Intrahost genome alterations in enterohemorrhagic Escherichia coli

Bacterial chromosomes are not fixed molecules; they evolve over the course of infections in human beings. During infection, a variety of strong selective pressures are exerted on the pathogen. The resulting genetic changes that occur in intestinal pathogens might influence clinical outcome and have an impact on diagnosis and epidemiology. Enterohemorrhagic Escherichia coli (EHEC) is a good example of this process. These zoonotic pathogens cause diarrhea, bloody diarrhea, and hemolytic uremic syndrome in human beings, whereas in their natural habitat they mostly are asymptomatic colonizers. Thus, EHEC must be able to quickly adapt from one milieu to another. The greatest challenge it might face is to infect human beings--profound chromosomal changes occur during the brief period that EHEC passes through the human gastrointestinal tract, leading to gains and losses of virulence determinants. The intensive study of human enteric factors that induce or modulate pathogen chromosome instability could provide important information about host-microbial interactions.

Cross-border comparison of the admission prevalence and clonal structure of meticillin-resistant Staphylococcus aureus

Since patient exchange between hospitals sharing a common catchment area might favour regional spread of meticillin-resistant Staphylococcus aureus (MRSA), the reliable detection of patients colonised at admission is crucial. Thus, hospitals in the Dutch-German border area EUREGIO MRSA-net aim at synchronising their local MRSA standards in order to prevent unidentified inter-hospital as well as cross-border spread. This assumes enhanced knowledge of MRSA prevalence and risk factors associated with MRSA carriage at admission. We conducted nasal MRSA screening of all inpatients admitted to 39 German hospitals (in the period 1 November to 30 November 2006) and to one Dutch hospital (in the period 1 July to 30 September 2007) in the EUREGIO MRSA-net. A total of 390 MRSA cases were detected among 25,540 patients screened. The admission prevalence was 1.6 MRSA/100 patients (6.5% of all S. aureus) in the German and 0.5 MRSA/100 patients (1.4% of all S. aureus) in the Dutch part of the border region. Overall, the predominating S. aureus protein A gene (spa) sequence types were t003, t032 and t011. One isolate (t044) carried Panton-Valentine leukocidin (PVL) encoding genes. Altogether, 79% and 67% of all MRSA patients in the German and Dutch regions respectively, were identifiable by the classical nosocomial risk factors assessed. In patients lacking all risk factors assessed, spa types t011 and t034 were predominant (P<0.001).

Analysis of collection of hemolytic uremic syndrome-associated enterohemorrhagic Escherichia coli

Multilocus sequence typing of 169 non-O157 enterohemorrhagic Escherichia coli (EHEC) isolated from patients with hemolytic uremic syndrome (HUS) demonstrated 29 different sequence types (STs); 78.1% of these strains clustered in 5 STs. From all STs and serotypes identified, we established a reference panel of EHEC associated with HUS (HUSEC collection).

Shiga toxin-negative attaching and effacing Escherichia coli: distinct clinical associations with bacterial phylogeny and virulence traits and inferred in-host pathogen evolution

BACKGROUND

Attaching and effacing Escherichia coli (AEEC) that lack Shiga toxin genes (stx) and the enteropathogenic E. coli adherence factor (EAF) plasmid (stx-/EAF-) are classified as atypical enteropathogenic E. coli and cause diarrhea worldwide. However, it is unknown whether there are bacterial lineage-specific human disease phenotypes. We compared stx-/EAF- AEEC recovered from patients (mostly children) with bloody and nonbloody diarrhea.

METHODS

stx-/EAF- AEEC were isolated using eae colony blot hybridization and were serotyped, tested (by polymerase chain reaction) for putative virulence genes, and analyzed for phylogenetic relationships by use of multilocus sequence typing.

RESULTS

During the period 1995-2007, stx-/EAF- AEEC were isolated as the only bacterial pathogens from stool specimens obtained from 18 (15.3%) of 118 patients with bloody diarrhea and from 141 (1.3%) of 10,550 patients with nonbloody diarrhea (P<.001). All but 1 of 18 strains recovered from patients with bloody diarrhea resembled enterohemorrhagic E. coli (EHEC) on the basis of serotypes, non-stx virulence profiles, and multilocus sequence types. In contrast, most (75.9%) of 141 stx-/EAF- AEEC recovered from patients with nonbloody diarrhea belonged to other serotypes and differed from the former strains phylogenetically and with regard to virulence genes. Three of 18 patients with bloody diarrhea and none of 141 patients with nonbloody diarrhea who shedded stx-/EAF- AEEC developed hemolytic uremic syndrome.

