Oligonucleotide microarray for molecular characterization and genotyping of Salmonella spp. strains

Camel as a transboundary vector for emerging exotic Salmonella serovars

The current study was conducted to shed light on the role of imported camels as a transboundary vector for emerging exotic Salmonella serovars. Fecal samples were collected from 206 camels directly after slaughtering including 25 local camels and 181 imported ones as well as stool specimens were obtained from 50 slaughterhouse workers at the same abattoir. The obtained samples were cultured while Salmonella serovars were identified through Gram's stain films, biochemical tests and serotyping with antisera kit. Moreover, the obtained Salmonella serovars were examined by PCR for the presence of invA and stn genes. The overall prevalence of Salmonella serovars among the examined camels was 8.3%. Stn gene was detected in the vast majority of exotic strains (11/14) 78.6% including emerging serovars such as Salmonella Saintpaul, S. Chester, S. Typhimurium whereas only one isolate from local camels carried stn gene (1/3) 33.3%. On the other hand, none of the examined humans yielded positive result. Our findings highlight the potential role of imported camels as a transboundary vector for exotic emerging Salomenella serovars.

Real time PCR gene profiling and detection of Salmonella using a novel target: The siiA gene

The objective of this study was to develop and evaluate a SYBR Green real time PCR method for the specific detection of Salmonella spp using a novel target, the siiA gene. Primer specificity testing was done on a panel of 76 Salmonella strains and 32 non-Salmonella strains. The primers directed against the siiA gene amplified all Salmonella strains tested, while non-Salmonella strains were not amplified. The melting temperatures of the 107 bp amplicons were consistently specific as they gave melting peaks around 75.5°C. The precision of the assay, based on intra and inter-run variations, was shown to be widely acceptable. In the second part of this study, 45 Salmonella strains were screened for the presence of 6 virulence-associated genes (sopB, cat2, safC, sefB and SC1248) located in several Salmonella Pathogenicity Islands (SPIs) and the spvC gene from the Salmonella virulence plasmid. The prevalence of these genes ranged from 51% to 100%. Variable virulence gene profiles were obtained even within the same serotype.

Development of a high-throughput DNA microarray for drug-resistant gene detection and its preliminary application

Most bacteria are resistant to a wide variety of antibiotics and other drugs, which decrease the effectiveness of clinical drug therapies. The present study developed a high-throughput DNA microarray for drug-resistant gene detection. A total of 115 specific oligonuclieotide probes with lengths of 42 nt to 45 nt and comparable Tm values were selected from 17 categories of drug-resistant genes in the National Center for Biotechnology Information database and were chemically synthesized. The entire bacterial DNA was extracted, randomly amplified, and labeled using Cy3-dCTP. The hybridization conditions of the microarray test were optimized to improve sensitivity and specificity. The drug-resistant genes were detected and genotyped using microarray analysis after hydration at 42°C for 4h with 2× hybridization solution. The microarray test sensitivity was 20ng/μL DNA. The performance of the microarray was validated using reference strains and clinical isolates. The results were consistent with direct DNA sequence analysis and drug susceptibility tests. The developed DNA microarray could be used to detect and screen drug-resistant bacteria rapidly and simultaneously. Thus, the present study could be helpful in effectively using antibiotics and controlling infectious diseases.

RGB colour coding of Y-shaped DNA for simultaneous tri-analyte solid phase hybridization detection

We present a new concept for tri-analyte DNA detection based on the idea of a Y-shaped capture probe which, after tri-target and fluorescently labeled reporter probe binding, becomes colour-coded to generate images in an RGB colour scheme. Hence, the RGB value of the resulting secondary pseudo-colour presented by the hybridized Y-DNA can be related to the ratio of the primary pseudo-colours present in its make-up, and thus to the ratio of the three target concentrations. As a proof of concept we detect sequences from the genes of the pathogenic bacterial strains Escherichia coli O157:H7, Vibrio cholera and Salmonella enteric in a semi-quantitative manner across the range 20-167 nM. The assay was relatively quick, with a time from hybridization to completed data interpretation of approximately 4 h.

