Multiplex real-time PCR for detection of Campylobacter, Salmonella, and Shigella. J Clin Microbiol. 2013;51:2822-2829. [PMID: 23761159 DOI: 10.1128/jcm.01397-13]

Prevalence and risk factors associated with the occurrence of Campylobacter sp. in children aged 6-24 months in peri-urban Nairobi, Kenya

Introduction

Campylobacter bacteria is a major cause of foodborne-related bacterial gastroenteritis in humans worldwide. It is known to cause diarrhea in young children which has been shown to directly affect their weight and height as a result of malnutrition. Severe cases of diarrhea can also lead to death. Most of the burden is experienced in resource-limited countries in Africa and Southeast Asia where the disease is linked to poor hygiene and sanitation. The objective of this study was to determine the prevalence of Campylobacter in children aged between 6 and 24 months in Nairobi, Kenya and identify potential risk factors associated with their occurrence.

Methods

A cross-sectional study was carried out between May to December 2021. A total of 585 randomly selected households were visited in two wards (Uthiru/Ruthimitu and Riruta) in Dagoretti South sub-county, Nairobi. A questionnaire regarding how children's food is handled, the major foods consumed, sanitation and hygiene, and animal ownership was conducted among caregivers to identify associated risk factors. Stool samples were collected from 540/585 children and screened for the presence of Campylobacter using culture-based methods and confirmed through PCR.

Results

Of the 540 children's stool samples processed, Campylobacter isolates were detected in 4.8% (26/540). Campylobacter jejuni (C. jejuni) was the most common species in 80.8% of positive samples compared to Campylobacter coli (C. coli) in 26.9% of samples. In six samples, both C. jejuni and C. coli were isolated, while in four samples, it was not possible to speciate the Campylobacter. Drinking cow's milk (OR 4.2, 95% CI 1.4 - 12.6) and the presence of animal feces in the compound (OR 3.4, 95% CI 1.1 - 10.3) were found to be statistically associated with Campylobacter carriage in children.

Discussion

The carriage of Campylobacter in children in this community indicates a need for further investigation on source attribution to understand transmission dynamics and inform where to target interventions. Awareness creation among caregivers on good personal and food hygiene is needed, including boiling milk before consumption. Implementation of biosecurity measures at the household level is highly recommended to reduce contact between animals and humans.

A microfluidic chip-based multiplex PCR-reverse dot blot hybridization technique for rapid detection of enteropathogenic bacteria

Diarrhea caused by enteropathogenic bacteria is a major public health issue worldwide, especially in developing countries. In this study, a microfluidic chip-based multiplex polymerase chain reaction (PCR)-reverse dot blot hybridization technology for the rapid and simultaneous detection of 11 enteropathogenic bacteria was developed and the entire process was completed within 3-4 h. The specificity of this method was analyzed using 11 types of pure target bacterial colonies and another 7 types of pure bacterial colonies, and its sensitivity was evaluated with the serial 10-fold dilution of 11 types of pure target bacterial colonies. The detection limit of this method was as low as 10³-10² CFU/mL, and it exhibited high specificity for enteropathogenic bacteria. A total of 60 clinical diarrheal fecal samples were detected using this method, the results of which were compared with those of the conventional reference method, which resulted in a positive coincident rate of 100% and a negative coincident rate of 93.75%. Based on the findings, it could be concluded that multiplex PCR-reverse dot blot hybridization based on the microfluidic chip is a rapid, economical, sensitive, specific, and high-throughput method for detecting enteropathogenic bacteria.

Development of a recombinase polymerase amplification assay with lateral flow dipstick (RPA-LFD) for rapid detection of Shigella spp. and enteroinvasive Escherichia coli

Shigella spp. and enteroinvasive Escherichia coli (EIEC) are widely distributed and can cause serious food-borne diseases for humans such as dysentery. Therefore, an efficient detection platform is needed to detect Shigella and EIEC quickly and sensitively. In this study, a method called recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD) was developed for rapid detection of Shigella and EIEC. RPA primers and LFD detection probes were designed for their shared virulence gene ipaH. Primers and probes were screened, and the primer concentration, and reaction time and temperature were optimized. According to the optimization results, the RPA reaction should be performed at 39°C, and when combined with LFD, it takes less than 25 min for detection with the naked eye. The developed RPA-LFD method specifically targets gene ipaH and has no cross-reactivity with other common food-borne pathogens. In addition, the minimum detection limit of RPA-LFD is 1.29×102 copies/μL. The detection of food sample showed that the RPA-LFD method was also verified for the detection of actual samples.

A Cutoff Determination of Real-Time Loop-Mediated Isothermal Amplification (LAMP) for End-Point Detection of Campylobacter jejuni in Chicken Meat

Campylobacter jejuni is one of the leading causes of foodborne illness worldwide. C. jejuni is commonly found in poultry. It is the most frequent cause of contamination and thus resulting in not only public health concerns but also economic impacts. To test for this bacterial contamination in food processing plants, this study attempted to employ a simple and rapid detection assay called loop-mediated isothermal amplification (LAMP). The best cutoff value for the positive determination of C. jejuni calculated using real-time LAMP quantification cycle (Cq) was derived from the receiver operating characteristic (ROC) curve modeling. The model showed an area under curve (AUC) of 0.936 (95% Wald CI: 0.903–0.970). Based on Youden’s J statistic, the optimal cutoff value which had the highest sensitivity and specificity from the model was calculated as 18.07. The LAMP assay had 96.9% sensitivity, 95.8% specificity, and 93.9 and 97.9% positive and negative predictive values, respectively, compared to a standard culture approach for C. jejuni identification. Among all non-C. jejuni strains, the LAMP assay gave each of 12.5% false-positive results to C. coli and E. coli (1 out of 8 samples). The assay can detect C. jejuni at the lowest concentration of 103 CFU/mL. Our results suggest a preliminary indicator for the application of end-point LAMP assays, such as turbidity and UV fluorescence tests, to detect C. jejuni in field operations. The LAMP assay is an alternative screening test for C. jejuni contamination in food samples. The method provides a rapid detection, which requires only 9 min with a cutoff value of Cq. We performed the extraction of DNA from pure cultures and the detection of C. jejuni using the LAMP assay within 3 h. However, we were not able to reduce the time for the process of enrichment involved in our study. Therefore, we suggest that alternative enrichment media and rapid DNA extraction methods should be considered for further study. Compared to other traditional methods, our proposed assay requires less equipment and time, which is applicable at any processing steps in the food production chain.

