The etiology of severe acute gastroenteritis among adults visiting emergency departments in the United States.

BACKGROUND: Acute gastroenteritis (AGE) remains a common cause of clinic visits and hospitalizations in the United States, but the etiology is rarely determined. METHODS: We performed a prospective, multicenter emergency department-based study of adults with AGE. Subjects were interviewed on presentation and 3-4 weeks later. Serum samples, rectal swab specimens, and/or whole stool specimens were collected at presentation, and serum was collected 3-4 weeks later. Fecal specimens were tested for a comprehensive panel of viral, bacterial, and parasitic pathogens; serum was tested for calicivirus antibodies. RESULTS: Pathogens were detected in 25% of 364 subjects, including 49% who provided a whole stool specimen. The most commonly detected pathogens were norovirus (26%), rotavirus (18%), and Salmonella species (5.3%). Pathogens were detected significantly more often from whole stool samples versus a rectal swab specimen alone. Nine percent of subjects who provided whole stool samples had >1 pathogen identified. CONCLUSIONS: Viruses, especially noroviruses, play a major role as agents of severe diarrhea in adults. Further studies to confirm the unexpectedly high prevalence of rotaviruses and to explore the causes of illness among patients from whom a pathogen cannot be determined are needed. Studies of enteric pathogens should require the collection of whole stool samples.

Multidrug-resistant typhoid fever with neurologic findings on the Malawi-Mozambique border.

BACKGROUND: Salmonella enterica serovar Typhi causes an estimated 22 million cases of typhoid fever and 216 000 deaths annually worldwide. We investigated an outbreak of unexplained febrile illnesses with neurologic findings, determined to be typhoid fever, along the Malawi-Mozambique border. METHODS: The investigation included active surveillance, interviews, examinations of ill and convalescent persons, medical chart reviews, and laboratory testing. Classification as a suspected case required fever and ≥1 other finding (eg, headache or abdominal pain); a probable case required fever and a positive rapid immunoglobulin M antibody test for typhoid (TUBEX TF); a confirmed case required isolation of Salmonella Typhi from blood or stool. Isolates underwent antimicrobial susceptibility testing and subtyping by pulsed-field gel electrophoresis (PFGE). RESULTS: We identified 303 cases from 18 villages with onset during March-November 2009; 214 were suspected, 43 were probable, and 46 were confirmed cases. Forty patients presented with focal neurologic abnormalities, including a constellation of upper motor neuron signs (n = 19), ataxia (n = 22), and parkinsonism (n = 8). Eleven patients died. All 42 isolates tested were resistant to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole; 4 were also resistant to nalidixic acid. Thirty-five of 42 isolates were indistinguishable by PFGE. CONCLUSIONS: The unusual neurologic manifestations posed a diagnostic challenge that was resolved through rapid typhoid antibody testing in the field and subsequent blood culture confirmation in the Malawi national reference laboratory. Extending laboratory diagnostic capacity, including blood culture, to populations at risk for typhoid fever in Africa will improve outbreak detection, response, and clinical treatment.

Control and prevention of viral gastroenteritis.

Diarrheal illness remains 1 of the top 5 causes of death in low-income and middle-income countries, especially for children <5 years of age. Introduction of universal childhood vaccination against rotaviruses has greatly reduced the incidence and severity of illness in upper-income and lower-income settings. For adults, norovirus is the leading cause of sporadic cases and outbreaks of diarrheal illness and is responsible for nearly 21 million episodes annually in the United States, of which 5.5 million are foodborne. Public health efforts to control and prevent norovirus illness have focused on rapid outbreak detection and source identification and control of transmission in institutional settings.

Complete Genome Sequences of Human Astrovirus Prototype Strains (Types 1 to 8).

We report the complete genome sequences of the eight human astrovirus Oxford prototype strains. These sequences share 94.9% to 99.9% nucleotide identity with open reading frame 2 (ORF2) genes of astrovirus genomes previously deposited in GenBank and include the first complete genome of human astrovirus type 7.

