1
|
Stanton E, Wahlig TA, Park D, Kaspar CW. Chronological set of E. coli O157:H7 bovine strains establishes a role for repeat sequences and mobile genetic elements in genome diversification. BMC Genomics 2020; 21:562. [PMID: 32807088 PMCID: PMC7430833 DOI: 10.1186/s12864-020-06943-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/23/2020] [Indexed: 11/21/2022] Open
Abstract
Background Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is a significant foodborne pathogen that resides asymptomatically within cattle and other ruminants. The EHEC genome harbors an extensive collection of mobile genetic elements (MGE), including multiple prophage, prophage-like elements, plasmids, and insertion sequence (IS) elements. Results A chronological collection of EHEC strains (FRIK804, FRIK1275, and FRIK1625) isolated from a Wisconsin dairy farm (farm X) comprised a closely related clade genetically differentiated by structural alterations to the chromosome. Comparison of the FRIK804 genome with a reference EHEC strain Sakai found a unique prophage like element (PLE, indel 1) and an inversion (1.15 Mb) situated symmetrically with respect to the terminus region. Detailed analysis determined the inversion was due to homologous recombination between repeat sequences in prophage. The three farm X strains were distinguished by the presence or absence of indel 3 (61 kbp) and indel 4 (48 kbp); FRIK804 contained both of these regions, FRIK1275 lacked indel 4, and indels 3 and 4 were both absent in FRIK1625. Indel 3 was the stx2 prophage and indel 4 involved a deletion between two adjacent prophage with shared repeat sequences. Both FRIK804 and FRIK1275 produced functional phage while FRIK1625 did not, which is consistent with indel 3. Due to their involvement in recombination events, direct and inverted repeat sequences were identified, and their locations mapped to the chromosome. FRIK804 had a greater number and overall length of repeat sequences than E. coli K12 strain MG1655. Repeat sequences were most commonly associated with MGE. Conclusions This research demonstrated that three EHEC strains from a Wisconsin dairy farm were closely related and distinguished by variability within prophage regions and other MGE. Chromosome alterations were associated with recombination events between repeat sequences. An inventory of direct and inverted repeat sequences found a greater abundance and total length of repeat sequences in the EHEC strains compared to E. coli strain MG1655. The locations of the repeat sequences were biased towards MGE. The findings from this study expand our understanding of the precise molecular events and elements that contributed to genetic diversification of wild-type EHEC in the bovine and farm environments.
Collapse
Affiliation(s)
- Eliot Stanton
- Department of Bacteriology, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI, 53706, USA
| | - Taylor A Wahlig
- Department of Bacteriology, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI, 53706, USA.,University of Utah, School of Medicine, 30 N 1900 E, Salt Lake City, UT, 84132, USA
| | - Dongjin Park
- Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Charles W Kaspar
- Department of Bacteriology, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI, 53706, USA. .,Food Research Institute, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI, 53706, USA.
| |
Collapse
|
2
|
Tarr GAM, Stokowski T, Shringi S, Tarr PI, Freedman SB, Oltean HN, Rabinowitz PM, Chui L. Contribution and Interaction of Shiga Toxin Genes to Escherichia coli O157:H7 Virulence. Toxins (Basel) 2019; 11:toxins11100607. [PMID: 31635282 PMCID: PMC6832461 DOI: 10.3390/toxins11100607] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 01/17/2023] Open
Abstract
Escherichia coli O157:H7 is the predominant cause of diarrhea-associated hemolytic uremic syndrome (HUS) worldwide. Its cardinal virulence traits are Shiga toxins, which are encoded by stx genes, the most common of which are stx1a, stx2a, and stx2c. The toxins these genes encode differ in their in vitro and experimental phenotypes, but the human population-level impact of these differences is poorly understood. Using Shiga toxin-encoding bacteriophage insertion typing and real-time polymerase chain reaction, we genotyped isolates from 936 E. coli O157:H7 cases and verified HUS status via chart review. We compared the HUS risk between isolates with stx2a and those with stx2a and another gene and estimated additive interaction of the stx genes. Adjusted for age and symptoms, the HUS incidence of E. coli O157:H7 containing stx2a alone was 4.4% greater (95% confidence interval (CI) −0.3%, 9.1%) than when it occurred with stx1a. When stx1a and stx2a occur together, the risk of HUS was 27.1% lower (95% CI −87.8%, −2.3%) than would be expected if interaction were not present. At the population level, temporal or geographic shifts toward these genotypes should be monitored, and stx genotype may be an important consideration in clinically predicting HUS among E. coli O157:H7 cases.