Development of a Duplex TaqMan Real-Time Polymerase Chain Reaction for Accurate Identification and Quantification of Salmonella Enteritidis from Laboratory Samples and Contaminated Chicken Eggs

Salmonella enteritidis is a major causative agent of foodborne illnesses worldwide. As the traditional serotyping and quantification methods are labor-intensive, time-consuming, and expensive, faster and more convenient molecular diagnostic methods are needed. In this study, we developed and validated a rapid duplex TaqMan real-time polymerase chain reaction (PCR) for the accurate identification and quantification of S. enteritidis. The primers and TaqMan probes were designed based on the S. enteritidis-specific gene lygD and the Salmonella genus-specific gene invA. The melt curve and gel electrophoresis analysis showed that the designed primers had potent specificity for the amplification of lygD and invA. The duplex real-time PCR specifically identified S. enteritidis from a panel of 40 Salmonella strains that represented 29 serovars and 12 non-Salmonella organisms. The duplex real-time PCR assay detected four copies of S. enteritidis DNA per reaction. The intra- and inter- assays indicated a high degree of reproducibility. The real-time PCR could accurately detect and quantify S. enteritidis in chicken organs after Salmonella infection. Furthermore, the assay identified 100% of the S. enteritidis and Salmonella genus isolates from chicken egg samples with superior sensitivity after 6 h of pre-enrichment compared to the traditional culture method. Additionally, the most-probable-number (MPN) combined with qPCR and a shortened incubation time (MPN-qPCR-SIT) method was developed for the population determination of S. enteritidis and compared with various enumeration methods. Thus, we have established and validated a new duplex real-time PCR assay and MPN-qPCR-SIT method for the accurate detection and quantification of S. enteritidis, which could contribute to meeting the need for fast detection and identification in prevention and control measures for food safety.

Development and Application of a Multiplex Fluorescent PCR for Shigella Detection and Species Identification

This study was to develop a multiplex fluorescent PCR for Shigella detection and species identification. Five primer pairs for Shigella detection and species identification were designed by Primer Premier 5.0. The multiplex fluorescent PCR was optimized by varying single parameter while other parameters were maintained. The multiplex fluorescent PCR assay could correctly detect Shigella and identify four Shigella species with a detection limits of 10 pg genomic DNA per reaction. Testing different strains and clinical samples confirmed the sensitivity and specificity of the multiplex fluorescent PCR. The newly developed multiplex fluorescent PCR assay is simple, sensitive and specific for Shigella detection and species identification. It has a potential to be used in routine Shigella detection and species identification in clinical laboratories.

Characterization of Extended-Spectrum Cephalosporin (ESC) Resistance in Salmonella Isolated from Chicken and Identification of High Frequency Transfer of blaCMY-2 Gene Harboring Plasmid In Vitro and In Vivo

Simple Summary

The prevalence of extended-spectrum cephalosporin (ESC)-resistant Salmonella is of great concern, as these strains with the same β-lactamase (bla) genes were found in human and poultry. The objective is to characterize ESC-resistant Salmonella isolated from chicken and to determine the transferability of β-lactamase gene-harboring plasmid in vitro and in vivo. ESC resistance genes in Salmonella isolated from chickens and presented a comprehensive analysis of the highly frequent transfer of the bla_CMY-2 gene in vitro and in vivo. In addition, this study has demonstrated the ease with which a bla_CMY-2 gene-harboring plasmid can be rapidly transferred between Salmonella and pathogenic E. coli within the intestinal tracts of mice, even without antimicrobial selective pressure. Given the potential risk of the frequent transfer of the bla_CMY-2 gene via the food chain to the human digestive tract, the molecular mechanism involved in the dissemination and maintenance of ESC resistance genes should be studied as further research in greater detail, and enhanced surveillance should be implemented to prevent the widespread of ESC resistant strains.

Abstract

A total of 136 Salmonella isolates from chicken feces and meat samples of the top 12 integrated chicken production companies throughout Korea were collected. Among the 17 ESC-resistant Salmonella; bla_CTX-M-15 was the most prevalent gene and two strains carried bla_TEM-1/bla_CTX-M-15 and bla_CMY-2, respectively. The transferable bla_CTX-M-15 gene was carried by IncFII plasmid in three isolates and the bla_CMY-2 gene carried by IncI1 plasmid in one isolate. bla_CMY-2 gene-harboring strain was selected as the donor based on the high frequency of bla_CMY-2 gene transfer in vitro and its transfer frequencies were determined at 10⁻³ transconjugants per recipient. The transfer of bla_CMY-2 gene-harboring plasmid derived from chicken isolate into a human pathogen; enteroinvasive Escherichia coli (EIEC), presented in mouse intestine with about 10⁻¹ transfer frequency without selective pressure. From the competition experiment; bla_CMY-2 gene-harboring transconjugant showed variable fitness burden depends on the parent strains. Our study demonstrated direct evidence that the bla_CMY-2 gene harboring Salmonella from chicken could frequently transfer its ESC-resistant gene to E. coli in a mouse intestine without antimicrobial pressure; resulting in the emergence of multidrug resistance in potentially virulent EIEC isolates of significance to human health; which can increase the risk of therapeutic inadequacy or failures.

