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Stapleton GS, Innes GK, Nachman KE, Casey JA, Patton AN, Price LB, Tartof SY, Davis MF. Assessing the difference in contamination of retail meat with multidrug-resistant bacteria using for-consumer package label claims that indicate on-farm antibiotic use practices- United States, 2016-2019. J Expo Sci Environ Epidemiol 2024:10.1038/s41370-024-00649-y. [PMID: 38374423 DOI: 10.1038/s41370-024-00649-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Antibiotic use in food-producing animals can select for antibiotic resistance in bacteria that can be transmitted to people through contamination of food products during meat processing. Contamination resulting in foodborne illness contributes to adverse health outcomes. Some livestock producers have implemented antibiotic use reduction strategies marketed to consumers on regulated retail meat packaging labels ("label claims"). OBJECTIVE We investigated whether retail meat label claims were associated with isolation of multidrug-resistant organisms (MDROs, resistant to ≥3 classes of antibiotics) from U.S. meat samples. METHODS We utilized retail meat data from the U.S. Food and Drug Administration National Antimicrobial Resistance Monitoring System (NARMS) collected during 2016-2019 for bacterial contamination of chicken breast, ground turkey, ground beef, and pork chops. We used modified Poisson regression models to compare the prevalence of MDRO contamination among meat samples with any antibiotic restriction label claims versus those without such claims (i.e., conventionally produced). RESULTS In NARMS, 62,338 meat samples were evaluated for bacterial growth from 2016-2019. Of these, 24,446 (39%) samples had label claims that indicated antibiotic use was restricted during animal production. MDROs were isolated from 2252 (4%) meat samples, of which 71% (n = 1591) were conventionally produced, and 29% (n = 661) had antibiotic restriction label claims. Compared with conventional samples, meat with antibiotic restriction label claims had a statistically lower prevalence of MDROs (adjusted prevalence ratio: 0.66; 95% CI: 0.61, 0.73). This relationship was consistent for the outcome of any bacterial growth. IMPACT This repeated cross-sectional analysis of a nationally representative retail meat surveillance database in the United States supports that retail meats labeled with antibiotic restriction claims were less likely to be contaminated with MDROs compared with retail meat without such claims during 2016-2019. These findings indicate the potential for the public to become exposed to bacterial pathogens via retail meat and emphasizes a possibility that consumers could reduce their exposure to environmental reservoirs of foodborne pathogens that are resistant to antibiotics.
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Affiliation(s)
- G Sean Stapleton
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Center for Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Gabriel K Innes
- Yuma Center for Excellence in Desert Agriculture, Yuma, AZ, USA
| | - Keeve E Nachman
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Joan A Casey
- Department of Environmental and Occupational Health Sciences, University of Washington School of Public Health, Seattle, WA, USA
| | - Andrew N Patton
- Geospatial Analysis Lab, University of San Francisco, Harney Science Center, San Francisco, CA, USA
| | - Lance B Price
- Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Sara Y Tartof
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, USA
| | - Meghan F Davis
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Molecular and Comparative Pathobiology & Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
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Park DE, Aziz M, Koch BJ, Roach K, Clabots C, Johnson JR, Price LB, Liu CM. Gut microbiome predictors of Escherichia coli sequence type 131 colonization and loss. EBioMedicine 2024; 99:104909. [PMID: 38096689 PMCID: PMC10758731 DOI: 10.1016/j.ebiom.2023.104909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 11/15/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Escherichia coli sequence type 131 (ST131), specifically its fluoroquinolone-resistant H30R clade (ST131-H30R), is a global multidrug-resistant pathogen. The gut microbiome's role in ST131-H30R intestinal carriage is undefined. METHODS Veterans and their household members underwent longitudinal fecal swab surveillance for ST131 in 2014-2018. The fecal microbiome was characterized by 16S rRNA qPCR and sequencing. We evaluated associations between ST131-H30R carriage and gut microbiome at baseline by random forest models to identify the most informative gut bacterial phyla and genera attributes for ST131 and ST131-H30R carriage status. Next, we assessed longitudinal associations between fecal microbiome and ST131-H30R carriage using a mixed-effects logistic regression with longitudinal measures. FINDINGS Of the 519 participants, 78 were carriers of ST131, among whom 49 had ST131-H30R. At the baseline timepoint, H30R-positive participants had higher proportional abundances of Actinobacteria phylum (mean: 4.9% vs. 3.1%) than ST131-negative participants. H30R-positive participants also had higher abundances of Collinsella (mean: 2.3% vs. 1.1%) and lower abundances of Alistipes (mean: 2.1% vs. 2.6%) than ST131-negative participants. In the longitudinal analysis, Collinsella abundance correlated positively with ST131-H30R carriage status and negatively with the loss of ST131-H30R. Conversely, Alistipes corresponded with the loss and persistent absence of ST131-H30R even in the presence of a household exposure. INTERPRETATION Abundances of specific fecal bacteria correlated with ST131-H30R carriage, persistence, and loss, suggesting their potential as targets for microbiome-based strategies to reduce carriage of ST131-H30R, a significant risk factor for invasive infections. FUNDING This work was supported in part by National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award numbers R21AI117654 and UM1AI104681 and the Office of Research and Development, Department of Veterans Affairs. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the Department of Veterans Affairs.
