Application of molecular genetic methods in diagnostics and epidemiology of food-borne bacterial pathogens

Genetic approach toward linkage of Iran 2012-2016 cholera outbreaks with 7th pandemic Vibrio cholerae

Vibrio cholerae, as a natural inhabitant of the marine environment is among the world-leading causes of diarrheal diseases. The present study aimed to investigate the genetic relatedness of Iran 2012-2016 V. cholerae outbreaks with 7th pandemic cholera and to further characterize the non-ST69/non-ST75 sequence types strains by whole-genome sequencing (WGS).Twenty V. cholerae isolates related to 2012, 2013, 2015 and 2016 cholera outbreaks were studied by two genotyping methods - Pulsed-field Gel Electrophoresis (PFGE) and Multi-locus Sequence Typing (MLST)-and by antimicrobial susceptibility testing. Seven sequence types (STs) and sixteen pulsotypes were detected. Sequence type 69 was the most abundant ST confirming that most (65%, 13/20) of the studied isolates collected in Iran between 2012 and 2016 belonged to the 7th pandemic clone. All these ST69 isolates (except two) exhibited similar pulsotypes. ST75 was the second most abundant ST. It was identified in 2015 and 2016. ST438, ST178, ST579 and STs of 983 and 984 (as newfound STs) each were only detected in one isolate. All strains collected in 2016 appeared as distinct STs and pulsotypes indicative of probable different originations. All ST69 strains were resistant to nalidixic acid. Moreover, resistance to nalidixic acid, trimethoprim-sulfamethoxazole and tetracycline was only observed in strains of ST69. These properties propose the ST69 as a unique genotype derived from a separate lineage with distinct resistance properties. The circulation of V. cholerae ST69 and its traits in recent years in Iran proposes the 7th pandemic strains as the ongoing causes of cholera outbreaks in this country, although the role of ST75 as the probable upcoming dominant ST should not be ignored.Genomic analysis of non-ST69/non-ST75 strains in this study showed ST579 is the most similar ST type to 7th pandemic sequence types, due to the presence of wild type-El Tor sequences of tcpA and VC-1319, VC-1320, VC-1577, VC-1578 genes (responsible for polymyxin resistance in El Tor biotype), the traits of rstC of RS1 phage in one strain of this ST type and the presence of VPI-1 and VSP-I islands in ST579 and ST178 strains. In silico analysis showed no significant presence of resistance genes/cassettes/plasmids within non-ST69/non-ST75 strains genomes. Overall, these data indicate the higher susceptibility of V. cholerae non-ST69/non-ST75 strains in comparison with more ubiquitous and more circulating ST69 and ST75 strains.In conclusion, the occurrence of small outbreaks and sporadic cholera cases due to V. cholerae ST69 in recent years in Iran shows the 7th pandemic strains as the persistent causes of cholera outbreaks in this country, although the role of ST75 as the second most contributed ST should not be ignored. The occurrence of non-ST69/non-ST75 sequence types with some virulence factors characteristics in border provinces in recent years is noteworthy, and further studies together with surveillance efforts are expected to determine their likely route of transport.

The Rapid Detection of Salmonella enterica, Listeria monocytogenes, and Staphylococcus aureus via Polymerase Chain Reaction Combined with Magnetic Beads and Capillary Electrophoresis

Food safety concerns regarding foodborne pathogen contamination have gained global attention due to its significant implications. In this study, we developed a detection system utilizing a PCR array combined with an automated magnetic bead-based system and CE technology to enable the detection of three foodborne pathogens, namely Salmonella enterica, Listeria monocytogenes, and Staphylococcus aureus. The results showed that our developed method could detect these pathogens at concentrations as low as 7.3 × 101, 6.7 × 102, and 6.9 × 102 cfu/mL, respectively, in the broth samples. In chicken samples, the limit of detection for these pathogens was 3.1 × 104, 3.5 × 103, and 3.9 × 102 cfu/g, respectively. The detection of these pathogens was accomplished without the necessity for sample enrichment, and the entire protocols, from sample preparation to amplicon analysis, were completed in approximately 3.5 h. Regarding the impact of the extraction method on detection capability, our study observed that an automated DNA extraction system based on the magnetic bead method demonstrated a 10-fold improvement or, at the very least, yielded similar results compared to the column-based method. These findings demonstrated that our developed model is effective in detecting low levels of these pathogens in the samples analyzed in this study. The PCR-CE method developed in this study may help monitor food safety in the future. It may also be extended to identify other foodborne pathogens across a wide range of food samples.

