Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii.

Escherichia coli, Escherichia albertii, and Escherichia fergusonii are closely related bacteria that can cause illness in humans, such as bacteremia, urinary tract infections and diarrhea. Current identification strategies for these three species vary in complexity and typically rely on the use of multiple phenotypic and genetic tests. To facilitate their rapid identification, we developed a multiplex PCR assay targeting conserved, species-specific genes. We used the Daydreamer™ (Pattern Genomics, USA) software platform to concurrently analyze whole genome sequence assemblies (WGS) from 150 Enterobacteriaceae genomes (107 E. coli, 5 Shigella spp., 21 E. albertii, 12 E. fergusonii and 5 other species) and design primers for the following species-specific regions: a 212bp region of the cyclic di-GMP regulator gene (cdgR, AW869_22935 from genome K-12 MG1655, CP014225) for E. coli/Shigella; a 393bp region of the DNA-binding transcriptional activator of cysteine biosynthesis gene (EAKF1_ch4033 from genome KF1, CP007025) for E. albertii; and a 575bp region of the palmitoleoyl-acyl carrier protein (ACP)-dependent acyltransferase (EFER_0790 from genome ATCC 35469, CU928158) for E. fergusonii. We incorporated the species-specific primers into a conventional multiplex PCR assay and assessed its performance with a collection of 97 Enterobacteriaceae strains. The assay was 100% sensitive and specific for detecting the expected species and offers a quick and accurate strategy for identifying E. coli, E. albertii, and E. fergusonii in either a single reaction or by in silico PCR with sequence assemblies.

Outbreaks of non-O157 Shiga toxin-producing Escherichia coli infection: USA.

Non-O157 Shiga toxin-producing Escherichia coli (STEC) infections are increasingly detected, but sources are not well established. We summarize outbreaks to 2010 in the USA. Single-aetiology outbreaks were defined as ⩾2 epidemiologically linked culture-confirmed non-O157 STEC infections; multiple-aetiology outbreaks also had laboratory evidence of ⩾2 infections caused by another enteric pathogen. Twenty-six states reported 46 outbreaks with 1727 illnesses and 144 hospitalizations. Of 38 single-aetiology outbreaks, 66% were caused by STEC O111 (n = 14) or O26 (n = 11), and 84% were transmitted through food (n = 17) or person-to-person spread (n = 15); food vehicles included dairy products, produce, and meats; childcare centres were the most common setting for person-to-person spread. Of single-aetiology outbreaks, a greater percentage of persons infected by Shiga toxin 2-positive strains had haemolytic uraemic syndrome compared with persons infected by Shiga toxin 1-only positive strains (7% vs. 0·8%). Compared with single-aetiology outbreaks, multiple-aetiology outbreaks were more frequently transmitted through water or animal contact.

Epidemiological features of a newly described serotype of Shigella boydii.

We report the clinical, microbiological, and epidemiological features of an emerging serotype, Shigella boydii 20. We interviewed patients about symptoms, and history of travel and visitors during the week before illness onset. Seventy-five per cent of the 56 patients were Hispanic. During the week before illness onset, 18 (32%) travelled abroad; 17 (94%) had visited Mexico. Eight (21%) out of 38 who had not travelled had foreign visitors. There were eight closely related patterns by PFGE with XbaI. S. boydii 20 may be related to travel to Mexico and Hispanic ethnicity. Prompt epidemiological investigation of clusters of S. boydii 20 infection may help identify specific vehicles and risk factors for infection.

Bacterial, viral and parasitic enteric pathogens associated with acute diarrhea in hospitalized children from northern Jordan.