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Affiliation(s)
- Daniel E Park
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Maliha Aziz
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, P.O. Box 5620, Flagstaff, AZ, 86011, USA; Department of Biological Sciences, Northern Arizona University, 617 S Beaver St., Flagstaff, AZ, 86011, USA
| | - Kelsey Roach
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Connie Clabots
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN, 55417, USA
| | - James R Johnson
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN, 55417, USA; Department of Medicine, University of Minnesota, 401 East River Parkway, VCRC 1st, UK Floor, Suite 131, Minneapolis, MN, 55455, USA
| | - Lance B Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Cindy M Liu
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA.
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3
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Innes GK, Patton AN, Nachman KE, Casey JA, Stapleton GS, Abraham AG, Price LB, Tartof SY, Davis MF. Distance and destination of retail meat alter multidrug resistant contamination in the United States food system. Sci Rep 2023; 13:21024. [PMID: 38030674 PMCID: PMC10687246 DOI: 10.1038/s41598-023-48197-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023] Open
Abstract
Antibiotic-resistant infections are a global concern, especially those caused by multidrug-resistant (MDR) bacteria, defined as those resistant to more than three drug classes. The animal agriculture industry contributes to the antimicrobial resistant foodborne illness burden via contaminated retail meat. In the United States, retail meat is shipped across the country. Therefore, understanding geospatial factors that influence MDR bacterial contamination is vital to protect consumers and inform interventions. Using data available from the United States Food and Drug Administration's National Antimicrobial Resistance Monitoring System (NARMS), we describe retail meat shipping distances using processor and retailer locations and investigated this distance as a risk factor for MDR bacteria meat contamination using log-binomial regression. Meat samples collected during 2012-2014 totaled 11,243, of which 4791 (42.61%) were contaminated with bacteria and 835 (17.43%) of those bacteria were MDR. All examined geospatial factors were associated with MDR bacteria meat contamination. After adjustment for year and meat type, we found higher prevalence of MDR contamination among meat processed in the south (relative adjusted prevalence ratio [aPR] 1.35; 95% CI 1.06-1.73 when compared to the next-highest region), sold in Maryland (aPR 1.12; 95% CI 0.95-1.32 when compared to the next-highest state), and shipped from 194 to 469 miles (aPR 1.59; 95% CI 1.31-1.94 when compared to meats that traveled < 194 miles). However, sensitivity analyses revealed that New York sold the meat with the highest prevalence of MDR Salmonella contamination (4.84%). In this secondary analysis of NARMS data, both geographic location where products were sold and the shipping distance were associated with microbial contamination on retail meat.
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Affiliation(s)
- Gabriel K Innes
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Yuma Center for Excellence in Desert Agriculture, Yuma, AZ, USA.
