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Due to health concerns associated with the increase of antimicrobial resistance in foodborne pathogens such as Salmonella, plant extracts have become important natural alternatives to known antimicrobials. The eradication effect of the water-soluble stinging nettle extracts with 2 mg/mL, 4 mg/mL, 6 mg/mL, 8 mg/mL, 12 mg/mL, 16 mg/mL, and 20 mg/mL concentrations, on pre-formed biofilms and swimming motility of Salmonella enterica subspecies enterica serovars, including Newport, Typhimurium, Enteritidis, Virchow, Othmarschen and Mikawasima, was investigated in vitro. Degradation of biofilm formation on spinach inoculated with each serovar was ascertained within different exposure time of 40 mg/mL concentrated extract as well. Moreover, major genes responsible for biofilm formation (i.e., rpoS, mlrA, ycfR, fimA, spiA and csgA) were screened in these isolates. The extract significantly decreased swimming motilities of Mikawasima and Virchow serovars. The highest reductions were found as 0.88 Log CFU/mL and 2.00 Log CFU/cm2 in vitro and on spinach, respectively.

The emerging situation of Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) in Turkey was investigated in terms of virulence genes and mobile genetic elements such as Salmonella genomic island 1 (SGI1) and class 1 (C1) integron to see whether increased multidrug resistance (MDR) and ability to cause human cases is a consequence of their possession. Screening of SGI1 (and its variants) and C1 integrons was done with conventional PCR, while screening of gene cassettes and virulence genes was conducted with real-time PCR for 70 S. Infantis isolates from poultry products. SGI1 or its variants were not detected in any of the isolates. Sixty-eight of 70 isolates were detected to carry one C1 integron of size 1.0 kb. These integrons were detected to carry ant(3 '')-Ia gene cassette explaining the streptomycin/spectinomycin resistance. Sequence analysis of gene cassettes belongs to four representing isolates which showed that, although their difference in isolation date and place, genetically, they are 99.9% similar. Virulence gene screening was introduced as genotypic virulence profiles. The most dominant profile for S. Infantis isolates, among twelve genes, was gatC-tcfA, which are known to be related to colonization at specific hosts. This study revealed the high percentage of C1 integron possession in S. Infantis isolates from poultry products in Turkey. It also showed the potential of S. Infantis strains to be resistant to more antimicrobial drugs. Moreover, a dominant profile of virulence genes that are uncommon for non-typhoidal Salmonella (NTS) serovars was detected, which might explain the enhanced growth at specified hosts.

This systematic review aimed to highlight the newest information on the effects of non-lactic acid probiotics on the foodborne pathogens. Following the PRISMA-P guidelines, electronic databases (PubMed, Medline, Cochrane Central, Web of Science, Scopus) was searched from their inception up to September 23, 2019. 83 studies met the inclusion criteria after the full-text analysis of 558 articles. Results demonstrated that the majority of the studies focused on spore-forming bacteria and species-specific direct antagonism as the mechanism of action. Nevertheless, further research with in-vivo experimental setups with gnotobiotic animals regarding immunomodulating effects and inhibition of biofilm formation is required.

Antimicrobial resistance of pathogenic microorganisms is an emerging public health concern. Intensive use of antibiotics in food animals might increase antimicrobial resistance in foodborne pathogens. Colistin is a last resort antibiotic for treatment of multidrug resistant (MDR) Gram negative pathogens. The recent antimicrobial resistance studies revealed a mobile antimicrobial resistance gene (mcr) that provides resistance to colistin. Furthermore, the gene has been found in different genera. Therefore, the aim of this study was to determine colistin resistance of Escherichia coli isolates (N=48) isolated in between 2011 and 2015 from food samples in Turkey. In addition, 5 mcr genes and their variants were screened by performing PCR on resistant isolates. 4 E. coli isolates were found resistant to colistin above the epidemiological cut-off value (Minimum inhibitory concentration (MIC) > 2mg/L). None of the resistant isolates had the mcr genes. Further studies with human and food isolates should be conducted to figure out which gene or genes are responsible for colistin resistance.