Chronic norovirus and adenovirus infection in a solid organ transplant recipient.

A 10-month-old boy developed chronic diarrhea 2 months after a combined liver, pancreas, and small bowel transplant. Norovirus and adenovirus were detected in multiple stool specimens during a 114-day period. Enteric viral infectious should be considered in solid organ transplant recipients with chronic diarrhea.

Comparing serologic response against enteric pathogens with reported diarrhea to assess the impact of improved household drinking water quality.

We evaluated enteric infection serology as an alternative outcome measure to diarrhea prevalence in a randomized controlled trial of household-based drinking water treatment; 492 households were randomly assigned to 5 household-based water treatment interventions or control. Individuals were followed weekly over 52 weeks to measure diarrhea prevalence. Study subjects of age

A large outbreak of Brainerd diarrhea associated with a restaurant in the Red River Valley, Texas.

BACKGROUND: In June 1996, an outbreak of chronic diarrhea was reported to the Texas Department of Health (Austin). METHODS: We initiated active case finding, performed 2 case-control studies, and conducted an extensive laboratory and environmental investigation. RESULTS: We identified 114 persons with diarrhea that lasted > or = 4 weeks. Symptoms among 102 patients who were studied included urgency (87%), fatigue (86%), fecal incontinence (74%), and weight loss (73%); the median maximum 24-h stool frequency was 15 stools. Diarrhea persisted for > 6 months in 87% and for > 1 year in 70% of patients who were observed. Fifty-one (89%) of 57 ill persons had eaten at a particular restaurant within 4 weeks before onset, compared with 8 (14%) of 59 matched control subjects (matched odds ratio [OR], undefined; 95% confidence interval [CI], 11.2-infinity). At the restaurant, patients were more likely than their unaffected dining companions to have drunk tap water (OR, 2.8; 95% CI, 1.0-9.9) and to have eaten several specific food items, and they were less likely to have drunk iced tea made from boiled water and store-bought ice (OR, 0.3; 95% CI, 0.05-1.0). A multivariable model that included consumption of tap water and salad bar tomatoes best fit the data. The restaurant had multiple sanitary and plumbing deficiencies. Extensive laboratory and environmental testing for bacterial, parasitic, mycotic, and viral agents did not identify an etiologic agent. CONCLUSIONS: The clinical, laboratory, and epidemiologic findings are consistent with those of previous outbreaks of Brainerd diarrhea. To our knowledge, this is the largest reported outbreak of Brainerd diarrhea associated with a restaurant.

Reduced evolutionary rate in reemerged Ebola virus transmission chains.

On 29 June 2015, Liberia's respite from Ebola virus disease (EVD) was interrupted for the second time by a renewed outbreak ("flare-up") of seven confirmed cases. We demonstrate that, similar to the March 2015 flare-up associated with sexual transmission, this new flare-up was a reemergence of a Liberian transmission chain originating from a persistently infected source rather than a reintroduction from a reservoir or a neighboring country with active transmission. Although distinct, Ebola virus (EBOV) genomes from both flare-ups exhibit significantly low genetic divergence, indicating a reduced rate of EBOV evolution during persistent infection. Using this rate of change as a signature, we identified two additional EVD clusters that possibly arose from persistently infected sources. These findings highlight the risk of EVD flare-ups even after an outbreak is declared over.

Norovirus and child care: challenges in outbreak control.

An infant with diarrhea attended a community playgroup. In the subsequent 48 hours, 6 of the 7 mothers and children reported gastroenteritis; fecal specimens from 5 persons tested positive for norovirus, with identical sequences. No breach of hygiene or contact with fecal matter was identified. Excluding the child with gastroenteritis from the playgroup could have prevented this outbreak.

Foodborne viral gastroenteritis: challenges and opportunities.

