@article{santos_d'souza_jaykus_ferket_sheldon_2007, title={Genotypes, serotypes, and antibiotic resistance profiles of Salmonella isolated from commercial North Carolina Turkey farms}, volume={70}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028X-70.6.1328}, abstractNote={This study was designed to determine the serotypes, genotypes, and antibiotic resistance (AbR) patterns of 42 Salmonella isolates recovered from either fecal or litter samples of 12 commercial turkey farms across two seasons (summer and winter) and two ages (3 and 19 weeks). Isolates were serotyped on the basis of the Kauffmann-White scheme. Genotyping was done by restriction digestion of cDNA (XbaI) and subsequent pulsed-field gel electrophoresis (PFGE). The AbR was determined with Sensititre susceptibility plates. Serovar Kentucky was the most prevalent serotype (26%), followed by Senftenberg (19%), Muenster (17%), Mbandaka (10%), Javiana (7%), Hadar (5%), Heidelberg (5%), 8,(20):nonmotile (5%), Agona (2%), Infantis (2%), and 4,12:r:-(2%). Serovars Kentucky, Heidelberg, Hadar, and 8,(20):nonmotile were isolated only from the 19-week-old bird samples, whereas Senftenberg and Muenster were isolated only from the young birds (3 weeks old). Isolates within any one serotype showed minor PFGE banding pattern differences, but dendogram analysis indicated that sequence variability between serotypes was more significant than within serotypes. Isolates were resistant to tetracycline (86%), sulfisoxazole (71%), streptomycin (64%), gentamicin (41%), ampicillin (36%), kanamycin (26%), sulfamethoxazole-trimethoprim (7%), nalidixic acid (5%), cefoxitin (2%), and ceftiofur (2%). One isolate (Muenster) was resistant to nine antibiotics (2%), and the others were resistant to six (7%), five (12%), four (10%), three (21%), two (24%), and one (10%) antibiotic. Only two isolates (5%) were susceptible to all antibiotics tested. The AbR patterns were affected by age; on average, strains recovered from young birds were resistant to more than four drugs compared with fewer than three in older birds (P < 0.05). This study showed that Salmonella enterica subsp. enterica serotypes, genotypes and AbR patterns were affected by bird age but not by season or farm.}, number={6}, journal={JOURNAL OF FOOD PROTECTION}, author={Santos, F. B. O. and D'Souza, D. H. and Jaykus, L. and Ferket, P. R. and Sheldon, B. W.}, year={2007}, month={Jun}, pages={1328–1333} }
 @article{dh d'souza_sair_williams_papafragkou_jean_moore_jaykus_2006, title={Persistence of caliciviruses on enviromnental surfaces and their transfer to food}, volume={108}, ISSN={["1879-3460"]}, DOI={10.1016/j.ijfoodmicro.2005.10.024}, abstractNote={The noroviruses (NoV) are a common cause of human gastroenteritis whose transmission by foodborne routes is well documented. Fecally contaminated surfaces are likely to contribute to this foodborne transmission and to the propagation of viral disease outbreaks. The purpose of this study was to (i) investigate the stability of NoV on various food preparation surfaces; and (ii) evaluate the degree of virus transfer from these surfaces to a model-ready-to-eat (RTE) food. For the virus persistence experiments, stainless steel, formica and ceramic coupons were artificially contaminated with Norwalk virus (NV), the prototype genogroup I NoV; NV RNA; or feline calicivirus (FCV) F9 (a NoV surrogate), stored at ambient temperature for up to 7 d, and periodically assayed for detection. In the transfer experiments, stainless steel coupons were inoculated with NV or FCV F9 and allowed to dry for 10, 30 and 60 min, after which lettuce leaves were exposed to the surface of the coupons at various contact pressures (10, 100, and 1000 g/9 cm2). Virus recovery was evaluated by RT-PCR (for NV and NV RNA) or by plaque assay (for FCV F9) using Crandell Reese Feline Kidney (CRFK) cells. NV and FCV were detected on all three surfaces for up to 7 d post-inoculation; for FCV, there was an approximate 6 to 7-log10 drop in virus titer over the 7 d evaluation period. By contrast, when stainless steel was inoculated with purified NV RNA, RT-PCR detection was not possible beyond 24 h. Transfer of both NV and FCV from stainless steel surfaces to lettuce occurred with relative ease. This study confirms lengthy NoV persistence on common food preparation surfaces and their ease of transfer, confirming a potential role for environmental contamination in the propagation of viral gastroenteritis.}, number={1}, journal={INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY}, author={DH D'Souza and Sair, A and Williams, K and Papafragkou, E and Jean, J and Moore, C and Jaykus, L}, year={2006}, month={Apr}, pages={84–91} }
 @article{jean_dh d'souza_jaykus_2004, title={Multiplex nucleic acid sequence-based amplification for simultaneous detection of several enteric viruses in model ready-to-eat foods}, volume={70}, ISSN={["0099-2240"]}, DOI={10.1128/AEM.70.11.6603-6610.2004}, abstractNote={ABSTRACT}, number={11}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Jean, J and DH D'Souza and Jaykus, LA}, year={2004}, month={Nov}, pages={6603–6610} }