Collapse
Affiliation(s)
- Gillian A M Tarr
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T3B 6A8, Canada.
| | - Taryn Stokowski
- Department of Laboratory Medicine and Pathology, University of Alberta and Alberta Public Labs, Edmonton, AB T6G 2J2, Canada.
| | - Smriti Shringi
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99163, USA.
| | - Phillip I Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Stephen B Freedman
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T3B 6A8, Canada.
| | - Hanna N Oltean
- Washington State Department of Health, Shoreline, WA 98155, USA.
| | - Peter M Rabinowitz
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta and Alberta Public Labs, Edmonton, AB T6G 2J2, Canada.
| |
Collapse
|
3
|
Ota M, Kamigaki T, Mimura S, Nakashima K, Ogami T. An enterohaemorrhagic Escherichia coli outbreak spread through the environment at an institute for people with intellectual disabilities in Japan in 2005. Western Pac Surveill Response J 2019; 10:14-21. [PMID: 31720050 PMCID: PMC6831959 DOI: 10.5365/wpsar.2017.8.4.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE An enterohaemorrhagic Escherichia coli (EHEC) outbreak at an institute with multiple facilities for children and adults with intellectual disabilities was investigated to characterize the cases and identify risk factors for infection. METHODS A case was defined as a resident, a staff member or a visitor at the institute from 16 May through 30 June 2005 testing positive for type 2 Vero toxin-producing EHEC O157:H7 (confirmed case) or exhibiting bloody diarrhoea for two or more days (probable case). We collected and analysed demographic, clinical, laboratory and individual behaviour data to identify possible risk factors for infection and infection routes. RESULTS We recorded 58 confirmed cases, of which 13 were symptomatic. One probable case was also found. The median age of the patients was 37 years (range: 6-59 years). Thirty-six patients (61%) were male. Thirteen patients (93%) had diarrhoea and six (43%) had abdominal pain. Two developed haemolytic-uraemic syndrome but recovered. All the patients were treated with antibiotics and tested negative after treatment. Some residents had problems with personal hygiene. The residents of one of the facilities who cleaned a particular restroom had 18.0 times higher odds of being infected with EHEC (95% confidence interval: 4.0-102.4) than those who did not. DISCUSSION The source of the outbreak could not be identified; however, the infection may have spread through environmental sources contaminated with EHEC. We recommend that institutional settings, particularly those that accommodate people with intellectual disabilities, clean restrooms as often as possible to reduce possible infection from contact with infected surfaces.
Collapse
Affiliation(s)
- Masaki Ota
- Research Institute of Tuberculosis, Tokyo, Japan
| | - Taro Kamigaki
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Satoshi Mimura
- Department of Respiratory Medicine, Japan Self Defense Force Central Hospital, Tokyo, Japan
| | - Kazutoshi Nakashima
- Department of Health Science, Faculty of Sports and Health Science, Daito Bunka University, Saitama, Japan
| | | |
Collapse
|
4
|
Keithlin J, Sargeant J, Thomas MK, Fazil A. Chronic sequelae of E. coli O157: systematic review and meta-analysis of the proportion of E. coli O157 cases that develop chronic sequelae. Foodborne Pathog Dis 2014; 11:79-95. [PMID: 24404780 PMCID: PMC3925333 DOI: 10.1089/fpd.2013.1572] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVE This was a systematic review and meta-analysis to determine the proportion of Escherichia coli O157 cases that develop chronic sequelae. DATA SOURCES We conducted a systematic review of articles published prior to July 2011 in Pubmed, Agricola, CabDirect, or Food Safety and Technology Abstracts. STUDY SELECTION Studies were selected that reported the number of E. coli O157 cases that developed reactive arthritis (ReA), hemolytic uremic syndrome (HUS), irritable bowel syndrome, inflammatory bowel disease, or Guillain Barré syndrome. METHODS Three levels of screening and data extraction of articles were conducted using predefined data fields. Meta-analysis was performed on unique outcome measures using a random-effects model, and heterogeneity was assessed using the I² value. Meta-regression was used to explore the influence of nine study-level variables on heterogeneity. RESULTS A total of 82 studies were identified reporting 141 different outcome measures; 81 reported on HUS and one reported on ReA. Depending on the number of cases of E. coli O157, the estimate for the proportion of E. coli O157 cases that develop HUS ranged from 17.2% in extra-small studies (<50 cases) to 4.2% in extra-large studies (>1000 cases). Heterogeneity was significantly associated with group size (p<0.0001); however, the majority of the heterogeneity was unexplained. CONCLUSIONS High unexplained heterogeneity indicated that the study-level factors examined had a minimal influence on the variation of estimates reported.