Dissemination of a multidrug resistant CTX-M-65 producer Salmonella enterica serovar Infantis clone between marketed chicken meat and children

The objective of the present study was to characterize Salmonella enterica serovar Infantis isolated from chicken meat determining their clonal relationships with S. Infantis isolated from children with diarrhea. Fifteen meat-recovered S. Infantis were analyzed. Susceptibility levels to 14 antibacterial agents, the presence of ESBL and that of inducible plasmid-mediated AmpC (i-pAmpC) were determined by phenotypical methods. The presence of ESBL and pAmpC was confirmed by PCR, and detected ESBL-encoding genes were sequenced and their transferability tested by conjugation. The presence of gyrA mutations as well as Class 1 integrons was determined by PCR. Clonal relationships were established by REP-PCR and RAPD. In addition, 25 clinical isolates of S. Infantis were included in clonality studies. All meat-recovered S. Infantis were MDR, showing resistance to ampicillin, nitrofurans and quinolones, while none was resistant to azithromycin, ceftazidime or imipenem. ESBL (bla_CTX-M-65) and i-pAmpC (bla_DHA) were detected in 2 and 5 isolates respectively (in one case concomitantly), with bla_CTX-M-65 being transferable through conjugation. In addition, 1 isolate presented a bla_SHV gene. All isolates presented D₈₇Y at GyrA, nalidixic acid active efflux pump and a Class 1 integron of ~1000 bp (aadA1). Clonal analysis showed that all isolates were related. Further they were identical to MDR bla_CTX-M-65-producing S. Infantis isolates causing children diarrhea in Lima. The dissemination of MDR bla_CTX-M-65-producing S. Infantis between marketed meat and children highlights a public health problem which needs be controlled at livestock level.

Transcriptomic Analysis, Motility and Biofilm Formation Characteristics of Salmonella typhimurium Exposed to Benzyl Isothiocyanate Treatment

Salmonella typhimurium (S. typhimurium) is a common foodborne pathogen that not only causes diseases and contaminates food, but also causes considerable economic losses. Therefore, it is necessary to find effective and feasible methods to control S. typhimurium. In this study, changes in S. typhimurium after treatment with benzyl isothiocyanate (BITC) were detected by transcriptomics to explore the antibacterial effect of BITC at subinhibitory concentration. The results showed that, in contrast to the control group (SC), the BITC-treated group (SQ_BITC) had 197 differentially expressed genes (DEGs), of which 115 were downregulated and 82 were upregulated. We screened out eight significantly downregulated virulence-related genes and verified gene expression by quantitative Real-time Polymerase Chain Reaction (qRT-PCR). We also selected motility and biofilm formation to observe the effects of BITC on the other virulence related factors of S. typhimurium. The results showed that both swimming and swarming were significantly inhibited. BITC also had a significant inhibitory effect on biofilm formation, and showed an effect on bacterial morphology. These results will be helpful for understanding the mechanism of the antibacterial action of BITC against S. typhimurium and other foodborne pathogens.

Detection and molecular typing of campylobacter isolates from human and animal faeces in coastal belt of Odisha, India

Introduction

Campylobacter-mediated diarrhoea is one of the major causes of gastroenteritis globally. A majority of the Campylobacter spp. that cause disease in humans have been isolated from animals. Faecal contamination of food and water is the identified frequent cause of human campylobacteriosis.

Methodology

In the present study, faecal samples from patients with symptoms of acute diarrhoea (n = 310) and domestic animals including cows (n = 60), sheep (n = 45) and goats (n = 45) were collected from the same localities in the peri-urban Bhubaneswar city. Genomic DNA isolation followed by polymerase chain reaction and sequencing was employed to analyse Campylobacter spp.-positive samples.

Results

Of the 460 faecal samples, 16.77% of human samples and 25.33% of animal samples were found to be positive for Campylobacter spp. Among animals, the isolation rate was highest in sheep followed by cows and goats with 9.33%, 8.66% and 7.33%, respectively. The highest number of Campylobacter-positive cases was diagnosed in infants of 2-5 years age. Concurrent infection of other pathogens in addition to Campylobacter spp. was frequently detected in the samples.

Conclusion

The present study showed the incidence of Campylobacter infections in human and different animal species in and around Bhubaneswar, Odisha. The analysis suggested that domestic animals can be the potential sources for human campylobacteriosis in the region.

Precise, direct, and rapid detection of Shigella Spa gene by a novel unmodified AuNPs-based optical genosensing system

Early detection of infectious bacteria is a necessity for combating infectious diseases. Due to low infectious dose of Shigella, rapid and sensitive detection is needed. Compared to the presented genes, Spa gene can be introduced as a novel sequence for all species of Shigella detection. Herein, the possibility of Spa genes for detection of four species of Shigella was investigated for the first time by AuNPs-based optical genosensing system. In this method, AuNP-DNA probes were hybridized with Spa gene sequence. When the complementary target is present, it prevents the aggregation of the complex under acid environment and the solution remains red whereas in the absence of the specific sequence, it turns to purple. Therefore, visual detection is possible with bare eye. The comparison of this Optical DNA biosensor and PCR-based method showed that the proposed method is simple, cost-effective, rapid operation, with high or comparable detection limit of (LOD and LOQ: 8.14 and 26.6 ng mLl^-1, respectively), without need of any expensive techniques, and equipments compared to the conventional methods. In conclusion, the described method may develop into a platform that could be utilized for detection of various bacterial species with high accuracy and prompt screening of samples.