A multiplex ligation detection assay for the characterization of Salmonella enterica strains

A proof of principle of a multi-target assay for genotyping Salmonella has been developed targeting 62 genomic marker sequences of Salmonella related to pathogenicity. The assay is based on multiplex ligation detection reaction (LDR) followed by customized ArrayTube® microarray detection. The feasibility of the developed assay was verified in a method comparison study with conventional PCR using 16 Salmonella 'test' strains comprising eight serovars. Subsequently, the feasibility of the LDR microarray assay was also tested by analyzing 41 strains belonging to 23 serovars. With the exception of four serovars each serovar was characterized by a unique virulence associated gene repertoire. The LDR microarray platform proved to be a convenient, rapid and easy to use tool with potential in tracing a Salmonella contamination in the food chain, for outbreak studies, and to provide data for risk assessors that support bio-traceability models.

High-throughput Universal Probe Salmonella Serotyping (UPSS) by nanoPCR

Salmonella enterica subsp. enterica serovar identification is of great importance with respect to outbreak monitoring and case verification. Therefore rapid, sensitive and cost efficient detection of Salmonella spp. is indispensable within microbiology labs. To amalgamate single tube isolate identification with Salmonella typing, we developed the high-throughput Universal Probe Salmonella Serotyping (UPSS) technique based on nano liter PCR. In comparison to the classical approach, where O- and H-antisera are applied, the UPSS relies on specific gene content amplification of Salmonella spp. by a universal TaqMan assay for all markers and identification of the specific amplicon pattern. To enable high-throughput technology we employed a chip format containing 1024 wells loaded by an automated liquid-handling system which allowed us to perform TaqMan PCR reactions in volumes of 100nL per well. Herein we present proof of principle of the UPSS method by the use of a test panel of 100 previously serotyped Salmonella isolates to successfully verify the usability, accuracy and feasibility of the newly developed UPSS approach. We found that the methodology of the UPSS technology is capable of unequivocally identifying 30 Salmonella serotypes on a single chip within 3 hours but can be highly parallelized by the use of multiple PCR machines. Therefore the UPSS method offers a robust and straightforward molecular alternative for Salmonella detection and typing that saves expensive chemistry and can be easily automated.

Development of microarray and multiplex polymerase chain reaction assays for identification of serovars and virulence genes in Salmonella enterica of human or animal origin

Salmonella enterica is an important enteric pathogen consisting of many serovars that can cause severe clinical diseases in animals and humans. Rapid identification of Salmonella isolates is especially important for epidemiologic monitoring and controlling outbreaks of disease. Although immunologic and DNA-based serovar identification methods are available for rapid identification of isolates, they are time consuming or costly or both. In the current study, 2 molecular methods for identification of Salmonella serovars were developed and validated. A 70-mer oligonucleotide spotted microarray was developed that consisted of probes that detected genes responsible for genetic variation among isolates of Salmonella that can be used for serotyping. A multiplex polymerase chain reaction (PCR) assay was also developed, which is capable of identifying 42 serovars, thus providing a valuable prediction of the pathogenicity of the isolates by detecting the presence of virulence genes sseL, invA, and spvC. The gene spvC was the best predictor of pathogenicity. In a blind study, traditional serologic methods were correlated at 93.3% with the microarray-based method and 100% with the multiplex PCR-based serovar determination.

Development of a DNA microarray to detect antimicrobial resistance genes identified in the National Center for Biotechnology Information database