| | - Andrew N Patton
- University of San Francisco Geospatial Analysis Lab, San Francisco, CA, USA
| | - Keeve E Nachman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Joan A Casey
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - G Sean Stapleton
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alison G Abraham
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Ophthalmology, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Lance B Price
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Sara Y Tartof
- Kaiser Permanente Southern California, Pasadena, CA, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, USA
| | - Meghan F Davis
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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4
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Nadimpalli ML, Stegger M, Viau R, Yith V, de Lauzanne A, Sem N, Borand L, Huynh BT, Brisse S, Passet V, Overballe-Petersen S, Aziz M, Gouali M, Jacobs J, Phe T, Hungate BA, Leshyk VO, Pickering AJ, Gravey F, Liu CM, Johnson TJ, Hello SL, Price LB. Plugging the leaks: antibiotic resistance at human-animal interfaces in low-resource settings. Front Ecol Environ 2023; 21:428-434. [PMID: 38464945 PMCID: PMC10923528 DOI: 10.1002/fee.2639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Antibiotic resistance is one of the greatest public health challenges of our time. International efforts to curb resistance have largely focused on drug development and limiting unnecessary antibiotic use. However, in areas where water, sanitation, and hygiene infrastructure is lacking, we propose that bacterial flow between humans and animals can exacerbate the emergence and spread of resistant pathogens. Here, we describe the consequences of poor environmental controls by comparing mobile resistance elements among Escherichia coli recovered from humans and meat in Cambodia, a middle-income country with substantial human-animal connectivity and unregulated antibiotic use. We identified identical mobile resistance elements and a conserved transposon region that were widely dispersed in both humans and animals, a phenomenon rarely observed in high-income settings. Our findings indicate that plugging leaks at human-animal interfaces should be a critical part of addressing antibiotic resistance in low- and especially middle-income countries.
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Affiliation(s)
- Maya L Nadimpalli
- Gangarosa Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, GA
- Stuart B Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, MA
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, DC
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia
| | - Roberto Viau
- Stuart B Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, MA
- Department of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA
| | - Vuthy Yith
- Laboratory of Environment and Food Safety, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Agathe de Lauzanne
- Epidemiology and Public Health Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Nita Sem
- Laboratory of Environment and Food Safety, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Laurence Borand
- Epidemiology and Public Health Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Bich-tram Huynh
- Université Paris-Saclay, UVSQ, Inserm, Anti-Infective Evasion and Pharmacoepidemiology Team, CESP, Montigny le Bretonneux, France
- UMR 1181, Inserm, University of Versailles Saint-Quentin-en-Yvelines, Saint-Quentin-en-Yvelines, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Virginie Passet
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | | | - Maliha Aziz
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, DC
| | - Malika Gouali
- Laboratory of Environment and Food Safety, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
- Enteric Bacterial Pathogens Unit, Institut Pasteur, Paris, France
| | - Jan Jacobs
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Thong Phe
- Sihanouk Hospital Center for Hope, Phnom Penh, Cambodia
| | - Bruce A Hungate
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ
| | - Victor O Leshyk
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ
| | - Amy J Pickering
- Stuart B Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, MA
- Department of Civil and Environmental Engineering, University of California–Berkeley, Berkeley, CA
| | - François Gravey
- Université de Caen Normandie, Université de Rouen Normandie, Inserm, DYNAMICURE UMR 1311, CHU Caen, Caen, France
- Department of Bacteriology, CHU Caen, Caen, France
| | - Cindy M Liu
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, DC
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St Paul, MN
| | - Simon Le Hello
- Enteric Bacterial Pathogens Unit, Institut Pasteur, Paris, France
- Université de Caen Normandie, Université de Rouen Normandie, Inserm, DYNAMICURE UMR 1311, CHU Caen, Caen, France
- Department of Bacteriology, CHU Caen, Caen, France
| | - Lance B Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, DC
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Liu CM, Aziz M, Park DE, Wu Z, Stegger M, Li M, Wang Y, Schmidlin K, Johnson TJ, Koch BJ, Hungate BA, Nordstrom L, Gauld L, Weaver B, Rolland D, Statham S, Hall B, Sariya S, Davis GS, Keim PS, Johnson JR, Price LB. Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections. One Health 2023; 16:100518. [PMID: 37363239 PMCID: PMC10288061 DOI: 10.1016/j.onehlt.2023.100518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
A one-health perspective may provide new and actionable information about Escherichia coli transmission. E. coli colonizes a broad range of vertebrates, including humans and food-production animals, and is a leading cause of bladder, kidney, and bloodstream infections in humans. Substantial evidence supports foodborne transmission of pathogenic E. coli strains from food animals to humans. However, the relative contribution of foodborne zoonotic E. coli (FZEC) to the human extraintestinal disease burden and the distinguishing characteristics of such strains remain undefined. Using a comparative genomic analysis of a large collection of contemporaneous, geographically-matched clinical and meat-source E. coli isolates (n = 3111), we identified 17 source-associated mobile genetic elements - predominantly plasmids and bacteriophages - and integrated them into a novel Bayesian latent class model to predict the origins of clinical E. coli isolates. We estimated that approximately 8 % of human extraintestinal E. coli infections (mostly urinary tract infections) in our study population were caused by FZEC. FZEC strains were equally likely to cause symptomatic disease as non-FZEC strains. Two FZEC lineages, ST131-H22 and ST58, appeared to have particularly high virulence potential. Our findings imply that FZEC strains collectively cause more urinary tract infections than does any single non-E. coli uropathogenic species (e.g., Klebsiella pneumoniae). Our novel approach can be applied in other settings to identify the highest-risk FZEC strains, determine their sources, and inform new one-health strategies to decrease the heavy public health burden imposed by extraintestinal E. coli infections.
