Use of two 16S DNA targeted oligonucleotides as PCR primers for the specific detection of Salmonella in foods

Investigation of prevalence and antimicrobial resistance of Salmonella in pet dogs and cats in Turkey

BACKGROUND

Although salmonellosis is considered to be a foodborne zoonotic disease, pets can play a significant role in the dissemination of antimicrobial-resistant Salmonella organisms to humans because of close contact with their owners.

OBJECTIVES

To determine the prevalence, risk factors, virulence factors, serotypes, and antimicrobial resistance profile of Salmonella in pet dogs and cats in Turkey and to assess the public health risk. Furthermore, to perform macroscopic comparison of lactic acid bacteria (LAB) in Salmonella-positive and Salmonella-negative animals.

METHODS

International Standards Organization (ISO) 6579-1:2017 and Food and Drug Administration (FDA) methods were used to compare the effectiveness of culture methods in the identification of Salmonella in 348 rectal swabs. Positive isolates were serotyped using the slide agglutination method according to the White-Kauffmann-Le Minor scheme and the presence of virulence genes (invA and stn) were evaluated by polymerase chain reaction (PCR). Antimicrobial activity was tested by Kirby-Bauer disk diffusion method according to Clinical and Laboratory Standards Institute (CLSI) guidelines.

RESULTS

Salmonella prevalence was 5.73% (9/157) in dogs and 0.0% (0/191) in cats. Eight (8/9) isolates were cultured with the ISO method and 5 (5/9) isolates were cultured with the FDA method. Macroscopic results revealed that Salmonella agents had no effect on LAB. Three different serotypes were detected and all isolates were positive for virulence genes. Antibiotic resistance profiling indicated that 11.1% of the isolates were MDR and the highest resistance was found for ciprofloxacin. MDR-resistant S. Virchow and carbapenem-resistant S. Enteritidis were detected from dog isolates. There was a significant difference between raw meat consumption and Salmonella carriage (p < 0.01).

CONCLUSIONS

Dogs could be potential carriers of Salmonella infection. The isolation of Salmonella in healthy dogs instead of dogs suffering from diarrhoea indicates that attention should be paid to asymptomatic carriage. The emergence of resistance among zoonotic Salmonella isolates poses a significant threat to public health.

Prevalence of Salmonella spp. and Escherichia coli in the feces of free-roaming wildlife throughout South Korea

Wildlife can carry pathogenic organisms, including viruses, bacteria, parasites, and fungi, which can spread to humans and cause mild to serious illnesses and even death. Spreading through animal feces, these pathogens significantly contributes to the global burden of human diseases. Therefore, the present study investigated the prevalence of zoonotic bacterial pathogens, such as Salmonella spp., Escherichia coli, and Shiga toxin-producing E. coli (STEC), in animal feces. Between September 2015 and August 2017, 699 wildlife fecal samples were collected from various agricultural production regions and mountainous areas in South Korea. Fecal samples were collected from wild mammals (85.26%, 596/699) and birds (14.73%, 103/699). Salmonella spp. and E. coli were present in 3% (21/699) and 45.63% (319/699) of the samples, respectively. Moreover, virulence genes stx1 and both stx1 and stx2 were detected in 13.30% (93/699) and 0.72% (5/699) of the samples, respectively. The 21 Salmonella spp. were detected in badgers (n = 5), leopard cats (n = 7), wild boars (n = 2), and magpies (n = 7); STEC was detected in roe deer, water deer, mice, and wild boars. Through phylogenetic and gene-network analyses, the Salmonella spp. isolates (n = 21 laboratory isolates, at least one isolate from each Salmonella-positive animal fecal sample, and n = 6 widely prevalent reference Salmonella serovars) were grouped into two major lineages: S. enterica subsp. enterica and S. enterica subsp. diarizonae. Similarly, 93 E. coli isolates belonged to stx1, including three major lineages (groups 1-3), and stx1 and stx2 detected groups. To the best of our knowledge, this is the first report of a wild leopard cat serving as a reservoir for Salmonella spp. in South Korea. The research findings can help manage the potential risk of wildlife contamination and improve precautionary measures to protect public health.

Salmonella Gallinarum in Small-Scale Commercial Layer Flocks: Occurrence, Molecular Diversity and Antibiogram

Salmonella Gallinarum is one of the most important bacterial pathogens associated with diminished egg production in poultry. The aim of this study was to understand the occurrence, molecular traits and antimicrobial resistance patterns of Salmonella Gallinarum strains isolated from small-scale commercial layer flocks with low level biosecurity standards in Bangladesh. A total of 765 samples, including cloacal swabs (535), visceral organs (50), and droppings (180), were collected from chickens of 12 layer flocks in 11 districts. Salmonella Gallinarum was isolated and characterized through culture-based method, followed by biochemical tests, sero-grouping, PCR assays, sequencing, and antibiogram. The identity of biochemically detected isolates of Salmonella Gallinarum was confirmed via genus-specific 16S rRNA gene based PCR, followed by invA and spvC genes based PCR assays. Occurrence of Salmonella Gallinarum was detected in overall 25.75% (197/765) samples, with a significantly (p < 0.05) higher incidence in visceral organs (42%) in comparison to cloacal swab (24%) and droppings (26%). Sequencing and subsequent phylogenetic analysis of invA and spvC genes in representative strains of Salmonella Gallinarum revealed a close genetic lineage, with a sequence similarity of 98.05–99.21% and 97.51–99.45%, respectively, to previously published sequences of the corresponding genes from the same serogroup strains. Remarkably, 66.5% (131/197) of the isolated strains of Salmonella Gallinarum were found to be resistant to 3 to 6 antimicrobial agents, and interpreted as multidrug resistant (MDR). The findings of this study underscore an inherent need of appropriate control measures to curb the widespread incidence of MDR Salmonella Gallinarum in small-scale commercial layer flocks, thereby, facilitating enhanced egg production and further support to the food security and safety in low resource settings.

