Probing the Degree of Coherence through the Full 1D to 3D Crossover

We experimentally study a gas of quantum degenerate ^{87}Rb atoms throughout the full dimensional crossover, from a one-dimensional (1D) system exhibiting phase fluctuations consistent with 1D theory to a three-dimensional (3D) phase-coherent system, thereby smoothly interpolating between these distinct, well-understood regimes. Using a hybrid trapping architecture combining an atom chip with a printed circuit board, we continuously adjust the system's dimensionality over a wide range while measuring the phase fluctuations through the power spectrum of density ripples in time-of-flight expansion. Our measurements confirm that the chemical potential μ controls the departure of the system from 3D and that the fluctuations are dependent on both μ and the temperature T. Through a rigorous study we quantitatively observe how inside the crossover the dependence on T gradually disappears as the system becomes 3D. Throughout the entire crossover the fluctuations are shown to be determined by the relative occupation of 1D axial collective excitations.

Assessing reproductive effects on fish populations: an evaluation of methods to predict the reproductive strategy of fishes

Many environmental monitoring programs include an assessment of the health of fish populations using a sentinel species and include an indicator of reproductive potential. Knowledge of the reproductive strategy of the fish species is critical for data interpretation but is not always known. The reproductive strategy of a species can be determined from detailed histological analyses of ovaries throughout the reproductive cycle; however, these studies can be costly and can delay the implementation of a monitoring program. Three quick and cost-effective methods of predicting the reproductive strategy (annual single spawning or annual multiple spawning) are evaluated in this study using predicted probabilities from binary logistic regression models as a means of classifying the reproductive strategies of 18 different fish species in Atlantic Canada. The first method was based on the hypothesis that the variability in the ovary weight-body weight relationship in prespawning females is higher in multiple spawners. This method did not have a good classification rate due to some multiple spawners having low variability. The other two methods involved predictor variables representing the proportion of oocytes in different stages of development and predictor variables representing the distribution of oocyte sizes during the prespawning season for 111 fish (25 different samples for species). Predicted probabilities from these regression models could be used to correctly classify the reproductive strategies of all 25 samples (development stage model) and all but one sample (oocyte size distribution model). These models can be used to estimate the reproductive strategy of a species from a single sample of fish collected during the prespawning period to support species selection and data interpretation in environmental monitoring programs.

Non-indigenous predators threaten ecosystem engineers: Interactive effects of green crab and oyster size on American oyster mortality

Non-indigenous green crabs (Carcinus maenas) are emerging as important predators of autogenic engineers like American oysters (Crassostrea virginica) throughout the eastern seaboard of Canada and the United States. To document the spreading distribution of green crabs, we carried out surveys in seven sites of Prince Edward Island during three fall seasons. To assess the potential impact of green crabs on oyster mortality in relation to predator and prey size, we conducted multiple predator-prey manipulations in the field and laboratory. The surveys confirmed an ongoing green crab spread into new productive oyster habitats while rapidly increasing in numbers in areas where crabs had established already. The experiments measured mortality rates on four sizes of oysters exposed to three sizes of crab, and lasted 3-5 days. The outcomes of experiments conducted in Vexar^® bags, laboratory tanks and field cages were consistent and were heavily dependent on both crab size and oyster size: while little predation occurred on large oysters, large and medium green crabs preyed heavily on small sizes. Oysters reached a refuge within the 35-55 mm shell length range; below that range, oysters suffered high mortality due to green crab predation and thus require management measures to enhance their survival. These results are most directly applicable to aquaculture operations and restoration initiatives but have implications for oyster sustainability.

Testing against "normal" with environmental data

Normal ranges are some fraction of a reference distribution deemed to represent an expected condition, typically 95%. They are frequently used as the basis for generic criteria for monitoring programs designed to test whether a sample is outside of "normal," as in reference-condition approach studies. Normal ranges are also the basis for criteria for more classic environmental effects monitoring programs designed to detect differences in mean responses between reference and exposure areas. Limits on normal ranges are estimated with error that varies depending largely on sample size. Direct comparison of a sample or a mean to estimated limits of a normal range will, with some frequency, lead to incorrect conclusions about whether a sample or a mean is inside or outside the normal range when the sample or the mean is near the limit. Those errors can have significant costs and risk implications. This article describes tests based on noncentral distributions that are appropriate for quantifying the likelihood that samples or means are outside a normal range. These noncentral tests reverse the burden of evidence (assuming that the sample or mean is at or outside normal), and thereby encourage proponents to collect more robust sample sizes that will demonstrate that the sample or mean is not at the limits or beyond the normal range. These noncentral equivalence and interval tests can be applied to uni- and multivariate responses, and to simple (e.g., upstream vs downstream) or more complex (e.g., before vs after, or upstream vs downstream) study designs. Statistical procedures for the various tests are illustrated with benthic invertebrate community data collected as part of the Regional Aquatics Monitoring Program (RAMP) in the vicinity of oil sands operations in northern Alberta, Canada. An Excel workbook with functions and calculations to carry out the various tests is provided in the online Supplemental Data. Integr Environ Assess Manag 2017;13:188-197. © 2016 SETAC.

Quantifying natural variability as a method to detect environmental change: Definitions of the normal range for a single observation and the mean of m observations

The normal range has been defined as the range that encloses 95% of reference values; in practice this range has been defined as the reference mean ± 2 standard deviations (SD). When sample sizes are small and reference data are not normally distributed, the mean ± 2 SDs do not enclose 95% of data values. Prediction intervals (PI) calculated using sample statistics are used in the present study to define the normal range for a single observation and the mean of m observations. The PIs provide confidence limits for the next randomly selected observation (or mean of m observations) from a population. The PIs are defined using normally distributed reference data; normality can typically be achieved with transformations of the data. Covariates can be used to explain some of the variability in the reference distribution, increasing the ability to detect change. When assumptions of normality are not met, alternative methods of defining the normal range are provided. The normal range can be used to quantify natural variability and assess change from the reference distribution. It can be used as an early warning indicator of change in environmental monitoring to identify the need for further investigation.