To understand the mechanisms and epidemiology of antimicrobial resistance (AR), the genetic elements responsible must be identified. Due to the myriad of possible genes, a high-density genotyping technique is needed for initial screening. To achieve this, AR genes in the National Center for Biotechnology Information GenBank database were identified by their annotations and compiled into a nonredundant list of 775 genes. A DNA microarray was constructed of 70mer oligonucelotide probes designed to detect these genes encoding resistances to aminoglycosides, beta-lactams, chloramphenicols, glycopeptides, heavy metals, lincosamides, macrolides, metronidazoles, polyketides, quaternary ammonium compounds, streptogramins, sulfonamides, tetracyclines, and trimethoprims as well as resistance transfer genes. The microarray was validated with two fully sequenced control strains of Salmonella enterica: Typhimurium LT2 (sensitive) and Typhi CT18 (multidrug resistance [MDR]). All resistance genes encoded on the MDR plasmid, pHCM1, harbored by CT18 were detected in that strain, whereas no resistance genes were detected in LT2. The microarray was also tested with a variety of bacteria, including MDR Salmonella enterica serovars, Escherichia coli, Campylobacter spp., Enterococcus spp., methicillin-resistant Staphylococcus aureus, Listeria spp., and Clostridium difficile. The results presented here demonstrate that a microarray can be designed to detect virtually all AR genes found in the National Center for Biotechnology Information database, thus reducing the subsequent assays necessary to identify specific resistance gene alleles.

Development and validation of a resistance and virulence gene microarray targeting Escherichia coli and Salmonella enterica

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

Advances in subtyping methods of foodborne disease pathogens

Current subtyping methods for the detection of foodborne disease outbreaks have limitations that reduce their use by public health laboratories. Recent advances in subtyping of foodborne disease pathogens utilize techniques that identify nucleic acid polymorphisms. Recent methods of nucleic acid characterization such as microarrays and mass spectrometry (MS) may provide improvements such as increasing speed and data portability while decreasing labor compared to current methods. This article discusses multiple-locus variable-number tandem-repeat analysis, single-nucleotide polymorphisms, nucleic acid sequencing, whole genome sequencing, variable absent or present loci, microarrays and MS as potential subtyping methods to enhance our ability to detect foodborne disease outbreaks.

First report of extended-spectrum-beta-lactamase-producing Salmonella enterica serovar Kentucky isolated from poultry in Ireland

Therapy of invasive human salmonellosis is complicated by increasing antimicrobial resistance. Food animals are the principal source of infection with nontyphoid Salmonella. We report the emergence of broad-spectrum-cephalosporin resistance in Salmonella enterica serovar Kentucky in poultry in Ireland.

DNA signature-based approaches for bacterial detection and identification

During the late eighties, environmental microbiologists realized the potential of the polymerase chain reaction (PCR) for the design of innovative approaches to study microbial communities or to detect and identify microorganisms in diverse and complex environments. In contrast to long-established methods of cultivation-based microbial identification, PCR-based techniques allow for the identification of microorganisms regardless of their culturability. A large number of reports have been published that describe PCR-inspired methods, frequently complemented by sequencing or hybridization profiling, to infer taxonomic and clonal microbial diversity or to detect and identify microorganisms using taxa-specific genomic markers. Typing methods have been particularly useful for microbial ecology-driven studies; however, they are not suitable for diagnostic purposes, such as the detection of specific species, strains or clones. Recently, comprehensive reviews have been written describing the panoply of typing methods available and describing their advantages and limitations; however, molecular approaches for bacterial detection and identification were either not considered or only vaguely discussed. This review focuses on DNA-based methods for bacterial detection and identification, highlighting strategies for selecting taxa-specific loci and emphasizing the molecular techniques and emerging technological solutions for increasing the detection specificity and sensitivity. The massive and increasing number of available bacterial sequences in databases, together with already employed bioinformatics tools, hold promise of more reliable, fast and cost-effective methods for bacterial identification in a wide range of samples in coming years. This tendency will foster the validation and certification of these methods and their routine implementation by certified diagnostic laboratories.

Poultry-associated Salmonella enterica subsp. enterica serovar 4,12:d:- reveals high clonality and a distinct pathogenicity gene repertoire

A European baseline survey during the years 2005 and 2006 has revealed that the monophasic Salmonella enterica subsp. enterica serovar 4,12:d:- was, with a prevalence of 23.6%, the most frequently isolated serovar in German broiler flocks. In Denmark and the United Kingdom, its serovar prevalences were 15.15% and 2.8%, respectively. Although poultry is a major source of human salmonellosis, serovar 4,12:d:- is rarely isolated in humans (approximately 0.09% per year). Molecular typing studies using pulsed-field gel electrophoresis and DNA microarray analysis show that the serovar is highly clonal and lacks genes with known contributions to pathogenicity. In contrast to other poultry-associated serovars, all strains were susceptible to 17 antimicrobial agents tested and did not encode any resistance determinant. Furthermore, serovar 4,12:d:- lacked the genes involved in galactonate metabolism and in the glycolysis and glyconeogenesis important for energy production in the cells. The conclusion of the study is that serovar 4,12:d:- seems to be primarily adapted to broilers and therefore causes only rare infections in humans.

