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A key challenge in cancer research is to identify the secreted factors that contribute to tumor cell survival. Nowhere is this more evident than in Hodgkin lymphoma, where malignant Hodgkin Reed Sternberg (HRS) cells comprise only 1-5% of the tumor mass, the remainder being infiltrating immune cells that presumably are required for the survival of the HRS cells. Until now, there has been no way to characterize the complex Hodgkin lymphoma tumor microenvironment at genome scale. Here, we performed genome-wide transcriptional profiling with spatial and single-cell resolution. We show that the neighborhood surrounding HRS cells forms a distinct niche involving 31 immune and stromal cell types and is enriched in CD4+ T cells, myeloid and follicular dendritic cells, while being depleted of plasma cells. Moreover, we used machine learning to nominate ligand-receptor pairs enriched in the HRS cell niche. Specifically, we identified IL13 as a candidate survival factor. In support of this hypothesis, recombinant IL13 augmented the proliferation of HRS cells in vitro . In addition, genome-wide CRISPR/Cas9 loss-of-function studies across more than 1,000 human cancer cell lines showed that IL4R and IL13RA1, the heterodimeric partners that constitute the IL13 receptor, were uniquely required for the survival of HRS cells. Moreover, monoclonal antibodies targeting either IL4R or IL13R phenocopied the genetic loss of function studies. IL13-targeting antibodies are already FDA-approved for atopic dermatitis, suggesting that clinical trials testing such agents should be explored in patients with Hodgkin lymphoma., Competing Interests: S.J.R. receives research support from Bristol Myers Squibb, Coherus, and KITE/Gilead. He is a member of the Scientific Advisory Board of Immunitas Therapeutics. F.C. is an academic founder of Curio Biosciences and Doppler Biosciences and a scientific advisor for Amber Bio. F.C 's interests were reviewed and managed by the Broad Institute per their conflict-of-interest policies. E.Z.M. is a founder of Curio Bioscience, inc. M.A.S. has received research funding from Bristol Myers Squibb, AstraZeneca, Bayer Abbvie, Genentech, and Novartis and has served on advisory boards for Bristol Myers Squibb and AstraZeneca. T.R.G. is a paid advisor and/or equity holder in Dewpoint Therapeutics, Sherlock Biosciences, Amplifyer Bio, and Braidwell, Inc. The remaining authors declare no competing interests.