CONCLUSIONS

Most stx-/EAF- AEEC associated with bloody diarrhea are plausibly EHEC that lost Shiga toxin during infection (EHEC-LST). To prevent serious complications of such infections, Shiga toxin-independent diagnostic strategies to accurately and rapidly identify such patients should be developed and applied. Multilocus sequence typing has potential to distinguish EHEC-LST from less pathogenic stx-/EAF- AEEC.

EUREGIO MRSA-net Twente/Münsterland – a Dutch-German cross-border network for the prevention and control of infections caused by methicillin-resistant Staphylococcus aureus

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Evidence for cost reduction based on pre-admission MRSA screening in general surgery

Colonization with methicillin-resistant Staphylococcus aureus (MRSA) is a risk factor for MRSA infection causing increased costs in patient's care and treatment. To evaluate cost efficiency, pre-admission MRSA screening and subsequent MRSA decolonization of patients admitted to the Department of General Surgery at the University Hospital of Münster were determined. In 2004, 2054 (89.3%) out of the total of 2299 hospital-admitted patients were screened for MRSA (1769 elective and 530 direct admissions); 1536 patients underwent pre-admission MRSA screening (86.8% of the 1769 elective admissions), of whom seven patients (0.5%) were MRSA-positive and five of these were successfully decolonized before admission. In case of direct admissions, i.e., emergency cases or transferral from other hospitals, 2.4% and 8.6% were MRSA-positive, respectively. There were 25 patients MRSA positive during their hospital stay, two of these were nosocomially acquired, which represent 0.1 nosocomial MRSA cases in 1000 in-patients. The average MRSA carrier was (65+/-15 years) older than the other patients (55+/-17 years), had a significantly higher rate of pulmonary disease, coronary heart disease and certain infections; and had a longer hospital stay (27 versus 10 days, p<0.05). The total costs of the MRSA screening were approximately 20,000 euro. Since the estimated costs for handling MRSA treatment and isolation during a hospital stay are 6000-10,000 euro for each affected patient, we estimated that approximately 20,000 euro could be saved by detecting and successfully decolonizing a total of five patients through pre-admission screening. In this calculation, additional costs due to the increased morbidity and mortality of MRSA carriers and the possible spread of MRSA through unrecognized colonization were not included. In conclusion, pre-admission screening for MRSA is an effective method to reduce the hospital burden of MRSA-colonized patients and the savings due to consistent decolonization before elective admission outweigh the costs of screening.

Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms

BACKGROUND

For typing of Staphylococcus aureus, DNA sequencing of the repeat region of the protein A (spa) gene is a well established discriminatory method for outbreak investigations. Recently, it was hypothesized that this region also reflects long-term epidemiology. However, no automated and objective algorithm existed to cluster different repeat regions. In this study, the Based Upon Repeat Pattern (BURP) implementation that is a heuristic variant of the newly described EDSI algorithm was investigated to infer the clonal relatedness of different spa types. For calibration of BURP parameters, 400 representative S. aureus strains with different spa types were characterized by MLST and clustered using eBURST as "gold standard" for their phylogeny. Typing concordance analysis between eBURST and BURP clustering (spa-CC) were performed using all possible BURP parameters to determine their optimal combination. BURP was subsequently evaluated with a strain collection reflecting the breadth of diversity of S. aureus (JCM 2002; 40:4544).

RESULTS

In total, the 400 strains exhibited 122 different MLST types. eBURST grouped them into 23 clonal complexes (CC; 354 isolates) and 33 singletons (46 isolates). BURP clustering of spa types using all possible parameter combinations and subsequent comparison with eBURST CCs resulted in concordances ranging from 8.2 to 96.2%. However, 96.2% concordance was reached only if spa types shorter than 8 repeats were excluded, which resulted in 37% excluded spa types. Therefore, the optimal combination of the BURP parameters was "exclude spa types shorter than 5 repeats" and "cluster spa types into spa-CC if cost distances are less than 4" exhibiting 95.3% concordance to eBURST. This algorithm identified 24 spa-CCs, 40 singletons, and excluded only 7.8% spa types. Analyzing the natural population with these parameters, the comparison of whole-genome micro-array groupings (at the level of 0.31 Pearson correlation index) and spa-CCs gave a concordance of 87.1%; BURP spa-CCs vs. manually grouped spa types resulted in 95.7% concordance.