To determine the etiology of acute diarrhea in Jordanian children under 5 years of age, we examined stool samples from 265 children admitted to the pediatric ward at Princess Rahma Hospital for Children, Irbid, Jordan, for parasites, rotavirus and enteric bacteria. Using both traditional and molecular diagnostic techniques, we detected enteropathogens in 66.4% of patients with diarrhea. A single enteric pathogen was detected in 50.9% of the children, and multiple pathogens were detected in 15.5%. The prevalence of enteropathogens identified was as follows: rotavirus (32.5%), enteropathogenic Escherichia coli (12.8%), enteroaggregative E. coli (10.2), enterotoxigenic E. coli (5.7%), Shigella spp. (4.9%), Entamoeba histolytica (4.9%), Salmonella spp. (4.5%), Campylobacter jejuni/coli (1.5%), Cryptosporidium spp. (1.5%), enteroinvasive E. coli (1.5%), eae-, Ehly-positive E. coli (0.8%), Giardia lamblia (0. 8%) and Yersinia enterocolitica (0.4%). No Vibrio cholerae, Shiga toxin-producing E. coli, microsporidia, adenovirus or small round virus were detected. Findings from this study demonstrate that rotavirus and several types of diarrheagenic E. coli, which are not screened for during routine examinations of stool samples in public health laboratories, were the most frequently detected enteropathogens in these children. Our findings highlight the value of using a combination of traditional and molecular techniques in the diagnosis of diarrheal disease in this population.

A prolonged outbreak of Shigella sonnei infections in traditionally observant Jewish communities in North America caused by a molecularly distinct bacterial subtype.

During 1994-1996, Shigella sonnei outbreaks occurred in 8 North American traditionally observant Jewish communities. These communities remain relatively separate from neighboring populations while maintaining close contact by travel with coreligionists in other cities. Epidemiologic investigations suggested community-to-community transmission via travel. Outbreak-related and control isolates of S. sonnei from each city were subtyped by pulsed-field gel electrophoresis (PFGE) to confirm an epidemiologic linkage between outbreaks. Forty-three (94%) of 46 outbreak-related isolates had closely related PFGE patterns, constituting a single subtype; 33 (94%) of 35 control isolates demonstrated unrelated PFGE patterns. Several patterns differing by < or = 3 bands were identified within the outbreak subtype; one of these accounted for 65% of outbreak isolates. Hence, a single subtype of S. sonnei caused an international outbreak involving 8 traditionally observant Jewish communities, but not neighboring populations, over a 2-year period, suggesting sustained propagation of the epidemic strain between communities.

Evaluation of commercial latex reagents for identification of O157 and H7 antigens of Escherichia coli.

Agglutination reactions obtained with three commercial latex reagents for detecting Escherichia coli O157 antigen (Oxoid Diagnostic Reagents, Hampshire, England; Pro-Lab Inc., Richmond Hill, Ontario, Canada; and Remel Microbiology Products, Lenexa, Kans.) and one for detecting H7 antigen (Remel) were compared with those obtained by standard serologic methods by using the Centers for Disease Control and Prevention (CDC) reference antisera for O157 and H7 antigens. For 159 strains of E. coli and related organisms, the Oxoid, Pro-Lab, and Remel O157 latex reagents each had a sensitivity and specificity of 100% compared with the CDC reference antiserum. For 106 strains of E. coli and related organisms that were not enhanced for motility through semisolid medium, the Remel H7 latex reagent had a sensitivity of 96% and a specificity of 100% compared with the standard tube agglutination method with CDC H7 antiserum. Measures to enhance motility were needed for some strains to detect the H7 antigen. Our findings demonstrate that the commercial latex reagents are good alternatives to standard serologic methods for identifying the O157 and H7 antigens of E. coli.

Isolation and characterization of a beta-D-glucuronidase-producing strain of Escherichia coli serotype O157:H7 in the United States.

A phenotypic variant of Escherichia coli serotype O157:H7 (G5101) was isolated from a patient with bloody diarrhea. Strain G5101 does not ferment sorbitol but is beta-D-glucuronidase and urease positive. Serotyping and colony hybridization using a serotype-specific DNA probe confirmed that the isolate was O157:H7. G5101 produces Shiga-like toxins I and II and contains an eae gene that is highly conserved in the O157:H7 serotype. This strain would have been missed by laboratories that screen for the sorbitol-negative, beta-D-glucuronidase-negative phenotype in isolating E. coli O157:H7 from clinical and food specimens.

Genetic polymorphism of the ipaH multicopy antigen gene in Shigella spps. and enteroinvasive Escherichia coli.