Collapse
Affiliation(s)
- Jessica Keithlin
- Centre for Public Health and Zoonoses, University of Guelph, Guelph, Ontario, Canada
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
| | - Jan Sargeant
- Centre for Public Health and Zoonoses, University of Guelph, Guelph, Ontario, Canada
- Department of Population Medicine, Ontario Veterinary College, Guelph, Ontario, Canada
| | - M. Kate Thomas
- Centre for Food-borne, Environmental, and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Aamir Fazil
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
| |
Collapse
|
5
|
Infections Associated with Group Childcare. PRINCIPLES AND PRACTICE OF PEDIATRIC INFECTIOUS DISEASES 2012. [PMCID: PMC7152480 DOI: 10.1016/b978-1-4377-2702-9.00102-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
6
|
Liu F, Guan W, Alam MJ, Shen Z, Zhang S, Li L, Shinoda S, Shi L. Pulsed-field Gel Electrophoresis Typing of Multidrug-resistant Vibrio parahaemolyticus Isolated from Various Sources of Seafood. ACTA ACUST UNITED AC 2009. [DOI: 10.1248/jhs.55.783] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Fang Liu
- College of Light Industry and Food Sciences, South China University of Technology
| | - Wenying Guan
- Institute of Microbiological Examination, Hebei Provincial Center for Disease Control and Prevention
| | - MJ. Alam
- Department of Diagnostic Medicine and Pathobiology, Kansas State University
| | - Zhixin Shen
- Institute of Microbiological Examination, Hebei Provincial Center for Disease Control and Prevention
| | - Shuhong Zhang
- Institute of Microbiological Examination, Hebei Provincial Center for Disease Control and Prevention
| | - Lin Li
- College of Light Industry and Food Sciences, South China University of Technology
| | | | - Lei Shi
- College of Light Industry and Food Sciences, South China University of Technology
| |
Collapse
|
7
|
Gilbert M, Monk C, Wang HL, Diplock K, Landry L. Screening policies for daycare attendees: lessons learned from an outbreak of E. coli O157:H7 in a daycare in Waterloo, Ontario. Canadian Journal of Public Health 2008. [PMID: 18767271 DOI: 10.1007/bf03403755] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
OBJECTIVES Control measures for enteric outbreaks in child care settings frequently include screening by stool cultures from symptomatic children only. We present evidence from an investigation of Escherichia coli (E. coli) O157:H7 in a daycare in Waterloo, Ontario to support implementation of a mandatory screening policy for all children during an outbreak. METHODS In addition to routine outbreak control measures employed by the health unit, stool samples from all children and staff were collected, with positive E. coli cultures typed by pulsed field gel electrophoresis (PFGE). We conducted a cohort study, using data from the environmental investigation and questionnaires administered to parents and staff, to look for risk factors for infection and to survey parent/staff knowledge regarding appropriate management of diarrhea. RESULTS Overall 11 E. coli O157:H7 cases were identified (7 lab-confirmed); 9 were children. No common source of infection was identified. Factors identified as possibly contributing to person-to-person transmission within the daycare included: i) the underreporting and possible attendance of symptomatic children despite alerting parents to the outbreak and requirements to keep symptomatic children at home, ii) possible transmission from an asymptomatic infected child, and iii) inconsistent understanding among parents and staff regarding diarrhea and appropriate management of a child with diarrhea. DISCUSSION/CONCLUSION This investigation reveals that in child care settings, E. coli O157:H7 outbreak screening policies based on reported symptoms only may be insufficient. We recommend that such policies be amended to include the collection of at least one stool culture from all children in attendance, regardless of symptom history.
Collapse
Affiliation(s)
- Mark Gilbert
- Canadian Field Epidemiology Program, Public Health Agency of Canada
| | | | | | | | | |
Collapse
|
8
|
Shane AL, Pickering LK. Infections Associated with Group Childcare. PRINCIPLES AND PRACTICE OF PEDIATRIC INFECTIOUS DISEASE 2008. [PMCID: PMC7310925 DOI: 10.1016/b978-0-7020-3468-8.50009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
|
9
|
Pearl DL, Louie M, Chui L, Doré K, Grimsrud KM, Martin SW, Michel P, Svenson LW, McEwen SA. The use of randomization tests to assess the degree of similarity in PFGE patterns of E. coli O157 isolates from known outbreaks and statistical space-time clusters. Epidemiol Infect 2007; 135:100-9. [PMID: 16740184 PMCID: PMC2870554 DOI: 10.1017/s0950268806006650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2006] [Indexed: 11/07/2022] Open
Abstract
Using isolates from reported cases of Escherichia coli O157 from Alberta, Canada in 2002, we applied randomization tests to determine if cases associated with an outbreak or statistical space-time cluster had more similar pulsed-field gel electrophoresis patterns, based on Dice coefficients, than expected by chance alone. Within each outbreak and space-time cluster, we assessed the mean, median, 25th percentile, 75th percentile, standard deviation, coefficient of variation, and interquartile range of the Dice coefficients of each pairwise comparison among the isolates. To assess the statistical significance of measures of location (e.g. mean) and variation (e.g. standard deviation) we created randomization distributions using all isolates or only isolates from sporadic cases. We determined that randomization tests are an appropriate tool for evaluating the similarity among isolates from cases that have been linked epidemiologically or statistically. We found little difference between using all cases or only sporadic cases when creating our randomization distributions.
Collapse
Affiliation(s)
- D L Pearl
- Department of Population Medicine, University of Guelph, Guelph, Ontario, Canada.