Stain-free Gram staining classification of pathogens via single-cell Raman spectroscopy combined with machine learning

Gram staining (GS) is one of the routine microbiological operations to classify bacteria based on the cell wall structure. Accurate GS classification of pathogens is of great significance since it helps correct administration of antimicrobial treatment. The laborious procedure and low sensitivity results related to conventional GS have resulted in reluctance among clinicians. In this study, we integrate confocal Raman spectroscopy and machine learning techniques to distinguish Gram-negative (GN) or Gram-positive (GP) bacteria. A single-cell Raman database including seven most common clinical pathogens (three GP strains and four GN strains) was constructed. Machine learning algorithms including the support-vector machine (SVM), k-nearest neighbors' algorithm (k-NN), gradient boosting machine (GBM), linear discriminant analysis (LDA), and t-distributed stochastic neighbor embedding (t-SNE) were trained to achieve the binary classification for GS. With such a relatively small database, the SVM model achieved the highest accuracy of 98.1%. The molecular signatures of GN and GP embedded in their Raman fingerprints were identified with hierarchical cluster analysis (HCA). The results indicated that Raman peaks for peptidoglycan and teichoic acid were the most significant factors that contributed to accurate classification. The Raman machine learning approach could greatly enhance the diagnosis of pathogenic infections.

Prevalence, Distribution, and Diversity of Salmonella Strains Isolated From a Subtropical Lake

This study investigated the prevalence, serovar distribution, antimicrobial resistance, and pulsed field gel electrophoresis (PFGE) typing of Salmonella enterica isolated from Lake Zapotlán, Jalisco, Mexico. Additionally, the association of the presence of Salmonella with physicochemical and environmental parameters was analyzed using Pearson correlation analysis and principal component analysis (PCA). Salmonella spp. were identified in 19 of 63 (30.15%) samples. The prevalence of Salmonella was positively correlated with air temperature, electrical conductivity, pH, and dissolved oxygen and negatively correlated with relative humidity, water temperature, turbidity, and precipitation. The predominant serotype identified was Agona (68.48%), followed by Weltevreden (5.26%), Typhimurium (5.26%), and serogroup B (21.05%). Overall, the highest detected antimicrobial resistance was toward colistin (73.68%), followed by sulfamethoxazole (63.15%), tetracycline (57.89%), nalidixic acid (52.63%), and trimethoprim (52.63%). All Salmonella strains were genetically diverse, with a total of 11 XbaI and four BlnI profiles on PFGE. The use of these two enzymes allowed differentiate strains of Salmonella of the same serotype. The results obtained in this study contribute to a better understanding of the Salmonella spp. ecology in an endorheic subtropical lake and provide information for decision makers to propose and implement effective strategies to control point and non-point sources of pathogen contamination.

Identifying geographic origins of the Escherichia coli isolates from food by a method based on single-nucleotide polymorphisms

BACKGROUND

E.coli is an important foodborne pathogen. Rapid and robust tracking of the source of E. coli is the key step to control foodborne infections.

RESULTS

In this study, a genotyping and tracing method based on highly discriminatory single nucleotide polymorphisms (SNPs) was developed to investigate the geographical origin of E. coli in food. A highly informative set of 12 SNPs was derived from 4 housekeeping genes in E. coli multilocus sequence typing (MLST) database. A collection of 253 E. coli isolates from food in 12 countries and regions were screened, resulting in a total of 61 profiles, 35 geographically specific SNP profiles were revealed and further verified by blind sample test. Also, the evolutionary relationship of 61 SNP profiles with different geographical origins was established by the enhanced analysis Based Upon Related Sequence Types (eBURST) analysis, which provided evidence that strains of different geographical origins owned the same ancestor strain.

CONCLUSIONS

Our study established a powerful method based on a set of 12 SNPs for identifying geographical origins. The blind sample analysis proved that this SNPs panel had a high traceability of E. coli in food. Furthermore, this method based on SNPs combined with eBURST analysis revealed the potential evolutionary relationship between E.coli strains of different geographical origins.