The Coronavirus Disease 2019 (COVID-19) pandemic has disproportionately impacted people who use drugs (PWUD). This study explored relationships between drug use, COVID-19 testing, vaccination, and infection. This cross-sectional study was conducted in Miami, Florida between March 2021 and October 2022 as part of the National Institutes of Health (NIH) Rapid Acceleration of Diagnostics-Underserved Populations (RADx-UP) initiative and the Miami Adult Studies on HIV (MASH) cohort. Users of cannabis, cocaine/crack, heroin/fentanyl, methamphetamines, hallucinogens, and/or prescription drug misuse in the previous 12 months were considered PWUD. Sociodemographic data, COVID-19 testing history, and vaccination-related beliefs were self-reported. Vaccinations were confirmed with medical records and positivity was determined with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. Statistical analyses included chi-square tests and logistic regression. Of 1,780 participants, median age was 57 years, 50.7% were male, 50.2% Non-Hispanic Black, and 66.0% reported an annual income less than $15,000. Nearly 28.0% used drugs. PWUD were less likely than non-users to self-report ever testing positive for SARS-CoV-2 (14.7% vs. 21.0%, p = 0.006). However, 2.6% of participants tested positive for SARS-CoV-2, with no significant differences between PWUD and non-users (3.7% vs. 2.2%, p = 0.076). PWUD were more likely than non-users to experience difficulties accessing testing (10.2% vs. 7.1%, p = 0.033), vaccine hesitancy (58.9% vs. 43.4%, p = 0.002) and had lower odds of receiving any dose of a COVID-19 vaccine compared to non-users (aOR, 0.63; 95% CI, 0.49-0.81; p<0.001). PWUD presented with greater difficulties accessing COVID-19 testing, greater vaccine hesitancy, and lower odds of vaccination. Testing and immunization plans that are tailored to the needs of PWUD and consider access, trust-building campaigns, and education may be needed., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Tamargo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: People with disabilities face heightened vulnerability to COVID-19., Objective: This study investigated (1) the relationships between disability and COVID-19-related challenges, testing, vaccination, and infection and (2) predictors of loss of healthcare coverage and postponement and avoidance of medical care during the pandemic., Methods: This cross-sectional study was conducted in Miami, Florida, between March 2021 and February 2022 as part of the NIH Rapid Acceleration of Diagnostics-Underserved Populations initiative. Disability was defined using a standard measure that assesses six universal functions. Participants reported sociodemographic data, COVID-19 testing, infection history, challenges, and healthcare history. Vaccinations were confirmed with medical records and COVID-19 positivity was assessed using real-time reverse transcription-polymerase chain reaction. Statistical analyses included multivariable logistic regression., Results: Among 1,689 participants with a median age of 57.0, 50.6% were male, and 48.9% were non-Hispanic Black. Disability was associated with greater odds of all assessed COVID-19 challenges: healthcare (aOR:1.60; 95% CI:1.23-2.07), housing (aOR:2.15; 95% CI:1.62-2.87), insufficient food (aOR:1.97; 95% CI:1.54-2.52), water scarcity (aOR:2.33; 95% CI:1.60-3.37), medications (aOR:2.04; 95% CI:1.51-2.77), and transportation (aOR:2.56; 95% CI:1.95-3.36). Those reporting employment disability were less likely to have received COVID-19 testing (81.1% vs. 85.3%, p = 0.026) or to have history of COVID-19 positivity (aOR:0.63; 95% CI:0.44-0.92). Disability predicted avoidance (aOR:2.76; 95% CI:1.95-3.91) and postponement (aOR: 2.24; 95% CI:1.72-2.91) of medical care., Conclusions: Disability is associated with higher odds of COVID-19 challenges and postponement and avoidance of medical care. Those reporting employment disability had a lower likelihood of COVID-19 testing. Public health responses to healthcare crises should prioritize the special challenges of people living with disabilities., Competing Interests: Declaration of competing interest No conflict declared., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Community collaboration is a cornerstone of modern public health efforts. This work aimed to use community-engaged research to explore COVID-19 vaccination, testing, and infection in a minoritized community. This study was conducted in Miami, Florida, from March 2021 to February 2022 in community partner sites and the Miami Adult Studies on HIV (MASH) cohort. Sociodemographic characteristics, vaccination and testing beliefs, and COVID-19 challenges were self-reported. COVID-19 vaccinations were verified with medical records, testing history was self-reported, and severe acute respiratory syndrome coronavirus 2 positivity was determined via real-time reverse transcription-polymerase chain reaction (rt-PCR). Of 1689 participants, the median age was 57, 51% were male, 49% were non-Hispanic Black, 66% reported an income < USD 15,000/year, and 75.9% received at least one dose of a COVID-19 vaccine. Belief that COVID-19 vaccination is effective was associated with lower odds of COVID-19 positivity and was the strongest predictor of vaccination. Challenges accessing health care, housing, food, and transportation were associated with lower odds of vaccination. Employment, health insurance, higher education, and greater perceived test accuracy were associated with greater odds of COVID-19 testing. Social determinants of health and the belief that vaccines are effective and tests are accurate predicted behaviors and thus should be considered during public health crises in vulnerable communities.