Norwalk-like viruses (NLVs) are estimated to be the most common causes of foodborne disease in the United States, accounting for two-thirds of all food-related illnesses. The epidemiologic features and disease burden associated with NLVs have, until recently, been poorly understood because of the lack of sensitive detection assays and the underuse of available diagnostic tools. However, the application of molecular techniques to diagnose and investigate outbreaks of infection during recent years has led to a growing appreciation of the importance of these agents. NLVs are a principal cause of outbreaks of acute-onset vomiting and diarrhea in all age groups-most commonly, via contamination of uncooked foods by infected foodhandlers, but also via foods contaminated at their sources, such as oysters and raspberries. NLVs may also account for >10% of sporadic cases of gastroenteritis in children and adults. Future research will focus on the development of easy-to-use diagnostic assays based on antigen and antibody detection as well as vaccine development. Implementation of simple prevention measures, including correct food-handling practices, will continue to be a priority.

Molecular epidemiology of outbreaks of viral gastroenteritis in New York State, 1998-1999.

This investigation evaluated the role of Norwalk-like virus (NLV) and other viruses (rotavirus, enteric adenovirus, and enterovirus) in 11 outbreaks of acute nonbacterial gastroenteritis that occurred in multiple settings in a span of 18 months in New York State. To determine the etiology of illness, patients' stool specimens were analyzed with a combination of reverse-transcription polymerase chain reaction (RT-PCR) and nucleotide sequencing, cell culture, and ELISA diagnostic techniques. NLV was detected from all of these outbreaks, with an overall detection rate of 64% (51 of 79) for all specimens tested. Repeated attempts to isolate other viral pathogens were unsuccessful. Phylogenetic analysis of a subset of 27 specimens from these outbreaks showed the presence of both genogroup I and genogroup II NLVs. A spectrum of different nucleotide sequences were detected, demonstrating interoutbreak sequence variation and unrelated infections. NLV is a significant causative agent of diarrhea outbreaks in New York State.

Molecular characterization of noroviruses detected in diarrheic stools of Michigan and Wisconsin dairy calves: circulation of two distinct subgroups.

Noroviruses have emerged as the leading worldwide cause of acute non-bacterial gastroenteritis in humans. The presence of noroviruses in diarrheic stool samples from calves on Michigan and Wisconsin dairy farms was investigated by RT-PCR. Norovirus-positive samples were found on all eight farms studied in Michigan and on 2 out of 14 farms in Wisconsin. Phylogenetic analyses of partial polymerase and capsid sequences, derived for a subset of these bovine noroviruses, showed that these strains formed a group which is genetically distinct from the human noroviruses, but more closely related to genogroup I than to genogroup II human noroviruses. Examination of 2 full and 10 additional partial capsid (ORF2) sequences of these bovine strains revealed the presence of two genetic subgroups or clusters of bovine noroviruses circulating on Michigan and Wisconsin farms. One subgroup is "Jena-like", the other "Newbury agent-2-like".

Prevalence of infection with waterborne pathogens: a seroepidemiologic study in children 6-36 months old in San Juan Sacatepequez, Guatemala.

Water and sanitation interventions in developing countries have historically been difficult to evaluate. We conducted a seroepidemiologic study with the following goals: 1) to determine the feasibility of using antibody markers as indicators of waterborne pathogen infection in the evaluation of water and sanitation intervention projects; 2) to characterize the epidemiology of waterborne diarrheal infections in rural Guatemala, and 3) to measure the age-specific prevalence of antibodies to waterborne pathogens. Between September and December 1999, all children 6-36 months of age in 10 study villages were invited to participate. We collected sufficient serum from 522 of 590 eligible children, and divided them into six-month age groups for analysis (6-12, 13-18, 19-24, 25-30, and 31-36 months). The prevalence of antibodies was lowest in children 6-12 months old compared with the four older age groups for the following pathogens: enterotoxigenic Escherichia coli (48%, 81%, 80%, 77%, and 83%), Norwalk virus (27%, 61%, 83%, 94%, and 94%), and Cryptosporidium parvum (27%, 53%, 70%, 67%, and 73%). The prevalence of total antibody to hepatitis A virus increased steadily in the three oldest age groups (40%, 28%, 46%, 60%, and 76%). In contrast, the prevalence of antibody to Helicobacter pylori was relatively constant in all five age groups (20%, 19%, 21%, 25%, and 25%). Serology appears to be an efficient and feasible approach for determining the prevalence of infection with selected waterborne pathogens in very young children. Such an approach may provide a suitable, sensitive, and economical alternative to the cumbersome stool collection methods that have previously been used for evaluation of water and sanitation projects.