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Affiliation(s)
- Cindy M. Liu
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
- The Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Room 210 Building 56, Applied Research & Development, 1395 S Knoles Drive, Flagstaff, AZ 86011, USA
| | - Maliha Aziz
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Daniel E. Park
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Zhenke Wu
- Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
- Michigan Institute for Data Science (MIDAS), University of Michigan, 500 Church Street, Suite 600, Ann Arbor, MI 48109, USA
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - Mengbing Li
- Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Yashan Wang
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Kara Schmidlin
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1365 Gortner Ave, St Paul, MN 55108, USA
| | - Benjamin J. Koch
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Lora Nordstrom
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Lori Gauld
- Flagstaff Medical Center, 1200 N. Beaver St. Flagstaff, AZ 86001, USA
| | - Brett Weaver
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Diana Rolland
- Flagstaff Medical Center, 1200 N. Beaver St. Flagstaff, AZ 86001, USA
| | - Sally Statham
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Brantley Hall
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sanjeev Sariya
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Gregg S. Davis
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Paul S. Keim
- The Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Room 210 Building 56, Applied Research & Development, 1395 S Knoles Drive, Flagstaff, AZ 86011, USA
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - James R. Johnson
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN 55417, USA
| | - Lance B. Price
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
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6
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Florea A, Casey JA, Nachman K, Price LB, Pomichowski ME, Takhar HS, Quinlivan V, Childs LD, Davis MF, Wei R, Hong V, Ku JH, Liu CM, Pressman A, Robinson S, Bruxvoort KJ, Salas SB, Tartof SY. Impact of California's Senate Bill 27 on Antimicrobial-Resistant Escherichia coli Urinary Tract Infection in Humans: Protocol for a Study of Methods and Baseline Data. JMIR Res Protoc 2023; 12:e45109. [PMID: 37145842 PMCID: PMC10199382 DOI: 10.2196/45109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/17/2023] [Accepted: 04/04/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Overuse of antibiotics contributes to antimicrobial resistance (AMR) and is a growing threat to human health worldwide. Previous work suggests a link between antimicrobial use in poultry and human AMR extraintestinal pathogenic Escherichia coli (E coli) urinary tract infections (UTIs). However, few US-based studies exist, and none have comprehensively assessed both foodborne and environmental pathways using advanced molecular and spatial epidemiologic methods in a quasi-experimental design. Recently, California enacted Senate Bill 27 (SB27), which changed previous policy to require a veterinarian's prescription for the use of antibiotic drugs, and which banned antibiotic use for disease prevention in livestock. This provided an opportunity to evaluate whether SB27 will result in a reduction in antimicrobial-resistant infections in humans. OBJECTIVE We describe in detail the methods implemented to achieve the overarching objective of this study to evaluate the impact of SB27 on downstream antibiotic resistance rates in human UTIs. METHODS A summary of the overall approach and the partnerships between Columbia University, George Washington University (GWU), Johns Hopkins Bloomberg School of Public Health, Kaiser Permanente Southern California (KPSC) Research and Evaluation, the Natural Resources Defense Council, Sanger Institute at Stanford University, Sutter Health Center for Health Systems Research, the University of Cambridge, and the University of Oxford is presented. The collection, quality control testing, and shipment of retail meat and clinical samples are described. Retail meat (chicken, beef, turkey, and pork) was purchased from stores throughout Southern California from 2017 to 2021. After processing at KPSC, it was shipped to GWU for testing. From 2016 to 2021, after clinical specimens were processed for routine clinical purposes and immediately before discarding, those with isolated colonies of E coli, Campylobacter, and Salmonella from KPSC members were collected and processed to be shipped for testing at GWU. Detailed methods of the isolation and testing as well as the whole-genome sequencing of the meat and clinical samples at GWU are described. KPSC electronic health record data were used to track UTI cases and AMR patterns among the cultured specimens. Similarly, Sutter Health electronic health record data were used to track UTI cases in its Northern California patient population. RESULTS From 2017 to 2021, overall, 12,616 retail meat samples were purchased from 472 unique stores across Southern California. In addition, 31,643 positive clinical cultures were collected from KPSC members during the same study period. CONCLUSIONS Here, we presented data collection methods for the study, which was conducted to evaluate the impact of SB27 on downstream antibiotic resistance rates in human UTI. To date, it is one of the largest studies of its kind to be conducted. The data collected during this study will be used as the foundation for future analyses specific to the various objectives of this large body of work. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/45109.