Reproductive strategies and seasonal changes in the somatic indices of seven small-bodied fishes in Atlantic Canada in relation to study design for environmental effects monitoring

Small-bodied fishes are more commonly being used in environmental effects monitoring (EEM) studies. There is a lack of understanding of the biological characteristics of many small-bodied species, which hinders study designs for monitoring studies. For example, 72% of fish population surveys in Canada's EEM program for pulp and paper mills that used small-bodied fishes were conducted outside of the reproductive period of the species. This resulted in an inadequate assessment of the EEM program's primary effect endpoint (reproduction) for these studies. The present study examined seasonal changes in liver size, gonad size, and condition in seven freshwater and estuarine small-bodied fishes in Atlantic Canada. These data were used to examine differences in reproductive strategies and patterns of energy storage among species. Female gonadal recrudescence in all seven species began primarily in the 2-month period in the spring before spawning. Male gonadal development was concurrent with females in five species; however, gonadal recrudescence began in the fall in male three-spined stickleback (Gasterosteus aculeatus) and slimy sculpin (Cottus cognatus). The spawning period for each species was estimated from the decline in relative ovary size after its seasonal maximum value in spring. The duration of the spawning period reflected the reproductive strategy (single vs multiple spawning) of the species. Optimal sampling periods to assess reproductive impacts in each species were determined based on seasonal changes in ovary size and were identified to be during the prespawning period when gonads are developing and variability in relative gonad size is at a minimum.

Negative consequences of using α = 0.05 for environmental monitoring decisions: a case study from a decade of Canada's Environmental Effects Monitoring Program

Using the traditional α = 0.05 significance level for null hypothesis significance tests makes assumptions about relative costs of Type I vs relevant Type II errors and inflates their combined probabilities. We have examined the results of 1254 monitoring tests conducted under the Canadian Environmental Effects Monitoring (EEM) program from 1992 to 2003, focusing on how the choice of α affected the relative probabilities and implied costs of Type I and Type II errors. Using α = 0.05 resulted in implied relative costs of Type I vs Type II errors that were both inconsistent among monitoring end points and also inconsistent with the philosophy of the monitoring program. Using α = 0.05 also resulted in combinations of Type I and II error that were 15-17% larger than those for "optimal" α levels set to minimize Type I and II errors for each study, and 12% of all monitoring tests would have reached opposite conclusions had they used these optimal α levels for decision-making. Thus, if the Canadian EEM program used study-specific optimal α levels, they would reduce the incidence of relevant errors and eliminate inconsistent implied relative costs of these errors. Environmental research and monitoring programs using α = 0.05 as a decision-making threshold should re-evaluate the usefulness of this "one-size-fits-all" approach.

Dealing with heterogeneous regression slopes in analysis of covariance: new methodology applied to environmental effects monitoring fish survey data

Analysis of covariance (ANCOVA) is a powerful statistical method which incorporates one or more covariates into the analysis to reduce error associated with measurement. ANCOVA (modeling response as a function of fish size) is frequently used to analyze environmental effects monitoring (EEM) fish survey data. In approximately 12% of fish survey data sets taken from cycles 1 to 3 of Environment Canada's EEM database for pulp and paper mills, the standard assumption of parallel regression slopes is not met. For the first three cycles of the EEM program, these data sets were classified as indicating a mill effect, but for the most part were excluded from subsequent analyses aimed at quantifying the effect. We present two different methods for initially dealing with data sets that exhibit heterogeneous slopes so that they can be analyzed using the parallel slope model. The first method identifies data sets where heterogeneous slopes are forced by a few high-influence observations. The second approach identifies data sets where a model with heterogeneous slopes is statistically, but not practically, significant: with a high coefficient of determination for the parallel slope model. These new methodologies are applied to EEM pulp and paper data sets and about 55% of cases with heterogeneous slopes can be described by a parallel slope model. We also discuss a third method that can be used to describe mill effects when regression slopes remain heterogeneous even after applying the above two methods, enabling comparison with a critical effect size. These new methodologies could benefit the EEM program by enabling more data sets to be incorporated into meta-analyses and be used to make more equitable mill monitoring decisions in the future.

Evaluation of antimicrobial resistance phenotypes for predicting multidrug-resistant Salmonella recovered from retail meats and humans in the United States

Although multidrug-resistant (MDR) non-Typhi Salmonella (NTS) strains are a concern in food production, determining resistance to multiple antimicrobial agents at slaughter or processing may be impractical. Single antimicrobial resistance results for predicting multidrug resistance are desirable. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value were used to determine each antimicrobial agent's ability to predict MDR phenotypes of human health significance: ACSSuT (resistance to at least ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, tetracycline) in NTS isolates, and MDR-AmpC-SN (resistance to ACSSuT, additional resistance to amoxicillin-clavulanate and to ceftiofur, and decreased susceptibility [MIC >= 2 microg/ml] to ceftriaxone) in NTS serotype Newport. The U.S. National Antimicrobial Resistance Monitoring System determined MICs to 15 or more antimicrobial agents for 9,955 NTS isolates from humans from 1999 to 2004 and 689 NTS isolates from retail meat from 2002 to 2004. A total of 847 (8.5%) human and 26 (3.8%) retail NTS isolates were ACSSuT; 995 (10.0%) human and 16 (2.3%) retail isolates were serotype Newport. Among Salmonella Newport, 204 (20.5%) human and 9 (56.3%) retail isolates were MDR-AmpC-SN. Chloramphenicol resistance provided the highest PPVs for ACSSuT among human (90.5%; 95% confidence interval, 88.4 to 92.3) and retail NTS isolates (96.3%; 95% confidence interval, 81.0 to 99.9). Resistance to ceftiofur and to amoxicillin-clavulanate and decreased susceptibility to ceftriaxone provided the highest PPVs (97.1, 98.1, and 98.6%, respectively) for MDR-AmpC-SN from humans. High PPVs for these agents applied to retail meat MDR-AmpC-SN, but isolate numbers were lower. Variations in MIC results may complicate ceftriaxone's predictive utility. Selecting specific antimicrobial resistance offers practical alternatives for predicting MDR phenotypes. Chloramphenicol resistance works best for ACSSuT-NTS, and resistance to ceftiofur, amoxicillin-clavulanate, or chloramphenicol works best for MDR-AmpC-SN.