Comparison of classical serotyping and PremiTest assay for routine identification of common Salmonella enterica serovars

The commercial PremiTest Salmonella kit uses a multiplexed DNA typing test aimed at identifying common serovars of Salmonella enterica. It was used in assays over a 9-month period in the Belgian reference laboratory that performs the routine identification of Salmonella strains of animal origin. A blind analysis of 754 strains was conducted in parallel by classical serotyping and the PremiTest assay. Full results were available for 685 strains (90.8%) by serotyping, while the remaining 69 strains were found to be nontypeable due to either a lack of surface antigen expression or autoagglutination properties. When the PremiTest assay (version 4.2) was performed with crude bacterial extracts, it identified 658 strains (87.3%), including most strains found to be nontypeable by serotyping. In contrast, it gave no, wrong, dual, or noninterpretable results for 96 strains, for which 23 were caused by assay failures. When purified DNA instead of crude extracts were tested, the number of strains successfully identified to the serovar level increased to 714 (94.7%), while all assay failures were cleared. Our conclusion is that, in its actual development stage, the application of the investigated kit to purified DNA samples offers a valuable alternative to classical serotyping for laboratories performing the routine identification of Salmonella strains belonging to commonly encountered serovars and isolated from a given geographical area, assuming that the system has been validated beforehand with a significant number of strains originating from that particular area.

A novel SHV-type beta-lactamase variant (SHV-89) in clinical isolates in China

Two clinical strains of Klebsiella pneumoniae (K. pneumoniae) and one isolate of Escherichia coli (E. coli) were collected from two large general hospitals in China. Conjugation experiment, susceptibility testing, isoelectric focusing, PCR, and sequencing techniques as well as clone, expression, purification and kinetics were carried out to describe the characterization of the novel SHV-tpye enzyme. The analysis of plasmid profiling and pulsed-field gel electrophoresis of the novel enzyme were performed to investigate epidemiology. These isolates had CTX-M-14 and SHV-89 beta-lactamases. SHV-89 beta-lactamase of pI 7.6 is a novel variant with two substitutions compared with the sequence of SHV-1: Leu35Gln and Met129Val. Its gene also had two silent mutations at positions 369 and 774, respectively. The results of substrate profiles and MIC determinations showed the activity of the novel enzyme was insufficient for the enzyme to count as an extended-spectrum beta-lactamase (ESBL). The substrates of the enzyme were also characterized. Furthermore, the three novel SHV enzyme-producing strains were epidemiologically unrelated. The emergence of a novel SHV-type beta-lactamase is rarely described in other areas. This study illustrates the importance of molecular survelliance in tracking SHV-producing strains in large teaching hospitals and emphasizes the need for epidemiological monitoring.

Salmonella serovar identification using PCR-based detection of gene presence and absence

There are more than 2,500 known Salmonella serovars, and some of these can be further subclassified into groups of strains that differ profoundly in their gene content. We refer to these groups of strains as "genovars." A compilation of comparative genomic hybridization data on 291 Salmonella isolates, including 250 S. enterica subspecies I strains from 32 serovars (52 genovars), was used to select a panel of 384 genes whose presence and absence among serovars and genovars was of potential taxonomic value. A subset of 146 genes was used for real-time PCR to successfully identify 12 serovars (16 genovars) in 24 S. enterica strains. A further subset of 64 genes was used to identify 8 serovars (9 genovars) in 12 multiplex PCR mixes on 11 S. enterica strains. These gene panels distinguish all tested S. enterica subspecies I serovars and their known genovars, almost all by two or more informative markers. Thus, a typing methodology based on these predictive genes would generally alert users if there is an error, an unexpected polymorphism, or a potential new genovar.