 @article{dh d'souza_jaykus_2003, title={Nucleic acid sequence based amplification for the rapid and sensitive detection of Salmonella enterica from foods}, volume={95}, ISSN={["1364-5072"]}, DOI={10.1046/j.1365-2672.2003.02106.x}, abstractNote={Aims: The purpose of this study was to apply nucleic acid sequence‐based amplification (NASBA) for the detection of Salmonella enterica serovar Enteritidis (S. Enteritidis) in representative foods.}, number={6}, journal={JOURNAL OF APPLIED MICROBIOLOGY}, author={DH D'Souza and Jaykus, LA}, year={2003}, pages={1343–1350} }
 @article{jean_d d'souza_jaykus_2003, title={Transcriptional enhancement of RT-PCR for rapid and sensitive detection of Noroviruses}, volume={226}, ISSN={["0378-1097"]}, DOI={10.1016/S0378-1097(03)00621-9}, abstractNote={Previously reported nucleic acid sequence-based amplification (NASBA) primers specific for the GII Noroviruses were adapted for reverse transcriptase-polymerase chain reaction (RT-PCR), and detection sensitivity was then enhanced by a subsequent in vitro transcription of the RT-PCR amplicons. The NASBA-derived primers performed comparably to other broadly reactive GII Norovirus primers with respect to detection limits (i.e. 1 RT-PCR amplifiable unit (RT-PCRU) per reaction). Detection limits improved by approximately 1 log(10) to 0.3 RT-PCRU per reaction when transcriptional enhancement and electrochemiluminescence (ECL) hybridization followed RT-PCR. The method shows promise for improved detection sensitivity in instances where very low levels of virus contamination might be anticipated.}, number={2}, journal={FEMS MICROBIOLOGY LETTERS}, author={Jean, J and D D'Souza and Jaykus, LA}, year={2003}, month={Sep}, pages={339–345} }
 @article{sair_dh d'souza_moe_jaykus_2002, title={Improved detection of human enteric viruses in foods by RT-PCR}, volume={100}, ISSN={["1879-0984"]}, DOI={10.1016/S0166-0934(01)00397-4}, abstractNote={Human enteric viruses (including hepatitis A virus (HAV) and Norwalk-like viruses (NLVs)) are now recognized as common causes of foodborne disease. While methods to detect these agents in clinical specimens have improved significantly over the last 10 years, applications to food samples have progressed more slowly. In an effort to improve the sensitivity and speed of virus detection from non-shellfish food commodities by reverse transcription-polymerase chain reaction (RT-PCR), we (i) evaluated multiple RNA extraction methods; (ii) compared alternative NLV primer sets; and (iii) developed a one-step RT-PCR method. Hamburger and lettuce samples, processed for virus concentration using a previously reported filtration–extraction–precipitation procedure, were inoculated with HAV or NV. Several RNA extraction methods (guanidinium isothiocyanate, microspin column, QIAshredder™ Homogenizer, and TRIzol) and primer pairs were compared for overall RNA yield (μg/ml), purity (A260/A280), and RT-PCR limits of detection. The use of TRIzol with the QIAshredder™ Homogenizer (TRIzol/Shred) yielded the best RT-PCR detection limits (<1 RT-PCR amplifiable units/reaction for NV), and the NVp110/NVp36 primer set was the most efficient for detecting NV from seeded food samples. A one-step RT-PCR protocol using the TRIzol/Shred extraction method and the NVp110/NVp36 or HAV3/HAV5 primer sets demonstrated improved sensitivity (>10-fold) over the routinely used two-step method. HAV RNA was detected by RT-PCR at initial inoculum levels corresponding to <10 and <100 PFU per 300 μl sample concentrate (corresponding to 6 g food sample) for hamburger and lettuce, respectively. NV RNA was detected by RT-PCR at initial inoculum levels <5 and <50 RT-PCR amplifiable units per 300 μl concentrate (corresponding to 6 g food sample) for hamburger and lettuce, respectively. Residual RT-PCR inhibitors were effectively removed as evidenced by the ability to detect viral RNA in food concentrates without prior dilution. The methods reported here show promise for rapid, sensitive detection of human enteric viruses in foods.}, number={1-2}, journal={JOURNAL OF VIROLOGICAL METHODS}, author={Sair, AI and DH D'Souza and Moe, CL and Jaykus, LA}, year={2002}, month={Feb}, pages={57–69} }
 @article{dh d'souza_jaykus_2002, title={Zirconium hydroxide effectively immobilizes and concentrates human enteric viruses}, volume={35}, ISSN={["1472-765X"]}, DOI={10.1046/j.1472-765X.2002.01206.x}, abstractNote={Background: Detection of human enteric viruses in foods and environmental samples requires concentration of viruses from complex matrices before application of molecular or cultural methods. Previous studies have described the use of zirconium hydroxide to concentrate bacteria from clinical, environmental, and food samples.}, number={5}, journal={LETTERS IN APPLIED MICROBIOLOGY}, author={DH D'Souza and Jaykus, LA}, year={2002}, pages={414–418} }