Sensitivity of Warm-Water Fishes and Rainbow Trout to Selected Contaminants.

Guidelines for developing water quality standards allow U.S. states to exclude toxicity data for the family Salmonidae (trout and salmon) when deriving guidelines for warm-water habitats. This practice reflects the belief that standards based on salmonid data may be overprotective of toxic effects on other fish taxa. In acute tests with six chemicals and eight fish species, the salmonid, Rainbow Trout (Oncorhynchus mykiss), was the most sensitive species tested with copper, zinc, and sulfate, but warm-water species were most sensitive to nickel, chloride, and ammonia. Overall, warm-water fishes, including sculpins (Cottidae) and sturgeons (Acipenseridae), were about as sensitive as salmonids in acute tests and in limited chronic testing with Lake Sturgeon (Acipenser fulvescens) and Mottled Sculpin (Cottus bairdi). In rankings of published acute values, invertebrate taxa were most sensitive for all six chemicals tested and there was no trend for greater sensitivity of salmonids compared to warm-water fish.

Metagenomic Approaches for Public Health Surveillance of Foodborne Infections: Opportunities and Challenges.

Foodborne disease surveillance in the United States is at a critical point. Clinical and diagnostic laboratories are using culture-independent diagnostic tests (CIDTs) to identify the pathogen causing foodborne illness from patient specimens. CIDTs are molecular tests that allow doctors to rapidly identify the bacteria causing illness within hours. CIDTs, unlike previous gold standard methods such as bacterial culture, do not produce an isolate that can be subtyped as part of the national molecular subtyping network for foodborne disease surveillance, PulseNet. Without subtype information, cases can no longer be linked using molecular data to identify potentially related cases that are part of an outbreak. In this review, we discuss the public health needs for a molecular subtyping approach directly from patient specimen and highlight different approaches, including amplicon and shotgun metagenomic sequencing.

Interpretation of Whole-Genome Sequencing for Enteric Disease Surveillance and Outbreak Investigation.

The routine use of whole-genome sequencing (WGS) as part of enteric disease surveillance is substantially enhancing our ability to detect and investigate outbreaks and to monitor disease trends. At the same time, it is revealing as never before the vast complexity of microbial and human interactions that contribute to outbreak ecology. Since WGS analysis is primarily used to characterize and compare microbial genomes with the goal of addressing epidemiological questions, it must be interpreted in an epidemiological context. In this article, we identify common challenges and pitfalls encountered when interpreting sequence data in an enteric disease surveillance and investigation context, and explain how to address them.

Salmonella epidemiology: A whirlwind of change.

The field of infectious disease epidemiology for Salmonella and other enteric pathogens is undergoing some of the most profound changes since the time of Kauffman and White. Rapid advances in "big data" technologies such as genomics and metagenomics are making it possible to monitor and control salmonellosis in new and exciting ways. Epidemiological methods are becoming increasingly robust through the routine use of standardized hypothesis-generating questionnaires, iterative open-ended interviewing, informational trace-backs and new modeling techniques for describing the attribution of disease to food sources. In addition, Salmonella epidemiology is facing important challenges and new opportunities due to the rapid adoption of culture independent diagnostic test panels by clinical laboratories. Where is this unprecedented wave of change taking us? This chapter will examine emerging trends in Salmonella epidemiology, and take a peek into the not-so-distant future.

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation.

Listeria monocytogenes (Lm) causes severe foodborne illness (listeriosis). Previous molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), were critical in detecting outbreaks that led to food safety improvements and declining incidence, but PFGE provides limited genetic resolution. A multiagency collaboration began performing real-time, whole-genome sequencing (WGS) on all US Lm isolates from patients, food, and the environment in September 2013, posting sequencing data into a public repository. Compared with the year before the project began, WGS, combined with epidemiologic and product trace-back data, detected more listeriosis clusters and solved more outbreaks (2 outbreaks in pre-WGS year, 5 in WGS year 1, and 9 in year 2). Whole-genome multilocus sequence typing and single nucleotide polymorphism analyses provided equivalent phylogenetic relationships relevant to investigations; results were most useful when interpreted in context of epidemiological data. WGS has transformed listeriosis outbreak surveillance and is being implemented for other foodborne pathogens.

Survival and Growth of Freshwater Pulmonate and Nonpulmonate Snails in 28-Day Exposures to Copper, Ammonia, and Pentachlorophenol.

