Development of a specific cytolethal distending toxin (cdt) gene (Eacdt)-based PCR assay for the detection of Escherichia albertii.

Many Escherichia albertii isolates, an emerging pathogen of human and birds, might have been misidentified due to the difficulty of differentiating this bacterium from Escherichia coli and Shigella spp. by routine biochemical tests, resulting in underestimation of E. albertii infections. We have developed a polymerase chain reaction (PCR) assay that targets E. albertii cytolethal distending toxin (Eacdt) genes, which include the genes previously identified as Escherichia coli cdt-II. This assay could generate a single 449-bp PCR product in each of 67 confirmed E. albertii strains but failed to produce PCR product from any of the tested non-E. albertii enteric strains belonging to 37 different species, indicating 100% sensitivity and specificity of the PCR assay. The detection limit was 10 CFU per PCR tube and could detect 105 CFU E. albertii per gram of spiked healthy human stool. The Eacdt gene-based PCR could be useful for simple, rapid, and accurate detection and identification of E. albertii.

Evaluation of a surface plasmon resonance imaging-based multiplex O-antigen serogrouping for Escherichia coli using eleven major serotypes of Shiga -toxin-producing E. coli.

The early detection of Shiga toxin-producing Escherichia coli (STEC) is important for early diagnosis and preventing the spread of STEC. Although the confirmatory test for STEC should be based on the detection of Shiga toxin using molecular analysis, isolation permits additional characterization of STEC using a variety of methods, including O:H serotyping. The conventional slide agglutination O-antigen serogrouping used in many clinical laboratories is laborious and time-consuming. Surface plasmon resonance (SPR)-based immunosensors are commonly used to investigate a large variety of bio-interactions such as antibody/antigen, peptide/antibody, DNA/DNA, and antibody/bacteria interactions. SPR imaging (SPRi) is characterized by multiplexing capabilities for rapidly screening (approximately 100 to several hundred sensorgrams in parallel) molecules. SPRi-based O-antigen serogrouping method for STEC was recently developed by detecting the interactions between O-antigen-specific antibodies and bacterial cells themselves. The aim of this study was to evaluate its performance for E. coli serogrouping using clinical STEC isolates by comparing the results of slide agglutination tests. We tested a total of 188 isolates, including O26, O45, O91, O103, O111, O115, O121, O128, O145, O157, and O159. The overall sensitivity of SPRi-based O-antigen serogrouping was 98.9%. Only two O157 isolates were misidentified as nontypeable and O121. The detection limits of all serotypes were distributed between 1.1 × 106 and 17.6 × 106 CFU/ml. Pulsed-field gel electrophoresis (PFGE) revealed the heterogeneity of the examined isolates. In conclusion, SPRi is a useful method for the O-antigen serogrouping of STEC isolates, but the further evaluation of non-O157 minor serogroups is needed.

High Prevalence of Diarrheagenic Escherichia coli among Children with Diarrhea in Kenya.

Diarrheagenic Escherichia coli (DEC) is an important agent of endemic and epidemic diarrhea worldwide, particularly in developing countries. DEC cannot be differentiated from commensal E. coli on selective media, although there are a few exceptions. Most studies use the colony isolation method, which cannot detect low numbers of DEC, and therefore, these studies might underestimate the incidence of DEC. In the present study, we employed a colony sweep method with real-time PCR targeting virulence genes of 5 categories of DEC; this technique can detect very low numbers of DEC among hundreds of commensal E. coli. DEC was detected in 171 (55.9%) of 306 children with diarrhea in Kenya. The prevalence of DEC in Kenya was notably higher than that (30 in 143, 21.0%) in Indonesia. Occurrences of multiple DEC infection in Kenya were frequent (69 in 306, 23.2%), suggesting that the source of DEC infection may be related to grossly contaminated food and water. In contrast, only 9 (6.0%) of 150 healthy adults in Kenya carried DEC. Considering that healthy adults naturally harbor non-DEC, it is interesting how children exclude DEC but not non-DEC as they grow up. Several mechanisms, such as mucosal immunity and intestinal microbiota, might be involved in the exclusion of DEC.