Analyses of prevalence and molecular typing reveal the spread of antimicrobial-resistant Salmonella infection across two breeder chicken farms

In this study, Salmonella prevalence and antimicrobial resistance were evaluated at various production stages in 2 geographically separated breeder farms (referred to as G and F). Day-old chicks for the breeder flock at farm F were purchased from farm G. A total of 219 Salmonella isolates, all identified as Salmonella enterica subsp. enterica serovar Enteritidis, were recovered from 1,430 samples (sick chicken carcasses and/or dead embryos). The isolation rates at breeder farms G and F were 10.53% (56/532) and 18.15% (163/898), respectively. Resistance to 4-6 antimicrobial agents was the most frequent phenotype during the laying stage at both farms, suggesting that chicks are exposed to higher risk of antimicrobial-resistant Salmonella infection during this stage of the breeding process. Using clustered regularly interspaced short palindromic repeat (CRISPR) typing, 5 CRISPR patterns were identified, out of which one pattern was shared by the 2 farms. In addition, pulsed-field gel electrophoresis (PFGE) typing result indicated that 2 clusters (PF-1 and PF-2) were shared among the 2 breeder farms, suggesting that strains were transmitted from breeder farm G to farm F via the trade of day-old chicks. Our findings suggested that the trade of day-old breeder chicks could be one of the potential Salmonella transmission routes, and antibiotics should be administered with caution during the laying stage.

Genotypic and phenotypic characterization of the food spoilage bacterium Brochothrix thermosphacta

Microbial food spoilage is responsible for significant economic losses. Brochothrix thermosphacta is one of the major bacteria involved in the spoilage of meat and seafood. Its growth and metabolic activities during food storage result in the production of metabolites associated with off-odors. In this study, we evaluated the genotypic and phenotypic diversity of this species. A collection of 161 B. thermosphacta strains isolated from different foods, spoiled or not, and from a slaughterhouse environment was constituted from various laboratory collections and completed with new isolates. A PCR test based on the rpoB gene was developed for a fast screening of B. thermosphacta isolates. Strains were typed by MALDI-TOF MS, rep-PCR, and PFGE. Each typing method separated strains into distinct groups, revealing significant intra-species diversity. These classifications did not correlate with the ecological origin of strains. The ability to produce acetoin and diacetyl, two molecules associated with B. thermosphacta spoilage, was evaluated in meat and shrimp juices. The production level was variable between strains and the spoilage ability on meat or shrimp juice did not correlate with the substrate origin of strains. Although the B. thermosphacta species encompasses ubiquitous strains, spoiling ability is both strain- and environment-dependent.

A systematic review characterizing on-farm sources of Campylobacter spp. for broiler chickens

Campylobacter and antimicrobial-resistant Campylobacter are frequently isolated from broiler chickens worldwide. In Canada, campylobacteriosis is the third leading cause of enteric disease and the regional emergence of ciprofloxacin-resistant Campylobacter in broiler chickens has raised a public health concern. This study aimed to identify, critically appraise, and synthesize literature on sources of Campylobacter in broilers at the farm level using systematic review methodology. Literature searches were conducted in January 2012 and included electronic searches in four bibliographic databases. Relevant studies in French or English (n = 95) conducted worldwide in any year and all study designs were included. Risk of Bias and GRADE criteria endorsed by the Cochrane collaboration was used to assess the internal validity of the study and overall confidence in the meta-analysis. The categories for on-farm sources were: broiler breeders/vertical transfer (number of studies = 32), animals (n = 57), humans (n = 26), environment (n = 54), and water (n = 63). Only three studies examined the antimicrobial resistance profiles of Campylobacter from these on-farm sources. Subgroups of data by source and outcome were analyzed using random effect meta-analysis. The highest risk for contaminating a new flock appears to be a contaminated barn environment due to insufficient cleaning and disinfection, insufficient downtime, and the presence of an adjacent broiler flock. Effective biosecurity enhancements from physical barriers to restricting human movement on the farm are recommended for consideration to enhance local on-farm food safety programs. Improved sampling procedures and standardized laboratory testing are needed for comparability across studies. Knowledge gaps that should be addressed include farm-level drug use and antimicrobial resistance information, further evaluation of the potential for vertical transfer, and improved genotyping methods to strengthen our understanding of Campylobacter epidemiology in broilers at the farm-level. This systematic review emphasizes the importance of improved industry-level and on-farm risk management strategies to reduce pre-harvest Campylobacter in broilers.