The ipaH loci comprise a multicopy antigen gene family unique to Shigella species and enteroinvasive Escherichia coli (EIEC). DNA probes derived from the Shigella flexneri serotype 5 ipaH7.8 gene were used to compare the molecular arrangement of ipaH alleles in a variety of Shigella and EIEC strains. Multiple copies of ipaH-homologous sequences were detected in all invasion plasmids examined. Oligonucleotide probes covering discrete 24 bp segments of the ipaH7.8 gene and sequences flanking the ipaH4.5 (probe H25) and ipaH2.5 (probe H24) loci were used to define the extent of homology among invasion plasmid copies of ipaH in S. flexneri serotypes 1, 2 and 5 and in S. sonnei. IpaH alleles carried by these invasion plasmids were not structurally equivalent and showed sequence divergence at their amino- and carboxy-terminal ends. The H25 probe was shown to correspond to an IS629 sequence genetically linked to the ipaH alleles, while the H24 probe defined a DNA sequence found only in Shigella invasion plasmids. Chromosomal DNA from invasion plasmid-cured S. flexneri and S. sonnei strains hybridized a core ipaH7.8 gene segment, indicating that portions of the ipaH7.8 structural gene were reiterated and contained within the shigellae chromosomes. Based on the specificity of the ipaH7.8 core probe and the detection of ipaH sequences on the invasion plasmids and chromosomes of Shigella strains, three polymorphic groups within a collection of forty S. dysenteriae 1 isolates received by the United States Centers for Disease Control in 1988 were identified using this probe. These results suggest that ipaH restriction fragment length polymorphisms may be useful in genetic lineage and epidemiologic studies of virulent shigellae.

Molecular subtyping of Salmonella enteritidis phage type 8 strains from the United States.

Salmonella enteritidis is now the most common serotype of the genus Salmonella reported in the United States. Bacteriophage typing has been helpful for subdividing S. enteritidis strains from different sources in the United States. Most S. enteritidis outbreaks reported were egg related, and the majority of them were caused by strains of phage type 8. To determine whether restriction fragment length polymorphism of the rRNA genes (ribotyping) and of the genomic DNAs from two lysogenic phages from S. enteritidis could be used to discriminate between S. enteritidis phage type 8 strains, we conducted Southern hybridization studies on 24 isolates from different outbreaks and six non-outbreak-associated strains using DNA probes for 16S and 23S rRNA genes and S. enteritidis typing phages 1 and 2 from the Ward typing system (L. R. Ward, J. D. H. de Sa, and B. Rowe, Epidemiol. Infect. 99:291-294, 1987). Of seven restriction endonucleases screened with the probe for rRNA genes, AccI provided the best discrimination between strains; six distinct patterns were observed. AccI ribosomal DNA patterns 1 to 6 were detected among 76.7, 3.3, 6.7, 3.3, 3.3, and 6.7% of isolates tested, respectively. Strains of AccI ribosomal DNA pattern 3 could be further subdivided into two additional patterns by using SmaI. Epidemiologically related strains had identical patterns. No discrimination between strains was achieved by probes for phages 1 and 2. No sequences homologous to the phage I probe were detected among phage type 8 strains, and all strains tested with six restriction enzymes had the same hybridization pattern with the phage 2 probe. These findings demonstrate that ribotyping with AccI and SmaI provides an additional means of discriminating between some phage type 8 strains; however, ribotyping and the phage 2 hybridization results from egg-related outbreak strains support previous findings that these strains are closely related.

Evaluation of a technique for identification of Shiga-like toxin-producing Escherichia coli by using polymerase chain reaction and digoxigenin-labeled probes.

A polymerase chain reaction (PCR) technique for the identification of Shiga-like toxin (SLT)-producing Escherichia coli was assessed by using 95 strains of SLT-producing E. coli and 5 Shigella dysenteriae type 1 strains. PCR was used for the amplification of slt gene sequences from whole bacterial colonies. A digoxigenin-labeled DNA probe was used for identification of the PCR products in a spot blot hybridization assay. Modifications were made to adapt this technique for the proper identification of 10 SLT-producing isolates which were refractory to the heat lysis step that was used to liberate whole-cell DNA for PCR and 6 isolates which gave nonspecific amplification products. The sensitivity and specificity of this assay were each 99% when compared with toxin neutralization results by using SLT-specific monoclonal antibodies. These values indicate that this detection technique could be suitable for use in a clinical laboratory.

Isolation of a Citrobacter freundii strain which carries the Escherichia coli O157 antigen.

A biochemically typical strain of Citrobacter freundii which carries the Escherichia coli O157 antigen is described. The significance of differentiating such strains from typical E. coli O157 strains is stressed.