Effects of pulp and paper mill effluent on fish: a temporal assessment of fish health across sampling cycles

The Canadian environmental effects monitoring (EEM) program is a regulated, cyclical, industry-funded program designed to determine whether receiving water impacts exist when a mill is in compliance with its discharge limits. The results from three cycles of the fish monitoring program (1992 to 2004) are available from over 200 surveys of fish compared between sites located upstream and downstream of pulp and paper mill effluent outfalls. Previous meta-analyses have shown a national average response pattern across cycles characterized by an increase in endpoints measuring energy storage and growth and a decrease in a reproductive endpoint, consistent with a response of nutrient enrichment in combination with some form of metabolic disruption. Although the national average pattern of effects was temporally consistent, there was some variability in the magnitude of effects among cycles. Questions were raised as to whether the intercycle variability was due to changes in effluent quality or due, at least in part, to other factors. The present study compares responses over the first three cycles, and shows that the choice of sentinel species is likely to be a major contributing factor to the variability in observed effects. Subset analyses using studies from mills that used the same sentinel species across cycles reveal fairly uniform responses and little evidence of significant improvements in overall fish health from cycles one to three. However, a meta-analysis using 1991 data collected from 10 mills before the implementation of the EEM program and data from the same mills collected during cycles one to three of the program reveal significantly reduced effects on relative liver weight and potential improvements in other endpoints.

Human Salmonella and concurrent decreased susceptibility to quinolones and extended-spectrum cephalosporins

For complicated infections, decreased susceptibility could compromise treatment with drugs from either antimicrobial class.

The National Antimicrobial Resistance Monitoring System monitors susceptibility among Enterobacteriaceae in humans in the United States. We studied isolates exhibiting decreased susceptibility to quinolones (nalidixic acid MIC >32 µg/mL or ciprofloxacin MIC >0.12 µg/mL) and extended-spectrum cephalosporins (ceftiofur or ceftriaxone MIC >2 µg/mL) during 1996–2004. Of non-Typhi Salmonella, 0.19% (27/14,043) met these criteria: 11 Senftenberg; 6 Typhimurium; 3 Newport; 2 Enteridis; and 1 each Agona, Haifa, Mbandaka, Saintpaul, and Uganda. Twenty-six isolates had gyrA mutations (11 at codon 83 only, 3 at codon 87 only, 12 at both). All Senftenberg isolates had parC mutations (S80I and T57S); 6 others had the T57S mutation. The Mbandaka isolate contained qnrB2. Eight isolates contained bla_CMY-2; 1 Senftenberg contained bla_CMY-23. One Senftenberg and 1Typhimurium isolate contained bla_SHV-12; the Mbandaka isolate contained bla_SHV-30. Nine Senftenberg isolates contained bla_OXA-1; 1 contained bla_OXA-9. Further studies should address patient outcomes, risk factors, and resistance dissemination prevention strategies.

Increase in nalidixic acid resistance among non-Typhi Salmonella enterica isolates in the United States from 1996 to 2003

Fluoroquinolones commonly are used to treat adult Salmonella infections. Fluoroquinolone treatment has failed for persons infected with nalidixic acid-resistant Salmonella. From 1996 to 2003, state public health laboratories forwarded 12,252 non-Typhi Salmonella enterica isolates to the Centers for Disease Control and Prevention for antimicrobial susceptibility testing; 203 (1.6%) of the isolates were nalidixic acid resistant, and 14 (7%) of those were ciprofloxacin resistant. Resistance to nalidixic acid significantly increased from 0.4% in 1996 to 2.3% in 2003. All ciprofloxacin-resistant isolates had at least one point mutation in the quinolone resistance determining region (QRDR) of gyrA and did not harbor qnr or have point mutations in the QRDR of gyrB, parC, or parE. Continued surveillance of antimicrobial resistance among non-Typhi S. enterica isolates is needed to mitigate the increasing prevalence of nalidixic acid resistance.

Enterococcus caccae sp. nov., isolated from human stools

The National Antimicrobial Resistance Monitoring System Laboratory at the Centers for Disease Control and Prevention (CDC) isolated two enterococcus-like strains that were referred to the CDC Streptococcus Laboratory for further identification. The isolates were recovered from human stool samples collected on different occasions from the same individual in Portland (OR, USA) in July 2000. Conventional physiological tests distinguished these strains from all known species of enterococci. Analyses of whole-cell-protein electrophoretic profiles showed the same unique profile for the two isolates, being most similar those of Enterococcus moraviensis and Enterococcus haemoperoxidus albeit not close enough to allow conclusive inclusion in any enterococcal species. Both isolates gave positive results in tests using the AccuProbe Enterococcus genetic probe, and Lancefield extracts reacted with CDC group D antiserum. Comparative 16S rRNA gene sequencing studies also revealed that these strains were closely related to the species E. moraviensis (99.6 % identity). The results of DNA–DNA relatedness experiments confirmed that these strains represented a single novel taxon. The highest level of DNA–DNA relatedness found between the novel taxon and any of the currently recognized species of Enterococcus was 32 %, for both E. moraviensis and E. haemoperoxidus. On the basis of this evidence, it is proposed that these stool isolates constitute a novel species, for which the name Enterococcus caccae sp. nov. is proposed. The type strain is 2215-02T (=SS-1777T=ATCC BAA-1240T=CCUG 51564T).

Plasmid-mediated quinolone resistance in non-Typhi serotypes of Salmonella enterica

BACKGROUND

Serious infections with Salmonella species are often treated with fluoroquinolones or extended-spectrum beta-lactams. Increasingly recognized in Enterobacteriaceae, plasmid-mediated quinolone resistance is encoded by qnr genes. Here, we report the presence of qnr variants in human isolates of non-Typhi serotypes of Salmonella enterica (hereafter referred to as non-Typhi Salmonella) from the United States National Antimicrobial Resistance Monitoring System for Enteric Bacteria.

METHODS

All non-Typhi Salmonella specimens from the United States National Antimicrobial Resistance Monitoring System for Enteric Bacteria collected from 1996 to 2003 with ciprofloxacin minimum inhibitory concentrations > or = 0.06 microg/mL (233 specimens) and a subset with minimum inhibitory concentrations < or = 0.03 microg/mL (102 specimens) were screened for all known qnr genes (A, B, and S) by polymerase chain reaction. For isolates with positive results, qnr and quinolone resistance-determining region sequences were determined. Plasmids containing qnr genes were characterized by conjugation or transformation.

RESULTS

Conjugative plasmids harboring qnrB variants were detected in 7 Salmonella enterica serotype Berta isolates and 1 Salmonella enterica serotype Mbandaka isolate. The S. Mbandaka plasmid also had an extended-spectrum beta -lactamase. Variants of qnrS on nonconjugative plasmids were detected in isolates of Salmonella enterica serotype Anatum and Salmonella enterica serotype Bovismorbificans.