Prevalence data of diarrheagenic E. coli in the fecal pellets of wild rodents using culture methods and PCR assay

Wild animals, such as rodents seem to be competent reservoir of bacteria-borne zoonotic diseases which disseminate in human. We investigated the presence of E. coli, Shiga toxin-producing E. coli (STEC), and Salmonella in the feces of six category wild rodent species (Apodemus agrarius, A. peninsulae, A. sylvaticus, Micromys minutus, Myodes regulus, and R. norvegicus) captured from different agricultural regions in South Korea. Among them, A. agrarius, which account for 65% of total (N = 52) individuals, are most widely distributed and abundant in various agroecosystems in South Korea. The bacterial identification was performed by cultural and molecular methods. In cultural method, the fecal cultures from 26 individuals formed colonies on E. coli-selective EMB agar media. Of them, the fecal cultures from 18 individuals also produced colonies on the Shiga toxin-producing E. coli-selective CT-SMAC agar media as well as the EMB agar media. In molecular method, polymerase chain reaction (PCR) was carried out to detect two virulence genes (stx1 and stx2) of isolated E. coli. The amplified dataset of stx1 and stx2 genes of E. coli were sequenced. In this manuscript, E. coli and STEC were detected but there were no Salmonella species. The wild rodents’ data would provide important information on reservoirs of those pathogenic bacteria.

Molecular identification of Neoechinorhynchus rutili parasite diagnosed in some fish species caught in Menzelet dam lake in Kahramanmaras province (Turkey)

This study details the molecular identification of the parasite Neoechinorhynchus rutili diagnosed in fish (Capoeta barroisi, Cyprinus carpio, Barbus rajanorum) caught in Menzelet Dam Lake in Kahramanmaras Province, Turkey. Parasite samples were obtained from the intestines of fish caught from January to June of 2013. The collected parasites were stored in sample vials containing 70% alcohol. Using staining methods and based on morphology, 120 N. rutili specimens were identified. DNA isolation of N. rutili was accomplished using special tissue sets for parasites. Specific primers were utilized in the molecular identification of N. rutili using polymerase chain reaction (PCR) and it was possible to verify that all of the parasites contained N. rutili molecules. In conclusion, using multiple methods we successfully identified and confirmed the presence of N. rutili parasites in the fish caught in Kahramanmaras Province. The process of identification of N. rutili using morphology and staining methods is time-consuming; however, PCR was successfully performed in a short time to accomplish the same results. The success of this study may lead to more original and extensive work aimed at the efficient molecular identification of parasitic agents found in fish.

Identification and characterization of Salmonella spp. from samples of broiler farms in selected districts of Bangladesh

Background and Aim:

Salmonella spp. are an important group of pathogens responsible for human and animal diseases. This study aimed to estimate the prevalence and identify and characterize of Salmonella spp. isolated from broiler farms of Gazipur, Tangail, and Dhaka districts of Bangladesh. This study also evaluated the difference of Salmonella positivity status between two groups of farms, good practices adapted in broiler rearing at the project intervened farms, and non-project intervened traditional farms.

Materials and Methods:

A total of 352 samples including 128 cloacal swabs, 32 whole carcasses, 64 feed, 64 water, and 64 attendants’ hand rinses were collected through convenient sampling technique from 16 poultry food safety project of Food and Agricultural Organization of United Nations Bangladesh intervened farms and other 16 non-project intervened farms in the same location. Various cultural based techniques and biochemical methods were employed for the estimation of prevalence, isolation, and identification of Salmonella spp. which was further evaluated by polymerase chain reaction. Antimicrobial susceptibility test using disk diffusion methods and serogrouping by slide agglutination test was accomplished for additional characterization.

Results:

Among the samples, an overall prevalence of Salmonella spp. was 31.25% (110/352) (95% confidence interval [CI]=26.44-36.38%). However, the prevalence of Salmonella spp. was 24.43% (43/176) (95% CI=18.28-31.47) in project intervened farms and 38.07% (67/176) (95% CI=30.87-45.68%) in non-intervened farms. Among the 110 isolates, 31.82% (35/110) were fitted under serogroup B, and the rest of the isolates 75 (68.18%) under serogroup D. Of 110 isolates, 82.72%, 77.27%, 81.82%, and 79.09% were susceptible to ciprofloxacin, gentamycin, norfloxacin, and streptomycin, respectively. In addition, 81.82% and 80% isolates were resistant to erythromycin and tetracycline, respectively. Isolated Salmonella spp. presented moderate resistance to both amoxicillin and azithromycin. Alarmingly, 80.91% (89/110) isolates were shown to be multidrug-resistant Salmonella spp.

Conclusion:

The study has presented a significant variation of the prevalence of Salmonella spp. between project intervened and non-project intervened farms, and this indicates project intervened farms are comparatively safer than the non-intervened farms considering public health and food safety grounds. This research outcome also has highlighted a substantial proportion of poultry origin multidrug resistance Salmonella spp. is a potential source of public health hazards. In this regard, proper awareness creation and motivational activities on good agriculture practices in poultry rearing and maintaining good personal hygiene at the farmers’ level are warranted through participatory training.

High-Throughput 16S rRNA Sequencing to Assess Potentially Active Bacteria and Foodborne Pathogens: A Case Example in Ready-to-Eat Food

Technologies to detect the entire bacterial diversity spectra and foodborne pathogens in food represent a fundamental advantage in the control of foodborne illness. Here, we applied high-throughput 16S rRNA sequencing of amplicons obtained by PCR and RT-PCR from extracted DNA and RNA targeting the entire bacterial community and the active bacterial fraction present in some of the most consumed and distributed ready-to-eat (RTE) salad brands in Europe. Customer demands for RTE food are increasing worldwide along with the number of associated foodborne illness and outbreaks. The total aerobic bacterial count in the analyzed samples was in the range of 2-4 × 10⁶ CFU/g (SD ± 1.54 × 10⁶). Culture validated methods did not detect Salmonella spp., Escherichia coli, and other fecal coliforms. 16S rRNA gene Illumina next-generation sequencing (NGS) data were congruent with these culture-based results and confirmed that these and other well-known foodborne bacterial pathogens, such as Listeria, were not detected. However, the fine-resolution of the NGS method unveiled the presence of the opportunistic pathogens Aeromonas hydrophyla and Rahnella aquatilis (relative frequency of 1.33-7.33%) that were metabolically active in addition to non-pathogenic, active members of Yersinia spp. (relative frequency of 0.0015-0.003%). The common ail and foxA marker genes of Yersinia enterocolitica were not detected by qPCR. Finally, our NGS data identified to non-pathogenic Pseudomonas spp. as the most abundant and metabolically active bacteria in the analyzed RTE salads (53-75% of bacterial abundance). Our data demonstrate the power of sequencing, in parallel, both 16S rRNA and rDNA to identify and discriminate those potentially and metabolically active bacteria and pathogens to provide a more complete view that facilitates the control of foodborne diseases, although further work should be conducted to determine the sensitivity of this method for targeting bacteria.