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Steele M, Ziebell K, Zhang Y, Benson A, Konczy P, Johnson R, Gannon V. Identification of Escherichia coli O157:H7 genomic regions conserved in strains with a genotype associated with human infection. Appl Environ Microbiol 2006; 73:22-31. [PMID: 17056689 PMCID: PMC1797103 DOI: 10.1128/aem.00982-06] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Beta-glucuronidase-negative, sorbitol-nonfermenting isolates of Shiga toxin-producing Escherichia coli O157 comprise part of a clone complex of related enterohemorrhagic E. coli isolates. High-resolution genotyping shows that the O157 populations have diverged into two different lineages that appear to have different ecologies. To identify genomic regions unique to the most common human-associated genotype, suppression subtractive hybridization was used to identify DNA sequences present in two clinical strains representing the human lineage I O157:H7 strains but absent from two bovine-derived lineage II strains. PCR assays were then used to test for the presence of these regions in 10 lineage I strains and 20 lineage II strains. Twelve conserved regions of genomic difference for lineage I (CRD(I)) were identified that were each present in at least seven of the lineage I strains but absent in most of the lineage II strains tested. The boundaries of the lineage I conserved regions were further delimited by PCR. Eleven of these CRD(I) were associated with E. coli Sakai S-loops 14, 16, 69, 72, 78, 82, 83, 91 to 93, 153, and 286, and the final CRD(I) was located on the pO157 virulence plasmid. Several potential virulence factors were identified within these regions, including a putative hemolysin-activating protein, an iron transport system, and several possible regulatory genes. Cluster analysis based on lineage I conserved regions showed that the presence/absence of these regions was congruent with the inferred phylogeny of the strains.
Collapse
Affiliation(s)
- Marina Steele
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 1st floor, C.F.I.A. Building, Lethbridge, AB T1J 3Z4, Canada
| | | | | | | | | | | | | |
Collapse
|
11
|
Iguchi A, Iyoda S, Terajima J, Watanabe H, Osawa R. Spontaneous recombination between homologous prophage regions causes large-scale inversions within the Escherichia coli O157:H7 chromosome. Gene 2006; 372:199-207. [PMID: 16516407 DOI: 10.1016/j.gene.2006.01.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Revised: 12/22/2005] [Accepted: 01/04/2006] [Indexed: 11/23/2022]
Abstract
It is known that XbaI-digested chromosomal DNAs of strains of Escherichia coli O157:H7 exhibit a wide variety in pulsed-field gel electrophoresis (PFGE) fragment patterns, which is used for epidemiological surveillance of this important pathogen. The variety in the restriction enzyme-digestion patterns suggests a wide genomic diversity, however, only a few studies have been conducted to investigate involvement of large-scale chromosomal rearrangements in development of the diversity. In this study, through rounds of subculturing E. coli O157:H7 strain EDL933, naturally occurring genome variation in the isolated derivatives was investigated. By comparing the PFGE patterns among clonally related derivatives, we found five types of large-scale inversions taking place within the chromosome. The five inversions found were across the replication axis and ranged from 250-kb to 1.4-Mb long, and all the corresponding recombination sites were associated with prophages or phage-like regions. Four inversions out of the five were resulted from recombination between pairs of lambda-like prophages disturbing the symmetry of the origin and terminus of the replication axis. These observations indicate that those prophage regions represent some of the hot spots for intrachromosomal recombination within the E. coli O157:H7 chromosome, where recombination between the prophage regions results not only in the large chromosomal inversions but might also in generation of chimeric phages.
Collapse
Affiliation(s)
- Atsushi Iguchi
- Department of Bioscience, Graduate School of Science and Technology, Kobe University, 1-1 Rokko-dai, Kobe, Hyogo, 657-8501, Japan
| | | | | | | | | |
Collapse
|
12
|
Yang Z, Kovar J, Kim J, Nietfeldt J, Smith DR, Moxley RA, Olson ME, Fey PD, Benson AK. Identification of common subpopulations of non-sorbitol-fermenting, beta-glucuronidase-negative Escherichia coli O157:H7 from bovine production environments and human clinical samples. Appl Environ Microbiol 2005; 70:6846-54. [PMID: 15528552 PMCID: PMC525184 DOI: 10.1128/aem.70.11.6846-6854.2004] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Non-sorbitol-fermenting, beta-glucuronidase-negative Escherichia coli O157:H7 strains are regarded as a clone complex, and populations from different geographical locations are believed to share a recent common ancestor. Despite their relatedness, high-resolution genotyping methods can detect significant genome variation among different populations. Phylogenetic analysis of high-resolution genotyping data from these strains has shown that subpopulations from geographically unlinked continents can be divided into two primary phylogenetic lineages, termed lineage I and lineage II, and limited studies of the distribution of these lineages suggest there could be differences in their propensity to cause disease in humans or to be transmitted to humans. Because the genotyping methods necessary to discriminate the two lineages are tedious and subjective, these methods are not particularly suited for studying the large sets of strains that are required to systematically evaluate the ecology and transmission characteristics of these lineages. To overcome this limitation, we have developed a lineage-specific polymorphism assay (LSPA) that can readily distinguish between the lineage I and lineage II subpopulations. In the studies reported here, we describe the development of a six-marker test (LSPA-6) and its validation in a side-by-side comparison with octamer-based genome scanning. Analysis of over 1,400 O157:H7 strains with the LSPA-6 demonstrated that five genotypes comprise over 91% of the strains, suggesting that these subpopulations may be widespread.