We performed toxicity tests with two species of pulmonate snails (Lymnaea stagnalis and Physa gyrina) and four taxa of nonpulmonate snails in the family Hydrobiidae (Pyrgulopsis robusta, Taylorconcha serpenticola, Fluminicola sp., and Fontigens aldrichi). Snails were maintained in static-renewal or recirculating culture systems with adults removed periodically to isolate cohorts of offspring for toxicity testing. This method successfully produced offspring for both species of pulmonate snails and for two hydrobiid species, P. robusta and Fluminicola sp. Toxicity tests were performed for 28 days with copper, ammonia, and pentachlorophenol in hard reconstituted water with endpoints of survival and growth. Tests were started with 1-week-old L. stagnalis, 2-week-old P. gyrina, 5- to 13-week-old P. robusta and Fluminicola sp., and older juveniles and adults of several hydrobiid species. For all three chemicals, chronic toxicity values for pulmonate snails were consistently greater than those for hydrobiid snails, and hydrobiids were among the most sensitive taxa in species sensitivity distributions for all three chemicals. These results suggest that the toxicant sensitivity of nonpulmonate snails in the family Hydrobiidae would not be adequately represented by results of toxicity testing with pulmonate snails.

Effect of Culture-Independent Diagnostic Tests on Future Emerging Infections Program Surveillance.

The Centers for Disease Control and Prevention Emerging Infections Program (EIP) network conducts population-based surveillance for pathogens of public health importance. Central to obtaining estimates of disease burden and tracking microbiological characteristics of these infections is accurate laboratory detection of pathogens. The use of culture-independent diagnostic tests (CIDTs) in clinical settings presents both opportunities and challenges to EIP surveillance. Because CIDTs offer better sensitivity than culture and are relatively easy to perform, their use could potentially improve estimates of disease burden. However, changes in clinical testing practices, use of tests with different sensitivities and specificities, and changes to case definitions make it challenging to monitor trends. Isolates are still needed for performing strain typing, antimicrobial resistance testing, and identifying other molecular characteristics of organisms. In this article, we outline current and future EIP activities to address issues associated with adoption of CIDTs, which may apply to other public health surveillance.

Bacterial enteric infections detected by culture-independent diagnostic tests--FoodNet, United States, 2012-2014.

The increased availability and rapid adoption of culture-independent diagnostic tests (CIDTs) is moving clinical detection of bacterial enteric infections away from culture-based methods. These new tests do not yield isolates that are currently needed for further tests to distinguish among strains or subtypes of Salmonella, Campylobacter, Shiga toxin-producing Escherichia coli, and other organisms. Public health surveillance relies on this detailed characterization of isolates to monitor trends and rapidly detect outbreaks; consequently, the increased use of CIDTs makes prevention and control of these infections more difficult. During 2012-2013, the Foodborne Diseases Active Surveillance Network (FoodNet*) identified a total of 38,666 culture-confirmed cases and positive CIDT reports of Campylobacter, Salmonella, Shigella, Shiga toxin-producing E. coli, Vibrio, and Yersinia. Among the 5,614 positive CIDT reports, 2,595 (46%) were not confirmed by culture. In addition, a 2014 survey of clinical laboratories serving the FoodNet surveillance area indicated that use of CIDTs by the laboratories varied by pathogen; only CIDT methods were used most often for detection of Campylobacter (10%) and STEC (19%). Maintaining surveillance of bacterial enteric infections in this period of transition will require enhanced surveillance methods and strategies for obtaining bacterial isolates.

An outbreak of foodborne illness among attendees of a wedding reception in Wisconsin likely caused by Arcobacter butzleri.

BACKGROUND: Arcobacter species, primarily Arcobacter butzleri, are widely distributed among animals, infrequently isolated from humans, and previously not associated with outbreaks of foodborne illness. We report results of an investigation of a foodborne outbreak that occurred among attendees of a wedding reception in Wisconsin, United States, and was likely caused by A. butzleri. METHODS: We conducted a case-control study among reception attendees and a laboratory investigation to determine the extent, source, and cause of the outbreak. A clinical case was defined as diarrhea in an attendee with illness onset ≤7 days following the wedding reception. RESULTS: The case-control study included 47 of 51 case patients and 43 non-ill attendees. Results demonstrated that consuming broasted chicken was the only factor significantly associated with illness (odds ratio 10.51; 95% confidence interval 1.28, 476.4). Five patients provided stool specimens. Comprehensive culture and polymerase chain reaction (PCR) testing did not detect common bacterial or viral pathogens. Subsequent testing with PCRs targeting 16S/23S rDNA of the three most clinically relevant Arcobacter spp. and the rpoB/C gene of A. butzleri provided products confirmed as A. butzleri (four patients) and A. cryaerophilus (one patient) by sequence analysis. CONCLUSIONS: The results of this investigation suggest that A. butzleri should be considered an agent that can cause outbreaks of foodborne illness. Rigorous investigation of outbreaks of undetermined etiology is valuable for incrementally increasing our understanding of emerging agents causing foodborne illnesses.