Distribution of virulence factors, determinants of antibiotic resistance and molecular fingerprinting of Salmonella species isolated from cattle and beef samples: suggestive evidence of animal-to-meat contamination

In this study, three hundred presumptive Salmonella strains isolated from cattle faeces and raw beef samples were subjected to both preliminary and confirmatory tests specific for Salmonella. PCR assays revealed that 100%, 20% and 26.7% of the isolates were positive for 16S rRNA, fliC and fljB gene fragments, respectively. Large proportions (62.4 to 94.3%) of these isolates were multiple antibiotic resistant (MAR) strains that were resistant to three or more antibiotics belonging to different classes. MAR phenotypes Ab1, Ab2, Ab3, Ab7, Ab8, Ab9, Ab26 and Ab27 were dominant among the isolates. Cluster analysis of antibiotic inhibition zone diameter data revealed two major clusters (clusters 1 and 2), and each cluster contained two sub-clusters (1A, 1B, 2A and 2B). PCR data revealed that 27.1% and 30.7% of the isolates possessed the spvC and invA virulent genes, respectively. There was a significant correlation between the possession of MAR phenotypes and virulent gene determinants. Analysis of restriction fragment length polymorphism (RFLP) of 16S rRNA gene fragments using EcoRI and HaeIII showed that large proportions of isolates from beef and cattle faeces produced similar genetic fingerprints. From these results, it is suggested that Salmonella species in cattle are transmitted to beef and, therefore, the consumption of undercooked beef could pose severe health complications on consumers. These findings provide baseline data that could be of great epidemiological importance and, thus, the need to utilise more sensitive typing tools in determining the genetic relatedness of isolates from different sources.

Occurrence, antimicrobial susceptibility patterns and genotypic relatedness of Salmonella spp. isolates from captive wildlife, their caretakers, feed and water in India

Occurrence of Salmonella spp. in captive wild animal species in India is largely unknown. The purpose of this study was to determine the occurrence of different Salmonella serotypes, antimicrobial resistance patterns and genotypic relatedness of recovered isolates. A total of 370 samples including faecal (n = 314), feed and water (n = 26) and caretakers stool swabs (n = 30) were collected from 40 different wild animal species in captivity, their caretakers, feed and water in four zoological gardens and wildlife enclosures in India. Salmonellae were isolated using conventional culture methods and tested for antimicrobial susceptibility with the Kirby–Bauer disc diffusion method. Salmonella isolates were serotyped and genotyping was performed using enterobacterial repetitive intergenic consensus (ERIC) PCR and 16S rRNA sequencing. Animal faecal samples were also subjected to direct PCR assay. Salmonella was detected in 10 of 314 (3.1%) faecal samples by isolation and 18 of 314 (5.7%) samples by direct PCR assay; one of 26 (3.8%) feed and water samples and five of 30 (16.7%) caretakers stool swabs by isolation. Salmonella was more commonly isolated in faecal samples from golden pheasants (25%; 2/8) and leopard (10%; 2/20). Salmonella enterica serotypes of known public health significance including S. Typhimurium (37.5%; 6/14), S. Kentucky (28.5%; 4/14) and S. Enteritidis (14.3%; 2/14) were identified. While the majority of the Salmonella isolates were pan-susceptible to the commonly used antibiotics. Seven (43.7%; 7/16) of the isolates were resistant to at least one antibiotic and one isolate each among them exhibited penta and tetra multidrug-resistant types. Three S. Kentucky serotype were identified in a same golden pheasants cage, two from the birds and one from the feed. This serotype was also isolated from its caretaker. Similarly, one isolate each of S. Typhimurium were recovered from ostrich and its caretaker. These isolates were found to be clonally related suggesting that wildlife may serve as reservoir for infections to humans and vice versa. These results emphasise the transmission of Salmonella among hosts via environmental contamination of feces to workers, visitors and other wildlife.

Periurban outbreaks of bovine calf scours in Northern India caused by Cryptosporidium in association with other enteropathogens

Bovine calf scours reported to be caused by multiple aetiologies resulting in heavy mortality in unweaned calves and huge economic loss to the dairy farmers. Among these, cryptosporidiosis is an emerging waterborne zoonoses and one of the important causes of neonatal calf diarrhoea. Poor immune response coupled with primary cryptosporidial infections predispose neonatal calves to multiple secondary infections resulting in their deaths. In the present study, faecal samples from 100 diarrhoeic calves randomly picked up out of 17 outbreaks of bovine calf diarrhoea in periurban Ludhiana, Punjab in Northern India were subjected to conventional (microscopy, modified Zeihl-Neelsen (mZN) staining) and immunological and molecular techniques (faecal antigen capture ELISA and PCR) for detection of primary Cryptosporidium parvum infection as well as other frequently reported concurrent pathogens, viz. rotavirus and coronavirus, Salmonella spp., Escherichia coli, Clostridium perfringens and Eimeria spp. The faecal antigen capture ELISA and PCR revealed 35% prevalence of C. parvum in contrast to 25% by mZN staining with a relatively higher prevalence (66·7%) in younger (8-14-day-old) calves. The detection rate of the other enteropathogens associated with C. parvum was 45·71% for C. perfringens followed by Salmonella spp (40·0%), rotavirus (36·0%), coronavirus (16·0%), E. coli (12·0%) and Eimeria spp (4·0%) The sensitivity for detection of C. parvum by ELISA and mZN staining in comparison to PCR was 97·14% and 72·72%, respectively. An important finding of the study was that C. parvum alone was found in only 10% of the diarrhoeic faecal samples, whereas, majority of the samples (90%) showed mixed infections ranging from a combination of two to five agents. This is the first documentary proof of C. parvum and associated pathogens responsible for severe periurban outbreaks of bovine calf diarrhoea culminating in heavy mortality from Northern India.