Development of a Surface Plasmon Resonance-Based Immunosensor for Detection of 10 Major O-Antigens on Shiga Toxin-Producing Escherichia coli, with a Gel Displacement Technique To Remove Bound Bacteria.

A surface plasmon resonance-based immunosensor (SPR-immunosensor) was developed for the detection of Shiga toxin-producing Escherichia coli (STEC) belonging to the O-antigen groups O26, O91, O103, O111, O115, O121, O128, O145, O157, and O159. The polyclonal antibodies (PoAbs) generated against each of the STEC O-antigen types in rabbits were purified and were immobilized on the sensor chip at 0.5 mg/mL. The limit of detection for STEC O157 by the SPR-immunosensor was found to be 6.3 × 10(4) cells for 75 s. Each of the examined 10 O-antigens on the STECs was detected by the corresponding PoAb with almost no reaction to the other PoAbs. The detected STECs were sufficiently removed from the PoAbs using gelatin or agarose gel without deactivation of the PoAbs, enabling repeatable use of the sensor chip. The developed SPR-immunosensor can be applied for the detection of multiple STEC O-antigens. Furthermore, the new antigen removal technique using the gel displacement approach can be utilized with various immunosensors to improve the detection of pathogens in clinical and public health settings.

Assessing the performance of novel software Strain Solution on automated discrimination of Escherichia coli serotypes and their mixtures using matrix-assisted laser desorption ionization-time of flight mass spectrometry.

O157, O26, and O111 are the most important O serogroups of enterohemorrhagic Escherichia coli worldwide. Recently we reported a strategy for discriminating these serotypes from the others using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) based on the S10-spc-alpha operon gene-encoded ribosomal protein mass spectrum (S10-GERMS) method. To realize the fully automated identification of microorganisms at species- or serotype-level with the concept of S10-GERMS method, novel software named Strain Solution for MALDI-TOF MS was developed. In this study, the Strain Solution was evaluated with a total of 45 E. coli isolates including O26, O91, O103, O111, O115, O121, O128, O145, O157, O159, and untyped serotypes. The Strain Solution could accurately discriminate 92% (11/12) of O157 strains, 100% (13/13) of O26 and O111 strains from the others with three biomarkers in an automated manner. In addition, this software could identify 2 different E. coli strains (K-12 as a non-O157 representative and O157) in mixed samples. The results suggest that Strain Solution will be useful for species- or serotype-level classification of microorganisms in the fields of food safety and diagnostics.

Development of multiplex PCR for rapid identification of four Salmonella serovars most commonly isolated in Japan.

More than 2,500 serovars of Salmonella species have been reported to date. A multiplex-PCR method was developed and evaluated for discriminating the four Salmonella enterica subsp enterica serovars, namely, S. Enteritidis, S. Typhimurium, S. Thompson and S. Infantis, most commonly isolated in Japan. Twenty-two serovars of 84 Salmonella strains and 7 species of non-Salmonella strains were evaluated using primer pairs specific for the detection of Salmonella spp. Multiplex PCR generated, with 100% specificity, the expected amplicon of 333, 413, 551 and 658 bp of S. Enteritidis, S. Infantis, S. Typhimurium, and S. Thompson, respectively, while an additional non-specific amplicon (about 1,000 bp) was observed for S. Infantis, but it had no practical impact in the bacterial detection. This multiplex PCR assay can be applied to identify and discriminate clinically significant strains of Salmonella serovars rapidly and accurately without the need for serological examination.

[Bacterial infections, what we can learn from each outbreak].

Studies on outbreaks or incidences of infectious diseases and food poisonings are the starting points in research. Analyses of the outbreaks will provide the mechanism by which the illnesses occur and the establishment of countermeasure. We report here some sensational outbreaks which recently occurred in Japan: 1) enterohemorrhagic Escherichia coli (EHEC) O157 outbreaks by pickled Chinese cabbage in Hokkaido, 2) EHEC O157/O111 outbreaks by raw beef in Toyama Prefecture, 3) parasitic food poisoning due to raw olive flounder consumption in the western Japan, and 4) botulism due to the consumption of vacuum packed food in Tottori Prefecture.