CONCLUSION

BURP is the first automated and objective tool to infer clonal relatedness from spa repeat regions. It is able to extract an evolutionary signal rather congruent to MLST and micro-array data.

Subtypes of the plasmid-encoded serine protease EspP in Shiga toxin-producing Escherichia coli: distribution, secretion, and proteolytic activity

We investigated the prevalence, distribution, and structure of espP in Shiga toxin-producing Escherichia coli (STEC) and assessed the secretion and proteolytic activity of the encoded autotransporter protein EspP (extracellular serine protease, plasmid encoded). espP was identified in 56 of 107 different STEC serotypes. Sequencing of a 3,747-bp region of the 3,900-bp espP gene distinguished four alleles (espPalpha, espPbeta, espPgamma, and espPdelta), with 99.9%, 99.2%, 95.3%, and 95.1% homology, respectively, to espP of E. coli O157:H7 strain EDL933. The espPbeta, espPgamma, and espPdelta genes contained unique insertions and/or clustered point mutations that enabled allele-specific PCRs; these demonstrated the presence of espPalpha, espPbeta, espPgamma, and espPdelta in STEC isolates belonging to 17, 16, 15, and 8 serotypes, respectively. Among four subtypes of EspP encoded by these alleles, EspPalpha (produced by enterohemorrhagic E. coli [EHEC] O157:H7 and the major non-O157 EHEC serotypes) and EspPgamma cleaved pepsin A, human coagulation factor V, and an oligopeptide alanine-alanine-proline-leucine-para-nitroaniline, whereas EspPbeta and EspPdelta either were not secreted or were proteolytically inactive. The lack of proteolysis correlated with point mutations near the active serine protease site. We conclude that espP is widely distributed among STEC strains and displays genetic heterogeneity, which can be used for subtyping and which affects EspP activity. The presence of proteolytically active EspP in EHEC serogroups O157, O26, O111, and O145, which are bona fide human pathogens, suggests that EspP might play a role as an EHEC virulence factor.

Enterohaemorrhagic Escherichia coli O26:H11/H-: a human pathogen in emergence

Enterohaemorrhagic Escherichia coli (EHEC) O26:H11 have emerged as the most important non-O157:H7 EHEC, with respect to their ability to cause diarrhoea and the haemolytic uraemic syndrome (HUS). HUS is a leading cause of acute renal failure in children, and is mainly caused by EHEC expressing Shiga toxins (Stx) 1 and/or 2. Since 1996, EHEC O26, which produce Stx2 only and appear to have enhanced virulence, have been increasingly isolated from HUS patients in Germany. In contrast, EHEC O26 found in cattle predominantly produce Stx1 as the sole Stx. Additional potential virulence factors of EHEC O26 include cytolysins (EHEC hemolysin), serine proteases (EspP), lymphotoxins (Efal) and adhesins (intimin). The genes encoding the virulence factors are located within pathogenicity islands (eae, efa1), bacteriophages (stx) or plasmids (EHEC-hlyA, espP). In addition, EHEC O26 possess, in contrast to other EHEC, the "high pathogenicity island" (HPI), which is also present in pathogenic Yersiniae. This island contains genes involved in the biosynthesis, regulation and transport of the siderophore yersiniabactin. Comparative genomic analyses between EHEC O26 and non-pathogenic E. coli, as well as investigations of mechanisms involved in the transfer of virulence genes, provide a deeper insight into the evolution of EHEC O26. These studies demonstrate how horizontal transfer of virulence genes, even from distantly related organisms, can lead in brief intervals to the rise of a highly virulent clone within a particular E. coli serotype.The classical bacteriological methods are no longer sufficient to determine the risk posed by EHEC O26. However, knowledge of the complete virulence profiles of these pathogens and understanding their stepwise evolution form a foundation for developing new strategies to prevent human infections and new methods for their laboratory diagnosis.