Molecular Typing of Campylobacter jejuni and Campylobacter coli Isolated from Various Retail Meats by MLST and PFGE

Campylobacter species are one of the leading causes of foodborne disease in the United States. Campylobacter jejuni and Campylobacter coli are the two main species of concern to human health and cause approximately 95% of human infections. Molecular typing methods, such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) are often used to source track foodborne bacterial pathogens. The aim of the present study was to compare PFGE and MLST in typing strains of C. jejuni and C. coli that were isolated from different Oklahoma retail meat sources. A total of 47 Campylobacter isolates (28 C. jejuni and 19 C. coli) isolated from various retail meat samples (beef, beef livers, pork, chicken, turkey, chicken livers, and chicken gizzards) were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). PFGE was able to group the 47 Campylobacter isolates into two major clusters (one for C. jejuni and one for C. coli) but failed to differentiate the isolates according to their source. MLST revealed 21 different sequence types (STs) that belonged to eight different clonal complexes. Twelve of the screened Campylobacter isolates (8 C. jejuni and 4 C. coli) did not show any defined STs. All the defined STs of C. coli isolates belonged to ST-828 complex. The majority of C. jejuni isolates belonged to ST-353, ST-607, ST-52, ST-61, and ST-21 complexes. It is worthy to mention that, while the majority of Campylobacter isolates in this study showed STs that are commonly associated with human infections along with other sources, most of the STs from chicken livers were solely reported in human cases. In conclusion, retail meat Campylobacter isolates tested in this study particularly those from chicken livers showed relatedness to STs commonly associated with humans. Molecular typing, particularly MLST, proved to be a helpful tool in suggesting this relatedness to Campylobacter human isolates.

A Comparison of Subtyping Methods for Differentiating Salmonella enterica Serovar Enteritidis Isolates Obtained from Food and Human Sources

Purpose:

To evaluate the abilities of these subtyping methods, we distinguished Salmonella Enteritidis (S. Enteritidis) isolated from food products and human clinical samples between 2009 and 2010 in Seoul using five subtyping methods.

Methods:

We determined the subtypes of 20 S. Enteritidis isolates from food and human sources using phage typing, antimicrobial susceptibility, pulsed-field gel electrophoresis (PFGE), repetitive sequence-based PCR (rep-PCR), and multi-locus sequence typing (MLST).

Results:

A total of 20 tested isolates were differentiated into six antimicrobial susceptibility patterns, three different phage types, four different PFGE profiles, seven rep-PCR patterns, and one MLST type. Food isolates were considerably more susceptible to antibiotics than human isolates. We were best able to discriminate among S. Enteritidis isolates using rep-PCR, and obtained the highest Simpson’s diversity index of 0.82, whereas other methods produced indices that were less than 0.71. PFGE pattern appeared to be more related to antimicrobial resistance and phage types of S. Enteritidis isolates than rep-PCR. MLST revealed identical alleles in all isolates at all seven loci examined, indicating no resolution.

Conclusion:

The results of this study suggest that rep-PCR provided the best discriminatory power for phenotypically similar S. Enteritidis isolates of food and human origins, whereas the discriminatory ability of MLST may be problematic because of the high sequence conservation of the targeted genes.

[Application of restriction fragment length polymorphism-polymerase chain reaction-flaA and resistotype to identify potential undiagnosed outbreaks of campylobacteriosis in Spain]

INTRODUCTION

Outbreaks of campylobacteriosis are infrequent and usually involve a low number of patients, although it is estimated that many more remain undiagnosed. The most successful techniques for outbreak investigation in Campylobacter spp. (PFGE, MLST) have the drawback of being laborious and not available in many laboratories.

METHODS

During the year 2008, 352 isolates of C. jejuni and C. coli from 16 hospitals were received in our laboratory. All strains were genotyped by RFLP-PCR-flaA (flaA type) and phenotyped with their resistotype. It was established that the strains of the same species from the same hospital, isolated over a period of up to 11 days, with MIC values of±1 dilution with the same flaA type could belong to an outbreak. Strains that met these criteria would be later subtyped by KpnI-PFGE and MLST.

RESULTS

A total of 23 out of 352 isolates, distributed in 10 groups, met the criteria for being associated with putative undiagnosed outbreaks. The similarity of the PFGE-profiles in 8 groups was greater than 95% among the isolates from each group. In 7 of the groups, the sequence types (MLST) were coincident.

CONCLUSIONS

The use of 2 easy markers (resistotype and RFLP-PCR-flaA) may detect isolates probably belonging to an undiagnosed outbreak of campylobacteriosis. Accurate diagnosis requires other molecular markers and epidemiological data of each isolate. The study suggests that, as in other countries, the number of outbreaks of campylobacteriosis in Spain is probably underestimated.