Serological cross-reactions between Escherichia coli O157 and other species of the genus Escherichia.

The antigenic relatedness of Escherichia coli O157 and four sorbitol-negative species of the genus Escherichia was examined. Isolates of Escherichia hermannii, E. fergusonii, E. vulneris, and E. blattae were tested in the tube agglutination assay by using polyclonal antisera and in the slide agglutination assay by using latex reagents. Only four isolates (17%) of E. hermannii exhibited serological cross-reactivity.

DNA probe analysis of diarrhoeagenic Escherichia coli: detection of EAF-positive isolates of traditional enteropathogenic E. coli serotypes among Bangladeshi paediatric diarrhoea patients.

Escherichia coli isolates from all surveillance patients less than or equal to 20 months of age seen for diarrhoea at the Dhaka Clinical Treatment Facility of the International Centre for Diarrhoeal Disease Research, Bangladesh between March 1 and August 31, 1988, were collected and hybridized with DNA probes to assess the potential importance of diarrhoeagenic E. coli among paediatric patients in Bangladesh. Of 396 patients evaluated, 18% were infected with enteropathogenic E. coli (EPEC) adherence factor (EAF)-positive E. coli, 23% were infected with enterotoxigenic E. coli (ETEC), 9% were infected with Shiga-like toxin-positive E. coli, and 13% were infected with diffuse adhesiveness-positive E. coli. None were infected with enteroinvasive E. coli. Ten percent of patients were colonized with more than one type of potential diarrhoeagenic E. coli. The majority of EAF-positive isolates were of traditional EPEC O:H serotypes. Although this was not a case-control study, the large number of EPEC and ETEC, which are recognized enteric pathogens, suggests these organisms are important causes of diarrhoeal diseases in this pediatric population.

A nested PCR followed by magnetic separation of amplified fragments for detection of Escherichia coli Shiga-like toxin genes.

The Shiga-like toxin (SLT) I and II genes in cytotoxic Escherichia coli strains were detected using a polymerase chain reaction (PCR) procedure. Identification and differentiation of SLT I and II was carried out using primers giving PCR-generated DNA fragments of different size for the two cytotoxins. A two-step PCR procedure utilizing three primers in a nested configuration for both SLT I and II was combined with magnetic separation to identify the toxin genes in a rapid, specific and sensitive test system designated DIANA (Detection of Immobilized Amplified Nucleic Acid). The first PCR was carried out using standard methods, and the product generated was used as primer in the second PCR. In this procedure one of the primers from the first PCR was used with biotin label, and the second (inner) primer was 32P-labelled. The double-stranded DNA fragments generated containing the two primers, were biotinylated on one 5' end and 32P-labelled on the other 5' end. These fragments were separated from the solution using streptavidin-coated super-paramagnetic microscopic beads. The test could detect and differentiate between SLT I and II in a positive/negative ratio of more than 20. The assay could detect five SLT-positive E. coli organisms in the 5 microliters test sample. The presence of 100-fold more SLT-negative strains in a sample did not adversely affect the test signal.

Restriction fragment length polymorphisms in rRNA operons for subtyping Shigella sonnei.

Shigella sonnei is the most frequent cause of shigellosis in the United States. Epidemiologic studies of this organism have been hampered by the lack of adequate typing procedures. Ribosomal DNA analysis (ribotyping), a method which analyzes restriction fragment length polymorphisms in the chromosomal genes that encode rRNA, has recently been shown to be useful for microbial species identification and subtyping. To determine whether ribotyping could be used to distinguish between S. sonnei isolates, we conducted Southern hybridization studies on isolates from 16 different geographic locations and from four recent outbreaks. S. sonnei genomic DNA fragments generated following digestion with SalI hybridized with Escherichia coli 16S and 23S rRNAs to produce six distinct patterns; strains with patterns 1, 2, and 3 were each further subdivided into two additional patterns by using PvuII, SmaI, and SstI, respectively. Epidemiologically related strains had identical patterns. Ribotyping appears to be a useful tool for epidemiologic studies of shigellosis caused by S. sonnei.

Surveillance of Escherichia coli O157 isolation and confirmation, United States, 1988.