Molecular Detection and Epidemiological Features of Selected Bacterial, Viral, and Parasitic Enteropathogens in Stool Specimens from Children with Acute Diarrhea in Thi-Qar Governorate, Iraq

Knowledge of etiology causes of diarrheal illness is essential for development and implementation of public health measures to prevent and control this disease syndrome. There are few published studies examining diarrhea in children aged <5 years in Iraq. This study aims to investigate the occurrences and epidemiology of selected bacterial (Salmonella spp. and Campylobacter spp.), viral (adenovirus, norovirus GI and GII, and astrovirus), and parasitic (Entamoeba spp. and Giardia spp.) agents in stool samples from 155 child diarrheal cases enrolled between March and August 2017, in a hospital-based cross-sectional study in Thi-Qar, southeastern Iraq. Using molecular techniques and sequence-based characterization, adenovirus was the most frequently detected enteropathogen (53/155 (34.2%)), followed by Salmonella spp. (23/155 (14.8%)), Entamoeba spp. (21/155 (13.5%)), and Campylobacter spp. (17/155 (10.9%)). Mixed infection with Salmonella spp. and Campylobacter spp. was evident, and the same was revealed between various enteric viruses, particularly adenovirus and norovirus. The most frequent co-infection pattern was between adenovirus and Campylobacter spp., in seven cases (7/155 (4.5%)). Whole-genome sequencing-derived typing data for Salmonella isolates (n = 23) revealed that sequence type 49 was the most prevalent in this sample set (15/23 (65.2%)). To the best of our knowledge, this study provides the first report on detection and identification of floR, bla_CARB-2, and mphA antimicrobial resistance genes in Salmonella isolated from children in the Middle East region. Logistic regression analysis pointed to few enteropathogen-specific correlations between child age, household water source, and breastfeeding patterns in relation to the outcome of detection of individual enteropathogens. This study presents the first published molecular investigation of multiple enteropathogens among children <5 years of age in Iraq. Our data provide supporting evidence for planning of childhood diarrhea management programs. It is important to build on this study and develop future longitudinal case-control research in order to elaborate the epidemiology of enteropathogens in childhood diarrhea in Iraq.

Effects of Different Papua New Guinea Sweetpotato Varieties on Performance and Level of Enteric Pathogens in Chickens

Simple Summary

The smallholder poultry industry in Papua New Guinea (PNG) has grown rapidly in the last decade. The cost of growing meat birds is high, as feed alone makes up to 80% of the total cost of production in PNG. Sweetpotato is currently used in a poultry feed as a cheaper alternative option compared to the more expensive commercially manufactured stockfeed in PNG. The PNG smallholder poultry production system involves many families who rear multiple batches of meat birds every year. These birds are sold mostly at the farm gate, at local provincial markets, or roadside markets. Consumption of contaminated chicken meat has been identified as one of the important food vehicles for food borne illness. This PNG-based study was conducted to understand whether the inclusion of local sweetpotato in poultry feed can influence the shedding of pathogens such as Clostridium perfringens, Salmonella and Campylobacter without causing negative effects on poultry performance. The results of this study releveled that Campylobacter and Salmonella levels in the broilers fed with the local sweetpotato diets can be influenced with inclusion of enzymes in the feed.

Abstract

In the last decade, research has targeted the evaluation of local feed ingredients for use in monogastric diets to alleviate the high cost of production of livestock at smallholder levels in Papua New Guinea (PNG). The PNG smallholder poultry production system involves many families who rear multiple batches of meat birds every year. This study was conducted to evaluate the levels of enteric pathogens in the caeca of broilers fed with sweetpotato diets with varying levels of non-starch polysaccharides (NSP). Selection of a sweetpotato variety for use in broiler diets should be based on the total NSP content. In particular, varieties with low soluble NSPs are economical to use as Apparent Metabolizable Energy (AME) values are within the desired range for poultry and there is minimal need to include enzymes to improve NSP digestibility. The use of varieties with a low total NSP is also advantageous as the numbers of Clostridium perfringens was lower in broilers fed with these sweetpotato varieties. The level of Campylobacter and Salmonella levels were high in the ceca of birds fed with the sweetpotato varieties with high total NSP. These levels can be reduced with the inclusion of enzymes. This information will assist in the efficient use of local varieties of sweetpotato in PNG by small holder poultry farmers for sustainable poultry production and the commercial industry.

Developments in Rapid Detection Methods for the Detection of Foodborne Campylobacter in the United States

The accurate and rapid detection of Campylobacter spp. is critical for optimal surveillance throughout poultry processing in the United States. The further development of highly specific and sensitive assays to detect Campylobacter in poultry matrices has tremendous utility and potential for aiding the reduction of foodborne illness. The introduction and development of molecular methods such as polymerase chain reaction (PCR) have enhanced the diagnostic capabilities of the food industry to identify the presence of foodborne pathogens throughout poultry production. Further innovations in various methodologies, such as immune-based typing and detection as well as high throughput analyses, will provide important epidemiological data such as the identification of unique or region-specific Campylobacter. Comparable to traditional microbiology and enrichment techniques, molecular techniques/methods have the potential to have improved sensitivity and specificity, as well as speed of data acquisition. This review will focus on the development and application of rapid molecular methods for identifying and quantifying Campylobacter in U.S. poultry and the emergence of novel methods that are faster and more precise than traditional microbiological techniques.

Prevalence, antimicrobial resistance, and virulence-associated genes of Campylobacter isolates from raw chicken meat in Shiraz, Iran

BACKGROUND

Campylobacter is recognized as a major cause of foodborne gastroenteritis in humans in many countries and may be transferred from animals to humans. The consumption of chicken meat is identified as a major cause of Campylobacter infection in humans.

AIMS

To find out the contamination rate of chicken meat with Campylobacter, the antimicrobial resistance (AMR) pattern, and the virulence-associated genes of the isolates.

METHODS

Ninety packed chicken meat from 7 main poultry slaughterhouses in Shiraz were analyzed for Campylobacter spp. isolation through microbiological methods. Specific primers were used for the identification of the Campylobacter isolates on species level by polymerase chain reaction (PCR). Antibiotic resistant profiles were determined using the disc diffusion method based on Clinical and Laboratory Standards Institute (CLSI) standards. All the isolates were screened for 7 virulence-associated genes, namely cdtA, cdtB, cdtC, cadF, pldA, cgtB, and virB11 by PCR.