Use of Pooled Samples for the Detection of Salmonella in Feces by Polymerase Chain Reaction

Many epidemiological studies of Salmonella rely on conventional bacteriological culture methods to detect Salmonella in fecal samples. These culture-based methods are inefficient for epidemiological studies in populations with a low prevalence of Salmonella. The objective of this study was to optimize a protocol that uses pooled Salmonella enrichment broth cultures of bovine feces and polymerase chain reaction (PCR) for the detection of the invA gene of Salmonella in feces. In one field trial, 196 animals were sampled, and all samples were tested by culture, invA PCR on individual samples, invA PCR on pools of 5 samples, and BAX PCR on individual samples. All assays showed a high agreement on individual samples (kappa ≥ 0.75). The invA PCR was run on each of 40 pools and detected 19 of 22 culture-positive pools. In another field trial, 152 samples were taken from 4 dairies, and the invA PCR was performed on pools of 5 samples in addition to bacteriological culture of individual samples. Salmonella was detected in 5 of the 32 pools (7 total positive samples) by both PCR and culture. One pool was PCR-positive but culture-negative. Pooling did not dramatically affect the performance of the invA PCR; most of the culture-positive samples were detected, including all of the samples when there were 4 or more Salmonella colonies on the agar plate. Based on these field trials, invA PCR on pooled samples appears to be an efficient method of Salmonella detection as long as Salmonella loads are not extremely low.

Exploring specific primers targeted against different genes for a multiplex PCR for detection of Listeria monocytogenes

The efficacy of six different sets of primers targeted against 16S rRNA and virulence genes such as ‘iap’, ‘hly’ and ‘prf’ was evaluated in separate PCR assays. The primer pairs targeted against 16S rRNA resulted into amplification of 1.2 kb PCR product. However, sets of primers targeted against different regions of ‘iap’ produced 371 and 660 bp PCR products, respectively. The primer pair targeted against ‘prf’ gene could produce 508 bp product. Three primer pairs targeted against different regions of ‘hly’, i.e., ‘hly’, ‘hly A’ and ‘hly K9’ were able to amplify 713, 276 and 384 bp products, respectively. The PCR conditions were also optimized in respect of two internal sets of primers falling within ‘iap’ and ‘hly’ genes that amplified 119 and 188 bp products to verify the PCR results obtained with respective external sets of primers. Three different combinations involving four sets of primers based on 16S rRNA, ‘iap’, ‘hly’ and ‘prf’ were explored in respective multiplex PCR assays in order to select a suitable combination. Combination 1 and 3 worked successfully as revealed by amplification of all the four bands of expected sizes on agarose gel. However, while optimizing the different parameters for developing a functional multiplex PCR, it was observed that in both these combinations, only two of the amplified products, i.e., 1.2 kb and 713 bp could be invariably detected. Hence, these two primers were combined in the multiplex PCR and the conditions were optimized for application in dairy foods for detection of Listeria monocytogenes.

Detection of Salmonella in chicken meat by insulated isothermal PCR

Consumption of Salmonella-contaminated foods, such as poultry and fresh eggs, is known to be one of the main causes of salmonellosis. Conventional PCR methods, including real-time PCR for rapid detection of Salmonella, in general require skilled technicians and costly instruments. A recently developed novel convective PCR, insulated isothermal PCR (iiPCR), is carried out in polycarbonate capillary tubes. In this study, we designed TaqMan probes and PCR primers based on the yrfH gene encoding a heat shock protein for the iiPCR detection of Salmonella in chicken meat samples. The TaqMan probe was labeled with 6-carboxyfluorescein and 6-carboxytetramethylrhodamine at the 5' and 3' ends, respectively. The PCR amplicon was 133 bp. A typical run of this iiPCR assay was completed within 1 h. Specific PCR products were obtained for 148 strains representing 49 serotypes of Salmonella tested. Under the same conditions, false-positive results were not obtained for 98 non-Salmonella strains tested, including strains of Enterobacteriaceae closely related to Salmonella. For chicken meat samples, with a 5-h enrichment step Salmonella at as low as 10⁰ CFU/g of poultry meat could be detected. Because the amplification signals from the probes are detectable at 520 nm, identification of the PCR products by gel electrophoresis is not required. Compared with conventional PCR, the iiPCR system requires less expertise and provides an economical, reliable, and rapid tool for result interpretation. Detection results can be obtained within 8 h, including the enrichment and DNA extraction steps.

Formation of biofilms under phage predation: considerations concerning a biofilm increase

Bacteriophages are emerging as strong candidates for combating bacterial biofilms. However, reports indicating that host populations can, in some cases, respond to phage predation by an increase in biofilm formation are of concern. This study investigates whether phage predation can enhance the formation of biofilm and if so, if this phenomenon is governed by the emergence of phage-resistance or by non-evolutionary mechanisms (eg spatial refuge). Single-species biofilms of three bacterial pathogens (Pseudomonas aeruginosa, Salmonella enterica serotype Typhimurium, and Staphylococcus aureus) were pretreated and post-treated with species-specific phages. Some of the phage treatments resulted in an increase in the levels of biofilm of their host. It is proposed that the phenotypic change brought about by acquiring phage resistance is the main reason for the increase in the level of biofilm of P. aeruginosa. For biofilms of S. aureus and S. enterica Typhimurium, although resistance was detected, increased formation of biofilm appeared to be a result of non-evolutionary mechanisms.

Dermanyssus gallinae in layer farms in Kosovo: a high risk for Salmonella prevalence

Background

The poultry red mite (PRM), Dermanyssus gallinae (D.g.) is a serious ectoparasitic pest of poultry and potential pathogen vector. The prevalence of D. g. and the prevalence of Salmonella spp. within mites on infested laying poultry farms were investigated in Kosovo.

Findings

In total, 14 populated layer farms located in the Southern Kosovo were assessed for D. g. presence. Another two farms in this region were investigated 6 months after depopulation. Investigated flocks were all maintained in cages, a common housing system in Kosovo. A total of eight farms were found to be infested with D. g. (50%) at varying levels, including the two depopulated farms. The detection of Salmonella spp. from D. g. was carried out using PCR. Out of the eight layer farms infested with D. g., Salmonella spp. was present in mites on three farms (37.5%).

Conclusions

This study confirms the high prevalence of D. g. in layer flocks in Kosovo and demonstrates the link between this mite and the presence of Salmonella spp. on infested farms.

