Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.

The use of culture-independent diagnostic tests (CIDTs), such as stool antigen tests, as standalone tests for the detection of Campylobacter in stool is increasing. We conducted a prospective, multicenter study to evaluate the performance of stool antigen CIDTs compared to culture and PCR for Campylobacter detection. Between July and October 2010, we tested 2,767 stool specimens from patients with gastrointestinal illness with the following methods: four types of Campylobacter selective media, four commercial stool antigen assays, and a commercial PCR assay. Illnesses from which specimens were positive by one or more culture media or at least one CIDT and PCR were designated "cases." A total of 95 specimens (3.4%) met the case definition. The stool antigen CIDTs ranged from 79.6% to 87.6% in sensitivity, 95.9 to 99.5% in specificity, and 41.3 to 84.3% in positive predictive value. Culture alone detected 80/89 (89.9% sensitivity) Campylobacter jejuni/Campylobacter coli-positive cases. Of the 209 noncases that were positive by at least one CIDT, only one (0.48%) was positive by all four stool antigen tests, and 73% were positive by just one stool antigen test. The questionable relevance of unconfirmed positive stool antigen CIDT results was supported by the finding that noncases were less likely than cases to have gastrointestinal symptoms. Thus, while the tests were convenient to use, the sensitivity, specificity, and positive predictive value of Campylobacter stool antigen tests were highly variable. Given the relatively low incidence of Campylobacter disease and the generally poor diagnostic test characteristics, this study calls into question the use of commercially available stool antigen CIDTs as standalone tests for direct detection of Campylobacter in stool. Campylobacter infection continues to be a major public health problem. Campylobacter jejuni and Campylobacter coli are pathogens transmitted commonly through food, causing an estimated 1.3 million cases of illness per year in the United States (1), and yet diagnosis can be challenging because the organism is difficult to isolate, grow, and identify. Recent reports describing clinical laboratory practices for Campylobacter diagnostics in Pennsylvania (2) and the Foodborne Diseases Active Surveillance Network (FoodNet) sites (3) highlight the wide range of testing practices in use; currently, no best-practice clinical or public health laboratory guidelines exist for laboratory diagnosis of Campylobacter infections. Direct plating onto a Campylobacter selective medium, followed by incubation at 42°C under microaerobic conditions for 72 h, has long been considered the "gold standard" for diagnosis (4).The use of culture-independent diagnostic tests (CIDTs) for Campylobacter testing on stool samples is increasing, which may have important implications for both patient management and public health surveillance efforts (5). Stool antigen tests to directly detect Campylobacter in fecal samples are fast and generate sameday results, but concerns regarding speci...

Environmental DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic methods for analysing metagenomic and amplicon datasets, which makes selecting adequate methods a significant challenge. A number of benchmark studies have been undertaken; however, these often present conflicting results. We have applied a network meta-analysis method to identify software methods that are generally accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some methods and computational strategies that produce robust predictions.

We report a cluster of pediatric cryptosporidiosis infections among solid organ transplant recipients at a summer camp in Georgia, USA. A retrospective cohort study was conducted to investigate the risk factors for infection. A total of 118 campers attended the camp during July 23‐28, 2017. The overall attack rate among campers during the outbreak was 11% (13/118). Sanger‐based amplicon sequencing of stool specimens from 7 (80%) campers identified Cryptosporidium hominis as the suspected etiologic agent. All infected campers were heart or kidney transplant recipients receiving immunosuppressive therapy. The median reported symptom duration was 12 days (range 6‐18 days) and 9 (69.2%) were hospitalized for at least one night (median length of stay 5 days, range 2‐16 days). There were no deaths or acute rejection events attributed to infection. The results of the epidemiologic and environmental investigation suggest a recreational pool as the presumed source, although there was no direct evidence to support this. Many long‐term interventions were implemented, and there have been no further outbreaks at the camp in the following two years. This outbreak demonstrates that cryptosporidiosis may be associated with notable burden in pediatric transplant recipients, and illustrates the challenges associated with source identification and containment.

Background: Discontinuation of contact precautions for methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE) have failed to show an increase in associated transmission or infections in adult healthcare settings. Pediatric experience is limited. Objective: We evaluated the impact of discontinuing contact precautions for MRSA, VRE, and extended-spectrum β-lactamase–producing gram-negative bacilli (ESBLs) on device-associated healthcare-associated infections (HAIs). Methods: In October 2018, contact precautions were discontinued for children with MRSA, VRE, and ESBLs in a large, tertiary-care pediatric healthcare system comprising 2 hospitals and 620 beds. Coincident interventions that potentially reduced HAIs included blood culture diagnostic stewardship (June 2018), a hand hygiene education initiative (July 2018), a handshake antibiotic stewardship program (December 2018) and multidisciplinary infection prevention rounding in the intensive care units (November 2018). Compliance with hand hygiene and HAI prevention bundles were monitored. Device-associated HAIs were identified using standard definitions. Annotated run charts were used to track the impact of interventions on changes in device-associated HAIs over time. Results: Average hand hygiene compliance was 91%. Compliance with HAI prevention bundles was 81% for ventilator-associated pneumonias, 90% for catheter-associated urinary tract infections, and 97% for central-line–associated bloodstream infections. Overall, device-associated HAIs decreased from 6.04 per 10,000 patient days to 3.25 per 10,000 patient days after October 2018 (Fig. 1). Prior to October 2018, MRSA, VRE and ESBLs accounted for 10% of device-associated HAIs. This rate decreased to 5% after October 2018. The decrease in HAIs was likely related to interventions such as infection prevention rounds and handshake stewardship. Conclusions: Discontinuation of contact precautions for children with MRSA, VRE, and ESBLs were not associated with increased device-associated HAIs, and such discontinuation is likely safe in the setting of robust infection prevention and antibiotic stewardship programs.Funding: NoneDisclosures: None