Collapse
Affiliation(s)
- Zhijie Yang
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska 68583-0919, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Lejeune JT, Abedon ST, Takemura K, Christie NP, Sreevatsan S. Human Escherichia coli O157:H7 genetic marker in isolates of bovine origin. Emerg Infect Dis 2004; 10:1482-5. [PMID: 15496255 PMCID: PMC3320398 DOI: 10.3201/eid1008.030784] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The antiterminator Q gene of bacteriophage 933W (Q933) was identified upstream of the stx2 gene in 90% of human disease–origin Escherichia coli O157:H7 isolates and in 44.5% of bovine isolates. Shiga toxin production was higher in Q933-positive isolates than Q933-negative isolates. This genetic marker may provide a useful molecular tool for epidemiologic studies.
Collapse
|
14
|
Aslani MM, Bouzari S. An epidemiological study on Verotoxin-producing Escherichia coli (VTEC) infection among population of northern region of Iran (Mazandaran and Golestan provinces). Eur J Epidemiol 2003; 18:345-9. [PMID: 12803375 DOI: 10.1023/a:1023602416726] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Faecal samples from 3268 randomly selected inhabitants of two provinces in the northern region of Iran were screened to detect Verotoxin-producing Escherichia coli (VTEC) using colony sweep polymyxin-B extraction method. Non-sorbitol fermentation phenotype and slide agglutination with O157 and H7 antisera used to detect this serotype. We found that 0.7% of the population were infected with VTEC, however none of the isolates belonged to O157:H7 serotype. We also found that children < 6 years of age were at highest risk of infection with VTEC (p < 0.05). Moreover, a significant association was found between the VTEC and diarrhoeal cases at the same age group (p < 0.001). Overall distribution of the VTEC isolates in the general population was found to be random, though a kind of clustered distribution could be noticed.
Collapse
|
15
|
Davis MA, Hancock DD, Besser TE, Call DR. Evaluation of pulsed-field gel electrophoresis as a tool for determining the degree of genetic relatedness between strains of Escherichia coli O157:H7. J Clin Microbiol 2003; 41:1843-9. [PMID: 12734215 PMCID: PMC154664 DOI: 10.1128/jcm.41.5.1843-1849.2003] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2002] [Revised: 09/29/2002] [Accepted: 01/29/2003] [Indexed: 11/20/2022] Open
Abstract
Pulsed-field gel electrophoresis (PFGE) has been used extensively to investigate the epidemiology of Escherichia coli O157:H7, although it has not been evaluated as a tool for establishing genetic relationships. This is a critical issue when molecular genetic data are used to make inferences about pathogen dissemination. To evaluate this further, genomic DNAs from 62 isolates of E. coli O157:H7 from different cattle herds were digested with XbaI and BlnI and subjected to PFGE. The correlation between the similarity coefficients for these two enzymes was only 0.53. Four additional restriction enzymes (NheI, PacI, SfiI, and SpeI) were used with DNAs from a subset of 14 isolates. The average correlations between similarity coefficients using sets of one, two, and three enzymes were 0.405, 0.568, and 0.648, respectively. Probing with lambda DNA demonstrated that some DNA fragments migrated equal distances in the gel but were composed of nonhomologous genetic material. Genome sequence data from EDL933 indicated that 40 PFGE fragments would be expected from complete XbaI digestion, yet only 19 distinguishable fragments were visible. Two reasons that similarity coefficients from single-enzyme PFGE are poor measures of relatedness (and hence are poorly correlated with other enzymes) are evident from this study: (i) matching bands do not always represent homologous genetic material and (ii) there are limitations to the power of PFGE to resolve bands of nearly identical size. The findings of the present study indicate that if genetic relationships must be inferred in the absence of epidemiologic data, six or more restriction enzymes would be needed to provide a reasonable estimate using PFGE.
Collapse
Affiliation(s)
- Margaret A Davis
- Field Disease Investigation Unit, Department of Veterinary Clinical Sciences, Washington State University, Pullman, Washington 99164, USA.