RESULTS

Out of 90 chicken meats, 26 (28.9%) Campylobacter spp. have been isolated. Resistance to ciprofloxacin (CIP), nalidixic acid (NA), and cefixime (CFM) was observed in all the isolates. Resistance to trimethoprim/sulfamethoxazole (SXT), tetracycline (TET), ampicillin (AMP), and chloramphenicol (CHO) was 80.8%, 88.5%, 76.9%, and 30.8%, respectively. Multidrug resistance (MDR) phenotype was observed in 80.8% of the Campylobacter isolates. All the isolates were positive for cdtA, cdtB, cdtC, and cadF genes. pldA and cgtB were detected in 65.4% and 15.4% of the isolates, respectively.

CONCLUSION

In this study, the presence of several virulence genes and an alarming level of MDR in Campylobacter spp. isolates were reported. Particularly, resistance to CIP and TET should be highlighted, since both are key drugs for the treatment of human campylobacteriosis.

A multiplex real-time PCR assay, based on invA and pagC genes, for the detection and quantification of Salmonella enterica from cattle lymph nodes

Cattle lymph nodes can harbor Salmonella and potentially contaminate beef products. We have developed and validated a new real-time PCR (qPCR) assay for the detection and quantification of Salmonella enterica in cattle lymph nodes. The assay targets both the invA and pagC genes, the most conserved molecular targets in Salmonella enterica. An 18S rRNA gene assay that amplifies from cattle and other animal species was also included as an internal control. Available DNA sequences for invA, pagC and 18S rRNA genes were used for primer and probe selections. Three Salmonella serotypes, S. Typhimurium, S. Anatum, and S. Montevideo, were used to assess the assay's analytical sensitivity. Correlation coefficients of standard curves generated for each target and for all three serotypes were >99% and qPCR amplification efficiencies were between 93% and 110%. Assay sensitivity was also determined using standard curve data generated from Salmonella-negative cattle lymph nodes spiked with 10-fold dilutions of the three Salmonella serotypes. Assay specificity was determined using Salmonella culture method, and qPCR testing on 36 Salmonella strains representing 33 serotypes, 38 Salmonella strains of unknown serotypes, 252 E. coli strains representing 40 serogroups, and 31 other bacterial strains representing 18 different species. A collection of 647 cattle lymph node samples from steers procured from the Midwest region of the US were tested by the qPCR, and compared to culture-method of detection. Salmonella prevalence by qPCR for pre-enriched and enriched lymph nodes was 19.8% (128/647) and 94.9% (614/647), respectively. A majority of qPCR positive pre-enriched samples (105/128) were at concentrations between 10⁴ and 10⁵ CFU/mL. Culture method detected Salmonella in 7.7% (50/647) and 80.7% (522/647) of pre- and post-enriched samples, respectively; 96.0% (48/50) of pre-enriched and 99.4% (519/522) of post-enriched culture-positive samples were also positive by qPCR. More samples tested positive by qPCR than by culture method, indicating that the real-time PCR assay was more sensitive. Our data indicate that this triplex qPCR can be used to accurately detect and quantify Salmonella enterica strains from cattle lymph node samples. The assay may serve as a useful tool to monitor the prevalence of Salmonella in beef production systems.

The other Campylobacters: Not innocent bystanders in endemic diarrhea and dysentery in children in low-income settings

Background

Campylobacter is one of the main causes of gastroenteritis worldwide. Most of the current knowledge about the epidemiology of this food-borne infection concerns two species, C. coli and C. jejuni. Recent studies conducted in developing countries and using novel diagnostic techniques have generated evidence of the increasing burden and importance of other Campylobacter species, i.e. non-C. coli/jejuni. We performed a nested case-control study to compare the prevalence of C. coli/jejuni and other Campylobacter in children with clinical dysentery and severe diarrhea as well as without diarrhea to better understand the clinical importance of infections with Campylobacter species other than C. coli/jejuni.

Methodology/Principal findings

Our nested case-control study of 439 stool samples included dysenteric stools, stools collected during severe diarrhea episodes, and asymptomatic stools which were systematically selected to be representative of clinical phenotypes from 9,160 stools collected during a birth cohort study of 201 children followed until two years of age. Other Campylobacter accounted for 76.4% of the 216 Campylobacter detections by qPCR and were more prevalent than C. coli/jejuni across all clinical groups. Other Campylobacter were also more prevalent than C. coli/jejuni across all age groups, with older children bearing a higher burden of other Campylobacter. Biomarkers of intestinal inflammation and injury (methylene blue, fecal occult test, myeloperoxidase or MPO) showed a strong association with dysentery, but mixed results with infection. MPO levels were generally higher among children infected with C. coli/jejuni, but Shigella-infected children suffering from dysentery recorded the highest levels (26,224 ng/mL); the lowest levels (10,625 ng/mL) were among asymptomatic children infected with other Campylobacter. Adjusting for age, sex, and Shigella infection, dysentery was significantly associated with C. coli/jejuni but not with other Campylobacter, whereas severe diarrhea was significantly associated with both C. coli/jejuni and other Campylobacter. Compared to asymptomatic children, children suffering from dysentery had a 14.6 odds of C. coli/jejuni infection (p-value < 0.001, 95% CI 5.5–38.7) but were equally likely to have other Campylobacter infections–odds ratio of 1.3 (0.434, 0.7–2.4). Children suffering from severe diarrhea were more likely than asymptomatic children to test positive for both C. coli/jejuni and other Campylobacter–OR of 2.8 (0.034, 1.1–7.1) and 1.9 (0.018, 1.1–3.1), respectively. Compared to the Campylobacter-free group, the odds of all diarrhea given C. coli/jejuni infection and other Campylobacter infection were 8.8 (<0.001, 3.0–25.7) and 2.4 (0.002, 1.4–4.2), respectively. Eliminating other Campylobacter in this population would eliminate 24.9% of the diarrhea cases, which is almost twice the population attributable fraction of 15.1% due to C. coli/jejuni.

Conclusions/Significance

Eighty-seven percent of the dysentery and 59.5% of the severe diarrhea samples were positive for Campylobacter, Shigella, or both, emphasizing the importance of targeting these pathogens to limit the impact of dysentery and severe diarrhea in children. Notably, the higher prevalence of other Campylobacter compared to C. coli/jejuni, their increasing burden during early childhood, and their association with severe diarrhea highlight the importance of these non-C. coli/jejuni Campylobacter species and suggest a need to clarify their importance in the etiology of clinical disease across different epidemiological contexts.