Prevalence of Vibrio cholerae O1 El Tor variant in a cholera-endemic zone of Kenya.

Since 2007, Kenya has experienced an increase in cholera outbreaks characterized by a high fatality rate. In this study, we characterized 81 Vibrio cholerae isolates from diarrhoeal stool samples in Nyanza, a cholera-endemic lake region of Kenya, for virulence properties, clonality and antibiotic susceptibility. Eighty of these isolates were V. cholerae O1 El Tor variants carrying the classical ctxB gene sequence, while one isolate was V. cholerae non-O1/O139. All of the El Tor variants were of clonal origin, as revealed by PFGE, and were susceptible to ampicillin, tetracycline, ciprofloxacin, fosfomycin, kanamycin and norfloxacin. However, the isolates showed resistance to sulfamethoxazole/trimethoprim and streptomycin, and intermediate resistance to nalidixic acid, chloramphenicol and imipenem. The non-O1/O139 isolate carried the cholix toxin II gene (chxA II) and was susceptible to all antimicrobials tested except ampicillin. We propose that an El Tor variant clone caused the Nyanza cholera outbreak of 2007-2008.

Antimicrobial resistance in Salmonella strains clinically isolated in Hyogo, Japan (2009-2012).

The purpose of this study was to examine the in vitro susceptibilities to antimicrobial agents and genetic diversity of 195 clinical strains of Salmonella spp., which were isolated and examined for the extended-spectrum ß-lactamase (ESBL) blaCTX-M gene and the presence of gyrA, gyrB, parC, and parE genes mutations in Hyogo, Japan, from 2009 to 2012. Forty-three of the 195 strains were antimicrobial resistant. Two Salmonella enterica subsp. enterica strains, 1 serovar Schwarzengrund, and 1 serovar Enteritidis were identified as ESBL-producing strains possessing blaCTX-M-15 and blaCTX-M-2, respectively. Among 8 nalidixic acid-resistant strains, 7 had mutations in gyrA alone or in gyrA and parC. In conclusion, we identified CTX-M ESBL-producing Salmonella clinical strains with multidrug resistance. Further studies are needed to monitor these serious drug-resistant Salmonella strains in Japan.

Frequency of diarrheagenic Escherichia coli among children in Surabaya, Indonesia.

Diarrheagenic Escherichia coli (DEC) is a major etiologic agent of childhood diarrhea in developing countries. We investigated the frequency of DEC in stool samples from 125 diarrheal children (age, 1-10 years) and 92 non-diarrheal children in Surabaya, Indonesia. The non-diarrheal children served as healthy controls. DEC was detected in 23 of 125 (18.4%) and 47 of 92 (51.1%) samples in the diarrheal and non-diarrheal children, respectively. Enteropathogenic E. coli was the most prevalent in the non-diarrheal children (25.0%), and its prevalence was significantly higher than that in the diarrheal children (0.8%) (P < 0.0001). Interestingly, Shiga toxin-producing E. coli (4.3%) was detected only in the non-diarrheal children (P = 0.031). This is the first study comparing between diarrheal children with non-diarrheal or healthy children to investigate the role of DEC in pediatric diarrheal diseases in Indonesia.

Inter-laboratory validation and applications of quantitative real-time PCR for the detection of Kudoa septempunctata in olive flounder (Paralichthys olivaceus).