This study aimed to understand the structure-property relationship in chitosan (CHI) based layer-by-layer (LbL) films and to correlate the surface properties with the biological characteristics of the multilayers. LbL films of CHI were prepared using two different types of polyacids, i.e. a polyphenol, tannic acid (TA) and a polycarboxylic acid, poly(acrylic acid) (PAA). The chemical nature and topology of the polyacid was found to be critical on LbL growth, stability under physiologically related conditions, surface morphology, wettability and drug release properties of the multilayers. The differences in surface properties provided remarkably different biological properties such as anti-adhesiveness against protein adsorption and antibacterial activity for Ciprofloxacin (CIP) incorporated films against Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Listeria monocytogenes (L. monocytogenes). Linearly growing TA/CHI films with relatively smooth surfaces resisted more against protein adsorption when the topmost layer and the protein carried like charges. On the other hand, exponentially growing PAA/CHI multilayers did not exhibit antiadhesive behaviour. Thick and loose PAA/CHI multilayers were able to release higher amount of CIP, thus presented enhanced antibacterial activity compared to thin and more intense TA/CHI films. Finally, we showed that pH affected the extent of association among the layers as well as drug release and antibacterial properties of the films. Our findings showed that TA/CHI films are more promising as antiadhesive surfaces, whereas PAA/CHI multilayers are more suitable for preparation of antibacterial surfaces. The fundamental findings of this study may form a basis for preparation of thin films for drug delivery applications and modification of biomaterial surfaces.

Foodborne diseases remain a major threat to global public health. Problems in detecting the threats at early stages in the supply chain due to defects in surveillance systems cannot be ignored. The primary goal of this article is to evaluate the capabilities of foodborne disease surveillance systems known for their effectiveness and functionality in order to highlight solutions for preventing and managing the outbreaks more effectively. For this purpose, early detection, notification and monitoring systems of the European Union (EU) and the United States were compared in terms of capability gaps and critical needs via an in-depth examination of two standout outbreaks.

WOS: 000354886300028 Some strains of Escherichia coli can be important food borne pathogens. Characterization and antimicrobial resistance testing of 28 E. coli isolates from random food samples obtained in Van, Turkey were performed. Primers for 6 indicator genes (fliC, stx1, stx2, eae, hlyA, and rfbE) for shiga toxin-producing E. coli and 5 indicator genes for each pathogroup (bfpA, aggR, ipaH, daaD, st, and lt) were used. E. coli isolates were also typed using pulsed field gel electrophoresis with the XbaI restriction enzyme. Antimicrobial susceptibility of E. coli isolates was determined using the disk diffusion method for 17 antimicrobials. E. coli isolates were non-pathogenic strains represented by 25 distinguishable PFGE patterns. Antimicrobial susceptibility testing revealed that more than 40% of the E. coli isolates showed resistance to ampicillin, sulphafurazole, and tetracycline. Antimicrobial susceptibility of commensal E. coli should be monitored because these bacteria are becoming reservoirs of antimicrobial resistance genes. Middle East Technical University (METU), Department of Food Engineering, Ankara, TurkeyMiddle East Technical University; METU Scientific Research Project (BAP)Middle East Technical University This study was supported by a grant from Middle East Technical University (METU), Department of Food Engineering, Ankara, Turkey. The METU Scientific Research Project (BAP) provided financial support. Dr. Kadir Halkman and Dr. Belkis Levent provided reference strains for STEC and pathogenic E. coli respectively. Dr. Martin Weidmann allowed use of bionumerics in the laboratory.

Bezelyelerde klorofilin termal degradasyon kinetiği ve görünür yeşil renkteki kayıp 70°, 80°, 90° ve 100 °C’de araştırılmıştır. Klorofil a ve klorofil b’nin parçalanması birinci dereceden bir kinetik model izlemektedir. Tristimulus kolorimetresi ile ölçülen -a, -a/b ve h (hue) değerlerindeki değişim ile ortaya konulan görünür yeşil renkteki kayıp da birinci dereceden reaksiyona uymaktadır. Klorofil a ve b için aktivasyon enerjileri sırasıyla 47.78 and 26.77 kJ mol-1olarak belirlenirken; -a, -a/b ve h değerleri için aktivasyon enerjileri 49.75, 56.04 and 55.06 kJ mol-1 olarak saptanmıştır.