Campylobacter is a major public health concern in developed and developing countries. C. coli and C. jejuni have long been considered to be the major disease-causing species, and clinical microbiologic approaches target these two species. However, less selective diagnostic approaches have shown the increasing importance of other Campylobacter species (i.e. non-C. coli/jejuni). Our case-control study investigated the association between diarrhea, C. coli/jejuni, and other Campylobacter among 439 stool samples from 201 children in peri-urban communities in Loreto, Peru. Three quarters of the 216 Campylobacter detections were associated with other Campylobacter, whose prevalence increased with age and was greater than that of C. coli/jejuni in all age and clinical groups (dysentery, severe diarrhea, and asymptomatic). Despite their lower prevalence, C. coli/jejuni were more strongly associated with higher levels of myeloperoxidase, clinical dysentery, and the presence of leukocytes and blood in the stool compared to other Campylobacter. Other Campylobacter were equally likely as C. coli/jejuni to be detected in severe diarrhea cases–odds ratio of 1.9 (p-value = 0.018, 95% CI 1.1–3.1) and 2.8 (0.034, 1.1–7.1), respectively. Removing C. coli/jejuni in this population would eliminate 15.1% of diarrhea compared to 24.9% if other Campylobacter were eliminated.

Impact of human Campylobacter infections in Southeast Asia: The contribution of the poultry sector

Campylobacter is globally recognized as a major cause of foodborne infection in humans, whilst the development of antimicrobial resistance and the possibility of repelling therapy increase the threat to public health. Poultry is the most frequent source of Campylobacter infection in humans, and southeast Asia is a global leader in poultry production, consumption, and exports. Though three of the world's top 20 most populated countries are located in southeast Asia, the true burden of Campylobacter infection in the region has not been fully elucidated. Based on published data, Campylobacter has been reported in humans, animals, and food commodities in the region. To our knowledge, this study is the first to review the status of human Campylobacter infection in southeast Asia and to discuss future perspectives. Gaining insight into the true burden of the infection and prevalence levels of Campylobacter spp. in the southeast Asian region is essential to ensuring global and regional food safety through facilitating improvements in surveillance systems, food safety regulations, and mitigation strategies.

Development of a multiplex qPCR in real time for quantification and differential diagnosis of Salmonella Gallinarum and Salmonella Pullorum

Currently there are 2659 Salmonella serovars. The host-specific biovars Salmonella Pullorum and Salmonella Gallinarum cause systemic infections in food-producing and wild birds. Fast diagnosis is crucial to control the dissemination in avian environments. The present work describes the development of a multiplex qPCR in real time using a low-cost DNA dye (SYBr Green) to identify and quantify these biovars. Primers were chosen based on genomic regions of difference (RoD) and optimized to control dimers. Primers pSGP detect both host-specific biovars but not other serovars and pSG and pSP differentiate biovars. Three amplicons showed different melting temperatures (Tm), allowing differentiation. The pSGP amplicon (97 bp) showed Tm of 78°C for both biovars. The pSG amplicon (273 bp) showed a Tm of 86.2°C for S. Gallinarum and pSP amplicon (260 bp) dissociated at 84.8°C for S. Pullorum identification. The multiplex qPCR in real time showed high sensitivity and was capable of quantifying 10⁸-10¹ CFU of these biovars.

Campylobacter hepaticus, the cause of spotty liver disease in chickens, is present throughout the small intestine and caeca of infected birds

Spotty liver disease (SLD) causes significant egg production losses and mortality in chickens and is therefore a disease of concern for some sectors of the poultry industry. Although the first reports of the disease came from the United States in the 1950s it is only recently that the organism that causes the disease was identified, isolated, and characterised as a new bacterial species, Campylobacter hepaticus. The first isolations of C. hepaticus were from the livers and bile of SLD affected birds. Isolates could only be recovered from samples that had a monoculture of C. hepaticus in the tissues, as a selective culturing method has not yet been developed. In non-selective growth conditions the slow growing C. hepaticus is quickly outgrown by many other members of the chicken microbiota. Therefore, it is currently not possible to use a culturing approach to evaluate C. hepaticus carriage in tissues, such as the gastrointestinal tract (GIT), that also carry complex microbial populations. As it is suspected that birds become infected via the faecal-oral route it is important that pathogen carriage in the GIT is investigated. In the present study, a specific and sensitive quantitative real-time PCR assay, based on the glycerol kinase gene of C. hepaticus, was developed. The assay facilitated the detection and quantification of C. hepaticus in tissue samples from clinical cases of SLD. It was shown that in infected birds C. hepaticus colonises the small intestine, increasing in abundance from duodenum to ileum, and is at highest levels within the ceaca. C. hepaticus was also readily detected in cloacal swabs, indicating that thecl-oral infection.

Advanced biosensors for detection of pathogens related to livestock and poultry

Infectious animal diseases caused by pathogenic microorganisms such as bacteria and viruses threaten the health and well-being of wildlife, livestock, and human populations, limit productivity and increase significantly economic losses to each sector. The pathogen detection is an important step for the diagnostics, successful treatment of animal infection diseases and control management in farms and field conditions. Current techniques employed to diagnose pathogens in livestock and poultry include classical plate-based methods and conventional biochemical methods as enzyme-linked immunosorbent assays (ELISA). These methods are time-consuming and frequently incapable to distinguish between low and highly pathogenic strains. Molecular techniques such as polymerase chain reaction (PCR) and real time PCR (RT-PCR) have also been proposed to be used to diagnose and identify relevant infectious disease in animals. However these DNA-based methodologies need isolated genetic materials and sophisticated instruments, being not suitable for in field analysis. Consequently, there is strong interest for developing new swift point-of-care biosensing systems for early detection of animal diseases with high sensitivity and specificity. In this review, we provide an overview of the innovative biosensing systems that can be applied for livestock pathogen detection. Different sensing strategies based on DNA receptors, glycan, aptamers and antibodies are presented. Besides devices still at development level some are validated according to standards of the World Organization for Animal Health and are commercially available. Especially, paper-based platforms proposed as an affordable, rapid and easy to perform sensing systems for implementation in field condition are included in this review.