Kudoa septempunctata, a myxosporean parasite, was recently identified as the causative agent of food poisoning resulting from the consumption of raw olive flounder (Paralichthys olivaceus). A single blind inter-laboratory study, involving 5 laboratories, was conducted to validate a quantitative real-time PCR assay for the detection of the parasite. We obtained relatively constant values for log rDNA copies/g from these laboratory analyses (SD = 0.35-0.86), suggesting the validity of the real-time PCR method for the detection of K. septempunctata in P. olivaceus. Detection of K. septempunctata in muscle tissue samples collected from both sides of the fish indicated that K. septempunctata infection spreads throughout the body of P. olivaceus. K. septempunctata infection in P. olivaceus is thought to occur during the early stage of fish growth because a K. septempunctata gene was detected in 1 of 300 P. olivaceus fry tested. Feeds seem not to be sources of infection. To prevent food poisoning due to K. septempunctata, the mechanism of infection and proliferation of K. septempunctata in P. olivaceus should be elucidated, and other hosts of the parasite should be identified. The sensitive real-time PCR method described here will be a useful tool for resolving these issues.

Identification of Kudoa septempunctata as the causative agent of novel food poisoning outbreaks in Japan by consumption of Paralichthys olivaceus in raw fish.

BACKGROUND: Outbreaks of an unidentified food-borne illness associated with the consumption of raw fish have increased in Japan since 2003. Those affected with this illness develop diarrhea and emesis within 2-20 hours after a meal including raw fish. No known causative agents such as bacteria, viruses, bacterial toxins, or toxic chemicals have been detected in the foods that were ingested. Fortunately, this illness is self-limiting with good prognosis in all cases. METHODS: We conducted an epidemiological analysis of outbreaks that occurred during 2008 and 2010 and analysed a fish sample from one outbreak by metagenomic DNA sequencing, real-time polymerase chain reaction, and direct microscopic observations. The pathogenicity of a putative risk factor identified by these techniques was assessed using the suckling-mouse test and a house musk shrew emetic assay. RESULTS: The epidemiological analysis of outbreaks in 24 municipalities involving >1300 subjects implicated an olive flounder (Paralichthys olivaceus) as the causative food source. The presence of Kudoa septempunctata, a recently-described myxosporean species in P. olivaceus, was prevalent in the causative foods. K. septempunctata induced watery stools and an elevated fluid accumulation ratio in suckling mice, as well as vomiting in house musk shrews. CONCLUSIONS: These results identify K. septempunctata as the etiological agent of this novel food-borne illness outbreak associated with consumption of raw P. olivaceus. This is the first report, to our knowledge, demonstrating the human pathogenicity of Kudoa spores.

Phenotypic and genotypic characterization of Vibrio cholerae clinically isolated in Surabaya, Indonesia.

The phenotypic and genotypic characteristics of 6 clinical strains of Vibrio cholerae isolated in Surabaya, Indonesia in 2009 were examined. The DNA fingerprints obtained suggested that these isolates were not from a single clone. Furthermore, all isolates produced cholera toxin and possessed the classical type of toxin B subunit gene, thus meaning that this is the first report of the occurrence of El Tor variants of V. cholerae in Indonesia. Although all isolates were sensitive to almost all antibiotics tested, including ampicillin, chloramphenicol, ciprofloxacin, gentamicin, levofloxacin, kanamycin, nalidixic acid, norfloxacin, streptomycin, trimethoprim-sulfamethoxazole, and tetracycline, and had no mutation in the gyrA and parC genes, they nevertheless possessed the class 1 integron that is a molecular vehicle for the acquisition of antibiotic resistance genes, suggesting that they have the potential to acquire the genetic element for drug resistance.

[Psittacosis outbreak at an avian exhibition].

Psittacosis outbreak due to Chlamydophila psittaci occurred among staff members at an avian exhibition of nearly 1,000 birds in Kobe, Japan, in December 2005. Staff members not trained about zoonosis or psittacosis used little protective attire such as masks and gloves when caring for their discharges. Two of 67 staff members contracted psittacosis pneumonia. Additional two suffered from pneumonia and 19 reported symptoms such as fever and cough, although none were diagnosed with psittacosis. The roughly 970 birds were kept without quarantine and identified by leg bands. Doxycycline administrated in drinking water and food failed to eradicate chlamydia, so all birds were captured, identified by leg band, and tested for chlamydia by PCR. Six were found to carry large amounts of chlamydia. Major outer membrane protein (MOMP) DNA sequence of chlamydia in a patient's bronchoalveolar lavage fluid (BALF) was identical to that derived from a channel-billed toucan kept in a closed aviary, and staff members may have been infected by inhaling excrement while working in the aviary. The MOMP DNA sequence was useful in comparing strains. We review the difficulty of diagnosing psittacosis and the knowledge and infection control measures required against it.