Milk has been the one of the main nutrient sources of human diet for centuries. Microbial studies on milk date back to the seventeenth century, when Kircher used a microscope, and observed the minute worms in milk. Two centuries later, in the1850s, Pasteur proved that the spoilage of milk resulting the sour taste was caused by microorganisms. Pasteur's discoveries on the effect of heat on undesirable microorganisms in beer and wine opened a new era in food science. Therefore, the process was named pasteurization. In the following years of his invention, pasteurization was conducted in Germany and the U.S.A. (Jay, Modern food microbiology. Aspen Publishing, Gaithersburg, MD, 2000). Another breakthrough in milk safety was refrigeration, which became popular after the 1950s. With the advances in heat treatment and low temperature storage, shelf life of pasteurized milk had been increased significantly. Today, pasteurization, partial sterilization, refrigeration, dehydration, and fermentation are commonly used to increase the shelf life of milk and dairy products. Besides these traditional methods, there are also novel methods used to prevent dairy products from spoilage and pathogen contamination such as high pressure processing an UV light. WOS:000431735400012

The food production system throughout the European Union, which includes farm production, harvesting, transport, processing, storage, marketing and consumption, is vast, complex and open. The high volume of trade in fresh vegetables and fruits contributes to the vulnerability to contamination, whether by accident or intent. Outbreak investigation is critical to understanding the sources of contamination and the steps required to minimize it. The fact that much of the trade in these commodities is international makes it critical that mediation efforts and cooperative research cross national barriers, just as the pathogens do. Enhancing the biosecurity of food production requires assessment of the following: how is the food production system currently organized, in what ways might it be vulnerable to contamination, either accidental or deliberate, what are the primary factors that would allow discrimination between deliberate vs. accidental outbreaks, how can the epidemiological and surveillance systems in Europe be strengthened to shorten outbreak response and mediation times, how can implicated fresh produce be traced to its source, and what forensically valid subtyping method(s) is/are available for detection and discrimination of associated foodborne pathogens.

Number of people being infected or intoxicated due to foodborne illness outbreaks reaches to millions annually. These outbreaks are also responsible from thousands of deaths and billions of dollars’ worth of damage every year. However it is considered as an essential portion for a healthy diet, the fresh produce, which is contaminated with Human Pathogens on Plants (HPOPs), is one of the major food items causing this damage. E.coli O104:H4 outbreak, occurred in Germany in 2011, has attracted a great attention on foodborne outbreaks caused by contaminated fresh produce, and especially the vulnerabilities and gaps in the foodborne illness surveillance systems. In the frame of this chapter, we focused on the most common foodborne pathogens on fresh produce, epdimiological and traceback investigations of the outbreaks caused by these pathogens in the last 5 years (November 2010–December 2015) in all around the World.

WOS: 000390071600012 PubMed ID: 27768932 192 Food samples (commonly consumed 8 food types), 355 animal samples (animal feces of bovine, ovine, goat and chicken) and 50 samples from clinical human cases in Sanliurfa city, Turkey in a year were collected to determine the Salmonella enterica subsp. enterica mosaic in Turkey. 161 Salmonella isolates represented 17 serotypes, 20 sequence types (STs) and 44 PFGE patterns (PTs). 3 serotypes, S. Enteritidis, S. Typhimurium and S. Kentucky, were recovered from three different hosts. The highest discriminatory power was obtained by PFGE (SID = 0.945), followed by MLST (SID = 0.902) and serotyping (SID = 0.885) for all isolates. The prevalence of antimicrobial resistance genes (aadA1, aadA2, strA, strB, aphA(1-lab) bla(TEM-1), bla(PSE-1), tetA) was highly correlated with phenotypic profiles of aminoglycoside, beta-lactam and tetracycline groups (kappa >0.85). From our knowledge, this is the first study reporting spatial and temporal distribution of Salmonella species through phenotypic and genetic approaches over farm to fork chain in Turkey. Thus, our data provided further information for evolution, ecology and transmission of Salmonella in Turkey. (C) 2016 Published by Elsevier B.V. Scientific and Technical Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [TUBITAK 3501(1120192)] We acknowledge Dr. Martin Wiedmann from Cornell University for using BioNumerics, Dr. Nihat Dilsiz from Harran University Medicine Faculty, Harran University Veterinary Faculty for the valuable discussion, and Dr. Tolga Can from Middle East Technical University, Computer Engineering for building a web-based database. This work is partially supported by The Scientific and Technical Council of Turkey Grant TUBITAK 3501(1120192).