Laboratory Criteria for Exclusion and Readmission of Potentially Infectious Persons in Sensitive Settings in the Age of Culture-Independent Diagnostic Tests: Report of a Multidisciplinary Workgroup.

Culture-independent diagnostic tests (CIDTs) are increasingly used for clinical diagnosis of gastrointestinal diseases such as salmonellosis, Shiga toxin-producing E. coli disease, and shigellosis because of their speed, convenience, and generally high-performance characteristics. These tests are also used to screen potentially infectious asymptomatic persons during outbreak investigations in sensitive settings such as childcare, food service, and healthcare. However, only limited performance data are available for CIDTs used on specimens from asymptomatic persons. The Association of Public Health Laboratories (APHL) and Council of State and Territorial Epidemiologists (CSTE) convened a workgroup to examine the available scientific data to inform interim decision-making related to exclusion and readmission criteria for potentially infectious persons in sensitive settings, the risks and benefits of different testing strategies, and to identify knowledge gaps for further research. This is the report on the Workgroup findings.

An assessment of the relation between metal contaminated sediment and freshwater mussel populations in the Big River, Missouri.

The Big River in southeast Missouri drains the largest historical lead mining area in the United States. Ongoing releases of metal contaminated sediments into this river are well documented and are suspected of suppressing freshwater mussel populations. We characterized the spatial extent of metal contaminated sediments and evaluated its relationship with mussel populations in the Big River. Mussels and sediments were collected at 34 sites with potential metal effects and 3 reference sites. Analysis of sediment samples showed that lead (Pb) and zinc (Zn) concentrations were 1.5 to 65 times greater than background concentrations in the reach extending 168 km downstream from Pb mining releases. Mussel abundance decreased acutely downstream from these releases where sediment Pb concentrations were highest and increased gradually as Pb sediment concentrations attenuated downstream. We compared current species richness with historical survey data from three reference rivers with similar physical habitat characteristics and human effects, but without Pb-contaminated sediment. Big River species richness was on average about one-half that expected based on reference stream populations and was 70-75 % lower in reaches with high median Pb concentrations. Sediment Zn and cadmium, and particularly Pb, had significant negative correlations with species richness and abundance. The association of sediment Pb concentrations with mussel community metrics in otherwise high-quality habitat indicates that Pb toxicity is likely responsible for depressed mussel populations observed within the Big River. We used concentration-response regressions of mussel density verses sediment Pb to determine that the Big River mussel community is adversely affected when sediment Pb concentrations are above 166 ppm, the concentration associated with 50 % decreases in mussel density. Based on this assessment of metals concentrations sediment and mussel fauna, our findings indicate that sediment in approximately 140 km of the Big River with suitable habitat has a toxic effect to mussels.

Impacts of culture-independent diagnostic practices on public health surveillance for bacterial enteric pathogens.

For decades, culture has been the mainstay of diagnostic testing for bacterial enteric pathogens. This paradigm is changing as clinical laboratories adopt culture-independent methods, such as antigen-based tests and nucleic acid-based assays. Public health surveillance for enteric infections addresses 4 interrelated but distinct objectives: case investigation for localized disease control; assessment of disease burden and trends to prioritize and assess impact of population-based control measures; outbreak detection; and microbiologic characterization to improve understanding of pathogens, their virulence mechanisms, and epidemiology. We summarize the challenges and opportunities that culture-independent tests present and suggest strategies, such as validation studies and development of culture-independent tests compatible with subtyping, that could be adopted to ensure that surveillance remains robust. Many of these approaches will require time and resources to implement, but they will be necessary to maintain a strong surveillance system. Public health practitioners must clearly explain the value of surveillance, especially how outbreak detection benefits the public, and collaborate with all stakeholders to develop solutions.

Sapovirus outbreaks in long-term care facilities, Oregon and Minnesota, USA, 2002-2009.

We tested fecal samples from 93 norovirus-negative gastroenteritis outbreaks; 21 outbreaks were caused by sapovirus. Of these, 71% were caused by sapovirus genogroup IV and 66% occurred in long-term care facilities. Future investigation of gastroenteritis outbreaks should include multi-organism testing.

Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent in enteric infections.