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Affiliation(s)
- Ana Florea
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Joan A Casey
- Columbia University Mailman School of Public Health, New York City, NY, United States
| | - Keeve Nachman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Lance B Price
- Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Magdalena E Pomichowski
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Harpreet S Takhar
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Vanessa Quinlivan
- Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Lee D Childs
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Meghan F Davis
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Rong Wei
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Vennis Hong
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Jennifer H Ku
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Cindy M Liu
- Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Alice Pressman
- Center for Health Systems Research, Sutter Health, Walnut Creek, CA, United States
| | - Sarah Robinson
- Center for Health Systems Research, Sutter Health, Walnut Creek, CA, United States
| | - Katia J Bruxvoort
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - S Bianca Salas
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Sara Y Tartof
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
- Department of Health Systems Science, Kaiser Permanente Bernard J Tyson School of Medicine, Pasadena, CA, United States
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7
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Aziz M, Palmer A, Iversen S, Salazar JE, Pham T, Roach K, Becker K, Kaspar U, Price LB, Baig S, Stegger M, Andersen PS, Liu CM. Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome. Sci Rep 2023; 13:6110. [PMID: 37059715 PMCID: PMC10103046 DOI: 10.1038/s41598-023-32709-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Dolosigranulum pigrum-a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the design and validation of a novel PCR assay targeting D. pigrum that is both sensitive and specific. We designed a PCR assay targeting murJ, a single-copy core species gene identified through the analysis of 21 D. pigrum whole genome sequences. The assay achieved 100% sensitivity and 100% specificity against D. pigrum and diverse bacterial isolates and an overall 91.1% sensitivity and 100% specificity using nasal swabs, detecting D. pigrum at a threshold of 1.0 × 104 D. pigrum 16S rRNA gene copies per swab. This assay adds a reliable and rapid D. pigrum detection tool to the microbiome researcher toolkit investigating the role of generalist and specialist bacteria in the nasal environment.
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Affiliation(s)
- Maliha Aziz
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Amber Palmer
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Søren Iversen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Juan E Salazar
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Tony Pham
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Kelsey Roach
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Ursula Kaspar
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Lance B Price
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Sharmin Baig
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Paal Skytt Andersen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Cindy M Liu
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA.
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8
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Li M, Park DE, Aziz M, Liu CM, Price LB, Wu Z. Integrating sample similarities into latent class analysis: a tree-structured shrinkage approach. Biometrics 2023; 79:264-279. [PMID: 34658017 PMCID: PMC10642217 DOI: 10.1111/biom.13580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/23/2021] [Accepted: 10/05/2021] [Indexed: 11/27/2022]
Abstract
This paper is concerned with using multivariate binary observations to estimate the probabilities of unobserved classes with scientific meanings. We focus on the setting where additional information about sample similarities is available and represented by a rooted weighted tree. Every leaf in the given tree contains multiple samples. Shorter distances over the tree between the leaves indicate a priori higher similarity in class probability vectors. We propose a novel data integrative extension to classical latent class models with tree-structured shrinkage. The proposed approach enables (1) borrowing of information across leaves, (2) estimating data-driven leaf groups with distinct vectors of class probabilities, and (3) individual-level probabilistic class assignment given the observed multivariate binary measurements. We derive and implement a scalable posterior inference algorithm in a variational Bayes framework. Extensive simulations show more accurate estimation of class probabilities than alternatives that suboptimally use the additional sample similarity information. A zoonotic infectious disease application is used to illustrate the proposed approach. The paper concludes by a brief discussion on model limitations and extensions.