The Hispanic, Latino, or Spanish (hereafter, "Hispanic") populations in the U.S. bear a disproportionate burden of COVID-19-related outcomes, including disease incidence and mortality. Developing culturally appropriate national public health services for Hispanic persons remains a challenge. This study examined the association of heritage and language preference with COVID-19 testing (tested vs. not tested) and vaccination (vaccinated vs. not vaccinated) outcomes among Hispanic participants from 18 Rapid Acceleration of Diagnostics-Underserved Populations (RADx-UP) projects (n = 3308; mean age = 44.1 years [SD = 14.9], 60% women; 83% spoke other than English at home). Generalized estimating equation models adjusted for age, gender, education level, income, insurance coverage, geographic region, comorbidities, and prior infection. Relative to Mexican heritage, individuals identifying as Puerto Rican or Dominican were more likely to test for COVID-19, and South American heritage was associated with higher testing and vaccination rates. Speaking Spanish or another language at home was associated with increased testing compared with speaking English at home for individuals who preferred not to report their heritage, and increased vaccination for those with Mexican, Cuban, or Central American heritage. This study highlights heterogeneity in testing and vaccination behaviors among Hispanic populations based on heritage and language preference, underscoring the diversity within the U.S. Hispanic community. In contrast to other studies on linguistic acculturation and health care utilization, our study found that a language other than English spoken at home was associated with greater vaccine uptake. That is, enculturation - the retention of Spanish language and presumably of Hispanic cultural norms - was linked with being vaccinated., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors. Published by Elsevier Inc.)

The gut-liver axis has been recognized as a potential pathway in which dietary factors may contribute to liver disease in people living with HIV (PLWH). The objective of this study was to explore associations between dietary quality, the fecal microbiome, the metabolome, and liver health in PLWH from the Miami Adult Studies on HIV (MASH) cohort. We performed a cross-sectional analysis of 50 PLWH from the MASH cohort and utilized the USDA Healthy Eating Index (HEI)-2015 to measure diet quality. A Fibrosis-4 Index (FIB-4) score < 1.45 was used as a strong indication that advanced liver fibrosis was not present. Stool samples and fasting blood plasma samples were collected. Bacterial composition was characterized using 16S rRNA sequencing. Metabolomics in plasma were determined using gas and liquid chromatography/mass spectrometry. Statistical analyses included biomarker identification using linear discriminant analysis effect size. Compared to participants with FIB-4 ≥ 1.45, participants with FIB-4 < 1.45 had higher intake of dairy ( p = 0.006). Fibrosis-4 Index score was inversely correlated with seafood and plant protein HEI component score ( r = -0.320, p = 0.022). The relative abundances of butyrate-producing taxa Ruminococcaceae, Roseburia , and Lachnospiraceae were higher in participants with FIB-4 < 1.45. Participants with FIB-4 < 1.45 also had higher levels of caffeine ( p = 0.045) and related metabolites such as trigonelline ( p = 0.008) and 1-methylurate ( p = 0.023). Dietary components appear to be associated with the fecal microbiome and metabolome, and liver health in PLWH. Future studies should investigate whether targeting specific dietary components may reduce liver-related morbidity and mortality in PLWH.

Objective: Over 19 million individuals globally have a cocaine use disorder, a significant public health crisis. Cocaine has also been associated with a pro-inflammatory state and recently with imbalances in the intestinal microbiota as compared to nonuse. The objective of this pilot study was to characterize the gut microbiota and plasma metabolites in people with HIV (PWH) who use cocaine compared with those who do not., Design: Cross-sectional study., Methods: A pilot study in PWH was conducted on 25 cocaine users and 25 cocaine nonusers from the Miami Adult Studies on HIV cohort. Stool samples and blood plasma were collected. Bacterial composition was characterized using 16S rRNA sequencing. Metabolomics in plasma were determined using gas and liquid chromatography/mass spectrometry., Results: The relative abundances of the Lachnopspira genus, Oscillospira genus, Bifidobacterium adolescentis species, and Euryarchaeota phylum were significantly higher in the cocaine- using PWH compared to cocaine-nonusing PWH. Cocaine-use was associated with higher levels of several metabolites: products of dopamine catabolism (3-methoxytyrosine and 3-methoxytyramine sulfate), phenylacetate, benzoate, butyrate, and butyrylglycine., Conclusions: Cocaine use was associated with higher abundances of taxa and metabolites known to be associated with pathogenic states that include gastrointestinal conditions. Understanding key intestinal bacterial functional pathways that are altered due to cocaine use in PWH will provide a better understanding of the relationships between the host intestinal microbiome and potentially provide novel treatments to improve health., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