Development of a panel of multiplex real-time polymerase chain reaction assays for simultaneous detection of major agents causing calf diarrhea in feces

Calf diarrhea is a major economic burden to the bovine industry. Since multiple infectious agents can be involved in calf diarrhea, and the detection of each of the causative agents by traditional methods is laborious and expensive, a panel of 2 multiplex real-time polymerase chain reaction (PCR) assays was developed for rapid and simultaneous detection of the 5 major bovine enteric pathogens (i.e., Bovine coronavirus [BCoV; formally known as Betacoronavirus 1], group A Bovine rotavirus [BRV], Salmonella spp., Escherichia coli K99(+), and Cryptosporidium parvum). The estimated detection limit (i.e., analytic sensitivity) of the panel was 0.1 TCID(50) (50% tissue culture infective dose) for BCoV and group A BRV; 5 and 0.5 colony-forming units for E. coli K99(+) and Salmonella, respectively; and 50 oocysts for Cryptosporidium per reaction. In testing 243 fecal samples obtained from submissions to the Iowa State University Veterinary Diagnostic Laboratory or from experimental animals with known infection status, the newly developed multiplex real-time PCR panel simultaneously detected all 5 pathogens directly from fecal samples and was more rapid and sensitive than the traditional diagnostic tests. The PCR panel showed 89%-97% agreement with those conventional diagnostic tests, demonstrating diagnostic sensitivity equal to or better than that of the conventional tests. In conclusion, the multiplex real-time PCR panel can be a tool for a timely and accurate diagnosis of calf diarrhea associated with BCoV, group A BRV, E. coli K99(+), Salmonella, and/or Cryptosporidium.

Prolonged impact of antibiotics on intestinal microbial ecology and susceptibility to enteric Salmonella infection

The impact of antibiotics on the host's protective microbiota and the resulting increased susceptibility to mucosal infection are poorly understood. In this study, antibiotic regimens commonly applied to murine enteritis models are used to examine the impact of antibiotics on the intestinal microbiota, the time course of recovery of the biota, and the resulting susceptibility to enteric Salmonella infection. Molecular analysis of the microbiota showed that antibiotic treatment has an impact on the colonization of the murine gut that is site and antibiotic dependent. While combinations of antibiotics were able to eliminate culturable bacteria, none of the antibiotic treatments were effective at sterilizing the intestinal tract. Recovery of total bacterial numbers occurs within 1 week after antibiotic withdrawal, but alterations in specific bacterial groups persist for several weeks. Increased Salmonella translocation associated with antibiotic pretreatment corrects rapidly in association with the recovery of the most dominant bacterial group, which parallels the recovery of total bacterial numbers. However, susceptibility to intestinal colonization and mucosal inflammation persists when mice are infected several weeks after withdrawal of antibiotics, correlating with subtle alterations in the intestinal microbiome involving alterations of specific bacterial groups. These results show that the colonizing microbiotas are integral to mucosal host protection, that specific features of the microbiome impact different aspects of enteric Salmonella pathogenesis, and that antibiotics can have prolonged deleterious effects on intestinal colonization resistance.

Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract

The commensal microbiota protects the murine host from enteric pathogens. Nevertheless, specific pathogens are able to colonize the intestinal tract and invade, despite the presence of an intact biota. Possibly, effective pathogens disrupt the indigenous microbiota, either directly through pathogen-commensal interaction, indirectly via the host mucosal immune response to the pathogen, or by a combination of these factors. This study investigates the effect of peroral Salmonella enterica serovar Typhimurium infection on the intestinal microbiota. Since the majority of the intestinal microbiota cannot be cultured by conventional techniques, molecular approaches using 16S rRNA sequences were applied. Several major bacterial groups were assayed using quantitative PCR. Administration of either the 50% lethal dose (LD(50)) or 10x LD(50) of Salmonella enterica serovar Typhimurium caused changes in the microbiota throughout the intestinal tract over the time course of infection. A 95% decrease in total bacterial number was noted in the cecum and large intestine with 10x LD(50) S. enterica serovar Typhimurium challenge at 7 days postinfection, concurrent with gross evidence of diarrhea. In addition, alterations in microbiota composition preceded the onset of diarrhea, suggesting the involvement of pathogen-commensal interactions and/or host responses unrelated to diarrhea. Microbiota alterations were not permanent and reverted to the microbiota of uninfected mice by 1 month postinfection. Infection with a Salmonella pathogenicity island 1 (SPI1) mutant did not result in microbiota alterations, while SPI2 mutant infections triggered partial changes. Neither mutant was capable of prolonged colonization or induction of mucosal inflammation. These data suggest that several Salmonella virulence factors, particularly those involved in the local mucosal host response, are required for disruption of the intestinal ecosystem.

Detection of Salmonella sp. in Dermanyssus gallinae using an FTA filter-based polymerase chain reaction

Salmonella spp. bacteria are responsible for some of the most important zoonoses worldwide. Because Dermanyssus gallinae (DeGeer) (Acari: Dermanyssidae) has been recently reported to be an experimental vector of Salmonella Enteritidis, it would be of benefit to evaluate the presence of this bacterium in mites. A molecular detection tool associating a simple filter-based DNA preparation with a specific 16S rDNA Salmonella sp. polymerase chain reaction (PCR) amplification was described. The limit of detection with this method was 2 x 10(4) bacteria per mite. To adapt this technique for large-scale studies, two sizes of mite pools were tested and a preliminary investigation was carried out on mites from 16 currently or previously contaminated farms. Mites sampled from one farm of each type were positive for Salmonella, suggesting that Dermanyssus could act as a reservoir between flocks. In further investigations, it will be necessary to carry out a large-scale study to assess the role of D. gallinae in the epidemiology of avian salmonellosis.

Detection and characterization of Salmonella associated with tropical seafood

The prevalence of Salmonella in seafood samples collected from the southwest coast of India was studied by conventional culture and by a DNA based molecular technique, polymerase chain reaction (PCR). While conventional culture techniques detected Salmonella in only 20 out of the 100 samples analyzed, direct enrichment lysate PCR detected 52 as positive for Salmonella. A set of three different PCR primers viz., hns, invA and invE were used. It was observed that hns primer detected Salmonella in a significantly higher number of samples. Fourteen out of nineteen isolates belonged to serovar S. enterica Weltevreden. S. Weltevreden isolates were genotyped yielding 4 different patterns both by RAPD and ERIC-PCR but when combined, the overall results discriminated the isolates of S. Weltevreden into 6 different types. This suggests that genetically diverse Salmonella Weltevreden are prevalent in seafood.

