levels of the SIPs. Sequence searches are also possible through a Basic Local Alignment Search Tool (BLAST) [Proper annotation of genes and other functionally relevant features is a major challenge in converting previously unknown genome sequences into resources that can be used by the research community. Recently, several tools such as CIPHER , GeneMarufflinks , 14 meth (BLAST)  interfac (BLAST) . By inteA. thaliana leaves under both abiotic or biotic stress conditions. We earlier identified genes potentially encoding oxidative stress-induced peptides (OSIPs) in A. thaliana using a Tiling array approach on leaves treated with the herbicide Paraquat [A. thaliana leaves after biotic stress caused by the fungal pathogen Botrytis cinerea (accession: GSE84002). B. cinerea-induced peptides (BIPs) of at least 10 amino acids were identified by six-frame translations of TARs. Additionally, in this study transcriptome analysis was performed on another set of A. thaliana leaves, after identical biotic and abiotic stress conditions, using a complementary RNA-seq approach (SRA accession : SRP080911). Both the Tiling array and RNA-seq data were subsequently analyzed with in-house scripts and the Tuxedo pipeline [Data for Arabidopsis unannotated secreted database (SecretedPeptides) were obtained upon request  and onlyParaquat , and coupipeline . The OSIA. thaliana leaves is described in De Coninck et al. [A. thaliana leaves collected 2 days post inoculation with the fungus B. cinerea was performed in a similar way .Tiling array analysis, performed on mRNA extracted from Paraquat-treated k et al. . Tiling A. thaliana leaves treated with Paraquat or B. cinerea . Homologous sequences were screened using the similarity search algorithm tBLASTn [Oryza sativa japonica, Triticum aestivum, Zea mays, Hordeum vulgare, Solanum lycopersicum, Vitis vinifera, Brassica rapa and Arabidopsis lyrata were downloaded from Ensembl through the FTP server (ftp://ftp.ensemblgenomes.org). The cutoff E-value was fixed at 0.001 and a 300 bp extra sequence was added on either side of the active region to not miss the chance of an in-frame start/stop codon  and nonsynonymous (dN) substitutions per site were estimated using PAML4.8 software [http://seqinr.r-forge.r-project.org/). The sequences were aligned using CLUSTALW2 using a default substitution matrix (BLOSUM62). The Gap Opening Penalty was set to default = 10 and the Gap Extension Penalty was set to 1. Using PAL2NAL.v14 [dN/dS score using codeml is explained in Additional file In order to understand the dynamics of molecular sequence evolution, the rates of synonymous , Tiling arrays, RNA-seq and EST analysis [The TARs were mapped to recent annotations in TAIR10. We also checked if the TARs overlap with any annotated ncRNAs such as in PLncDB. PLncDB currently deposits lncRNA information of several analysis . The gffanalysis .http://xfam.org) [http://www.geneontology.org/external2go/pfam2go). This is an automated mapping of GO terms to Pfam domains. Pfam2GO annotations are not available for all the domains. Standalone version of SignalP [http://prosite.expasy.org/scanprosite/) for detecting PROSITE signature matches [http://elm.eu.org/) was used to detect functional sites in the putative peptides [In order to assign functional roles to the peptides, data was collected across several resources. The sORFs/peptides predicted by other research groups were collected and pooled together  . hmmsearfam.org)  package  SignalP  was used SignalP  was used matches . PROSITEpeptides . As the The Markov Cluster Algorithm (mcl) was used to group all the peptide sequences in ARA-PEPs into putative clusters . All thehttp://getbootstrap.com/), JavaScript and jQuery (https://jquery.com/). ARA-PEPs hosts JBrowse-1.12-0 which is a dynamic and fast genome browser that integrates gene structure and genomic attributes, expression data, etc. We have also embedded other JavaScript visualization tools such as pVIz.js, a protein feature viewer for visualization of TM domains [http://www.highcharts.com/ have been integrated to visualize the data. These tools are compatible with any browser without the need of any external plugins. The web application has been successfully tested on Chrome 49, Firefox 41.0.2, Opera 28, Safari 9.1, Internet Explorer 11.Resulting tables from the data processing pipeline were loaded into a MySQL database and were normalized to remove data redundancy , JavaScript and jQuery (https://jquery.com/). These tools are compatible with any browser without the need of any external plugins. The web application has been successfully tested on Chrome 49, Firefox 41.0.2, Opera 28, Safari 9.1, Internet Explorer 11. Copyright 2016 KU Leuven Computational Systems Biology, distributed under MIT license.ARA-PEPs is available from