Due to health benefits of the fresh fruits and vegetables, the consumption of the minimally processed refrigerated (MPR) and packaged produce has been increased in the USA and EU countries. For MPR and packaged product production, fresh produces and vegetables are first examined for quality purposes and then washed, cut, dried, sanitized, and packaged. When these processes are performed under insufficient sanitary conditions, foodborne outbreaks become inevitable. The most common foodborne agents, causing outbreaks in MPR and packaged produce, are pathogenic bacteria (i.e., Listeria monocytogenes, Clostridium botulinum, Shiga toxin-producing Escherichia coli O157:H7, Salmonella spp., Campylobacter jejuni, Yersinia enterocolitica, Aeromonas hydrophila), viral pathogens (i.e., hepatitis A, Norwalk virus), and parasites (i.e., Giardia lamblia). To prevent these MPR and packaged produce-related outbreaks, the ecology of microorganisms and fresh produces and fruits should be well known. Therefore, the detection methods and their improvements are crucial. To advance the safety and quality of the MPR and packaged produce, here we provided the most common foodborne pathogens in these products and their rapid, standardized, and easy-to-use identification methods.

Due to the increase in consumption of fresh produce regarding to the health demand in the last decades, a considerable portion of foodborne outbreaks has been trackbacked to contaminated fresh produce, which have appeared as highly possible vehicles for foodborne outbreaks nowadays. Delays in detection of pathogens and mycotoxins on fresh produce hindered the trace-back investigations in finding the source and revealed the urgent need of rapid and reliable methods. In the frame of this review, we summarized available fast, reliable and standardized methods (conventional, molecular, rapid and recently developed methods) used for detection of the most common foodborne pathogens and mycotoxins which are the most likely causative agents of outbreaks caused by contaminated fresh produce.

Salmonella represents an important zoonotic pathogen worldwide, but the transmission dynamics between humans and animals as well as within animal populations are incompletely understood. We characterized Salmonella isolates from cattle and humans in two geographic regions of the United States, the Pacific Northwest and the Northeast, using three common subtyping methods (pulsed-field gel electrophoresis [PFGE], multilocus variable number of tandem repeat analysis [MLVA], and multilocus sequence typing [MLST]). In addition, we analyzed the distribution of antimicrobial resistance among human and cattle Salmonella isolates from the two study areas and characterized Salmonella persistence on individual dairy farms. For both Salmonella enterica subsp. enterica serotypes Newport and Typhimurium, we found multidrug resistance to be significantly associated with bovine origin of isolates, with the odds of multidrug resistance for Newport isolates from cattle approximately 18 times higher than for Newport isolates from humans. Isolates from the Northwest were significantly more likely to be multidrug resistant than those from the Northeast, and susceptible and resistant isolates appeared to represent distinct Salmonella subtypes. We detected evidence for strain diversification during Salmonella persistence on farms, which included changes in antimicrobial resistance as well as genetic changes manifested in PFGE and MLVA pattern shifts. While discriminatory power was serotype dependent, the combination of PFGE data with either MLVA or resistance typing data consistently allowed for improved subtype discrimination. Our results are consistent with the idea that cattle are an important reservoir of multidrug-resistant Salmonella infections in humans. In addition, the study provides evidence for the value of including antimicrobial resistance data in epidemiological investigations and highlights the benefits and potential problems of combining subtyping methods.