Molecular Differentiation of Shigella Spp. from Enteroinvasive E. Coli

A real-time polymerase chain reaction (PCR) assay, amplifying the genes encoding lactose permease (lacY) and invasion plasmid antigen H (ipaH), was run on 121 isolates phenotypically classified as Shigella spp., enteroinvasive Escherichia coli (EIEC), or EIEC O nontypable (ONT). The results were compared with data from a generic E. coli multiple-locus variable-number of tandem repeat analysis (MLVA) and a Shigella MLVA.

The real-time PCR verified all Shigella spp. (n = 53) as Shigella (lacY negative) and all EIEC O121 (n = 15) and EIEC O124 (n = 2) as EIEC (lacY positive). However, the real-time PCR typed EIEC O164 as either EIEC (n = 2) or Shigella (n = 2) and, thus, was not suited for classifying this group of isolates. Interestingly, the majority (42/47, 89.4%) of the EIEC ONT were classified as Shigella (lacY negative) by the real-time PCR, and in nearly all cases, (92.9%, 39/42) data from both MLVA assays supported these findings. Overall, in 94.7% (114/121) of the isolates, the results from the real-time PCR were substantiated by the results from the MLVA assays.

In conclusion, the real-time PCR assay was fast and accurate in differentiating Shigella spp. from EIEC, with the exception of the EIEC O164 group. This molecular assay was particularly pragmatic for the challenging EIEC ONT group.

Evaluation of a multiplex PCR assay for detection of cytomegalovirus in stool samples from patients with ulcerative colitis

AIM: To evaluate a multiplex PCR assay for the detection of bacterial and viral enteropathogens in stool samples from patients with ulcerative colitis (UC).

METHODS: We prospectively analyzed 300 individuals, including immunocompetent patients, immunocompromised patients, and patients with UC. Stool samples were collected from the recto-sigmoid region of the colon by endoscopy. The samples were qualitatively analyzed for bacterial and viral enteropathogens with a multiplex PCR assay using a Seeplex^® Kit. Additional clinical and laboratory data were collected from the medical records.

RESULTS: A multiplex PCR assay detected 397 pathogens (191 bacteria and 206 viruses) in 215 samples (71.7%). The most frequently detected bacteria were Escherichia coli H7, 85 (28.3%); followed by Aeromonas spp., 43 (14.3%); and Clostridium perfringens, 36 (12.0%) samples. The most prevalent viruses were Epstein-Barr virus (EBV), 90 (30.0%); followed by human herpes virus-6 (HHV-6), 53 (17.7%); and cytomegalovirus (CMV), 37 (12.3%) samples. The prevalence rate of CMV infection was significantly higher in the immunocompromised group than in the immunocompetent group (P < 0.01). CMV infection was more common in patients with UC (26/71; 36.6%) than in the immunocompetent patients excluding UC (6/188; 3.2%) (P < 0.01). CMV infection was more prevalent in UC active patients (25/58; 43.1%) than in UC inactive patients (1/13; 7.7%) (P < 0.05). Among 4 groups which defined by the UC activity and immunosuppressive drugs, the prevalence rate of CMV infection was highest in the UC active patients with immunosuppressive drugs (19/34; 55.8%). Epstein-Barr virus (EBV) infection was more common in the immunocompromised patients excluding UC (18/41; 43.9%) than in the immunocompetent patients excluding UC (47/188; 25.0%) (P < 0.05). The simultaneous presence of CMV and EBV and/or HHV6 in UC active patients (14/58; 24.1%) was greater than in immunocompromised patients excluding UC (5/41; 12.2%) (P < 0.05).

CONCLUSION: The multiplex PCR assay that was used to analyze the stool samples in this study may serve as a non-invasive approach that can be used to exclude the possibility of CMV infection in patients with active UC who are treated with immunosuppressive therapy.

Association Between Shigella Infection and Diarrhea Varies Based on Location and Age of Children

Molecular identification of the invasion plasmid antigen-H (ipaH) gene has been established as a useful detection mechanism for Shigella spp. The Global Enteric Multicenter Study (GEMS) identified the etiology and burden of moderate-to-severe diarrhea (MSD) in sub-Saharan Africa and south Asia using a case-control study and traditional culture techniques. Here, we used quantitative polymerase chain reaction (qPCR) to identify Shigella spp. in 2,611 stool specimens from GEMS and compared these results to those using culture. Demographic and nutritional characteristics were assessed as possible risk factors. The qPCR identified more cases of shigellosis than culture; however, the distribution of demographic characteristics was similar by both methods. In regression models adjusting for Shigella quantity, age, and site, children who were exclusively breast-fed had significantly lower odds of MSD compared with children who were not breast-fed (odds ratio [OR] = 0.47, 95% confidence interval (CI) = 0.28-0.81). The association between Shigella quantity and MSD increased with age, with a peak in children of 24-35 months of age (OR = 8.2, 95% CI = 4.3-15.7) and the relationship between Shigella quantity and disease was greatest in Bangladesh (OR = 13.2, 95% CI = 7.3-23.8). This study found that qPCR identified more cases of Shigella and age, site, and breast-feeding status were significant risk factors for MSD.