In 1989, to examine patterns of testing for Escherichia coli O157:H7 in state public health laboratories (SPHLs), CDC conducted a survey to determine the availability and type of Escherichia coli O157:H7 testing in SPHLs during 1988 and the number of isolates confirmed at SPHLs if such testing was available. The results were compared with information on isolates submitted for confirmatory testing at CDC in 1988. Thirty-nine (78%) of the 51 SPHLs were testing for E. coli O157:H7 in 1988; 26 confirmed at least one E. coli O157 isolate in that year. CDC confirmed isolates from three additional states. A total of 489 E. coli O157:H7 or E. coli O157:NM isolates were identified, with the largest numbers being reported from Washington (156), Oregon (64), Minnesota (63), and Massachusetts (36). These results show that E. coli O157 has been detected in most areas of the United States. Infections are apparently concentrated in northern states; however, improved surveillance data are needed to determine regional incidence and trends.

Molecular epidemiologic techniques in analysis of epidemic and endemic Shigella dysenteriae type 1 strains.

During 1988 the number of Shigella dysenteriae type 1 infections reported in the United States increased fivefold. To determine if recent isolates from Mexico were related to those that caused epidemics of dysentery worldwide, Southern hybridization analysis was done with Shiga toxin and ribosomal RNA gene probes. Western hemisphere and Eastern Hemisphere strains differed by the size of a single EcoRI fragment carrying the Shiga toxin genes. Three ribosomal DNA (rDNA) patterns were observed, which correlated with the strain's continental origin for 81 of 83 isolates tested. Together the Shiga toxin and rDNA probe results indicated that recent Mexican isolates were chromosomally similar to earlier Central American isolates and distinct from Asian and African strains. This suggests there has been no significant exchange of organisms between continents in recent decades and that the 1988 outbreak in Mexico was caused by strains present in Central America since at least 1962.

The use of plasmid profiles and nucleic acid probes in epidemiologic investigations of foodborne, diarrheal diseases.

The application of nucleic acid analyses to investigations of infectious disease outbreaks has resulted in useful molecular strain markers that distinguish the epidemic clone of a particular pathogen and help identify specific vehicles of infection. We have successfully used plasmid profile analysis, restriction endonuclease digestion of plasmid and whole-cell DNAs, and nucleic acid hybridization to investigate recent outbreaks of foodborne diarrheal illness. Plasmid analysis has been important in identifying epidemic strains of Salmonella enteritidis and Escherichia coli O157:H7. In a culture survey of S. enteritidis isolates from humans and a variety of animals, including chickens and chicken eggs, we identified 16 distinct plasmid profiles and used these to differentiate strains, especially within commonly occurring phage types (Colindale 8 and 13a). HindIII digests of plasmid DNA were useful in distinguishing plasmids of similar mass but dissimilar enzyme target sequences; they clearly distinguished S. enteritidis strains causing systemic infections in children in parts of Africa from U.S. isolates. Investigations of outbreaks of hemorrhagic colitis have also been assisted by plasmid analysis. Restriction endonuclease digests of whole-cell DNA and Southern blot analysis, hybridizing with E. coli 16S and 23S rRNA (ribotyping), have been effective subtyping techniques, especially for plasmidless isolates of Campylobacter jejuni. In five outbreaks of C. jejuni infections, ribotyping of PvuII and ClaI digests distinguished individual epidemic strains within one commonly occurring C. jejuni serotype (Penner 2, Lior 4). Preliminary data show that ribotyping of NcoI digests can also distinguish individual epidemic strains of E. coli O157:H7 and may provide a more stable marker than plasmid profiles. Specific DNA probes derived from cloned virulence genes of E. coli have been invaluable in epidemic investigations and surveys. Using colony hybridization, we found in one survey of stool specimens from 174 dairy cattle that 11% of animals were asymptomatically carrying Shiga-like toxigenic E. coli other than O157:H7. We also found that newly synthesized oligonucleotide probes for the Shiga-like toxins I and II agreed 100% with cloned gene probes in a study of 613 E. coli strains. Future studies of these organisms will include the use of additional synthetic oligonucleotides as primers to amplify the toxin genes directly in patient and animal specimens by the polymerase chain reaction. There is a continuing and expanding role for molecular approaches in epidemiological investigations. The DNA methods described above are not based on the often complex expression of phenotypic characteristics, and, unlike sensitive and specific techniques such as phage typing, a single method can be used to study a variety of Gram-positive and negative bacterial pathogens.