Distribution of capsular and surface polysaccharide serotypes of Staphylococcus aureus

Because of its ability to cause serious and fatal infections, Staphylococcus aureus remains one of the most feared microorganisms. Methicillin-resistant S. aureus (MRSA) has long been a common pathogen in healthcare facilities, but within the past decade, it has emerged as a problematic pathogen in the community setting as well. The severe consequences of infection heighten the importance of prevention. To analyze the potential applicability of a putative S. aureus polysaccharide conjugate vaccine, we tested 714 German methicillin-susceptible S. aureus (MSSA) and MRSA strains for their capsular and surface polysaccharide serotype by slide agglutination with specific antibodies (anti-T5-DT, anti-T8-DT, anti-336-rEPA). The strain serotypes were confirmed by immunodiffusion using lysostaphin-digested cell lysates. Regarding MRSA strains representing 86 unique spa types and thus covering >90% of MRSA spa types registered, 39 (45.3%) were type 5, 36 (41.9%) were type 8, and 11 (12.8%) were type 336. Of particular interest, type 336 was the second most common serotype among MRSA isolates collected from 10 different laboratories (40 isolates per site) covering university hospitals, general hospitals, and clinics throughout Germany. Type 8-positive strains were more prevalent among isolates recovered from anterior nares of patients who did not subsequently develop S. aureus bacteremia compared with those who became bacteremic with this pathogen. In conclusion, the addition of the newly described type 336 to a capsular polysaccharide-protein conjugate vaccine could extend the coverage substantially and would include virtually all MSSA and MRSA strains currently circulating in Germany.

Staphylococcus pettenkoferi sp. nov., a novel coagulase-negative staphylococcal species isolated from human clinical specimens

Five coagulase-negative, novobiocin-susceptible staphylococcal strains were isolated from human blood cultures in different German and Belgian medical facilities. A novel species, ‘Staphylococcus pettenkoferi’ was proposed recently to accommodate two of these strains (B3117T and A6664), although the name was not validly published. All five strains belonged to the genus Staphylococcus because they were non-motile, Gram-positive, catalase-positive cocci with peptidoglycan type (A3α type l-lys–gly2–4–l-Ser–Gly), menaquinone pattern (MK-7, MK-6 and MK-8) and major cellular fatty acids (ai-C15 : 0, ai-C17 : 0 and i-C15 : 0) that corresponded to those of staphylococci. Phenotypically, the isolates most closely resembled Staphylococcus capitis subsp. capitis and Staphylococcus auricularis, but they could be distinguished from these species by physiological tests and chemotaxonomic investigations. The results of DNA–DNA hybridization, chemotaxonomic investigations and 16S rRNA gene and RNA polymerase B gene (rpoB) sequence analysis enabled strains B3117T, K6999, 229 and 230 to be differentiated genotypically and phenotypically from known Staphylococcus species, indicating that these isolates are representatives of a novel species. The name Staphylococcus pettenkoferi sp. nov. is proposed for this novel species, with strain B3117T (=CIP 107711T=CCUG 51270T) as the type strain. Due to differences in the results of physiological and chemotaxonomic investigations and DNA–DNA hybridization data, strain A6664 was not included in the description of the novel species.

Prevalence, Virulence Profiles, and Clinical Significance of Shiga Toxin-Negative Variants of Enterohemorrhagic Escherichia coli O157 Infection in Humans

BACKGROUND

Escherichia coli O157, of the H7 clone, exists in humans and in the environment as Shiga toxin (Stx)-positive and Stx-negative variants. Stx production by infecting organisms is considered to be a critical requirement for the development of hemolytic uremic syndrome (HUS), which occurs in approximately 15% of E. coli O157-infected patients. It is unknown if loss of the stx gene during the early stage of an enterohemorrhagic E. coli infection prevents HUS, or if absence of the stx gene from E. coli O157 reduces or ablates virulence.

METHODS

We determined the frequency of stx-positive and stx-negative E. coli O157 isolates in stool samples obtained from patients who experienced sporadic cases of diarrhea or HUS, as well as the frequency in samples obtained during outbreaks, and investigated the clinical course of the disease.

RESULTS

Among E. coli O157 isolates obtained from samples related to sporadic cases of diarrhea, stx-negative strains accounted for 4%. The proportion of stx-negative strains was significantly higher among sorbitol-fermenting, nonmotile E. coli O157 isolates (12.7%) than among non-sorbitol-fermenting E. coli O157:H7 or nonmotile isolates (0.8%; P<.001). stx-Negative sorbitol-fermenting E. coli O157 isolates were also observed in samples related to 3 HUS outbreaks and 1 outbreak of diarrhea caused by sorbitol-fermenting, nonmotile enterohemorrhagic E. coli O157; additionally, they were the only pathogens that were isolated in 2 other outbreaks of diarrhea without HUS.