| | | | | | | |
Collapse
|
16
|
Bopp DJ, Sauders BD, Waring AL, Ackelsberg J, Dumas N, Braun-Howland E, Dziewulski D, Wallace BJ, Kelly M, Halse T, Musser KA, Smith PF, Morse DL, Limberger RJ. Detection, isolation, and molecular subtyping of Escherichia coli O157:H7 and Campylobacter jejuni associated with a large waterborne outbreak. J Clin Microbiol 2003; 41:174-80. [PMID: 12517844 PMCID: PMC149601 DOI: 10.1128/jcm.41.1.174-180.2003] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The largest reported outbreak of waterborne Escherichia coli O157:H7 in the United States occurred in upstate New York following a county fair in August 1999. Culture methods were used to isolate E. coli O157:H7 from specimens from 128 of 775 patients with suspected infections. Campylobacter jejuni was also isolated from stools of 44 persons who developed diarrheal illness after attending this fair. There was one case of a confirmed coinfection with E. coli O157:H7 and C. jejuni. Molecular detection of stx(1) and stx(2) Shiga toxin genes, immunomagnetic separation (IMS), and selective culture enrichment were utilized to detect and isolate E. coli O157:H7 from an unchlorinated well and its distribution points, a dry well, and a nearby septic tank. PCR for stx(1) and stx(2) was shown to provide a useful screen for toxin-producing E. coli O157:H7, and IMS subculture improved recovery. Pulsed-field gel electrophoresis (PFGE) was used to compare patient and environmental E. coli O157:H7 isolates. Among patient isolates, 117 of 128 (91.5%) were type 1 or 1a (three or fewer bands different). Among the water distribution system isolates, 13 of 19 (68%) were type 1 or 1a. Additionally, PFGE of C. jejuni isolates revealed that 29 of 35 (83%) had indistinguishable PFGE patterns. The PFGE results implicated the water distribution system as the main source of the E. coli O157:H7 outbreak. This investigation demonstrates the potential for outbreaks involving more than one pathogen and the importance of analyzing isolates from multiple patients and environmental samples to develop a better understanding of bacterial transmission during an outbreak.
Collapse
Affiliation(s)
- Dianna J Bopp
- Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Shere JA, Kaspar CW, Bartlett KJ, Linden SE, Norell B, Francey S, Schaefer DM. Shedding of Escherichia coli O157:H7 in dairy cattle housed in a confined environment following waterborne inoculation. Appl Environ Microbiol 2002; 68:1947-54. [PMID: 11916717 PMCID: PMC123869 DOI: 10.1128/aem.68.4.1947-1954.2002] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2001] [Accepted: 01/16/2002] [Indexed: 11/20/2022] Open
Abstract
A study of Escherichia coli O157:H7 transmission and shedding was conducted with bull calves housed in individual pens within a confined environment. For comparative purposes, the numbers and duration of E. coli O157:H7 shedding in naturally infected calves were monitored after a single purchased calf (calf 156) tested positive prior to inoculation. During the next 8 days, the calves in adjacent pens and a pen directly across a walkway from calf 156 began to shed this serotype O157:H7 strain. Five of the eight calves in this room shed this O157:H7 strain at some time during the following 8 weeks. The numbers of E. coli O157:H7 isolates shed in these calves varied from 60 to 10(5) CFU/g of feces, and the duration of shedding ranged from 17 to >31 days. The genomic DNAs from isolates recovered from these calves were indistinguishable when compared by using XbaI digestion and pulsed-field gel electrophoresis. Inoculation of calves with 1 liter of water containing ca. 10(3) to 10(4) CFU of E. coli O157:H7/ml resulted in shedding in 10 of 12 calves (trial 1, 4 of 4 calves; trial 2, 6 of 8 calves). The inoculated calves shed the inoculation strain (FRIK 1275) as early as 24 h after administration. The duration of shedding varied from 18 to >43 days at levels from 10(2) to 10(6) CFU/g of feces. The numbers of doses necessary to initiate shedding varied among calves, and two calves in trial 2 never shed FRIK 1275 after four doses (ca. 10(6) CFU per dose). Results from this study confirm previous reports of animal-to-animal and waterborne dissemination of E. coli O157:H7 and highlight the need for an effective water treatment to reduce the spread of this pathogen in cattle.
Collapse
Affiliation(s)
- J A Shere
- United States Department of Agriculture, Animal, Plant Health Inspection Service, Veterinary Services, Madison, Wisconsin 53719, USA
| | | | | | | | | | | | | |
Collapse
|
18
|
Kim J, Nietfeldt J, Ju J, Wise J, Fegan N, Desmarchelier P, Benson AK. Ancestral divergence, genome diversification, and phylogeographic variation in subpopulations of sorbitol-negative, beta-glucuronidase-negative enterohemorrhagic Escherichia coli O157. J Bacteriol 2001; 183:6885-97. [PMID: 11698378 PMCID: PMC95530 DOI: 10.1128/jb.183.23.6885-6897.2001] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The O157:H7 lineage of enterohemorrhagic Escherichia coli is a geographically disseminated complex of highly related genotypes that share common ancestry. The common clone that is found worldwide carries several markers of events in its evolution, including markers for acquisition of virulence genes and loss of physiological characteristics, such as sorbitol fermentation ability and beta-glucuronidase production. Populations of variants that are distinct with respect to motility and the sorbitol and beta-glucuronidase markers appear to have diverged at several points along the inferred evolutionary pathway. In addition to these variants, distinct subpopulations of the contemporary non-sorbitol-fermenting, beta-glucuronidase-negative O157:H7 clone were recently detected among bovine and human clinical isolates in the United States by using high-resolution genome comparison. In order to determine if these recently described subpopulations were derived from a regional or ancestral divergence event, we used octamer-based genome scanning, marker sorting, and DNA sequence analysis to examine their phylogenetic relationship to populations of non-sorbitol-fermenting, beta-glucuronidase negative O157:H7 and O157:H- strains from Australia. The inferred phylogeny is consistent with the hypothesis that subpopulations on each continent resulted from geographic spread of an ancestral divergence event and subsequent expansion of distinct subpopulations. Marker sorting and DNA sequence analyses identified sets of monophyletic markers consistent with the pattern of divergence and demonstrated that phylogeographic variation occurred through emergence of regional subclones and concentration of regional polymorphisms among distinct subpopulations. DNA sequence analysis of representative polyphyletic markers showed that genome diversity accrued through random drift and bacteriophage-mediated events.