Objective: Determine if cocaine use impacts gut permeability, promotes microbial translocation and immune activation in people living with HIV (PLWH) using effective antiretroviral therapy (ART)., Methods: Cross-sectional analysis of 100 PLWH (ART ≥6 months, HIV-RNA <200 copies/mL) from the Miami Adult Studies on HIV (MASH) cohort. Cocaine use was assessed by self-report, urine screen, and blood benzoylecgonine (BE). Blood samples were collected to assess gut permeability (intestinal fatty acid-binding protein, I-FABP), microbial translocation (lipopolysaccharide, LPS), immune activation (sCD14, sCD27, and sCD163) and markers of inflammation (hs-CRP, TNF-α and IL-6). Multiple linear regression models were used to analyze the relationships of cocaine use., Results: A total of 37 cocaine users and 63 cocaine non-users were evaluated. Cocaine users had higher levels of I-FABP (7.92±0.35 vs. 7.69±0.56 pg/mL, P = 0.029) and LPS (0.76±0.24 vs. 0.54±0.27 EU/mL, P<0.001) than cocaine non-users. Cocaine use was also associated with the levels of LPS (P<0.001), I-FABP (P = 0.033), and sCD163 (P = 0.010) after adjusting for covariates. Cocaine users had 5.15 times higher odds to exhibit higher LPS levels than non-users (OR: 5.15 95% CI: 1.89-13.9; P<0.001). Blood levels of BE were directly correlated with LPS (rho = 0.276, P = 0.028), sCD14 (rho = 0.274, P = 0.031), and sCD163 (rho = 0.250, P = 0.049)., Conclusions: Cocaine use was associated with markers of gut permeability, microbial translocation, and immune activation in virally suppressed PLWH. Mitigation of cocaine use may prevent further gastrointestinal damage and immune activation in PLWH., Competing Interests: The authors have declared that no competing interests exist. Dr. RN Mandler, an employee of the National Institute on Drug Abuse, is an author and did review and approve the manuscript as a part of his authorship role as a Scientific Official. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Background: Smoking has been associated with mental disorders (MD). People who smoke are at a higher risk of contracting COVID-19 and experiencing more severe symptoms of the illness. This study aimed to investigate the relationship between cigarette smoking and MD before and during the COVID-19 pandemic and whether it was influenced by COVID-19-related stress in the MASH cohort. Methods: An ambispective design was used with data collected during the pandemic (July/August 2020) by the COVID-19-Related Worry Scale, a parameter for stress, and data collected at the participants’ last cohort visit before the pandemic (December 2019). Results: In our sample of 314 participants, 58.6% were living with HIV, 39.2% had MD, 52.5% smoked before, and 47.8% smoked during the pandemic. Participants with MD were twice as likely to smoke cigarettes both before (aOR = 2.02, 95% CI: 1.21−3.37, p = 0.007) and during the pandemic (aOR = 2.10, 95% CI: 1.24−3.56, p = 0.006); and experienced higher levels of stress measured by the COVID-19-Related Worry Scale (8.59 [5.0−10.0] vs. 7.65 [5.0−10.0]; p = 0.026) compared to those without MD. Participants with MD and high levels of stress smoked more days per month (20.1 [0−30] days) than those with lower levels of stress (9.2 [0−30] days, p = 0.021), and more than those with high levels of stress, but no MD (2.6 [0−30] days, p < 0.001). Conclusions: Cigarette smoking decreased in the MASH cohort during the pandemic, but increased in participants with MD and higher levels of stress.