Rapid Detection of Viruses Using Loop-Mediated Isothermal Amplification (LAMP): A Review

Most of the diseases caused by viral infection are found to be fatal, and the diagnosis is difficult due to confusion with other causative agents. So, a highly efficient molecular-based advance detection technique, i.e., loop-mediated isothermal amplification (LAMP) method, is developed for diagnosis of viral infections by various workers. It is based on amplification of DNA at very low level under isothermal conditions, using a set of four specifically designed primers and a DNA polymerase with strand displacement activity. This technique is found to be superior than most of the molecular techniques like PCR, RT-PCR, and real-time PCR due to its high specificity, sensitivity, and rapidity. Major advantage of LAMP method is its cost-effectiveness as it can be done simply by using water bath or dry bath. Here, in this review information regarding almost all the effective LAMP techniques which is developed so far for diagnosis of numerous viral pathogens is presented.

Comparison of five molecular subtyping methods for differentiation of Salmonella Kentucky isolates in Tunisia

Salmonellosis is one of the most common causes of food-borne infection worldwide. In the last decade, Salmonella enterica serovar Kentucky has shown an increase in different parts of the world with the concurrent emergence of multidrug-resistant isolates. These drug-resistant types spread from Africa and the Middle East to Europe and Asia. Although S. Kentucky serovar is of potential human relevance, there is currently no standardized fingerprinting method for it, in Tunisia. In the present study, a collection of 57 Salmonella Kentucky isolates were analyzed using plasmid profiling, pulsed-field gel electrophoresis (PFGE), ribotyping, enterobacterial repetitive intergenic consensus (ERIC) fingerprinting, and Random Amplification of Polymorphic DNA. Plasmid profiling showed a discriminatory index (D) of 0.290, and only 9 out of 57 (16%) isolates carried plasmids, which represents a limitation of this technique. Fingerprinting of genomic DNA by PFGE and ribotyping produced 4 and 5 patterns, respectively. Distinct PFGE patterns (SX1, SX2, SX3, and SX4) were generated for only 28 strains out of 57 (49.1%) with a D value of 0.647. RAPD fingerprinting with primers RAPD1 and RAPD2 produced 4 and 20 patterns, respectively. ERIC fingerprinting revealed 14 different patterns with a high discriminatory index (D) of 0.903. When the methods were combined, the best combination of two methods was ERIC-2 with RAPD2. These results indicates that a single method cannot be relied upon for discriminating between S. Kentucky strains, and a combination of typing methods such ERIC2 and RAPD2 allows further discrimination.

Simultaneous analysis of multiple enzymes increases accuracy of pulsed-field gel electrophoresis in assigning genetic relationships among homogeneous Salmonella strains

Due to a highly homogeneous genetic composition, the subtyping of Salmonella enterica serovar Enteritidis strains to an epidemiologically relevant level remains intangible for pulsed-field gel electrophoresis (PFGE). We reported previously on a highly discriminatory PFGE-based subtyping scheme for S. enterica serovar Enteritidis that relies on a single combined cluster analysis of multiple restriction enzymes. However, the ability of a subtyping method to correctly infer genetic relatedness among outbreak strains is also essential for effective molecular epidemiological traceback. In this study, genetic and phylogenetic analyses were performed to assess whether concatenated enzyme methods can cluster closely related salmonellae into epidemiologically relevant hierarchies. PFGE profiles were generated by use of six restriction enzymes (XbaI, BlnI, SpeI, SfiI, PacI, and NotI) for 74 strains each of S. enterica serovar Enteritidis and S. enterica serovar Typhimurium. Correlation analysis of Dice similarity coefficients for all pairwise strain comparisons underscored the importance of combining multiple enzymes for the accurate assignment of genetic relatedness among Salmonella strains. The mean correlation increased from 81% and 41% for single-enzyme PFGE up to 99% and 96% for five-enzyme combined PFGE for S. enterica serovar Enteritidis and S. enterica serovar Typhimurium strains, respectively. Data regressions approached 100% correlation among Dice similarities for S. enterica serovar Enteritidis and S. enterica serovar Typhimurium strains when a minimum of six enzymes were concatenated. Phylogenetic congruence measures singled out XbaI, BlnI, SfiI, and PacI as most concordant for S. enterica serovar Enteritidis, while XbaI, BlnI, and SpeI were most concordant among S. enterica serovar Typhimurium strains. Together, these data indicate that PFGE coupled with sufficient enzyme numbers and combinations is capable of discerning accurate genetic relationships among Salmonella serovars comprising highly homogeneous strain complexes.