CONCLUSIONS

Plasmid-mediated quinolone resistance appears to be widely distributed, though it is still uncommon in non-Typhi Salmonella isolates from the United States, including strains that are quinolone susceptible by the criteria of the Clinical and Laboratory Standards Institute (formerly the National Committee for Clinical Laboratory Standards). The presence of this gene in non-Typhi Salmonella that causes infection in humans suggests potential for spread through the food supply, which is a public health concern.

Salmonella resistant to extended-spectrum cephalosporins: prevalence and epidemiology

Salmonella resistant to extended-spectrum cephalosporins (ESCs) have emerged worldwide since 1988. By 2004, 43 countries had reported this public health problem. Resistance was mediated by classical extended-spectrum beta-lactamases, plasmid-mediated cephalosporinases, and recently a class A carbapenemase. Of these, CMY-2 is the most widely disseminated enzyme. Salmonella enterica serotype Typhimurium and S. enterica serotype Enteritidis are the most common serovars associated with ESC resistance in human infections. Many outbreaks in humans have been reported, most often among children and neonates. ESC-resistant Salmonella is frequently recovered from animals and food, with poultry as primary food source, suggesting that humans are often infected by these routes.

Beta-lactam resistance and Enterobacteriaceae, United States

Extended-spectrum cephalosporins (ESC) are an important drug class for treating severe Salmonella infections. We screened the human collection from the National Antimicrobial Resistance Monitoring System 2000 for ESC resistance mechanisms. Of non-Typhi Salmonella tested, 3.2% (44/1,378) contained bla_CMY genes. Novel findings included bla_CMY-positive Escherichia coli O157:H7 and a bla_SHV-positive Salmonella isolate. CMY-positive isolates showed a ceftriaxone MIC >2 µg/mL.

The clonal spread of multidrug-resistant non-typhi Salmonella serotypes

Non-typhoid Salmonella are one of the most important organisms causing food-borne diseases worldwide. There have been significant increases in developed countries in recent years in the occurrence of resistance, in particular multidrug resistance phenotypes, in non-typhoid Salmonella spp. Such increases have been observed in many countries, not only within the European community but also the Americas and Southeast Asia. Of particular concern is the increasing detection of Salmonella isolates displaying resistance to key antimicrobials, notably fluoroquinolones and third-generation cephalosporins. An important factor associated with this increase in multidrug resistance among particular Salmonella spp. is the national and international spread of certain clonal genotypes, the most recent being the global epidemic spread of multidrug-resistant S. Typhimurium DT104, since the early 1990s. In this review, we describe examples where particular antimicrobial-resistant Salmonella serotypes emerged, persisted for periods of time, and then quickly decreased in prevalence.

Interpretation of Pulsed-Field Gel Electrophoresis Patterns in Foodborne Disease Investigations and Surveillance

Since the establishment of the well-known Tenover criteria in 1995 (Tenover et al., 1995), relatively few papers have been published about the interpretation of subtyping data generated by pulsed-field gel electrophoresis (PFGE). This paper describes the approach that has been used in the PulseNet network during the past 10 years. PFGE data must always be interpreted in the proper epidemiological context and PFGE data can not alone prove an epidemiological connection. The Tenover criteria are not generally applicable to the interpretation of PFGE subtyping data of foodborne pathogens. The reproducibility of the method with a particular organism, the quality of the PFGE gel, the variability of the organism being subtyped, and the prevalence of the pattern in question must always be considered. Only isolates displaying indistinguishable patterns should be included in the detection of clusters of infections or the initial case definition in a point-source outbreak. More variability (patterns differing from each other in two to three band positions) may be accepted if the outbreak has been going on for some time or if person-person spread is a prominent feature. If epidemiological information is sufficiently strong, isolates with markedly different PFGE patterns may be included in an outbreak.

Surveillance for human Salmonella infections in the United States

Surveillance for human Salmonella infections plays a critical role in understanding and controlling foodborne illness due to Salmonella. Along with its public health partners, the Centers for Disease Control and Prevention (CDC) has several surveillance systems that collect information on Salmonella infections in the United States. The National Salmonella Surveillance System, begun in 1962, receives reports of laboratory-confirmed Salmonella infections through state public health laboratories. Salmonella outbreaks are reported by state and local health departments through the Foodborne Disease Outbreak Reporting System, which became a Web-based, electronic system (eFORS) in 2001. PulseNet facilitates the detection of clusters of Salmonella infections through standardized molecular subtyping (DNA "fingerprinting") of isolates and maintenance of "fingerprint" databases. The National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS) monitors antimicrobial resistance in Salmonella by susceptibility testing of every 20th Salmonella isolate received by state and local public health laboratories. FootNet is an active surveillance system that monitors Salmonella infections in sentinel areas, providing population-based estimates of infection rates. Efforts are underway to electronically link all of the Salmonella surveillance systems at CDC to facilitate optimum use of available data and minimize duplication.

Standardization of Pulsed-Field Gel Electrophoresis Protocols for the Subtyping ofEscherichia coliO157:H7,Salmonella, andShigellafor PulseNet

Standardized rapid pulsed-field gel electrophoresis (PFGE) protocols for the subtyping of Escherichia coli O157:H7, Salmonella serotypes, and Shigella species are described. These protocols are used by laboratories in PulseNet, a network of state and local health departments, and other public health laboratories that perform real-time PFGE subtyping of these bacterial foodborne pathogens for surveillance and outbreak investigations. Development and standardization of these protocols consisted of a thorough optimization of reagents and reaction conditions to ensure that the protocols yielded consistent results and high-quality PFGE pattern data in all the PulseNet participating laboratories. These rapid PFGE protocols are based on the original 3-4-day standardized procedure developed at Centers for Disease Control and Prevention that was validated in 1996 and 1997 by eight independent laboratories. By using these rapid standardized PFGE protocols, PulseNet laboratories are able to subtype foodborne pathogens in approximately 24 h, allowing for the early detection of foodborne disease case clusters and often aiding in the identification of the source responsible for the infections.

Multidrug-resistant Salmonella Typhimurium in four animal facilities

Within each of 4 outbreaks of S. Typhimurium among humans and animals at companion animal care facilities, isolates were identical or nearly identical.