CONCLUSIONS

Strains of stx-negative E. coli O157 isolated from stool samples of patients are either inherently stx-negative strains that cause mostly uncomplicated diarrhea, or strains that descended from enterohemorrhagic E. coli O157 by the loss of the stx gene during infection; the latter strains may still cause severe disease.

Staphylococcal Chromosomal CassettemecType I,spaType, and Expression of Pls Are Determinants of Reduced Cellular Invasiveness of Methicillin‐ResistantStaphylococcus aureusIsolates

We have shown previously that pls, which codes for the surface protein Pls of methicillin-resistant Staphylococcus aureus (MRSA), reduces adhesion to immobilized fibronectin, fibrinogen, laminin, and immunoglobulin G as well as invasion of host cells. Here, we tested a collection of 66 clinical MRSA isolates--48 negative for pls/Pls (pls(-)/Pls(-)), 15 positive for pls/Pls (pls(+)/Pls(+)), and 3 harboring the pls gene but not expressing Pls (pls(+)/Pls(-))--for cellular invasiveness. Invasion of 293 cells by pls(+)/Pls(+) strains was lower than that by the pls(-)/Pls(-) strains (median [range], 36% [22%-70%] vs. 93% [25%-162%]). The 3 pls(+)/Pls(-) strains (median [range], 95% [63%-103%]) were as invasive as the pls(-)/Pls(-) strains. In addition, we identified a pls(+)/Pls(+) staphylococcal chromosomal cassette mec (SCCmec) IV strain. In conclusion, 3 properties--pls/Pls, SCCmec type, and spa type--strongly predicted the cellular invasiveness of MRSA strains, as indicated by good clustering. In contrast, the spa type-deduced multilocus sequence typing clonal complex (MLST-CC) was not able to predict the invasiveness of MRSA strains equally well. The underlying mechanism remains to be elucidated.

Shiga toxin gene loss and transfer in vitro and in vivo during enterohemorrhagic Escherichia coli O26 infection in humans

Escherichia coli serogroup O26 consists of enterohemorrhagic E. coli (EHEC) and atypical enteropathogenic E. coli (aEPEC). The former produces Shiga toxins (Stx), major determinants of EHEC pathogenicity, encoded by bacteriophages; the latter is Stx negative. We have isolated EHEC O26 from patient stools early in illness and aEPEC O26 from stools later in illness, and vice versa. Intrapatient EHEC and aEPEC isolates had quite similar pulsed-field gel electrophoresis (PFGE) patterns, suggesting that they might have arisen by conversion between the EHEC and aEPEC pathotypes during infection. To test this hypothesis, we asked whether EHEC O26 can lose stx genes and whether aEPEC O26 can be lysogenized with Stx-encoding phages from EHEC O26 in vitro. The stx2 loss associated with the loss of Stx2-encoding phages occurred in 10% to 14% of colonies tested. Conversely, Stx2- and, to a lesser extent, Stx1-encoding bacteriophages from EHEC O26 lysogenized aEPEC O26 isolates, converting them to EHEC strains. In the lysogens and EHEC O26 donors, Stx2-converting bacteriophages integrated in yecE or wrbA. The loss and gain of Stx-converting bacteriophages diversifies PFGE patterns; this parallels findings of similar but not identical PFGE patterns in the intrapatient EHEC and aEPEC O26 isolates. EHEC O26 and aEPEC O26 thus exist as a dynamic system whose members undergo ephemeral interconversions via loss and gain of Stx-encoding phages to yield different pathotypes. The suggested occurrence of this process in the human intestine has diagnostic, clinical, epidemiological, and evolutionary implications.

Structural and functional differences between disease-associated genes of enterohaemorrhagic Escherichia coli O111