Determination of a universal nucleic acid extraction procedure for PCR detection of gastroenteritis viruses in faecal specimens.

Four nucleic acid extraction protocols were examined for their suitability for extraction of the ssRNA, dsRNA and dsDNA genomes of gastroenteritis viruses, for PCR detection. Protocol (A), employed specimen lysis with guanidinium thiocyanate, extraction with phenol-chloroform-isoamyl alcohol and nucleic acid purification by size-fractionated silica particles. Protocol (B), utilised specimen lysis with guanidinium thiocyanate and nucleic acid purification by silica, followed by phenol-chloroform-isoamyl alcohol extraction. Protocol (C), employed specimen lysis with guanidinium thiocyanate and nucleic acid purification by RNAID glass powder. Protocol (D), employed specimen lysis with sodium dodecyl sulphate, proteinase K digestion and extraction with phenol-chloroform-isoamyl alcohol. Of the four protocols, (B) appeared to be a suitable candidate 'universal' nucleic acid extraction procedure for PCR detection of different viral agents of gastroenteritis in a single nucleic acid extract of a faecal specimen, irrespective of genome composition. Omission of the phenol-chloroform extraction step did not affect negatively the ability of protocol (B) to allow PCR detection of gastroenteritis viruses in faecal specimens. PCR detection of NLVs, astroviruses, rotaviruses and adenoviruses, in single nucleic acid extracts of faecal specimens obtained from the field, confirmed the universality of the modified protocol (B). We propose the modified protocol (B) as a 'universal' nucleic acid extraction procedure, for monoplex PCR detection of gastroenteritis viruses in single nucleic acid extracts of faecal specimens and for development of multiplex PCR for their simultaneous detection.

Development of a rapid method using nucleic acid sequence-based amplification for the detection of astrovirus.

We have developed a rapid method to detect astrovirus in fecal specimens utilizing nucleic acid sequence-based amplification (NASBA) and several detection methodologies, including a sandwich hybridization assay based on DNA-tagged liposomes (liposome-strip detection assay). RNA was extracted from 65 stool specimens that were positive for astrovirus by enzyme immunoassay and was amplified by both NASBA and reverse transcriptase PCR (RT-PCR). Also extracted and amplified were 19 specimens containing rotavirus, 20 specimens containing norovirus, five specimens containing adenovirus, 15 water negative control specimens, and eight specimens containing astrovirus reference strains. NASBA products were detected by electrochemiluminescence detection (ECL) and by liposome-strip detection; RT-PCR products were detected by ethidium bromide staining following gel electrophoresis and by liquid hybridization assay (LHA). There was no significant difference in the detection rates of NASBA- and RT-PCR-based assays, with one exception in which the NASBA/ECL assay detected astrovirus in eight specimens that tested negative by the RT-PCR/LHA assay. These results suggest that these NASBA-based detection methods have detection rates that are as good as or better than those of RT-PCR-based methods. Both NASBA and liposome-strip detection may be useful for field studies and environmental testing because these methods are rapid and do not require specialized equipment.

Norovirus detection and genotyping for children with gastroenteritis, Brazil.

During 1998-2005, we analyzed stool samples from 289 children in Rio de Janeiro to detect and genotype no-rovirus strains. Previous tests showed all samples to be negative for rotavirus and adenovirus. Of 42 (14.5%) no-rovirus-positive specimens, 20 (47.6%) were identified as genogroup GI and 22 (52.3%) as GII.