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Affiliation(s)
- Mengbing Li
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel E. Park
- Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| | - Maliha Aziz
- Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| | - Cindy M. Liu
- Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| | - Lance B. Price
- Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| | - Zhenke Wu
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
- Michigan Institute for Data Science (MIDAS), University of Michigan, Ann Arbor, Michigan, USA
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9
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Price LB, Rogers L, Lo K. Policy reforms for antibiotic use claims in livestock. Science 2022; 376:130-132. [PMID: 35389795 DOI: 10.1126/science.abj1823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Antibiotics detected in "raised without antibiotics" cattle underscore the need to ensure the integrity of labeling claims.
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Affiliation(s)
- Lance B Price
- Antibiotic Resistance Action Center, Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Laura Rogers
- Antibiotic Resistance Action Center, Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Kevin Lo
- Food In-Depth, San Mateo, CA, USA
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10
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Randad PR, Larsen J, Kaya H, Pisanic N, Ordak C, Price LB, Aziz M, Nadimpalli ML, Rhodes S, Stewart JR, Love DC, Mohr D, Davis MF, Miller LS, Hall D, Carroll KC, Perl TM, Heaney CD. Transmission of Antimicrobial-Resistant Staphylococcus aureus Clonal Complex 9 between Pigs and Humans, United States. Emerg Infect Dis 2021; 27:740-748. [PMID: 33622471 PMCID: PMC7920674 DOI: 10.3201/eid2703.191775] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transmission of livestock-associated Staphylococcus aureus clonal complex 9 (LA-SA CC9) between pigs raised on industrial hog operations (IHOs) and humans in the United States is poorly understood. We analyzed whole-genome sequences from 32 international S. aureus CC9 isolates and 49 LA-SA CC9 isolates from IHO pigs and humans who work on or live near IHOs in 10 pig-producing counties in North Carolina, USA. Bioinformatic analysis of sequence data from the 81 isolates demonstrated 3 major LA-SA CC9 clades. North Carolina isolates all fell within a single clade (C3). High-resolution phylogenetic analysis of C3 revealed 2 subclades of intermingled IHO pig and human isolates differing by 0–34 single-nucleotide polymorphisms. Our findings suggest that LA-SA CC9 from pigs and humans share a common source and provide evidence of transmission of antimicrobial-resistant LA-SA CC9 between IHO pigs and humans who work on or live near IHOs in North Carolina.
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11
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Sieber RN, Urth TR, Petersen A, Møller CH, Price LB, Skov RL, Larsen AR, Stegger M, Larsen J. Phage-Mediated Immune Evasion and Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus in Humans. Emerg Infect Dis 2021; 26. [PMID: 33079052 PMCID: PMC7588543 DOI: 10.3201/eid2611.201442] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
These bacteria are capable of adapting to humans, leading to increased spread into the community and healthcare settings. Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) can acquire phage-encoded immune modulators, such as the immune evasion cluster (IEC), which protects bacteria from components of the human innate immune system, and the enzyme TarP, which protects against antibody-mediated immune recognition. We used whole-genome sequencing and epidemiologic investigations to study the effects of IEC- and tarP-harboring phages on household transmission of LA-MRSA in North Denmark Region during 2004–2011. We reviewed information about all patients throughout Denmark who experienced LA-MRSA infection during 2007–2018 to determine whether IEC is associated with increased spread into the general population. Horizontal acquisition of IEC in the human host was associated with increased household transmission of LA-MRSA and spillover into the community and healthcare settings, whereas we found no evidence to suggest that IEC-positive LA-MRSA isolates have become self-sustainable in the general population. By contrast, TarP did not seem to influence household transmission of LA-MRSA.