Two outbreaks of Shiga toxin-producing Escherichia coli O121:H19 associated with wheat flour, in the United States of America and Canada, involved strains with an unusual phenotype, delayed lactose utilization (DLU). These strains do not ferment lactose when initially cultured on MacConkey agar (MAC), but lactose fermentation occurs following subculture to a second plate of MAC. The prevalence of DLU was determined by examining the β-galactosidase activity of 49 strains of E. coli O121, and of 37 other strains of E. coli. Twenty four of forty three O121:H19 and one O121:NM displayed DLU. Two strains (O121:NM and O145:H34) did not have detectable β-galactosidase activity. β-glucuronidase activity of O121 strains was also determined. All but six DLU strains had normal β-glucuronidase activity. β-glucuronidase activity was suppressed on MAC for 17 of 23 O121 non-DLU strains. Genomic analysis found that DLU strains possessed an insertion sequence, IS600 (1267 bp), between lacZ (β-galactosidase) and lacY (β-galactoside permease), that was not present in strains exhibiting normal lactose utilization. The insert might reduce the expression of β-galactoside permease, delaying import of lactose, resulting in the DLU phenotype. The high probability of DLU should be considered when using lactose-containing media for the isolation of STEC O121., (Crown Copyright © 2021. Published by Elsevier Ltd. All rights reserved.)

Persistent immune activation is a hallmark of human immunodeficiency virus (HIV) infection and thought to play a role on chronic diseases in people with HIV (PWH). Food insecurity is disproportionately prevalent in PWH and is associated with adverse health outcomes. We determined whether food insecurity was associated with increased plasma levels of soluble CD14, CD27, and CD163 in 323 antiretroviral-treated PWH from the Miami Adult Studies on HIV cohort. Nearly half (42.7%) of participants were food insecure, and 85.5% were virally suppressed (<200 copies/mL). Food insecurity was independently associated with higher levels of soluble CD14 and soluble CD27. Very low food security was associated with increased soluble CD163 levels among those with lower CD4+ cell counts. Food insecurity may promote immune activation in PWH, suggesting a biological link between food insecurity and chronic disease among PWH. Improving financial security and access to high-quality diets could reduce the burden of disease in this highly vulnerable population., (© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)

The objective of this study was to determine sources of Shiga toxin-producing Escherichia coli O157 (STEC O157) infection among visitors to Farm X and develop public health recommendations. A case-control study was conducted. Case-patients were defined as the first ill child (aged <18 years) in the household with laboratory-confirmed STEC O157, or physician-diagnosed hemolytic uremic syndrome with laboratory confirmation by serology, who visited Farm X in the 10 days prior to illness. Controls were selected from Farm X visitors aged <18 years, without symptoms during the same time period as case-patients. Environment and animal fecal samples collected from Farm X were cultured; isolates from Farm X were compared with patient isolates using whole genome sequencing (WGS). Case-patients were more likely than controls to have sat on hay bales at the doe barn (adjusted odds ratio: 4.55; 95% confidence interval: 1.41-16.13). No handwashing stations were available; limited hand sanitizer was provided. Overall, 37% (29 of 78) of animal and environmental samples collected were positive for STEC ; of these, 62% (18 of 29) yielded STEC O157 highly related by WGS to patient isolates. STEC O157 environmental contamination and fecal shedding by goats at Farm X was extensive. Farms should provide handwashing stations with soap, running water, and disposable towels. Access to animal areas, including animal pens and enclosures, should be limited for young children who are at risk for severe outcomes from STEC O157 infection. National recommendations should be adopted to reduce disease transmission., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Nichols, Gacek, Phan, Gambino-Shirley, Gollarza, Schroeder, Mercante, Mullins, Blackstock, Laughlin, Olson, Pizzo, Nguyen, Mank, Holmes-Talbot, McNutt, Noel, Muyombwe, Razeq, Lis, Sherman, Kasacek, Whitlock, Strockbine, Martin, Vidyaprakash, McCormack and Cartter.)