A new species of parvovirus, tentatively named human bocavirus 4 (HBoV4), was genetically characterized. Among 641 feces samples obtained from children and adults, the most commonly detected bocavirus species were, in descending order, HBoV2, HBoV3, HBoV4, and HBoV1, with an HBoV2 prevalence of 21% and 26% in Nigerian and Tunisian children, respectively. HBoV3 or HBoV4 species were found in 12 of 192 patients with non-polio acute flaccid paralysis in Tunisia and Nigeria and 0 of 96 healthy Tunisian contacts (P = .01). Evidence of extensive recombination at the NP1 and VP1 gene boundary between and within bocavirus species was found. The high degree of genetic diversity seen among the human bocaviruses found in feces specimens, relative to the highly homogeneous HBoV1, suggest that this worldwide-distributed respiratory pathogen may have recently evolved from an enteric bocavirus after acquiring an expanded tropism favoring the respiratory tract. Elucidating the possible role of the newly identified enteric bocaviruses in human diseases, including acute flaccid paralysis and diarrhea, will require further epidemiological studies.

Modeling the Bioavailability of Nickel and Zinc to Ceriodaphnia dubia and Neocloeon triangulifer in Toxicity Tests with Natural Waters.

We studied biotic ligand model (BLM) predictions of the toxicity of nickel (Ni) and zinc (Zn) in natural waters from Illinois and Minnesota, USA, which had combinations of pH, hardness, and dissolved organic carbon (DOC) more extreme than 99.7% of waters in a nationwide database. We conducted 7-day chronic tests with Ceriodaphnia dubia and 96-hour acute and 14-day chronic tests with Neocloeon triangulifer and estimated median lethal concentrations and 20% effect concentrations for both species. Toxicity of Ni and Zn to both species differed among test waters by factors from 8 (Zn tests with C. dubia) to 35 (Zn tests with N. triangulifer). For both species and metals, tests with Minnesota waters (low pH and hardness, high DOC) showed lower toxicity than Illinois waters (high pH and high hardness, low DOC). Recalibration of the Ni BLM to be more responsive to pH-related changes improved predictions of Ni toxicity, especially for C. dubia. For the Zn BLM, we compared several input data scenarios, which generally had minor effects on model performance scores (MPS). A scenario that included inputs of modeled dissolved inorganic carbon and measured Al and Fe(III) produced the highest MPS values for tests with both C. dubia and N. triangulifer. Overall, the BLM framework successfully modeled variation in toxicity for both Zn and Ni across wide ranges of water chemistry in tests with both standard and novel test organisms. Environ Toxicol Chem 2021;40:3049-3062. © 2021 SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

A novel picornavirus associated with gastroenteritis.

A novel picornavirus genome was sequenced, showing 42.6%, 35.2%, and 44.6% of deduced amino acid identities corresponding to the P1, P2, and P3 regions, respectively, of the Aichi virus. Divergent strains of this new virus, which we named salivirus, were detected in 18 stool samples from Nigeria, Tunisia, Nepal, and the United States. A statistical association was seen between virus shedding and unexplained cases of gastroenteritis in Nepal (P = 0.0056). Viruses with approximately 90% nucleotide similarity, named klassevirus, were also recently reported in three cases of unexplained diarrhea from the United States and Australia and in sewage from Spain, reflecting a global distribution and supporting a pathogenic role for this new group of picornaviruses.

The role, challenges, and support of pulsenet laboratories in detecting foodborne disease outbreaks.

In recent years, there have been several high-profile nationwide foodborne outbreaks due to enteric organisms in food products, including Salmonella Typhimurium in peanut products, Salmonella Saintpaul in peppers, and Escherichia coli O157:H7 in spinach. PulseNet, the national molecular subtyping network for foodborne disease surveillance, played a key role in detecting each of these outbreaks. PulseNet laboratories use bacterial subtyping methods to rapidly detect clusters of foodborne disease, which are often the first indication that an outbreak is occurring. Rapid outbreak detection reduces ongoing transmission through product recalls, restaurant closures, and other mechanisms. By greatly increasing the sensitivity of outbreak detection, PulseNet allows us to identify and correct problems with our food production and distribution systems that would not otherwise have come to our attention. Annually, millions of potentially preventable cases of foodborne illness result in billions of dollars in lost productivity and health-care expenses. We describe the critical role PulseNet laboratories play in the detection of foodborne outbreaks and discuss current challenges and potential improvements for PulseNet laboratories to more rapidly identify future foodborne outbreaks.