In 1999 and 2000, 3 state health departments reported 4 outbreaks of gastrointestinal illness due to Salmonella enterica serotype Typhimurium in employees, clients, and client animals from 3 companion animal veterinary clinics and 1 animal shelter. More than 45 persons and companion animals became ill. Four independent investigations resulted in the testing of 19 human samples and >200 animal samples; 18 persons and 36 animals were culture-positive for S. Typhimurium. One outbreak was due to multidrug-resistant S. Typhimurium R-type ACKSSuT, while the other 3 were due to multidrug-resistant S. Typhimurium R-type ACSSuT DT104. This report documents nosocomial transmission of S. Typhimurium and demonstrates that companion animal facilities may serve as foci of transmission for salmonellae between animals and humans if adequate precautions are not followed.

Hospitalization and antimicrobial resistance in Salmonella outbreaks, 1984-2002

Few studies have evaluated the health consequences of antimicrobial-resistant Salmonella strains associated with outbreaks. Among 32 outbreaks occurring in the United States from 1984 to 2002, 22% of 13,286 persons in 10 Salmonella-resistant outbreaks were hospitalized, compared with 8% of 2,194 persons in 22 outbreaks caused by pansusceptible Salmonella strains (p<0.01).

Invasive Infection with Multidrug‐ResistantSalmonella entericaSerotype Typhimurium Definitive Type 104 among HIV‐Infected Adults

BACKGROUND

Multidrug-resistant Salmonella enterica serotype Typhimurium definitive type 104 (MRDT104), with resistance to at least ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (R-type ACSSuT), was first detected in the United States in 1985, and the prevalence increased to account for nearly 7% of Salmonella infections in 1998.

METHODS

A retrospective study of S. Typhimurium infections in an urban health care system assessed whether infection with an antibiotic-resistant strain--and specifically MRDT104--was associated with invasive disease or HIV infection. Sixty cases of S. Typhimurium infection were identified.

RESULTS

Of the 50 isolates available for analysis, 30 (60%) were MRDT104. Pathogens were isolated from blood in 25 (83%) of 30 patients infected with MRDT104, compared with 10 (50%) of 20 patients who were infected with non-MRDT104 strains (P = .01). Among isolates obtained from 32 HIV-infected patients, 19 (95%) of 20 MRDT104 isolates were from blood specimens, compared with 8 (66%) of 12 non-MRDT104 isolates (P = .05).

CONCLUSIONS

MRDT104 accounted for the majority of S. Typhimurium infections in this patient population, and MRDT104 infections were more invasive than non-MRDT104 infections, particularly in HIV-infected persons.

Analysis of Salmonella enterica serotype Typhi pulsed-field gel electrophoresis patterns associated with international travel

Typhoid fever is a significant cause of morbidity and mortality worldwide, causing an estimated 16 million cases and 600,000 deaths annually. Although overall rates of the disease have dramatically decreased in the United States, the number of travel-related infections has increased in recent decades. Drug resistance among Salmonella enterica serotype Typhi strains has emerged worldwide, making antimicrobial susceptibility testing an important function in public health laboratories. Pulsed-field gel electrophoresis (PFGE) subtyping of food-borne and waterborne pathogens has proven to be a valuable tool for the detection of outbreaks and laboratory-based surveillance. This retrospective study examined the distribution of PFGE patterns of S. enterica serotype Typhi isolates from patients with a history of international travel. Isolates were collected as part of a passive laboratory-based antimicrobial susceptibility surveillance study. Isolates were PFGE subtyped by using the restriction enzyme XbaI to restrict the total genomic DNA. Isolates indistinguishable with XbaI were further characterized using the restriction enzyme BlnI. A total of 139 isolates were typed, representing travel to 31 countries. Restriction fragment patterns consisted of 14 to 18 fragments ranging in size from 580 to 40 kbp. Seventy-nine unique PFGE patterns were generated using XbaI. Isolates from the same geographic region did not necessarily have similar PFGE patterns. Of the 139 isolates, 46 (33%) were resistant to more than one antimicrobial agent (multidrug resistant [MDR]). Twenty-seven (59%) of 46 MDR isolates had indistinguishable PFGE patterns with both XbaI and BlnI. It appears that MDR S. enterica serotype Typhi has emerged as a predominant clone in Southeast Asia and the Indian subcontinent.

Antimicrobial use in agriculture: controlling the transfer of antimicrobial resistance to humans

Salmonella and Campylobacter infections occur commonly in children. Some of these infections are severe, requiring treatment with antimicrobial agents. Many classes of antimicrobial agents that are used in humans also are used in food animals for growth promotion, disease prevention, and therapy. The use of such antimicrobial agents in food animals increases the likelihood that human bacterial pathogens that have food animal reservoirs, such as Salmonella or Campylobacter, will develop cross-resistance to drugs approved for use in human medicine. Resistance determinants also may be transmitted from food animals to humans through the food supply with bacteria that usually are commensal, such as Escherichia coli and enterococci. Clinicians should be aware that antimicrobial resistance is increasing in food-borne pathogens and that patients who are taking antimicrobial agents for any reason are at increased risk for acquiring antimicrobial-resistant food-borne infections. Several European countries have demonstrated that restricting the use of antimicrobial agents in food animals can be followed by a decrease in antimicrobial resistance in humans without compromising animal health or significantly increasing the cost of production. Appropriate use of antimicrobial agents in humans and food animals is an important factor in maintaining their effectiveness.

Antimicrobial-resistant nontyphoidal Salmonella is associated with excess bloodstream infections and hospitalizations

BACKGROUND

Nontyphoidal Salmonella is a leading cause of foodborne illness. Few studies have explored the health consequences of antimicrobial-resistant Salmonella.

METHODS

The National Antimicrobial Resistance Monitoring System (NARMS) performs susceptibility testing on nontyphoidal Salmonella isolates. The Foodborne Diseases Active Surveillance Network (FoodNet) ascertains outcomes for patients with culture-confirmed Salmonella infection, in 9 states, each of which participates in NARMS. We analyzed the frequency of bloodstream infection and hospitalization among patients with resistant infections. Isolates defined as resistant to a clinically important agent were resistant to 1 or more of the following agents: ampicillin, ceftriaxone, ciprofloxacin, gentamicin, and/or trimethoprim-sulfamethoxazole.