Identification of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with 16S ribosomal DNA-based oligonucleotide array hybridization

Rapid identification of the genus and species of bacteria in foods and clinical specimens is important. In this report, DNA sequences of bacterial 16S rDNA were used to develop the oligonucleotide array for the identification of bacterial strains of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. Most of these bacterial strains may cause food-borne outbreaks or sporadic cases. A rapid (<4 h) detection method that used universal PCR primers to amplify the variable regions of bacterial 16S rDNA, followed by reverse hybridization of the PCR products, which were biotin labeled, to the oligonucleotides arrayed on the chip was developed. Fifteen oligonucleotide probes were selected and spotted on the nylon strip to determine the array hybridization patterns. It was successful in discriminating Bacillus spp., E. coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with identification, in general, to the genus level, not species level. As 182 randomly selected strains were assayed, the detection rate was found higher than 98%. Except for 3 strains, the remaining 179 strains were correctly identified and no cross reactions were observed. These 179 strains generated five hybridization patterns. Adding more oligonucleotide probes to the array may allow the detection of more bacterial genera and species without significantly increasing the complexity or cost.

Comparison of a membrane surface adhesion recovery method with an IMS method for use in a polymerase chain reaction method to detect Escherichia coli O157:H7 in minced beef

In this study, enrichment procedures and two recovery methods, a membrane surface adhesion technique and an immunomagnetic separation (IMS), were compared for use in conjunction with a multiplex polymerase chain reaction (PCR) method with a view to describing a fast (24 h) and economical test for detection of Escherichia coli O157:H7 in meat samples. The study showed no significant difference between three different enrichment media (BHI, E. coli (E.C.) broth+novobiocin, modified tryptone soya broth (mTSB)+novobiocin) or two incubation temperatures (37 or 41.5 degrees C) for growth of E. coli O157:H7 in minced beef. Minced beef samples inoculated with E. coli O157:H7 at 40 cfu g(-1) were incubated at 37 degrees C for 16 h in E.C. broth+novobiocin reaching numbers of (log(10)7.82-8.70). E. coli O157:H7 were recovered by attachment to polycarbonate membranes immersed in the enriched cultures for 15 min or by immunomagnetic separation. Subsequent treatment of recovered membranes or IMS beads with lysis buffer and phenol/chloroform/isoamyl alcohol was used to extract the DNA from the extracted E. coli O157:H7 cells. The results show when E. coli O157:H7 was present at high levels in the enriched meat sample (log(10)9.6-7.5 cfu ml(-1); >16-h enrichment), the membrane and IMS techniques recovered similar levels of the pathogen and the microorganism was detectable by PCR using both methods. At lower levels of E. coli O157:H7 (log(10)6.4), only the IMS method could recover the pathogen but at levels below this neither method could recover sufficient numbers of the pathogens to allow detection. The conclusion of the study is that with sufficient enrichment time (16 h) the membrane surface adhesion membrane extraction method used in combination with multiplex PCR has the potential for a rapid and economical detection method.

AnDiaTec Salmonella sp. PCR-ELISA for analysis of food samples

A commercially available PCR kit (AnDiaTec Salmonella sp. PCR-ELISA) was developed and evaluated for the detection of Salmonella sp. in food samples. The test is based on PCR amplification and hybridization of the amplified DNA to a microtiter plate followed by the detection of PCR product in the manner of an enzyme-linked immunosorbent assay test. The sensitivity and specificity were evaluated first with Salmonella pure cultures and artificially contaminated food samples, including food types for which an inhibition of the PCR reaction was expected. Both experiments proved a very good sensitivity, specificity, and reliability of the test with a very broad range of food types. In a second evaluation study, more than 1,100 food samples of different types were tested in parallel with the PCR method and with the International Standardization Organization 6579 bacteriological reference method. The results of this evaluation study and the results from other experiments on dilutions of artificially contaminated food samples led to the establishment of a positive-negative cutoff value (optical density at 450 nm of more than 0.9) with respect to the conventional bacteriological method. Using this positive-negative cutoff, 98% agreement to the bacteriological method was obtained.

Evaluation of the specificity of Salmonella PCR primers using various intestinal bacterial species

AIMS

Nine sets of PCR primers targeting Salmonella were evaluated for their specificity with pure cultures of intestinal-associated bacteria prior to their application to Salmonella detection in faecal samples.

METHODS AND RESULTS

Gene targets of PCR primers included: 16S rDNA, a Salmonella pathogenicity island I virulence gene, Salmonella enterotoxin gene (stn), invA gene, Fur-regulated gene, histidine transport operon, junction between SipB and SipC virulence genes, Salmonella-specific repetitive DNA fragment, and multiplex targeting invA gene and spvC gene of the virulence plasmid. Fifty-two Salmonella strains were used to determine sensitivity; five strains from related genera and 45 intestinal bacteria were used to evaluate specificity. All primers amplified DNA from Salmonella strains, although two primer sets failed to amplify Salmonella DNA from either Salmonella bongori (hilA) or subgroups VI or VII (16S rDNA). There was no detected amplification of DNA from related bacterial genera with any of nine PCR assays. Six of the PCR assays amplified DNA for some intestinal bacteria.

CONCLUSIONS

Only three primer pairs were determined to be suitable for application of PCR amplification of Salmonella in faecal samples - 16S rDNA, stn and histidine transport operon. We are currently evaluating their sensitivity of detection of Salmonella in faecal samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrated the importance of internal lab validation of PCR primers prior to application to the type of samples of interest. Information from this evaluation can be applied in other labs to facilitate choosing Salmonella PCR primers.

Detection of Salmonella spp. in tropical seafood by polymerase chain reaction

The incidence of Salmonella spp. in tropical seafood was studied using standard microbiological techniques and polymerase chain reaction (PCR). Six of 20 finfish (30%), 4 of 20 clams (20%) and 1 of 20 shrimp (5%) were positive by culture techniques and by PCR. In a comparative study of different selective enrichment broths and selective plating media, more than one enrichment broth and selective agar were found to be necessary for efficient detection of Salmonella from seafood. Selenite cystine broth (SCB) was found to be more efficient compared to tetrathionate broth (TTB) while both bismuth sulfite agar (BSA) and hektoen enteric agar (HEA) were equally effective as selective plating media for fish. In the case of clams, HEA was found to be more effective. The presence of Salmonella spp. could be detected by PCR amplification of DNA extracted directly from the enrichment broths. In two cases, enrichment broths that were positive by PCR did not yield Salmonella by conventional methods.