Multiple outbreaks of gastroenteritis due to a single strain of genotype GII/4 norovirus in Kobe, Japan, 2006: risk factors for norovirus spread in health care settings.

A large number of gastroenteritis outbreaks due to a norovirus GII/4 strain and its variants occurred during November and December 2006 in Kobe, Japan. Of the 118 outbreaks, 6 were foodborne and 112 were caused by person-to-person transmission in healthcare settings such as nursing homes and hospitals. The distribution of norovirus outbreaks in healthcare settings was skewed, particularly in the south coastal area. Moreover, several outbreaks occurred within 1 km(2) in various areas. Outbreaks in neighboring settings, especially within 1 km, and travel from the sources of outbreaks were risk factors for the spread of the norovirus. The use of ineffective disinfectants such as alcohol and benzalkonium chloride might also have helped to spread the infection.

High incidence of enteroaggregative Escherichia coli among food handlers in three areas of Kenya: a possible transmission route of travelers' diarrhea.

BACKGROUND: Contaminated food and water are acknowledged vehicles for the transmission of travelers' diarrhea (TD). Importance of food handlers as reservoirs of enteroaggregative Escherichia coli (EAEC), enteropathogenic E coli (EPEC), and Shiga toxin-producing E coli (STEC) causing TD has not been clearly demonstrated. METHODS: We undertook a 1-year prospective study to determine the presence and selected risk factors of carriage of EAEC, EPEC, and STEC by 1,399 food handlers working in tourist hotels in three popular tourist destinations of Kenya. Enterotoxigenic E coli (ETEC) was not sought in this study. RESULTS: During the period April 2003 to May 2004, EAEC harboring the aggR gene were detected from 29 (2.1%) subjects and EPEC harboring the eaeA gene and STEC harboring the stx2 gene were detected from 11 (0.8%) and 2 (0.1%) of the study subjects, respectively. Mean age of subjects with EAEC was significantly lower (24.6 y) than the rest of the study population (28.2 y) (p < 0.05). Pit latrines usage was significantly associated with the isolation of EAEC (<0.001) but not with EPEC and STEC. Four of the 29 EAEC isolates were sensitive to all antibiotics tested, and 19 (65.5%) were multidrug resistant (MDR). Antibiotic resistance varied from 6.9% for cefuroxime to 72.4% for co-trimoxazole. Six EPEC isolates (6/13, 46.2%) showed multidrug resistance. Cluster analysis of the pulsed-field gel electrophoresis (PFGE) profiles showed that the EAEC isolates belonged to two clonally unrelated genotypes. CONCLUSIONS: We conclude that food handlers working in tourist hotels are important carriers of EAEC that could cause TD and a high proportion of the EAEC are MDR. The isolation of MDR EAEC from food handlers working in tourist hotels is of potential public health importance. There is a need for a study employing molecular methods including PFGE to examine carriage of similar pathogens in food handlers, processed foods, and travelers consuming the food who develop diarrhea.

Evaluation of colony-based examinations of diarrheagenic Escherichia coli in stool specimens: low probability of detection because of low concentrations, particularly during the early stage of gastroenteritis.

To evaluate traditional colony-based examinations of diarrheagenic Escherichia coli (DEC), we analyzed the proportions of 5 categories of DEC among E. coli in stool specimens from patients with gastroenteritis using real-time polymerase chain reaction with novel primers and probes. Among 81 DEC isolates, 48 (59.3%) were present at proportions of < or = 10%, whereas only 17 (21.0%) reached >50%. Low concentrations (< or = 10%) of DEC were found, particularly in most (71.8%) stool specimens collected within 48 h after the onset of illness, although such specimens were conventionally collected as close to the time of diarrhea onset as possible. Because the probability of detecting < or = 10% DEC by colony-based examinations is very low, traditional laboratory methods might not detect most DEC infections, especially at the start of gastroenteritis. Thus, a diagnosis of DEC infections requires a molecular method that targets not individual colonies but E. coli clusters.