Collapse
Affiliation(s)
- J Kim
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583-0919, USA
| | | | | | | | | | | | | |
Collapse
|
19
|
Bettelheim KA, Bennett-Wood V, Lightfoot D, Wright PJ, Marshall JA. Simultaneous isolation of verotoxin-producing strains of Escherichia coli O128:H2 and viruses in gastroenteritis outbreaks. Comp Immunol Microbiol Infect Dis 2001; 24:135-42. [PMID: 11247046 DOI: 10.1016/s0147-9571(00)00023-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three outbreaks of gastroenteritis from which the Verotoxin producing Escherichia coli serotype O128:H2 was isolated are reported. In addition Norwalk-like viruses were detected in patients from two of the outbreaks and astrovirus in the third outbreak. While it cannot be specifically determined which of these agents played the major role in these outbreaks, the findings suggest that the viral agents need to be considered in investigations of gastroenteritis outbreaks, regardless of whether bacterial enteropathogens have also been isolated. This study points to a strong need to investigate gastroenteritis outbreaks for both bacterial and viral agents and to review in detail the asymptomatic carriage rate of Verotoxin-producing bacteria and gastroenteritis-associated viral agents; these areas of public health significance have been largely neglected.
Collapse
Affiliation(s)
- K A Bettelheim
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | | | | | | | | |
Collapse
|
20
|
Murase T, Yamada M, Muto T, Matsushima A, Yamai S. Fecal excretion of Salmonella enterica serovar typhimurium following a food-borne outbreak. J Clin Microbiol 2000; 38:3495-7. [PMID: 10970414 PMCID: PMC87417 DOI: 10.1128/jcm.38.9.3495-3497.2000] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fecal excretion of Salmonella enterica serovar Typhimurium organisms was observed in patients and in people not showing symptoms who were involved in an outbreak of food-borne infection with this organism. Excretion of organisms was prolonged in the patients who were given antimicrobial drugs compared with those who were not. The isolates were indistinguishable by their pulsed-field gel electrophoresis patterns and biotyping from the strain recovered from the roast pork that had been consumed by all of the people. This indicates that these isolates obtained from the infected people had originated in the contaminated pork.
Collapse
Affiliation(s)
- T Murase
- Department of Bacteriology and Pathology, Kanagawa Prefectural Public Health Laboratory, Yokohama 241-0815, Japan.
| | | | | | | | | |
Collapse
|
21
|
Preston MA, Johnson W, Khakhria R, Borczyk A. Epidemiologic subtyping of Escherichia coli serogroup O157 strains isolated in Ontario by phage typing and pulsed-field gel electrophoresis. J Clin Microbiol 2000; 38:2366-8. [PMID: 10835004 PMCID: PMC86805 DOI: 10.1128/jcm.38.6.2366-2368.2000] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phage typing and DNA macrorestriction fragment analysis by pulsed-field gel electrophoresis (PFGE) were evaluated for use in the epidemiological subtyping of Escherichia coli serogroup O157 strains isolated in Ontario, Canada. Among 30 strains isolated from patients with sporadic cases of infection, 22 distinct XbaI macrorestriction patterns were identified and 17 strains exhibited unique PFGE patterns. In contrast, phage typing identified only seven different phage types and 17 strains belonged to the same phage type. A total of 25 phage type-macrorestriction pattern combinations were identified among the strains from patients with sporadic cases of infection. PFGE subtyping differentiated between unrelated strains that exhibited the same phage type, and in one group of strains, phage typing differentiated between strains of the same PFGE subtype. Both typing procedures correctly identified outbreak-related isolates as belonging to the same type in four separate outbreaks. Each outbreak strain was characterized by a distinct macrorestriction pattern, while phage typing subdivided the outbreak strains into only three different types. A small percentage of outbreak-related isolates had PFGE patterns that differed slightly (one or two DNA fragment differences) from that of the outbreak strain. On the other hand, each isolate from the same outbreak belonged to the same phage type as that of the outbreak strain. We conclude that phage typing and PFGE fingerprinting represent complementary procedures for the subtyping of E. coli serogroup O157 and that the combined use of these procedures provides optimal discrimination.