Background: Socioeconomic disadvantages and potential immunocompromise raise particular concerns for people living with HIV (PLWH) and other marginalized communities during the COVID-19 pandemic. In this study, we explored COVID-19 testing and the impact of the pandemic among participants from the Miami Adult Studies on HIV cohort, predominantly composed of low-income minorities living with and without HIV., Methods: Between July and August 2020, a telephone survey was administered to 299 Miami Adult Studies on HIV participants to assess COVID-19 testing, prevention behaviors, and psychosocial stressors. Health care utilization, antiretroviral adherence, food insecurity, and substance use during the pandemic were compared with those of their last cohort visit (7.8 ± 2.9 months earlier)., Results: Half of surveyed participants had been tested for COVID-19, 8 had tested positive and 2 had been hospitalized. PLWH (n = 183) were 42% times less likely than HIV-uninfected participants to have been tested. However, after adjustment for age, employment, COVID-19 symptoms, mental health care, and substance use, the effect of HIV status was no longer significant. PLWH were more likely to have seen a health care provider, use face coverings, and avoid public transportation and less likely to be food insecure and drink hazardously. There were significant changes in substance use patterns during the pandemic when compared with those before., Conclusion: PLWH, compared with their HIV-uninfected peers, were more likely to engage in preventive measures and health care during the pandemic, potentially reducing their exposure to COVID-19. There were no reported changes in antiretroviral adherence or health care utilization, but there were changes in substance use; these need to be monitored as this crisis progresses., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Primary cutaneous follicle center lymphomas (PCFCLs) are indolent B-cell lymphomas that predominantly remain skin restricted and manageable with skin-directed therapy. Conversely, secondary cutaneous involvement by usual systemic follicular lymphoma (secondary cutaneous follicular lymphoma [SCFL]) has a worse prognosis and often necessitates systemic therapy. Unfortunately, no histopathologic or genetic features reliably differentiate PCFCL from SCFL at diagnosis. Imaging may miss low-burden internal disease in some cases of SCFLs, leading to misclassification as PCFCL. Whereas usual systemic FL is well characterized genetically, the genomic landscapes of PCFCL and SCFL are unknown. Herein, we analyzed clinicopathologic and immunophenotypic data from 30 cases of PCFCL and 10 of SCFL and performed whole-exome sequencing on 18 specimens of PCFCL and 6 of SCFL. During a median follow-up of 7 years, 26 (87%) of the PCFCLs remained skin restricted. In the remaining 4 cases, systemic disease developed within 3 years of diagnosis. Although the SCFLs universally expressed BCL2 and had BCL2 rearrangements, 73% of the PCFCLs lacked BCL2 expression, and only 8% of skin-restricted PCFCLs had BCL2 rearrangements. SCFLs showed low proliferation fractions, whereas 75% of PCFCLs had proliferation fractions >30%. Of the SCFLs, 67% had characteristic loss-of-function CREBBP or KMT2D mutations vs none in skin-restricted PCFCL. Both SCFL and skin-restricted PCFCL showed frequent TNFRSF14 loss-of-function mutations and copy number loss at chromosome 1p36. These data together establish PCFCL as a unique entity with biological features distinct from usual systemic FL and SCFL. We propose 3 criteria based on BCL2 rearrangement, chromatin-modifying gene mutations (CREBBP, KMT2D, EZH2, and EP300), and proliferation index to classify cutaneous FL specimens based on the likelihood of concurrent or future systemic spread., (© 2021 by The American Society of Hematology.)