We analysed 72 clinical isolates of enterohaemorrhagic Escherichia coli (EHEC) O111 from patients with diarrhoea or haemolytic uraemic syndrome (HUS) isolated during the period from 1955 to 2005 and identified six motile strains (flagellar antigens 8, 10 and 11); the remaining 66 (92%) were nonmotile (NM) and could not be typed by conventional H serotyping. To improve subtyping methodologies, we determined genotypes of the flagellin-encoding fliC. Three fliC genotypes were found which were identical to those of motile EHEC O111 with H antigens 8, 10 and 11 and designated fliC(H8), fliC(H10) and fliC(H11). The IS629 insertion element was present, identically located, in six epidemiologically unrelated isolates with fliC(H8). The prevalence of the fliC genotypes in the 72 EHEC O111 strains were fliC(H8) (89%), fliC(H10) (7%) and fliC(H11) (4%). Within these fliC genotypes, a high degree of homogeneity for the presence of disease-associated genes was found. The adhesins-encoding genes eae and efa-1 were present in all strains with fliC(H8) and fliC(H11), but absent from strains with fliC(H10). The latter strains have not been reported previously. Strains with fliC(H10) and fliC(H11), but not those with fliC(H8), retained intact cadA and cadC loci and decarboxylated lysine. Three different stx genotypes including stx(1), stx(2) and stx(1)/stx(2) were determined among the 72 EHEC O111. We observed a significant increase over time in the frequency of strains harbouring both stx(1) and stx(2). The presence of stx(2) both alone and in combination with stx(1) was significantly (chi(2)=23.16, P<0.00001, CI(95) [2.29; 9.76]) associated with HUS. Therefore, the emergence of EHEC O111 should be monitored carefully. We conclude that EHEC O111 strains can be differentiated using specific loci required for motility, adherence, Stx production, and lysine decarboxylation. The divergence within EHEC O111 makes it possible to subtype these emerging pathogens in the laboratory thereby providing a basis for further investigations into their ecological niches and survival capabilities.

EUREGIO-Projekt MRSA-net Twente/Münsterland

Over the last years, Germany has observed an increase in the prevalence of methicillin-resistant Staphylococcus (MRSA) in all S. aureus isolates from 2 % to about 25 % whereas in The Netherlands this proportion has continuously been kept below 1 % thanks to a consistent "search & destroy" policy. Both countries increasingly register so-called community-acquired (CA) MRSA which are a threat also to the healthy population without any known risk factor for MRSA carriership. The EUREGIO project "MRSA-net Twente/Münsterland" has made it its main goal to set up a German-Dutch network serving as a basis for a quality association which includes all those who are actively involved in health care provision on both sides of the border and to implement a coordinated strategy for MRSA control and prevention. The project is being carried out with the financial support of the European Union under the INTERREG-IIIA Community initiative and of the Ministry of Economics of the State of North Rhine-Westphalia. The epidemiological backbone of the MRSA-net is a genetic-based MRSA typing strategy (spa-typing) which has been developed by the Institute for Hygiene, University Hospital, Münster and which allows regional and cross-border comparability of laboratory results. The Faculty of Behavioural Sciences of the University of Twente examines MRSA hygiene protocols with regard to their acceptability and realisability with the intention of developing user-friendly, target group-oriented MRSA protocols for the EUREGIO. The health departments involved in the project play a central role in the coordination of the network partners in the municipalities. By performing their function of surveillance in accordance with Sections 23 and 36 of the Infectious Disease Control Act they provide an important contribution to enhancing MRSA control and prevention strategies. Thanks to its cross-border cooperation and exchange of knowledge and technology the EUREGIO project "MRSA-net" contributes to controlling the proliferation of MRSA in the EUREGIO and thus to removing obstacles to the free cross-border movement of patients and personnel.

Chromosomal dynamism in progeny of outbreak-related sorbitol-fermenting enterohemorrhagic Escherichia coli O157:NM

Sorbitol-fermenting (SF) enterohemorrhagic Escherichia coli (EHEC) O157:NM (nonmotile) is a unique clone that causes outbreaks of hemorrhagic colitis and hemolytic-uremic syndrome. In well-defined clusters of cases, we have observed significant variability in pulsed-field gel electrophoresis (PFGE) patterns which could indicate coinfection by different strains. An analysis of randomly selected progeny colonies of an outbreak strain after subcultivation demonstrated that they displayed either the cognate PFGE outbreak pattern or one of four additional patterns and were <89% similar. These profound alterations were associated with changes in the genomic position of one of two Shiga toxin 2-encoding genes (stx2) in the outbreak strain or with the loss of this gene. The two stx2 alleles in the outbreak strain were identical but were flanked with phage-related sequences with only 77% sequence identity. Neither of these phages produced plaques, but one lysogenized E. coli K-12 and integrated in yecE in the lysogens and the wild-type strain. The presence of two stx2 genes which correlated with increased production of Stx2 in vitro but not with the clinical outcome of infection was also found in 14 (21%) of 67 SF EHEC O157:NM isolates from sporadic cases of human disease. The variability of PFGE patterns for the progeny of a single colony must be considered when interpreting PFGE patterns in SF EHEC O157-associated outbreaks.