Collapse
Affiliation(s)
- M A Preston
- Central Public Health Laboratory, Ministry of Health, Toronto, Ontario M9P 3T1.
| | | | | | | |
Collapse
|
22
|
Jarvisa GN, Kizoulisa MG, Diez-Gonzaleza F, Russellab JB. The genetic diversity of predominant Escherichia coli strains isolated from cattle fed various amounts of hay and grain(1). FEMS Microbiol Ecol 2000; 32:225-233. [PMID: 10858581 DOI: 10.1111/j.1574-6941.2000.tb00715.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
When the 16S rDNA of predominant Escherichia coli strains from cattle was digested with HhaI and HaeIII, the strains could be sub-divided into four operational taxonomic units. When genomic DNA was digested with XbaI, strains could be grouped into 24 pulsed-field gel electrophoresis genotypes (>95% Dice similarity) and five clades (>20% Dice similarity). Diet (hay versus grain) and gastrointestinal compartment (rumen versus colon) did not have a large impact on diversity. However, both analyses indicated that the cows (n=2) had different E. coli populations. When all 22 colonic strains were inoculated into a maltose-limited chemostat, only a single genotype persisted. Based on these results, the genetic diversity of E. coli in the cattle is very great and this bacterium can occupy different niches.
Collapse
|
23
|
Abstract
Multilocus sequence typing (MLST) provides a new approach to molecular epidemiology that can identify and track the global spread of virulent or antibiotic-resistant isolates of bacterial pathogens using the Internet. MLST databases, together with interrogation software, are available for Neisseria meningitidis and Streptococcus pneumoniae and databases for Streptococcus pyogenes and Staphylococcus aureus will be released shortly.
Collapse
Affiliation(s)
- M C Enright
- Wellcome Trust Centre for the Epidemiology of Infectious Disease, Dept of Zoology, University of Oxford, Oxford, UK OX1 3FY
| | | |
Collapse
|
24
|
Kim J, Nietfeldt J, Benson AK. Octamer-based genome scanning distinguishes a unique subpopulation of Escherichia coli O157:H7 strains in cattle. Proc Natl Acad Sci U S A 1999; 96:13288-93. [PMID: 10557313 PMCID: PMC23940 DOI: 10.1073/pnas.96.23.13288] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multilocus-genotyping methods have shown that Escherichia coli O157:H7 is a geographically disseminated clone. However, high-resolution methods such as pulse-field gel electrophoresis demonstrate significant genomic diversity among different isolates. To assess the genetic relationship of human and bovine isolates of E. coli O157:H7 in detail, we have developed an octamer-based genome-scanning methodology, which compares the distance between over-represented, strand-biased octamers that occur in the genome. Comparison of octamer-based genome-scanning products derived from >1 megabase of the genome demonstrated the existence of two distinct lineages of E. coli O157:H7 that are disseminated within the United States. Human and bovine isolates are nonrandomly distributed among the lineages, suggesting that one of these lineages may be less virulent for humans or may not be efficiently transmitted to humans from bovine sources. Restriction fragment length polymorphism analysis with lambdoid phage genomes indicates that phage-mediated events are associated with divergence of the lineages, thereby providing one explanation for the degree of diversity that is observed among E. coli O157:H7 by other molecular-fingerprinting methods.
Collapse
Affiliation(s)
- J Kim
- Department of Food Science and Technology, University of Nebraska, 330 Food Industry Complex, Lincoln, NE, 68583-0919, USA
| | | | | |
Collapse
|
25
|
Caeiro JP, Mathewson JJ, Smith MA, Jiang ZD, Kaplan MA, Dupont HL. Etiology of outpatient pediatric nondysenteric diarrhea: a multicenter study in the United States. Pediatr Infect Dis J 1999; 18:94-7. [PMID: 10048678 DOI: 10.1097/00006454-199902000-00003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Few data have been published recently on the etiology of outpatient pediatric diarrhea in the US. METHODS We determined the etiology of acute, nondysenteric diarrhea among 147 children between 2 and 11 years old presenting to 9 outpatient clinics in various regions of the US between August, 1991, and August, 1993. Enteropathogens were sought by conventional laboratory methods. The various diarrheagenic Escherichia coli were sought. RESULTS A recognized etiologic agent was detected in the stools of 89 (60.5%) children and 15 (10) patients had multiple agents detected. Rotavirus was found in 43 (29.3%) of the children, with a spring and winter peak in occurrence. Giardia lamblia was identified in 22 (15%) cases with a spring peak. HEp-2 cell-adherent E. coli were found in 15 (10.2%). Other agents found included: enteric adenovirus in 7 (4.8%); Salmonella in 5 (3.4%); enterohemorrhagic E. coli in 5 (3.4%); enteropathogenic E. coli in 2 (1.4%); enterotoxigenic E. coli in 2 (1.4%); Entamoeba histolytica in 1 (0.70%); and Campylobacter jejuni in 1 (0.7%). CONCLUSIONS In addition to the presence of conventional enteropathogens, diarrheagenic E. coli (HEp-2 cell-adherent E. coli, enterohemorrhagic E. coli, enteropathogenic E. coli and enterotoxigenic E. coli) were associated with endemic pediatric diarrhea in the US.
Collapse
Affiliation(s)
- J P Caeiro
- Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | | |
Collapse
|