RESULTS

During 1996-2001, NARMS received 7370 serotyped, nontyphoidal Salmonella isolates from blood or stool. Bloodstream infection occurred more frequently among patients infected with an isolate resistant to > or =1 clinically important agent (adjusted odds ratio [OR], 1.6; 95% confidence interval [CI], 1.2-2.1), compared with patients with pansusceptible infection. During 1996-2001, FoodNet staff ascertained outcomes for 1415 patients who had isolates tested in NARMS. Hospitalization with bloodstream infection occurred more frequently among patients infected with an isolate resistant to > or =1 clinically important agent (adjusted OR, 3.1; 95% CI, 1.4-6.6), compared with patients with pansusceptible infection.

CONCLUSIONS

Patients with antimicrobial-resistant nontyphoidal Salmonella infection were more likely to have bloodstream infection and to be hospitalized than were patients with pansusceptible infection. Mitigation of antimicrobial resistance in Salmonella will likely benefit human health.

Vagococcus carniphilus sp. nov., isolated from ground beef

Nine enterococcus-like strains were referred to the Streptococcus Laboratory at the Centers for Disease Control and Prevention (CDC) for further identification from the National Antimicrobial Resistance Monitoring System Laboratory at the CDC. The cultures were isolated from ground beef purchased from retail in Oregon in 2000. Conventional biochemical testing and analysis of whole-cell protein electrophoretic profiles distinguished these strains from known species of enterococci and vagococci. Comparative 16S rRNA gene sequencing studies revealed that these strains were most closely related to the species Vagococcus fluvialis. DNA–DNA reassociation studies confirmed that these nine strains represented a new taxon. The relative binding ratio was 87 % or greater at the optimal temperature, and the divergence was less than 1 % for strains hybridized against the isolate designated the type strain. DNA–DNA relatedness was 25 % to V. fluvialis and 9 % or less to the other three species of Vagococcus. DNA–DNA relatedness was 33 % or less to the 25 currently described species of Enterococcus. On the basis of this evidence, it is proposed that these strains be classified as Vagococcus carniphilus sp. nov. The type strain of V. carniphilus is 1843-02T (=ATCC BAA-640T=CCUG 46823T). The clinical significance (if any) of these strains is yet to be determined.

Multidrug-resistant strains of Salmonella enterica Typhimurium, United States, 1997-1998

To evaluate multidrug-resistant strains of Salmonella enterica serotype Typhimurium, including definitive type 104 (DT104) in the United States, we reviewed data from the National Antimicrobial Resistance Monitoring System (NARMS). In 1997 to 1998, 703 (25%) of 2,767 serotyped Salmonella isolates received at NARMS were S. Typhimurium; antimicrobial susceptibility testing and phage typing were completed for 697. Fifty-eight percent (402) were resistant to > or = 1 antimicrobial agent. Three multidrug-resistant (> or = 5 drugs) strains accounted for (74%) 296 of all resistant isolates. Ceftriaxone resistance was present in 8 (3%), and nalidixic acid resistance in 4 (1%), of these multidrug-resistant strains. By phage typing, 259 (37%) of S. Typhimurium isolates were DT104, 209 (30%) were of undefined type and 103 (15%) were untypable. Fifty percent (202) of resistant (> or = 1 drug) isolates were DT104. Multidrug-resistant S. Typhimurium isolates, particularly DT104, account for a substantial proportion of S. Typhimurium isolates; ceftriaxone resistance is exhibited by some of these strains.

Antimicrobial resistance among Campylobacter strains, United States, 1997-2001

We summarize antimicrobial resistance surveillance data in human and chicken isolates of Campylobacter. Isolates were from a sentinel county study from 1989 through 1990 and from nine state health departments participating in National Antimicrobial Resistance Monitoring System for enteric bacteria (NARMS) from 1997 through 2001. None of the 297 C. jejuni or C. coli isolates tested from 1989 through 1990 was ciprofloxacin-resistant. From 1997 through 2001, a total of 1,553 human Campylobacter isolates were characterized: 1,471 (95%) were C. jejuni, 63 (4%) were C. coli, and 19 (1%) were other Campylobacter species. The prevalence of ciprofloxacin-resistant Campylobacter was 13% (28 of 217) in 1997 and 19% (75 of 384) in 2001; erythromycin resistance was 2% (4 of 217) in 1997 and 2% (8 of 384) in 2001. Ciprofloxacin-resistant Campylobacter was isolated from 10% of 180 chicken products purchased from grocery stores in three states in 1999. Ciprofloxacin resistance has emerged among Campylobacter since 1990 and has increased in prevalence since 1997.

Insertions, deletions, and single-nucleotide polymorphisms at rare restriction enzyme sites enhance discriminatory power of polymorphic amplified typing sequences, a novel strain typing system for Escherichia coli O157:H7

Polymorphic amplified typing sequences (PATS) for Escherichia coli O157:H7 (O157) was previously based on indels containing XbaI restriction enzyme sites occurring in O-island sequences of the O157 genome. This strain-typing system, referred to as XbaI-based PATS, typed every O157 isolate tested in a reproducible, rapid, straightforward, and easy-to-interpret manner and had technical advantages over pulsed-field gel electrophoresis (PFGE). However, the system was less discriminatory than PFGE and was unable to differentiate fully between unrelated isolates. To overcome this drawback, we enhanced PATS by using another infrequently cutting restriction enzyme, AvrII (also known as BlnI), to identify additional polymorphic regions that could increase the discriminatory ability of PATS typing. Referred to as AvrII-based PATS, the system identified seven new polymorphic regions in the O157 genome. Unlike XbaI, polymorphisms involving AvrII sites were caused by both indels and single-nucleotide polymorphisms occurring in O-island and backbone sequences of the O157 genome. AvrII-based PATS by itself provided poor discrimination of the O157 isolates tested. However, when primer pairs amplifying the seven polymorphic AvrII sites were combined with those amplifying the eight polymorphic XbaI sites (combined PATS), the discriminatory power of PATS was enhanced. Combined PATS matched related O157 isolates better than PFGE while differentiating between unrelated isolates. PATS typed every O157 isolate tested and directly targeted polymorphic sequences responsible for differences in the restriction digest patterns of O157 genomic DNA, utilizing PCR rather than relying on gel electrophoresis. This enabled PATS to resolve the ambiguity in PFGE typing, including that arising from the "more distantly related" and "untypeable" profiles.