An outbreak of rotavirus infection among adults in an institution for rehabilitation: long-term residence in a closed community as a risk factor for rotavirus illness.

An outbreak of group A rotavirus infection resulted in gastroenteritis among disabled adults in an isolated rehabilitation institution in Kobe, Japan. Of the 95 residents, 16 were diagnosed with rotavirus illness. The causative agent was a single strain of typical human group A rotavirus belonging to VP7 serotype G2, VP4 genotype P[4], and NSP4 genotype A. Mean duration of stay was significantly longer for residents with rotavirus illness (22.1+/-11.8 years) than for residents without the disease (13.5+/-10.6 years; P=0.01). Age, sex, disability and location of resident rooms displayed no significant relationships with illness. These observations suggest that long-term residence in a closed community, which might be related to absence of immuno-stimulation, represents a risk factor for rotavirus illness.

Improvement in the detection rate of diarrhoeagenic bacteria in human stool specimens by a rapid real-time PCR assay.

A rapid laboratory system has been developed and evaluated that can simultaneously identify major diarrhoeagenic bacteria, including Salmonella enterica, Vibrio parahaemolyticus, Campylobacter jejuni and Shiga toxin-producing Escherichia coli, in stool specimens by real-time PCR. Specific identification was achieved by using selective TaqMan probes, detecting two targets in each pathogen. A positive result was scored only when both targets of a pathogen were amplified and the difference between threshold cycles for detection was less than five. Diagnosis of enteric bacterial infections using this highly sensitive method, including DNA extraction and real-time PCR, requires only 3 h. Forty stool specimens related to suspected food poisoning outbreaks were analysed: 16 (40%) of these samples were found to be positive for diarrhoeagenic bacteria using a conventional culture method; 28 (70%) were positive using the real-time PCR assay. Of the 12 PCR-positive but culture-negative cases, 11 patients had consumed pathogen-contaminated or high-risk food. Analysis of faecal samples from 105 outpatients who complained of diarrhoea and/or abdominal pain identified 19 (18%) patients as being positive for diarrhoeagenic bacteria using the culture method. An additional six (6%) patients were found to be positive by PCR analysis.

Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae.

BACKGROUND: Vibrio parahaemolyticus, a gram-negative marine bacterium, is a worldwide cause of food-borne gastroenteritis. V parahaemolyticus strains of a few specific serotypes, probably derived from a common clonal ancestor, have lately caused a pandemic of gastroenteritis. The organism is phylogenetically close to V cholerae, the causative agent of cholera. METHODS: The whole genome sequence of a clinical V parahaemolyticus strain RIMD2210633 was established by shotgun sequencing. The coding sequences were identified by use of Gambler and Glimmer programs. Comparative analysis with the V cholerae genome was undertaken with MUMmer. FINDINGS: The genome consisted of two circular chromosomes of 3288558 bp and 1877212 bp; it contained 4832 genes. Comparison of the V parahaemolyticus genome with that of V cholerae showed many rearrangements within and between the two chromosomes. Genes for the type III secretion system (TTSS) were identified in the genome of V parahaemolyticus; V cholerae does not have these genes. INTERPRETATION: The TTSS is a central virulence factor of diarrhoea-causing bacteria such as shigella, salmonella, and enteropathogenic Escherichia coli, which cause gastroenteritis by invading or intimately interacting with intestinal epithelial cells. Our results suggest that V parahaemolyticus and V cholerae use distinct mechanisms to establish infection. This finding explains clinical features of V parahaemolyticus infections, which commonly include inflammatory diarrhoea and in some cases systemic manifestations such as septicaemia, distinct from those of V cholerae infections, which are generally associated with non-inflammatory diarrhoea.