Optomagnetic read-out enables easy, rapid, and cost-efficient qualitative biplex detection of bacterial DNA sequences

There is an increasing need to develop novel bioassay methods for low-cost, rapid, and easy-to-use multiplex detection of pathogens in various fields ranging from human infectious disease diagnosis, drinking water quality control, to food safety applications. Due to their unique advantages, magnetic and optomagnetic bioassay principles are particularly promising for biodetection platforms that will be used in developing countries. In this paper, an optomagnetic method for rapid and cost-efficient qualitative biplex detection of bacterial DNA sequences is demonstrated. Within less than two hours, the assay gives an answer to whether none, both, or only one of the bacterial DNA sequences is present in the sample. The assay relies on hybridization of oligonucleotide-functionalized magnetic nanobeads of two different sizes to rolling circle amplification (RCA) products originating from two different bacterial targets. The different bead sizes are equipped with different oligonucleotide probes, complementary to only one of the RCA products, and the read-out is carried out in the same sample volume. In an optomagnetic setup, the frequency modulation of transmitted laser light in response to an applied AC magnetic field is measured. The presented methodology is potentially interesting for low-cost screening of pathogens relating to both human and veterinary medicine in resource-poor regions of the world.

Update on molecular epidemiology of Shigella infection

PURPOSE OF REVIEW

Shigella spp. are important etiologic agents of diarrhea worldwide. This review summarizes the recent findings on the epidemiology, diagnosis, virulence genes, and pathobiology of Shigella infection.

RECENT FINDINGS

Shigella flexneri and Shigella sonnei have been identified as the main serogroups circulating in developing and developed countries, respectively. However, a shift in the dominant species from S. flexneri to S. sonnei has been observed in countries that have experienced recent improvements in socioeconomic conditions. Despite the increasing usage of molecular methods in the diagnosis and virulence characterization of Shigella strains, researchers have been unsuccessful in finding a specific target gene for this bacillus. New research has demonstrated the role of proteins whose expressions are temperature-regulated, as well as genes involved in the processes of adhesion, invasion, dissemination, and inflammation, aiding in the clarification of the complex pathobiology of shigellosis.

SUMMARY

Knowledge about the epidemiologic profile of circulating serogroups of Shigella and an understanding of its pathobiology as well as of the virulence genes is important for the development of preventive measures and interventions to reduce the worldwide spread of shigellosis.

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.

Rapid identification of Campylobacter jejuni from poultry carcasses and slaughtering environment samples by real-time PCR

The objective of this study was to develop a real-time PCR assay for rapid identification of Campylobacter jejuni and to apply the method in analyzing samples from poultry processing. A C. jejuni-specific primer set targeting a portion of the C. jejuni hippuricase gene was developed. The specificity of the newly designed primer pair was verified using 5 C. jejuni strains and 20 other bacterial strains. Sensitivity was determined to be as low as 1 genome copy per reaction. A total of 73 samples were collected at different sites along the processing line during 2 visits to a poultry slaughterhouse and were examined by direct plating onto modified charcoal cefoperazone deoxycholate agar or after enrichment in Bolton broth followed by plating on modified charcoal cefoperazone deoxycholate agar. The newly developed real-time PCR assay was used to identify the presumptive colonies as belonging to C. jejuni. A real-time PCR assay targeting 16S ribosomal RNA was also applied to determine Campylobacter spp. prevalence. Results from the real-time PCR analysis indicated considerable variability in Campylobacter contamination, with incidence rates of 72.7 and 27.6% for sampling days A and B, respectively. Campylobacter was isolated from 100% of prescalded and preeviscerated carcasses on sampling day A. In contrast, on sampling day B, the highest number of Campylobacter-positive carcasses was recovered after evisceration (60%). The chilling process significantly reduced (P < 0.05) Campylobacter population, but the percentage of positive samples on sampling day A increased to 80%. All samples collected from the processing environment, except scalding tank 3 and the prechiller and chiller tanks, were 100% positive on day A, whereas no campylobacters were isolated from machinery on sampling day B. Our results revealed the widespread of C. jejuni in poultry processing and proved that the newly developed real-time PCR assay is a simple, specific, and inexpensive method for rapid C. jejuni identification. The newly developed PCR method can be easily used in laboratories for reliable and unambiguous identification of C. jejuni in poultry samples.

Biosensors for whole-cell bacterial detection

Bacterial pathogens are important targets for detection and identification in medicine, food safety, public health, and security. Bacterial infection is a common cause of morbidity and mortality worldwide. In spite of the availability of antibiotics, these infections are often misdiagnosed or there is an unacceptable delay in diagnosis. Current methods of bacterial detection rely upon laboratory-based techniques such as cell culture, microscopic analysis, and biochemical assays. These procedures are time-consuming and costly and require specialist equipment and trained users. Portable stand-alone biosensors can facilitate rapid detection and diagnosis at the point of care. Biosensors will be particularly useful where a clear diagnosis informs treatment, in critical illness (e.g., meningitis) or to prevent further disease spread (e.g., in case of food-borne pathogens or sexually transmitted diseases). Detection of bacteria is also becoming increasingly important in antibioterrorism measures (e.g., anthrax detection). In this review, we discuss recent progress in the use of biosensors for the detection of whole bacterial cells for sensitive and earlier identification of bacteria without the need for sample processing. There is a particular focus on electrochemical biosensors, especially impedance-based systems, as these present key advantages in terms of ease of miniaturization, lack of reagents, sensitivity, and low cost.

Targeted and highly multiplexed detection of microorganisms by employing an ensemble of molecular probes

The vast majority of microscopic life on earth consists of microbes that do not grow in laboratory culture. To profile the microbial diversity in environmental and clinical samples, we have devised and employed molecular probe technology, which detects and identifies bacteria that do and do not grow in culture. The only requirement is a short sequence of contiguous bases (currently 60 bases) unique to the genome of the organism of interest. The procedure is relatively fast, inexpensive, customizable, robust, and culture independent and uses commercially available reagents and instruments. In this communication, we report improving the specificity of the molecular probes substantially and increasing the complexity of the molecular probe set by over an order of magnitude (>1,200 probes) and introduce a new final readout method based upon Illumina sequencing. In addition, we employed molecular probes to identify the bacteria from vaginal swabs and demonstrate how a deliberate selection of molecular probes can identify less abundant bacteria even in the presence of much more abundant species.