Detection of Salmonella from chicken rinses and chicken hot dogs with the automated BAX PCR system

The BAX system with automated PCR detection was compared with standard cultural procedures for the detection of naturally occurring and spiked Salmonella in 183 chicken carcass rinses and 90 chicken hot dogs. The automated assay procedure consists of overnight growth (16 to 18 h) of the sample in buffered peptone broth at 35 degrees C, transfer of the sample to lysis tubes, incubation and lysis of the cells, transfer of the sample to PCR tubes, and placement of tubes into the cycler-detector, which runs automatically. The automated PCR detection assay takes about 4 h after 16 to 24 h of overnight preenrichment. The culture procedure consists of preerichment, enrichment, plating, and serological confirmation and takes about 72 h. Three trials involving 10 to 31 samples were carried out for each product. Some samples were spiked with Salmonella Typhimurium, Salmonella Heidelberg, Salmonella Montevideo, and Salmonella Enteritidis at 1 to 250 cells per ml of rinse or 1 to 250 cells per g of meat. For unspiked chicken rinses, Salmonella was detected in 2 of 61 samples with the automated system and in 1 of 61 samples with the culture method. Salmonella was recovered from 111 of 122 spiked samples with the automated PCR system and from 113 of 122 spiked samples with the culture method. For chicken hot dogs, Salmonella was detected in all 60 of the spiked samples with both the automated PCR and the culture procedures. For the 30 unspiked samples, Salmonella was recovered from 19 samples with the automated PCR system and from 10 samples with the culture method. The automated PCR system provided reliable Salmonella screening of chicken product samples within 24 h.

Application of the PCR technique for a rapid, specific and sensitive detection of Salmonella spp. in foods

We report here the use of a PCR based assay modified by us for the detection of Salmonella spp. in foods, based on amplification of a 236 bp Salmonella specific hin/H2 region [Way et al. (1993) Applied and Environmental Microbiology 59, 1473-1479], using Ampli Taq Gold polymerase. Using this assay we were able to detect all the Salmonella serovars tested. The limit of detection was 1 fg of purified target DNA or N x 10(0) (1-3 cells) cfu ml(-1) of pure bacterial culture. This assay could detect N x 10(0) cfu Salmonella cells g(-1) of the food sample unambiguously in presence of endogenous microflora following 6 h enrichment, thus requires a duration of approximately 10 h for the full processing from DNA template preparation, PCR and visualization of DNA product on agarose gel. The main advantage of this PCR detection method is its sensitivity, and specificity. We also tried to adopt DNA template isolation method simply by boiling the bacterial cells thereby reducing the possibility of contamination, cutting the processing time and cost considerably. This can be an added advantage for the use of this system in simple lab setups.

Designing of polymerase chain reaction primers for the detection of Salmonella enteritidis in foods and faecal samples

AIMS

In this study, novel insertion element (IE) DNA targeted polymerase chain reaction (PCR) primers were designed and further used for the specific detection of Salmonella enteritidis in foods and faecal samples.

METHODS AND RESULTS

Polymerase chain reaction primers, based upon their IE gene sequence (accession number Z83734), were developed for the detection of Salm. enteritidis. These primers were termed IE1L-IE1R and IE2L-IE3R. The cell lysate, rather than the extracted DNA, was used as template and preculturing of bacterial material was carried out prior to the PCR assay. The specificities of these developed primers were to be confirmed further. The PCR procedure developed was used to examine 170 endogenously contaminated samples, including poultry, seafood, meats, faecal specimens and some feed samples. Salmonella enteritidis was detected in 5.29% (nine of 170) of the samples.

CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY

Two sets of novel PCR primers, based upon their IE gene sequence, have been developed. These primers demonstrated the ability to be used for the specific detection of Salm. enteritidis. When PCR primers IE1L-IE1R were used for the detection of artificially Salm. enteritidis-contaminated food samples, as few as 1 cell ml(-1) sample could be detected using this PCR process.

Combination of immunomagnetic separation and polymerase chain reaction for the simultaneous detection of Listeria monocytogenes and Salmonella spp. in food samples

A method that combined the immunomagnetic separation (IMS) technique and the multiplex polymerase chain reaction (PCR) method (i.e., the IMS-mPCR method) was developed for simultaneous detection of Listreria monocytogenes and Salmonella spp. in food samples. When only the multiplex PCR method was used, it was found that if cell numbers of each of the two target organisms (L. monocytogenes and Salmonella spp.) were above the detection limit, but differed by more than 2 logs-e.g., n x 10(7) to n x 10(4) or n x 10(6) to n x 10(3)--the organism presenting the lower numbers might go undetected. Following the enrichment step with universal preenrichment (UP) broth, if an IMS method using equal quantities of anti-Listeria and anti-Salmonella immunomagnetic beads was performed prior to PCR, both pathogens could be detected unambiguously. Such results could be obtained for target organisms in food samples, such as milk, dairy, and meat products, if similar enrichment and IMS steps were performed prior to PCR.

Bacillus cereus group strains, their hemolysin BL activity, and their detection in foods using a 16S RNA and hemolysin BL gene-targeted multiplex polymerase chain reaction system

Hemolysin BL (HBL) is a major virulence factor for Bacillus cereus group strains. It is also a target enterotoxin for the most commonly used B. cereus detection kit, i.e., the B. cereus enterotoxin (diarrheal type) reversed passive latex agglutination (BCET-RPLA) test kit. A survey of the HBL activities and the cytotoxicities to the Chinese hamster ovary (CHO) cells for the B. cereus group strains, however, showed that although only part of the B. cereus group strains are HBL active, all strains show cytotoxicity to the CHO cells. Thus, methods that allow the detection of not only the HBL but also of the B. cereus group strains are important. In this study, by comparison of the gene sequences of the 16S rRNA for B. cereus group and other bacteria strains, we designed primers B16S1 and B16S2 specific to all the B. cereus group strains. In addition, because HBL is a major enterotoxin, we also designed HBL gene-specific polymerase chain reaction (PCR) primers, i.e., Hm1 and Hm2, that generated the same results as those of the hemolysis and BCET-RPLA assays. Primers B16S1/B16S2 and Hm1/Hm2 could be combined into a multiplex PCR system for the simultaneous detection of B. cereus group cells and the possible presence of their HBL enterotoxins. Also, all these PCR systems allowed the detection of n x 10(0) CFU B. cereus cells per g of food sample if an 8-h enrichment step was performed prior to the PCR.