Phage-type specific markers identified by Diversity Arrays Technology (DArT) analysis of Salmonella enterica ssp. enterica serovars Enteritidis and Typhimurium

Diversity Arrays Technology (DArT) was applied to differentiate between S. enterica serovar Enteritidis and Typhimurium strains, respectively. Ten and eleven, mainly phage and plasmid-related markers were identified for serovars Enteritidis and Typhimurium. In combination, these markers can be used for subtyping among and within phage types.

Clonal relationships determined by multilocus sequence typing among enteropathogenicEscherichia coliisolated in Brazil

Enteropathogenic Escherichia coli (EPEC) infections are a leading cause of infantile diarrhea in developing nations. Multilocus sequence typing (MLST) characterizes bacterial strains based on the sequences of internal fragments in housekeeping genes. Little is known about strains of EPEC analyzed by MLST from Brazil. In this study, a diverse collection of 29 EPEC strains isolated from patients with diarrhea, admitted to the University Hospital of Ribeirao Preto, was characterized by MLST. Strain analysis demonstrated 22 different sequence types (STs), of which almost half (48%) were new, indicating a high genotype diversity. The 22 STs were divided by eBURST into 12 clonal complexes. It was not possible to correlate typical and atypical EPEC with other strains in the MLST database. This is the first study that analyzed EPEC strains from South America that are included in the E. coli MLST database. Nine (31%) out of 29 strains are part of the CC10 clonal complex, the major clonal complex in the database, which comprises 174 strains and 86 different STs, suggesting that these strains might be the most important intestinal pathogenic E. coli worldwide. Genetic relationships between typical and atypical EPEC, enterohemorrhagic E. coli, and enteroaggregative E. coli strains were not established by MLST.

Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases

Loop-mediated isothermal amplification (LAMP) is an established nucleic acid amplification method offering rapid, accurate, and cost-effective diagnosis of infectious diseases. This technology has been developed into commercially available detection kits for a variety of pathogens including bacteria and viruses. The current focus on LAMP methodology is as a diagnostic system to be employed in resource-limited laboratories in developing countries, where many fatal tropical diseases are endemic. The combination of LAMP and novel microfluidic technologies such as Lab-on-a-chip may facilitate the realization of genetic point-of-care testing systems to be used by both developed and developing countries in the near future. This review will describe the historical, current, and future developments of such technologies.

Predicting Salmonella enterica serotypes by repetitive sequence-based PCR

Repetitive extragenic palindromic sequence-based PCR (rep-PCR) utilizing a semi-automated system, was evaluated as a method to determine Salmonella serotypes. A group of 216 Salmonella isolates belonging to 13 frequently isolated serotypes and one rarer serotype from poultry were used to create a DNA fingerprint library with the DiversiLab System software. Subsequently, a blinded set of 44 poultry isolates were fingerprinted and queried against the library in an attempt to putatively assign a serotype designation to each Salmonella isolate. The query isolates were previously typed employing standard serological techniques. Utilizing pair-wise similarity percentages as calculated by the Pearson correlation coefficient, the predicted serotype of 28 isolates matched the serological typing result. For eight isolates, rep-PCR results were interpreted as one of two very closely-related serotypes, Hadar and the rarer Istanbul. Traditional serological assays have difficulty distinguishing between these groups, and sequencing interspacer regions of the rrfH gene was unable to differentiate among isolates of these two serovars. Six of the remaining isolates resulted in no match to the database (similarity values <95%) and these indeed proved to be serotypes not included in the original library. The two remaining samples proved discrepant at the 95% similarity threshold, however examination of electropherograms clearly indicated fingerprint variability between query and library samples, suggesting an expanded rep-PCR library will be necessary for increased utility. Since serological assays can take several days to weeks to provide information, the DiversiLab System holds promise for more rapid serotype classification for members of this group.

Microarray for molecular typing of Salmonella enterica serovars

We describe the development of a spotted array for the delineation of the most common 14 disease-causing Salmonella serovars in the United States. Our array consists of 414 70 mers targeting core genes of Salmonella enterica, subspecies I specific genes, fimbrial genes, pathogenicity islands, Gifsy elements and other variable genes. Using this array we were able to identify a unique gene presence/absence profile for each of the targeted serovar which was used as the serovar differentiating criteria. Based on this profile, we developed a Matlab programme that compares the profile of an unknown sample to all 14 reference serovar profiles and give out the closest serovar match. Since we have included probes targeting most of the virulence genes and variable genes in Salmonella, in addition to using for serovar detection this array could also be used for studying the virulence gene content and also for evaluating the genetic relation between different isolates of Salmonella.