Background: Produce-associated outbreaks of Shiga toxin-producing Escherichia coli (STEC) were first identified in 1991. In April 2018, New Jersey and Pennsylvania officials reported a cluster of STEC O157 infections associated with multiple locations of a restaurant chain. The Centers for Disease Control and Prevention (CDC) queried PulseNet, the national laboratory network for foodborne disease surveillance, for additional cases and began a national investigation., Methods: A case was defined as an infection between 13 March and 22 August 2018 with 1 of the 22 identified outbreak-associated E. coli O157:H7 or E. coli O61 pulsed-field gel electrophoresis pattern combinations, or with a strain STEC O157 that was closely related to the main outbreak strain by whole-genome sequencing. We conducted epidemiologic and traceback investigations to identify illness subclusters and common sources. A US Food and Drug Administration-led environmental assessment, which tested water, soil, manure, compost, and scat samples, was conducted to evaluate potential sources of STEC contamination., Results: We identified 240 case-patients from 37 states; 104 were hospitalized, 28 developed hemolytic uremic syndrome, and 5 died. Of 179 people who were interviewed, 152 (85%) reported consuming romaine lettuce in the week before illness onset. Twenty subclusters were identified. Product traceback from subcluster restaurants identified numerous romaine lettuce distributors and growers; all lettuce originated from the Yuma growing region. Water samples collected from an irrigation canal in the region yielded the outbreak strain of STEC O157., Conclusions: We report on the largest multistate leafy greens-linked STEC O157 outbreak in several decades. The investigation highlights the complexities associated with investigating outbreaks involving widespread environmental contamination., (Published by Oxford University Press for the Infectious Diseases Society of America 2019.)

Competing Interests: All authors have completed and submitted the ICMJE form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

Competing Interests: All authors have completed and submitted the ICMJE form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

Competing Interests: All authors have completed and submitted the ICMJE form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

Competing Interests: All authors have completed and submitted the ICMJE form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

The U.S. Food and Drug Administration Escherichia coli Identification (FDA-ECID) microarray provides rapid molecular characterization of E. coli. The effectiveness of the FDA-ECID for characterizing Shiga toxin-producing E. coli (STEC) was evaluated by three federal laboratories and one reference laboratory with a panel of 54 reference E. coli strains from the External Quality Assurance program. Strains were tested by FDA-ECID for molecular serotyping (O and H antigens), Shiga toxin subtyping, and the presence of the ehxA and eae genes for enterohemolysin and intimin, respectively. The FDA-ECID O typing was 96% reproducible among the four laboratories and 94% accurate compared with the reference External Quality Assurance data. Discrepancies were due to the absence of O41 target loci on the array and to two pairs of O types with identical target sequences. H typing was 96% reproducible and 100% accurate, with discrepancies due to two strains from one laboratory that were identified as mixed by FDA-ECID. Shiga toxin (Stx) type 1 subtyping was 100% reproducible and accurate, and Stx2 subtyping was 100% reproducible but only 64% accurate. FDA-ECID identified most Stx2 subtypes but had difficulty distinguishing among stx 2a , stx 2c , and stx 2d genes because of close similarities of these sequences. FDA-ECID was 100% effective for detecting ehxA and eae and accurately subtyped the eae alleles. This interlaboratory study revealed that FDA-ECID for STEC characterization was highly reproducible for molecular serotyping, stx and eae subtyping, and ehxA detection. However, the array was less useful for distinguishing among the highly homologous O antigen genes and the stx 2a , stx 2c , and stx 2d subtypes.

Shiga toxin-producing Escherichia coli (STEC) is an enteric foodborne pathogen that can cause mild to severe illness. Here, we report the availability of high-quality whole-genome sequences for 77 STEC strains generated using the PacBio sequencing platform.

Shigella spp. are enteric pathogens that cause shigellosis. We report here the high-quality whole-genome sequences of 59 historical Shigella strains that represent the four species and a variety of serotypes.