Immobilization with metal hydroxides as a means to concentrate food-borne bacteria for detection by cultural and molecular methods

The application of nucleic acid amplification methods to the detection of food-borne pathogens could be facilitated by concentrating the organisms from the food matrix before detection. This study evaluated the utility of metal hydroxide immobilization for the concentration of bacterial cells from dairy foods prior to detection by cultural and molecular methods. Using reconstituted nonfat dry milk (NFDM) as a model, two food-borne pathogens (Listeria monocytogenes and Salmonella enterica serovar Enteritidis) were concentrated from 25-ml samples by the sequential steps of clarification and high-speed centrifugation (designated primary concentration) and immobilization with zirconium hydroxide and low-speed centrifugation (designated secondary concentration). Sample volume reduction after immobilization with zirconium hydroxide was 50-fold, with total bacterial recoveries ranging from 78 to 96% of input for serovar Enteritidis and 65 to 96% of input for L. monocytogenes. Immobilized bacteria remained viable and could be enumerated by standard cultural procedures. When followed by RNA extraction and subsequent detection by reverse transcription (RT)-PCR, detection limits of 10(1) to 10(2) CFU/25 ml of reconstituted NFDM were achieved for both organisms. The bacterial-immobilization step was relatively nonspecific, resulting in recovery of >50% of the input cells when evaluated on a panel of representative bacterial strains of significance to foods. The method could be adapted to more complex dairy products, such as whole milk and ice cream, for which bacterial recoveries after immobilization ranged from 64 to >100%, with subsequent RT-PCR detection limits of >/=10(2) CFU/ml for whole milk and >/=10(1) CFU for ice cream for both serovar Enteritidis and L. monocytogenes. The bacterial-immobilization method is easy, rapid, and inexpensive and may have applications for the concentration of a wide variety of food-borne bacteria prior to detection by both conventional and alternative methods.

Detection of low numbers of Salmonella in environmental water, sewage and food samples by a nested polymerase chain reaction assay

A polymerase chain reaction (PCR) assay with two nested pairs of primers selected from conserved sequences within a 2.3 kb randomly cloned DNA fragment from the Salmonella typhimurium chromosome was developed. The nested PCR assay correctly identified 128 of a total of 129 Salmonella strains belonging to subspecies I, II, IIIb and IV. One strain of Salm. arizona (ssp. IIIa) tested negative. No PCR products were obtained from any of the 31 non-Salmonella strains examined. The sensitivity of the assay was 2 cfu, as determined by analysis of proteinase K-treated boiled lysates of Salm. typhimurium. The performance of the assay was evaluated for environmental water, sewage and food samples spiked with Salm. typhimurium. Water and sewage samples were filtered and filters were enriched overnight in a non-selective medium. Prior to PCR, the broth cultures were subjected to a rapid and simple preparation procedure consisting of centrifugation, proteinase K treatment and boiling. This assay enabled detection of 10 cfu 100 ml(-1) water with background levels of up to 8700 heterotrophic organisms ml(-1) and 10000 cfu of coliform organisms 100 ml(-1) water. Spiked food samples were analysed with and without overnight enrichment in a non-selective medium using the same assay as above. Nested PCR performed on enriched broths enabled detection of <10 cfu g(-1) food. Variable results were obtained for food samples examined without prior enrichment and most results were negative. This rapid and simple assay provides a sensitive and specific means of screening drinking water or environmental water samples, as well as food samples, for the presence of Salmonella spp.

Rapid detection of stressed Salmonella spp. in dairy and egg products using immunomagnetic separation and PCR

The rapid detection of an average of 5.9 stressed Salmonella cells in 25 g of food product using immunomagnetic separation (IMS) and PCR is described. For pasteurised egg yolk, egg yolk powder, ice-cream, whole egg, egg white and cheeses made from pasteurised milk PCR was applied after 16 h of preenrichment in buffered peptone water (BPW) using IMS and alkaline lysis as sample preparation method. For whole egg and egg white the BPW was supplemented with iron. For milk powder, and raw milk cheeses, the 16-h preenrichment in BPW was followed by IMS and a 4-h enrichment in Rappaport-Vassiliadis broth. In the latter case, PCR was applied on the enrichment medium after centrifugation and alkaline lysis. For PCR the primers ST11 and ST15 (Aabo et al., 1993) producing a fragment of 429 bp were used. An internal PCR control, designed to be co-amplified with the target DNA using the same primers but producing a smaller fragment of 240 bp, was used.

Use of polymerase chain reaction and restriction enzyme analysis to directly detect and identify Salmonella typhimurium in food

A primer set of oligonucleotides (Salm 3 and Salm 4) from the invA gene of Salmonellae has been evaluated for the specific detection of Salmonella spp. by the polymerase chain reaction (PCR). This primer set amplified 33 Salmonella serovars but did not amplify 16 non-Salmonella bacteria. Moreover, after PCR amplification, it was possible to identify Salm. typhimurium by restriction enzyme analysis. The PCR-RE method developed could represent a helpful tool for detecting Salmonella spp., and for directly and rapidly identifying Salm. typhimurium in food.

Development of a PCR microplate-capture hybridization method for simple, fast and sensitive detection of Salmonella serovars in food

The authors have developed an easy and rapid detection and identification system for Salmonella spp. in food. The gene inv A was selected as the target sequence. Oligonucleotides derived from conserved regions of this gene were able to exclusively prime the amplification of a 389 bp fragment when Salmonella spp. DNA was used as the template. An internal Salmonella spp. specific DNA probe was used for confirmation of the amplified polymerase chain reaction(PCR)product, by Southern blot or microplate-capture hybridization assay. In this fashion the sensitivity of the method was increased 100-fold (4.5 fg total DNA). To validate the method, a total of 75 food samples were tested. The PCR-microplate capture hybridization assay is easy to perform and much faster than traditional detection methods for Salmonella spp. in food. Hybridization in microtitre plates is more readily observed than in Southern blot and is more sensitive than conventional agarose gel electrophoresis.