Assessing genetic heterogeneity within bacterial species isolated from gastrointestinal and environmental samples: how many isolates does it take?

Strain typing of bacterial isolates is increasingly used to identify sources of infection or product contamination and to elucidate routes of transmission of pathogens or spoilage organisms. Usually, the number of bacterial isolates belonging to the same species that is analyzed per sample is determined by convention, convenience, laboratory capacity, or financial resources. Statistical considerations and knowledge of the heterogeneity of bacterial populations in various sources can be used to determine the number of isolates per sample that is actually needed to address specific research questions. We present data for intestinal Escherichia coli, Listeria monocytogenes, Klebsiella pneumoniae, and Streptococcus uberis from gastrointestinal, fecal, or soil samples characterized by ribotyping, pulsed-field gel electrophoresis, and PCR-based strain-typing methods. In contrast to previous studies, all calculations were performed with a single computer program, employing software that is freely available and with in-depth explanation of the choice and derivation of prior distributions. Also, some of the model assumptions were relaxed to allow analysis of the special case of two (groups of) strains that are observed with different probabilities. Sample size calculations, with a Bayesian method of inference, show that from 2 to 20 isolates per sample need to be characterized to detect all strains that are present in a sample with 95% certainty. Such high numbers of isolates per sample are rarely typed in real life due to financial or logistic constraints. This implies that investigators are not gaining maximal information on strain heterogeneity and that sources and transmission pathways may go undetected.

Emergence of a tetracycline-resistant Campylobacter jejuni clone associated with outbreaks of ovine abortion in the United States

Campylobacter infection is one of the major causes of ovine abortions worldwide. Historically, Campylobacter fetus subsp. fetus was the major cause of Campylobacter-associated abortion in sheep; however, Campylobacter jejuni is increasingly associated with sheep abortions. We examined the species distribution, genotypes, and antimicrobial susceptibilities of abortion-associated Campylobacter isolates obtained from multiple lambing seasons on different farms in Iowa, Idaho, South Dakota, and California. We found that C. jejuni has replaced C. fetus as the predominant Campylobacter species causing sheep abortion in the United States. Most strikingly, the vast majority (66 of 71) of the C. jejuni isolates associated with sheep abortion belong to a single genetic clone, as determined by pulsed-field gel electrophoresis, multilocus sequence typing, and cmp gene (encoding the major outer membrane protein) sequence typing. The in vitro antimicrobial susceptibilities of these isolates to the antibiotics that are routinely used in food animal production were determined using the agar dilution test. All of the 74 isolates were susceptible to tilmicosin, florfenicol, tulathromycin, and enrofloxacin, and 97% were sensitive to tylosin. However, all were resistant to tetracyclines, the only antibiotics currently approved in the United States for the treatment of Campylobacter abortion in sheep. This finding suggests that feeding tetracycline for the prevention of Campylobacter abortions is ineffective and that other antibiotics should be used for the treatment of sheep abortions in the United States. Together, these results indicate that a single tetracycline-resistant C. jejuni clone has emerged as the major cause of Campylobacter-associated sheep abortion in the United States.

[Systemic granulomatosis of infectious origin]

PURPOSE

Granulomatous diseases are defined by specific histological features, following the local recruitment of macrophages and lymphocytes. Many infections can lead to the development of granuloma.

CURRENT KNOWLEDGE AND KEY POINTS

Microorganisms responsible for granuloma include mainly mycobacteria, many viral and fungal species, as well as schistosoma in endemic areas. Nevertheless, almost all microorganisms can lead to granuloma, especially if their clearance needs macrophages pathway. New immunosuppressive drugs such as tumor necrosis factor antagonists are associated with a high risk of infectious granulomatous complications. All patients with granuloma must be carefully screened to find a potential underlying infection, since an immunosuppressive therapy could be otherwise considered. We here review the general diagnostic process with a specific glance to the main organs.

FUTURE PROSPECTS AND PROJECTS

Without clinical or epidemiological clue, diagnosis can be very tedious. New molecular tools now assist classical microbiological and histological techniques. Their specificity and sensitivity have recently been better characterized, and their use will probably increase in the near future for the diagnosis of infectious granuloma. They may also lead to discover new infectious aetiologies of granulomatous diseases formerly considered as idiopathic. We describe here the main microorganisms that can be responsible for granuloma, with a specific focus on the use of new diagnostic tools.