Hurricane Maria made landfall in Puerto Rico on September 20, 2017, causing major damage to infrastructure and severely limiting access to potable water, electric power, transportation, and communications. Public services that were affected included operations of the Puerto Rico Department of Health (PRDOH), which provides critical laboratory testing and surveillance for diseases and other health hazards. PRDOH requested assistance from CDC for the restoration of laboratory infrastructure, surveillance capacity, and diagnostic testing for selected priority diseases, including influenza, rabies, leptospirosis, salmonellosis, and tuberculosis. PRDOH, CDC, and the Association of Public Health Laboratories (APHL) collaborated to conduct rapid needs assessments and, with assistance from the CDC Foundation, implement a temporary transport system for shipping samples from Puerto Rico to the continental United States for surveillance and diagnostic and confirmatory testing. This report describes the initial laboratory emergency response and engagement efforts among federal, state, and nongovernmental partners to reestablish public health laboratory services severely affected by Hurricane Maria. The implementation of a sample transport system allowed Puerto Rico to reinitiate priority infectious disease surveillance and laboratory testing for patient and public health interventions, while awaiting the rebuilding and reinstatement of PRDOH laboratory services., Competing Interests: No conflicts of interest were reported.

Competing Interests: No conflicts of interest were reported.

Drug-resistant Shigella sonnei poses a clinical and public health challenge. We report here the high-quality draft whole-genome sequences of four outbreak-associated S. sonnei isolates; three were resistant to two or more antibiotics, and one was resistant to streptomycin only.

Enterobacteriaceae carrying plasmid-mediated colistin resistance have been found around the world. We report here the high-quality whole-genome sequence of an Escherichia coli O157:H48 isolate (2016C-3936C1) from Connecticut that carried the mcr-1 resistance gene on an IncX4-type plasmid., (Copyright © 2017 Lindsey et al.)

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen. We report here the high-quality draft whole-genome sequences of five STEC strains isolated from clinical cases in the United States. This report is for STEC of serotypes O55:H7, O79:H7, O91:H14, O153:H2, and O156:H25., (Copyright © 2016 Lindsey et al.)

On May 9, 2014, a physician at hospital A in American Samoa noticed an abnormally high number of children presenting to the emergency department with bloody diarrhea. Based on preliminary testing of stool specimens, Entamoeba histolytica infection was suspected as a possible cause. Shigella was also suspected in a subset of samples. On May 22, the American Samoa Department of Health requested assistance from CDC with the outbreak investigation. The goals of the investigation were to establish the presence of an outbreak, characterize its epidemiology and etiology, and recommend control measures. The CDC field team reviewed the emergency department log book for cases of diarrheal illness during April 15-June 13, 2014. During this period, 280 cases of diarrheal illness were recorded, with a peak occurring on May 10. Twice as many cases occurred during this period in 2014 compared with the same period in 2011, the most recent year for which comparable surveillance data were available. Cases were widely distributed across the island. The highest number of cases occurred in children aged 0-9 years. Across age groups, cases were similarly distributed among males and females. These patterns are not consistent with the epidemiology of disease caused by E. histolytica, which tends to cause more cases in males of all ages.

Shiga toxin-producing Escherichia coli (STEC) are a common cause for food-borne diarrheal illness outbreaks and sporadic cases. Here, we report the availability of the draft genome sequences of 228 STEC strains representing 32 serotypes with known pulsed-field gel electrophoresis (PFGE) types and epidemiological relationships, as well as 12 strains representing other diarrheagenic E. coli pathotypes., (Copyright © 2014 Trees et al.)

Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen. Here, we report the draft whole-genome sequences of nine STEC strains isolated from clinical cases in the United States. This is the first report of such information for STEC of serotypes O69, H11, O145:H25, O118:H16, O91:H21, O146:H21, O45:H2, O128:H2, and O121:H19., (Copyright © 2014 Lindsey et al.)