A macroinvertebrate assessment of Ozark streams located in lead-zinc mining areas of the Viburnum Trend in southeastern Missouri, USA.

The Viburnum Trend lead-zinc mining subdistrict is located in the southeast Missouri portion of the Ozark Plateau. In 2003 and 2004, we assessed the ecological effects of mining in several watersheds in the region. We included macroinvertebrate surveys, habitat assessments, and analysis of metals in sediment, pore water, and aquatic biota. Macroinvertebrates were sampled at 21 sites to determine aquatic life impairment status (full, partial, or nonsupport) and relative biotic condition scores. Macroinvertebrate biotic condition scores were significantly correlated with cadmium, nickel, lead, zinc, and specific conductance in 2003 (r = -0.61 to -0.68) and with cadmium, lead, and pore water toxic units in 2004 (r = -0.55 to -0.57). Reference sites were fully supporting of aquatic life and had the lowest metals concentrations and among the highest biotic condition scores in both years. Sites directly downstream from mining and related activities were partially supporting, with biotic condition scores 10% to 58% lower than reference sites. Sites located greater distances downstream from mining activities had intermediate scores and concentrations of metals. Results indicate that elevated concentrations of metals originating from mining activities were the underlying cause of aquatic life impairment in several of the streams studied. There was general concurrence among the adversely affected sites in how the various indicators responded to mining activities during the overall study.

Influence of remediation on sediment toxicity within the Grand Calumet River, Indiana, USA.

The Grand Calumet River (GCR), located in northern Indiana, is contaminated due to a wide range of historical industrial activities. This study was conducted to determine the influence of sediment remediation within the GCR on concentrations of chemical contaminants and toxicity to sediment-dwelling organisms. Between 2005 and 2016, sediments with high concentrations of metals and toxic organic compounds were remediated through a combination of removal, addition of activated carbon and organoclay amendments, and capping with sand or relatively uncontaminated sediment. Short-term and long-term sediment toxicity tests with the amphipod Hyalella azteca, the midge Chironomus dilutus, and the mussel Lampsilis siliquoidea were conducted with samples collected in 2013, 2015, and 2017, from 29 sites, including both remediated and non-remediated sites. Sediment chemistry and toxicity data for three groups of remediated sites (US Steel, West Branch, and East Branch) were compared to samples from contaminated but unremediated sites and to relatively uncontaminated reference sites. In general, remediated sediments had lower levels of PAHs, PCBs and metals, although sediments from the US Steel area still had elevated levels of PAH, PCB and chromium. Sediments from the three remediated sites and from reference sites showed significantly reduced toxic effects in short-term sediment bioassays, compared to unremediated sites. Variation in the long-term success of remediation may reflect site-specific factors such as the type of remediation and the potential for recontamination from uncontrolled sources.

Characteristics of O157 versus non-O157 Shiga toxin-producing Escherichia coli infections in Minnesota, 2000-2006.

BACKGROUND: Escherichia coli O157:H7 (O157) is the Shiga toxin-producing E. coli (STEC) serotype most frequently isolated and most often associated with hemolytic uremic syndrome (HUS) in the United States. Non-O157 STEC serotypes can also cause serious illness, but their impact as pathogens remains undefined. We compared characteristics of non-O157 and O157 STEC infections identified through sentinel surveillance. METHODS: Sentinel sites included a metropolitan health maintenance organization laboratory and a hospital laboratory serving a small city and rural area. We received sorbitol-MacConkey agar plates from every stool culture performed at both sites during 2000-2006. Colony sweeps were screened for stx1 and stx2 by polymerase chain reaction. E. coli identity, serotype, and presence of stx1 and/or stx2 were confirmed on individual isolates. RESULTS: Two hundred six STEC isolates were identified: 108 (52%) were non-O157 serotypes, and 98 (48%) were O157. Of non-O157 cases, 54% involved bloody diarrhea, and 8% involved hospitalization. Non-O157 isolates with at least stx2 were not more likely to cause severe illness (bloody diarrhea, hospitalization, or HUS) than were non-O157 isolates with only stx1. O157 cases were more likely than non-O157 cases to involve bloody diarrhea (78% vs 54%; P < .001), hospitalization (34% vs 8%; P < .001 and HUS (7% vs 0%; P = .005). When including only isolates with at least stx2, O157 cases were still more likely to involve bloody diarrhea (78% vs 56%; P = .02) and hospitalization (33% vs 12%; P = .01) than non-O157 cases. CONCLUSIONS: Differences in severity among STEC infections could not be explained by stx2, suggesting that additional factors are important in STEC virulence.