Multiple-locus variable-number tandem repeat analysis of Salmonella Enteritidis isolates from human and non-human sources using a single multiplex PCR

Simplified multiple-locus variable-number tandem repeat analysis (MLVA) was developed using one-shot multiplex PCR for seven variable-number tandem repeats (VNTR) markers with high diversity capacity. MLVA, phage typing, and PFGE methods were applied on 34 diverse Salmonella Enteritidis isolates from human and non-human sources. MLVA detected allelic variations that helped to classify the S. Enteritidis isolates into more evenly distributed subtypes than other methods. MLVA-based S. Enteritidis clonal groups were largely associated with sources of the isolates. Nei's diversity indices for polymorphism ranged from 0.25 to 0.70 for seven VNTR loci markers. Based on Simpson's and Shannon's diversity indices, MLVA had a higher discriminatory power than pulsed field gel electrophoresis (PFGE), phage typing, or multilocus enzyme electrophoresis. Therefore, MLVA may be used along with PFGE to enhance the effectiveness of the molecular epidemiologic investigation of S. Enteritidis infections.

Development and application of an oligonucleotide microarray for the detection of food-borne bacterial pathogens

The rapid and accurate detection and identification of food-borne pathogenic bacteria is critical for food safety. In this paper, we describe a rapid (<4 h) high-throughput detection and identification system that uses universal polymerase chain reaction (PCR) primers to amplify a variable region of bacterial the 16S rRNA gene, followed by reverse hybridization of the products to species-specific oligonucleotide probes on a chip. This procedure was successful in discriminating 204 strains of bacteria from pure culture belonging to 13 genera of bacteria. When this method was applied directly to 115 strains of bacteria isolated from foods, 112/115 (97.4%) were correctly identified; two strains were indistinguishable due to weak signal, while one failed to produce a PCR product. The array was used to detect and successfully identify two strains of bacteria from food poisoning outbreak samples, giving results through hybridization that were identical to those obtained by traditional methods. The sensitivity of the microarray assay was 10(2) CFU of bacteria. Thus, the oligonucleotide microarray is a powerful tool for the detection and identification of pathogens from foods.

Molecular characterization and antibiotic resistance profiling of Salmonella isolated from retail Turkey meat products

Contaminated poultry meat has been identified as one of the principal foodborne sources of Salmonella. Molecular characterization of Salmonella is important in addressing methods to control this pathogen. Seventy-four retail turkey meat samples were collected from various stores in Fargo, North Dakota in the fall of 2003. Salmonella was recovered from 30 samples using the standard conventional culture method (FSIS, USDA). Isolated Salmonella were characterized by serotyping, pulsed-field gel electrophoresis (PFGE) analysis, plasmid analysis, and antibiotic resistance profiling. Five serotypes were identified among the isolates: Newport (n = 12), Hadar (n = 8), Heidelberg (n = 7), 4,12:nonmotile (n = 2), and Reading (n = 1). XbaI PFGE analysis revealed 13 PFGE types and succeeded in grouping the isolates according to their serotypes. Plasmid profiling identified 5 plasmid types (with 1 or 2 plasmids) among eleven isolates that harbored plasmids. Seventeen isolates were resistant to antibiotics. The Heidelberg serotype showed resistance to multiple antibiotics: 1 isolate had resistance to gentamicin, sulfamethoxazole, and streptomycin, and 6 isolates had resistance to tetracycline, gentamycin, sulfamethoxazole, kanamycin, and streptomycin. The Hadar serotype isolates were resistant to 2 or 3 antibiotics: tetracycline and streptomycin (1 isolate); tetracycline and kanamycin (1 isolate); and tetracycline, kanamycin, and streptomycin (6 isolates). The 4,12:nonmotile serotype isolates showed resistance to tetracycline only. The Newport and the Reading serotypes were susceptible to all 16 of the antimicrobials tested.

Use of molecular epidemiology in veterinary practice

Molecular epidemiology is a relatively new branch of epidemiology that uses molecular biology methods to study health and disease in populations. This article gives an introduction to molecular epidemiologic terminology and methodology and its usefulness in large animal medicine and veterinary public health. Applications in source tracing and vaccine studies and insights into transmission dynamics, host specificity, and niche adaptation of infectious organisms are presented. Examples are drawn from a variety of diseases, organisms, and host species and range from the global level to the individual-animal level.