Pulsed-field gel electrophoresis (PFGE) characterization of 335 temporally and spatially matched clinical, bovine, and human Salmonella enterica subsp. enterica isolates revealed 167 XbaI PFGE patterns. These isolates were previously classified into 51 serotypes and 73 sequence types, as determined by multilocus sequence typing. Discriminatory power of PFGE (Simpson's index, D = 0.991) was considerably higher than that of multilocus sequence typing (D = 0.920) or serotyping (D = 0.913). Although 128 PFGE types each only represented a single isolate, 8 PFGE types represented >4 isolates, including (i) three serotype Enteritidis and Heidelberg patterns that were only identified among human isolates, (ii) two PFGE patterns (each representing serotypes Bardo and Newport) that were significantly more common among bovine isolates as compared with human isolates; (iii) two PFGE types that each includes two serotypes (4,5,12:i:- and Typhimurium; Thompson and 1,7:-:1,5); and (iv) one PFGE type that includes eight Typhimurium isolates from humans and cattle. Characterization of isolates collected over multiple farm visits indicated that given specific PFGE types persisted over time on 11 farms. On an additional seven farms, isolates with a given sequence type represented multiple PFGE type, which typically only differed by

Salmonella spp. are one of the most common causes of bacterial food-borne diseases worldwide (34). In the United States nontyphoidal Salmonella serotypes cause an estimated 1.4 million human salmonellosis cases, including approximately 550 deaths annually (27). Serotyping with the Kaufmann-White scheme is used commonly as a first step to differentiate Salmonella isolates. Serotyping of Salmonella isolates is based on lipopolysaccharide moieties on the cell surface (O antigens) and the flagellar proteins (H antigens), as well as capsular protein antigens (Vi antigen), which are only found in a few Salmonella serotypes (e.g., Salmonella enterica serotype Typhi). According to the Kaufmann-White scheme, Salmonella includes over 2,500 recognized serotypes (20). Many Salmonella bacteria are motile due to peritrichous flagella (28), which include a basal body, a propeller, and a hook. The motility of Salmonella depends on the rotation of the flagellar propeller (i.e., the filament), which includes either FliC (phase 1 antigen) or FljB (phase 2 antigen) flagellin (11). Most Salmonella serotypes, including Salmonella enterica serotype Typhimurium, are biphasic, meaning that they can express two distinct flagellar antigens (i.e., phase 1 and phase 2 antigens). Regulation of phase 1 and 2 antigen expression is under the control of the recombinase Hin. This recombinase facilitates inversion of a promoter element so that it either (i) transcribes fljB (which encodes the phase 2 antigen FljB) and fljA (which encodes a repressor of fliC, the gene encoding the phase 1 antigen FliC) (4, 37) or (ii) does not transcribe either of these genes. If this promoter is located in an orientation that does not allow for transcription of fljB and fljA, the lack of a repression of fliC transcription leads to expression of phase 1 flagellar antigens. Salmonella enterica serotype 4,5,12:i:− is a serotype that appears to be antigenically similar and genetically closely related to Salmonella serotype Typhimurium (which has the antigenic formula 4,5,12:i:1,2) but lacks expression of the second-phase flagellar antigen, which is 1,2 in Salmonella serotype Typhimurium (28). Salmonella serotype 4,5,12:i:− was the sixth most common Salmonella serotype among cases of human disease in the United States in 2006 (10) and the fourth most common serotype among human isolates in Spain in 1998 (18). Overall, the prevalence of Salmonella serotype 4,5,12:i:− among human cases has increased considerably in many countries in the world over the last 10 years (9, 10, 18, 29, 36). This Salmonella serotype has also been responsible for a number of human salmonellosis outbreaks over the last decades, including in Spain (1998), the United States (2004 and 2007), and Luxemburg (2006). Salmonella serotype 4,5,12:i:− has been isolated, particularly over the last decade, from a number of different foods and animals (1, 6, 13, 29, 38). While a number of separate studies, using molecular subtyping and characterization tools (e.g., genomic microarrays and PCR assays to test for gene presence/absence), have shown that Salmonella serotype 4,5,12:i:− isolates from Spain (15, 18) and the United States (1, 2, 38) are genetically closely related to Salmonella serotype Typhimurium, we are not aware of any comparative studies of Salmonella serotype 4,5,12:i:− isolates from Europe and the United States that have been published to date. In order to provide a better understanding of the transmission, ecology, and evolution of Salmonella serotype 4,5,12:i:−, we have assembled a collection of 190 Salmonella serotype 4,5,12:i:− and Typhimurium isolates from various sources and from two countries, the United States and Spain. These isolates were characterized by different molecular subtyping methods (i.e., multilocus sequence typing [MLST] and pulsed-field gel electrophoresis [PFGE]), followed by characterization of selected isolates for genomic deletions that may be responsible for the lack of phase 2 flagellum expression.