Prior antimicrobial agent use increases the risk of sporadic infections with multidrug-resistant Salmonella enterica serotype Typhimurium: a FoodNet case-control study, 1996-1997

Several strains of multidrug-resistant (MDR) Salmonella serotype Typhimurium, including MDR S. Typhimurium definitive type 104, cause almost 10% of Salmonella infections among humans in the United States. To determine the risk factors for acquiring sporadic MDR S. Typhimurium infection, we conducted a population-based, case-control study using data from the Foodborne Diseases Active Surveillance Network (FoodNet) during 1996-1997. S. Typhimurium isolates from 5 FoodNet surveillance areas (California, Connecticut, Georgia, Minnesota, and Oregon) were tested for antimicrobial resistance and phage typing. Telephone interviews were conducted with ill persons and matched control subjects. Compared with both control subjects and patients infected with pansensitive strains of S. Typhimurium, patients with MDR S. Typhimurium infection were significantly more likely to have received an antimicrobial agent, particularly an agent to which the Salmonella isolate was resistant, during the 4 weeks preceding illness onset. Prudent antimicrobial agent use among humans and among veterinarians and food-animal producers is necessary to reduce the burden of drug-resistant salmonellosis in humans.

Emergence of Multidrug‐ResistantSalmonella entericaSerotype Newport Infections Resistant to Expanded‐Spectrum Cephalosporins in the United States

We describe a field investigation in New England that identified the emergence and epidemiology of new strains of multidrug-resistant Salmonella, Newport-MDRAmpC, and summarize the Center for Disease Control and Prevention's surveillance data for these infections. In Massachusetts, the prevalence of Newport-MDRAmpC among Salmonella serotype Newport isolates obtained from humans increased from 0% (0/14) in 1998 to 53% (32/60) in 2001 (P<.001). In a retrospective case-control study, infection with Newport-MDRAmpC was domestically acquired and was associated with exposure to a dairy farm. Isolates from both humans and cattle had indistinguishable or closely related antibiograms and pulsed-field gel electrophoresis patterns. Nationally, the prevalence of ceftriaxone-resistant Salmonella increased from 0.5% in 1998 to 2.4% in 2001; 85% of the isolates in 2001 were Newport-MDRAmpC, and at least 27 states have isolated these strains from humans, cattle, or ground beef. These data document the widespread emergence of Newport-MDRAmpC strains in the United States and show that the 5-fold increase in the prevalence of Salmonella resistant to expanded-spectrum cephalosporins, between 1998 and 2001, is primarily due to the emergence of Newport-MDRAmpC strains.

Reevaluating fluoroquinolone breakpoints for Salmonella enterica serotype Typhi and for non-Typhi salmonellae

Salmonella enterica infections cause considerable morbidity and mortality worldwide. Antimicrobial therapy may be life-saving for patients with extraintestinal infections with S. enterica serotype Typhi or non-Typhi salmonellae. Because antimicrobial resistance to several classes of traditional first-line drugs has emerged in the past several decades, the quinolone antimicrobial agents, particularly the fluoroquinolones, have become the drugs of choice. Recently, resistance to nalidixic acid has emerged among both Typhi and non-Typhi Salmonella serotypes. Such Salmonella isolates typically also have decreased susceptibility to fluoroquinolones, although minimum inhibitory concentrations of the fluoroquinolones usually are within the susceptible range of the interpretive criteria of the NCCLS. A growing body of clinical and microbiological evidence indicates that such nalidixic acid-resistant S. enterica infections also exhibit a decreased clinical response to fluoroquinolones. In this article, we recommend that laboratories test extraintestinal Salmonella isolates for nalidixic acid resistance, we recommend that short-course fluoroquinolone therapy be avoided for infection with nalidixic acid-resistant extraintestinal salmonellae, and we summarize existing data and data needs that would contribute to reevaluation of the current NCCLS fluoroquinolone breakpoints for salmonellae.

Characterization of plasmids carrying CMY-2 from expanded-spectrum cephalosporin-resistant Salmonella strains isolated in the United States between 1996 and 1998

Sequencing of DNA from 15 expanded-spectrum cephalosporin (e.g., ceftriaxone)-resistant Salmonella isolates obtained in the United States revealed that resistance to ceftriaxone in all isolates was mediated by cmy-2. Hybridization patterns revealed three plasmid structures containing cmy-2 in these 15 isolates. These data suggest that the spread of cmy-2 among Salmonella strains is occurring through mobilization of the cmy-2 gene into different plasmid backbones and consequent horizontal transfer by conjugation.

Salmonella enterica serotype Typhimurium DT104 isolated from humans, United States, 1985, 1990, and 1995

First isolated from an ill person in 1985, multidrug-resistant Salmonella enterica serotype Typhimurium DT104 emerged in the mid-1990s as a strain of Salmonella frequently isolated from humans in the United States. We compared the integron content, plasmid profile, and XbaI pulsed-field gel electrophoresis (PFGE) patterns of multidrug-resistant S. Typhimurium DT104 (MR-DT104) isolated from humans in the United States in 1985, 1990, and 1995. All isolates contained a 60-mDa plasmid and had indistinguishable PFGE and integron profiles, supporting the idea of a clonal relationship between recent and historical isolates. The data suggest that the widespread emergence of MR-DT104 in humans and animals in the 1990s may have been due to the dissemination of a strain already present in the United States rather than the introduction of a new strain.

Polymorphic amplified typing sequences provide a novel approach to Escherichia coli O157:H7 strain typing

Escherichia coli O157:H7 (O157) strains are commonly typed by pulsed-field gel electrophoresis (PFGE) following digestion of genomic DNA with the restriction enzyme XbaI. We have shown that O157 strains differ from each other by a series of discrete insertions or deletions, some of which contain recognition sites for XbaI, suggesting that these insertions and deletions are responsible for the differences in PFGE patterns. We have devised a new O157 strain typing protocol, polymorphic amplified typing sequences (PATS), based on this information. We designed PCR primer pairs to amplify genomic DNA flanking each of 40 individual XbaI sites in the genomes of two O157 reference strains. These primer pairs were tested with 44 O157 isolates, 2 each from 22 different outbreaks of infection. Thirty-two primer pairs amplified identical fragments from all 44 isolates, while eight primer pairs amplified regions that were polymorphic between isolates. The isolates could be differentiated solely on the basis of which of the eight polymorphic amplicons was detected. PATS correctly identified 21 of 22 outbreak pairs as being identical or highly related, whereas PFGE correctly identified 14 of the 22 outbreak pairs as being identical or highly related; PATS was also able to type isolates from three outbreaks that were untypeable by PFGE. However, PATS was less sensitive than PFGE in discriminating between outbreaks. These data suggest that typing by PATS may provide a simple procedure for strain typing of O157 and other bacteria and that further evaluation of the utility of this method for epidemiologic investigations is warranted.

Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms

Escherichia coli O157:H7 (O157) strains demonstrate varied pulsed-field gel electrophoresis patterns following XbaI digestion, which enable epidemiological surveillance of this important human pathogen. The genetic events underlying PFGE differences between strains, however, are not defined. We investigated the mechanisms for strain variation in O157 by recovering and examining nucleotide sequences flanking each of the XbaI restriction enzyme sites in the genome. Our analysis demonstrated that differences between O157 strains were due to discrete insertions or deletions that contained the XbaI sites polymorphic between strains rather than single-nucleotide polymorphisms in the XbaI sites themselves. These insertions and deletions were found to be uniquely localized within the regions of the genome that are specific to O157 compared to E. coli K-12 (O islands), suggesting that strain-to-strain variation occurs in these O islands. These results may be utilized to devise novel strain-typing tools for this pathogen.

Increased myocardial Rab GTPase expression: a consequence and cause of cardiomyopathy

The Ras-like Rab GTPases regulate vesicle transport in endocytosis and exocytosis. We found that cardiac Rabs1, 4, and 6 are upregulated in a dilated cardiomyopathy model overexpressing beta(2)-adrenergic receptors. To determine if increased Rab GTPase expression can contribute to cardiomyopathy, we transgenically overexpressed in mouse hearts prototypical Rab1a, the small G protein that regulates vesicle transport from endoplasmic reticulum to and through Golgi. In multiple independent mouse lines, Rab1a overexpression caused cardiac hypertrophy that progressed in a time- and transgene dose-dependent manner to heart failure. Isolated cardiac myocytes were hypertrophied and exhibited contractile depression with impaired calcium reuptake. Ultrastructural analysis revealed enlarged Golgi stacks and increased transitional vesicles in ventricular myocytes, with increased secretory atrial natriuretic peptide granules and degenerative myelin figures in atrial myocytes; immunogold studies localized Rab1a to these abnormal vesicular structures. A survey of hypertrophy signaling molecules revealed increased protein kinase C (PKC) alpha and delta, and confocal microscopy showed abnormal subcellular distribution of PKCalpha in Rab1a transgenics. These results indicate that increased expression of Rab1 GTPase in myocardium distorts subcellular localization of proteins and is sufficient to cause cardiac hypertrophy and failure.

Expression of estrogen receptor isoforms alpha and beta messenger RNA in vaginal tissue of premenopausal and postmenopausal women

OBJECTIVE

To determine the messenger RNA expression patterns of estrogen receptor (ER)alpha and ER beta in human vaginal tissue.

STUDY DESIGN

Reverse transcriptase-polymerase chain reaction was performed on tissue samples of 75 patients having anterior colporrhaphy (25 premenopausal, 25 postmenopausal receiving estrogen replacement therapy [ERT], 25 postmenopausal not receiving ERT). Levels of mRNA were normalized and ratios were calculated to assess relative levels of expression.

RESULTS

All samples showed expression of the ER alpha isoform. Significant differences existed in ER alpha expression among the 3 cohorts (P =.023). Greater differences (P <.001) existed in ER beta expression. For both isoforms, the premenopausal group had the highest level, and the postmenopausal group receiving ERT had the lowest level. No significant difference in ER beta expression existed between postmenopausal groups.

CONCLUSION

Significant differences exist between premenopausal and postmenopausal women in presence and expression of ER alpha and ER beta in vaginal tissue. Expression of ER beta markedly declines in menopause, regardless of ERT use.

Rapid pulsed-field gel electrophoresis protocol for subtyping of Campylobacter jejuni

We developed a rapid pulsed-field gel electrophoresis (PFGE) protocol for subtyping Campylobacter isolates based on the standardized protocols used by PulseNet laboratories for the subtyping of other food-borne bacterial pathogens. Various combinations of buffers, reagents, reaction conditions (e.g., cell suspension concentration, lysis time, lysis temperature, and restriction enzyme concentration), and electrophoretic parameters were evaluated in an effort to devise a protocol that is simple, rapid, and robust. PFGE analysis of Campylobacter isolates can be completed in 24 to 30 h using this protocol, whereas the most widely used current protocols require 3 to 4 days to complete. Comparison of PFGE patterns obtained in six laboratories showed that subtyping results obtained using this protocol are highly reproducible.

The United States National Prospective Hemolytic Uremic Syndrome Study: microbiologic, serologic, clinical, and epidemiologic findings

The frequency of Shiga toxin-producing Escherichia coli (STEC) serotypes associated with postdiarrheal hemolytic uremic syndrome (HUS) cases among children and adults in the United States and the proportion with IgM or IgG lipopolysaccharide antibodies to E. coli O157 were determined by use of a nationwide sample from January 1987 through December 1991. Among 83 patients, STEC were isolated from 30 (43%) of 70 whose stool cultures yielded bacterial growth (25 E. coli O157 isolates and 5 non-O157 STEC isolates). Fifty-three (80%) of 66 patients with serum samples had positive O157 lipopolysaccharide antibody titers. Of the 83 patients, 60 (72%) had evidence of STEC infection, including 6 of 8 adults whose illnesses also met criteria for thrombotic thrombocytopenic purpura. Data from a subset of patients suggest that E. coli O157 was the cause of > or = 80% of the STEC infections. All 3 women who were postpartum had evidence of E. coli O157 infection. STEC infection should be considered the likely cause for all persons with postdiarrheal HUS.

PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States

PulseNet, the national molecular subtyping network for foodborne disease surveillance, was established by the Centers for Disease Control and Prevention and several state health department laboratories to facilitate subtyping bacterial foodborne pathogens for epidemiologic purposes. PulseNet, which began in 1996 with 10 laboratories typing a single pathogen (Escherichia coli O157:H7), now includes 46 state and 2 local public health laboratories and the food safety laboratories of the U.S. Food and Drug Administration and the U.S. Department of Agriculture. Four foodborne pathogens (E. coli O157:H7; nontyphoidal Salmonella serotypes, Listeria monocytogenes and Shigella) are being subtyped, and other bacterial, viral, and parasitic organisms will be added soon.