Norovirus classification and proposed strain nomenclature.

Without a virus culture system, genetic analysis becomes the principal method to classify norovirus (NoV) strains. Currently, classification of NoV strains beneath the species level has been based on sequences from different regions of the viral genome. As a result, the phylogenetic insights of some virus were not appropriately interpreted, and no consensus has been reached to establish a uniform classification scheme. To provide a consistent and reliable scientific basis for classifying NoVs, we analyzed the amino acid sequences for the major capsid protein of 164 NoV strains by first using an alignment based on the predicted 3D structures. A Bayesian tree was generated, and the maximum likelihood pairwise distances of the aligned sequences were used to evaluate the results from the uncorrected pairwise distance method. Analyses of the pairwise distances demonstrated three clearly resolved peaks, suggesting that NoV strains beneath the species level can be classified at three levels: strain (S), cluster (C), and genogroup (G). The uncorrected pairwise distance ranges for S, C, and G were 0-14.1%, 14.3-43.8%, and 44.9-61.4%, respectively. A scheme with 29 genetic clusters [8 in genogroup 1 (G1), 17 in G2, 2 in G3, and 1 each in G4 and G5] was defined on the basis of the tree topology with the standards provided and was supported by the distance analysis. Of these, five clusters in G2 and one in G1 are newly described. This analysis can serve as the basis for a standardized nomenclature to genetically describe NoV strains.

Molecular and epidemiologic trends of caliciviruses associated with outbreaks of acute gastroenteritis in the United States, 2000-2004.

Between July 2000 and June 2004, fecal specimens from 270 outbreaks of acute gastroenteritis were sent to the Centers for Disease Control and Prevention by local or state health departments for calicivirus testing. Of the 226 outbreaks that met the criteria for inclusion in the present study, caliciviruses were detected in 184 (81%) by reverse-transcription polymerase chain reaction and nucleotide sequencing. Nursing homes, retirement centers, and hospitals were the most frequently reported settings, and person-to-person contact was the most common mode of transmission, followed by foodborne spread. Overall, genogroup II norovirus (NoV) strains were the most abundant (79%), followed by genogroup I NoV strains (19%) and sapovirus (2%). Nucleotide-sequence analysis indicated a great diversity of NoV strains and implicated the emergence of one particular sequence variant in outbreaks occurring between July 2002 and June 2003. The public health impact of caliciviruses will not be fully appreciated, nor will interventions be completely evaluated, until methods to detect these viruses are more routinely used.

Use of TaqMan real-time reverse transcription-PCR for rapid detection, quantification, and typing of norovirus.

Noroviruses (NoVs) are the most commonly identified cause of outbreaks and sporadic cases of acute gastroenteritis. We evaluated and optimized NoV-specific TaqMan real-time reverse transcription (RT)-PCR assays for the rapid detection and typing of NoV strains belonging to genogroups GI and GII and adapted them to the LightCycler platform. We expanded the detection ability of the assays by developing an assay that detects the GIV NoV strain. The assays were validated with 92 clinical samples and 33 water samples from confirmed NoV outbreaks and suspected NoV contamination cases. The assays detected NoV RNA in all of the clinical specimens previously confirmed positive by conventional RT-PCR and sequencing. Additionally, the TaqMan assays successfully detected NoV RNA in water samples containing low viral concentrations and inhibitors of RT and/or PCR, whereas the conventional method with region B primers required dilution of the inhibitors. By means of serially diluted NoV T7 RNA transcripts, a potential detection limit of <10 transcript copies per reaction mixture was observed with the GII assay and a potential detection limit of <100 transcript copies per reaction mixture was observed with the GI assay. These results and the ability to detect virus in water that was negative by RT-PCR demonstrate the higher sensitivity of the TaqMan assay compared with that of a conventional RT-PCR assay. The TaqMan methods dramatically decrease the turnaround time by eliminating post-PCR processing. These assays have proven useful in assisting scientists in public health and diagnostic laboratories report findings quickly to outbreak management teams.