Objective—To determine the duration of fecal shedding of and serologic response to Salmonella spp after natural infection in dairy calves and characterize Salmonella organisms recovered from these herds. Design—Longitudinal study. Animals—Calves from 2 dairy herds (A and B) in the northeast United States that were identified at the beginning of a Salmonella outbreak. Procedures—Fecal samples were collected twice per week (herd A) or once per week (herd B); blood samples were collected for serologic testing once per week in both herds. Bacteriologic culture of fecal samples was performed, and Salmonella isolates were characterized by serotype, pulsed-field gel electrophoresis (PFGE) pattern, and antimicrobial resistance profile. Results—All Salmonella isolates from herd A were serovar Typhimurium var Copenhagen, had the same PFGE pattern, and were resistant to at least 9 antimicrobials. All isolates from herd B were Salmonella Typhimurium, represented 2 PFGE patterns, and were susceptible to all antimicrobials evaluated. The estimated duration of fecal shedding was 14 days in herd A and 9 days in herd B. Few calves were seropositive for antibody against Salmonella lipopolysaccharide within the first week after birth (0 of 20 in herd A and 13 of 79 in herd B) or seroconverted (6 in herd A and 4 in herd B). Fecal shedding was more common in calves that seroconverted, but overall, there was not a strong association between seropositivity and fecal shedding of Salmonella organisms. Conclusions and Clinical Relevance—Although the herds differed in serologic response and Salmonella subtype, the duration of fecal shedding among calves was similar between herds.

In recent years, the proportion of Salmonella enterica infections represented by S. enterica serovar Newport has increased markedly among humans and animals. Multilocus variable-number tandem-repeat analysis (MLVA) has proven to be useful in discriminating other highly clonal Salmonella serovars. Here, we report on the development of a highly discriminatory MLVA for Salmonella serovar Newport.

Salmonella spp. represent one of the most common causes of bacterial foodborne illnesses around the world. The species Salmonella enterica contains more than 2500 serotypes, and emergence of new human pathogenic Salmonella strains and serotypes represents a major public health issue. Salmonella enterica subsp. enterica serotype 4,5,12:i:– represents a monophasic variant of Salmonella Typhimurium, which has rarely been identified before the mid-1990s. The prevalence of this serotype among human salmonellosis cases has increased considerably since the mid-1990s and Salmonella 4,5,12:i:– currently (i.e., the first decade of the 2000s) represents one of the most common serotypes among human cases in many countries around the world. This paper discusses our current knowledge of the global ecology, epidemiology, transmission, and evolution of this emerging Salmonella serotype.

Nontyphoidal salmonellosis has been characterized by a pattern of dissemination of clonal Salmonella enterica. The most well-known example of this was S. enterica serovar Typhimurium definitive phage type 104 (DT104), a clone that emerged and disseminated globally in the 1990s (1). Other examples of epidemic clones include Salmonella serovar Wien, which spread from North Africa through Europe in the 1970s; S. Typhimurium phage type 10 (DT10), which disseminated across Canada in the 1970s; and other phage types of S. Typhimurium associated with cattle that disseminated widely in Europe during the 1980s (2). More recently, multidrug-resistant (MDR) S. Agona was disseminated in poultry in Belgium; MDR S. Paratyphi B dT+ in Germany, Belgium, and the Netherlands; and MDR S. Newport that harbors the plasmid-mediated AmpC resistance in the United States (3). Epidemic clones may remain largely restricted to the animal reservoir for years before their incidence rises among human infections: S. Typhimurium phage type 204c disseminated throughout the United Kingdom in cattle from 1980 through 1984, but its proportion among human S. Typhimurium infections was not high during that period (4). Some epidemic clones, for example DT10 and DT104, expanded in the absence of a specific resistance advantage (1). The mechanisms underlying emergence, dissemination, and subsequent decline of novel Salmonella clones are unknown, although some researchers have hypothesized that fitness-associated genetic factors may allow more efficient dissemination in specific hosts and environments (5) and that acquisition of these fitness genes may be phage mediated (6). One approach to understanding clonal replacement events is to conduct prospective surveillance of Salmonella infections in animal and human hosts. We initiated such a study to compare human- and animal-origin Salmonella strains by serovar, antimicrobial drug resistance pattern, and pulsed-field gel electrophoresis (PFGE).

Although Turkey is one of the major producers of fruits and vegetables in the world, there has been no information available on the prevalence of pathogens in fresh produce. To fill this gap, we collected 503 fresh produce samples including tomato, parsley, iceberg lettuce, green-leaf lettuce and five different fresh pepper varieties (i.e., green, kapya, bell, mazamort and Charleston) from 3 major districts within 9 supermarkets and 3 bazaars in Ankara, Turkey to investigate the presence of Salmonella. Salmonella was detected in 0.8% (4/503) of samples by conventional culturing method with molecular confirmation conducted through polymerase chain reaction (PCR). For further characterization of isolates, serotyping, antimicrobial susceptibility testing, multi-locus sequence typing (MLST; aroC, thrA, purE, sucA, hisD, hemD and dnaN) and pulsed-field gel electrophoresis (PFGE) were performed. Salmonella enterica subsp. enterica serotypes Anatum, Charity, Enteritidis and Mikawasima were isolated from two parsley, one pepper and one lettuce samples, respectively. MLST resulted in 4 sequence types (STs) for each serotype, including one novel ST for serotype Mikawasima. Similarly, PFGE revealed four different XbaI PFGE patterns. The results of this survey, obtained by the most common subtyping methods (i.e. serotyping, MLST and PFGE) worldwide, contributes to the development of a national database in Turkey, which is essential for investigating the evolutionary pathways, geographical distribution and genetic diversity of Salmonella strains.

During the year 2004, 178 human and 158 bovine clinical Salmonella isolates were collected across New York State to better understand the transmission dynamics and genetic determinants of antimicrobial resistance among human and bovine hosts. Serotyping, sequence typing, and pulsed-field gel electrophoresis typing results have been reported previously. Here we tested all isolates for phenotypic susceptibility to 15 antimicrobial drugs that are part of the National Antimicrobial Monitoring System bovine susceptibility panel. PCR was performed on a representative subset of unique isolates (n = 53) to screen for the presence of 21 known antimicrobial resistance genes (i.e., ampC, bla(TEM) (1), bla(CMY) (2), bla(PSE) (1), cat1, cat2, cmlA, flo, aadA1, aadA2, aacC2, strA, strB, aphA1-IAB, dhrfI, dhrfXII, sulI, sulII, tetA, tetB, and tetG); selected fluoroquinolone- and nalidixic acid-resistant (n = 3) and -sensitive (n = 6) isolates were also tested for known resistance-conferring mutations in gyrA and parC. Genes responsible for antimicrobial resistance were shared among isolates of human and bovine origin. However, bovine isolates were significantly more likely than human isolates to be multidrug resistant (P < 0.0001; Fisher's exact test). Our analyses showed perfect categorical agreement between phenotypic and genotypic resistance for beta-lactam and chloramphenicol. Our data confirm that resistance profiles of amoxicillin-clavulanic acid, chloramphenicol, kanamycin, and tetracycline were strongly associated with the presence of bla(CMY) or ampC, flo, aphA1-IAB, and tetA, respectively. Our findings provide evidence for the clinical value of genotypic resistance typing if incorporating multiple known genes that can confer a phenotypic resistance profile.

A microarray was developed to simultaneously screen Escherichia coli and Salmonella enterica for multiple genetic traits. The final array included 203 60-mer oligonucleotide probes, including 117 for resistance genes, 16 for virulence genes, 25 for replicon markers, and 45 other markers. Validity of the array was tested by assessing inter-laboratory agreement among four collaborating groups using a blinded study design. Internal validation indicated that the assay was reliable (area under the receiver-operator characteristic curve=0.97). Inter-laboratory agreement, however, was poor when estimated using the intraclass correlation coefficient, which ranged from 0.27 (95% confidence interval 0.24, 0.29) to 0.29 (0.23, 0.34). These findings suggest that extensive testing and procedure standardization will be needed before bacterial genotyping arrays can be readily shared between laboratories.

A collection of 179 human and 156 bovine clinicalSalmonellaisolates obtained from across New York state over the course of 1 year was characterized using serotyping and a multilocus sequence typing (MLST) scheme based on the sequencing of three genes (fimA,manB, andmdh). The 335 isolates were differentiated into 52 serotypes and 72 sequence types (STs). Analyses of bovine isolates collected on different farms over time indicated that specific subtypes can persist over time on a given farm; in particular, a number of farms showed evidence for the persistence of a specificSalmonella entericaserotype Newport sequence type. Serotypes and STs were not randomly distributed among human and bovine isolates, and selected serotypes and STs were associated exclusively with either human or bovine sources. A number of common STs were geographically widespread. For example, ST6, which includes isolates representing serotype Typhimurium as well as the emerging serotype 4,5,12:i:-, was found among human and bovine isolates in a number of counties in New York state. Phylogenetic analyses supported the possibility that serotype 4,5,12:i:- is closely related toSalmonellaserotype Typhimurium.Salmonellaserotype Newport was found to represent two distinct evolutionary lineages that differ in their frequencies among human and bovine isolates. A number ofSalmonellaisolates carried two copies ofmanB(33 isolates) or showed small deletion events infimA(nine isolates); these duplication and deletion events may provide mechanisms for the rapid diversification ofSalmonellasurface molecules. We conclude that the combined use of an economical three-gene MLST scheme and serotyping can provide considerable new insights into the evolution and transmission ofSalmonella.

Background The bacterium Salmonella enterica includes a diversity of serotypes that cause disease in humans and different animal species. Some Salmonella serotypes show a broad host range, some are host restricted and exclusively associated with one particular host, and some are associated with one particular host species, but able to cause disease in other host species and are thus considered "host adapted". Five Salmonella genome sequences, representing a broad host range serotype (Typhimurium), two host restricted serotypes (Typhi [two genomes] and Paratyphi) and one host adapted serotype (Choleraesuis) were used to identify core genome genes that show evidence for recombination and positive selection. Results Overall, 3323 orthologous genes were identified in all 5 Salmonella genomes analyzed. Use of four different methods to assess homologous recombination identified 270 genes that showed evidence for recombination with at least one of these methods (false discovery rate [FDR] ompC, a gene encoding an outer membrane protein, which has also been found to be under positive selection in other bacteria. A total of 8, 16, 7, and 5 genes showed evidence for positive selection in Choleraesuis, Typhi, Typhimurium, and Paratyphi branch analyses, respectively. Sequencing and evolutionary analyses of four genes in an additional 42 isolates representing 23 serotypes confirmed branch specific positive selection and recombination patterns. Conclusion Our data show that, among the four serotypes analyzed, (i) less than 10% of Salmonella genes in the core genome show evidence for homologous recombination, (ii) a number of Salmonella genes are under positive selection, including genes that appear to contribute to virulence, and (iii) branch specific positive selection contributes to the evolution of host restricted Salmonella serotypes.