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12
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Innes GK, Nachman KE, Abraham AG, Casey JA, Patton AN, Price LB, Tartof SY, Davis MF. Contamination of Retail Meat Samples with Multidrug-Resistant Organisms in Relation to Organic and Conventional Production and Processing: A Cross-Sectional Analysis of Data from the United States National Antimicrobial Resistance Monitoring System, 2012-2017. Environ Health Perspect 2021; 129:57004. [PMID: 33978452 PMCID: PMC8114881 DOI: 10.1289/ehp7327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND During food animal production, animals are exposed to, colonized by, and sometimes infected with bacteria that may contaminate animal products with susceptible and multidrug-resistant organisms (MDRO). The United States' Organic Foods Production Act resulted in decreased antibiotic use in some animal production operations. Some studies have reported that decreased antibiotic use is associated with reduced MDRO on meat. OBJECTIVES The aim of this study was to investigate associations of meat production and processing methods with MDRO and overall bacterial contamination of retail meats. METHODS Bacterial contamination data from 2012 to 2017 for chicken breast, ground beef, ground turkey, and pork chops were downloaded from the National Antimicrobial Resistance Monitoring System. Poisson regression models with robust variance were used to estimate associations with MDRO contamination and any contamination (adjusted for year and meat type) overall, and according to bacteria genus (Salmonella, Campylobacter, Enterococcus, Escherichia coli) and meat type. RESULTS A total of 39,349 retail meat samples were linked to 216 conventional, 123 split (conventional and organic), and three organic processing facilities. MDRO contamination was similar in conventionally produced meats processed at split vs. conventional facilities but was significantly lower in organically produced meats processed at split facilities [adjusted prevalance ratio (aPR)=0.43; 95% CI: 0.30, 0.63]. Meat processed by split vs. conventional processors had higher or similar MDRO contamination for all tested bacterial genera except Campylobacter (aPR=0.29; 95% CI: 0.13, 0.64). The prevalence of any contamination was lower in samples processed at split vs. conventional facilities for aggregated samples (aPR=0.70; 95% CI: 0.68, 0.73) and all meat types and bacterial genera. DISCUSSION Organically produced and processed retail meat samples had a significantly lower prevalence of MDRO than conventionally produced and processed samples had, whereas meat from split processors had a lower prevalence of any contamination than samples from conventional processors had. Additional studies are needed to confirm findings and clarify specific production and processing practices that might explain them. https://doi.org/10.1289/EHP7327.
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Affiliation(s)
- Gabriel K. Innes
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Keeve E. Nachman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Alison G. Abraham
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Epidemiology, School of Public Health University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Joan A. Casey
- Mailman School of Public Heath, Columbia University, New York, New York, USA
| | - Andrew N. Patton
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Lance B. Price
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Sara Y. Tartof
- Kaiser Permanente Southern California, Pasadena, California, USA
| | - Meghan F. Davis
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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13
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Rhodes S, Christenson E, Nguyen A, Larsen J, Price LB, Stewart J. Getting ahead of antibiotic-resistant Staphylococcus aureus in U.S. hogs. Environ Res 2021; 196:110954. [PMID: 33676950 PMCID: PMC8119327 DOI: 10.1016/j.envres.2021.110954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Antibiotic-resistant strains of Staphylococcus aureus, an opportunistic bacterial pathogen, have emerged in industrial livestock operations and agricultural settings. In the United States, there is limited access to industrial livestock operations and farm-level antibiotic use data. As a result, studies often rely on retail meat as a proxy for direct animal sampling. To move beyond this limitation and assess S. aureus colonization in hogs, we purchased the heads of recently-slaughtered hogs and compared S. aureus populations in those raised on industrial hog operations versus those raised without antibiotics. S. aureus isolates were analyzed for antibiotic resistance and putative genotypic markers of livestock adaptation. Although methicillin-resistant S. aureus (MRSA) was not detected in this study, all of the hogs from industrial hog operations (n = 9/9) carried multidrug-resistant S. aureus (MDRSA) with two livestock-adaptation markers (scn-negative and clonal complex (CC) 9 or 398) compared to 11% of hogs raised without antibiotics (n = 1/9). Hogs from industrial operations were 9.0 times (95% confidence interval (CI): 1.4-57.1) as likely to carry livestock-adapted S. aureus and 4.5 times (95% CI: 1.3-15.3) as likely to carry MDRSA as hogs raised without antibiotics. In contrast, the majority of antibiotic-free hogs (67%, n = 6/9) contained human-adapted S. aureus (i.e. scn-positive, CC1) compared to 11% (n = 1/9) of IHO hogs. These results indicate that antibiotic use in IHO hogs may make them more conducive hosts to antibiotic-resistant, livestock-adapted S. aureus strains when compared to hogs raised without antibiotics. Our results are important, as they provide strong evidence that antibiotic use practices influence the S. aureus populations carried by U.S. hogs, supporting the need for increased access to routine monitoring of hog operations for antibiotic resistance management using a One Health framework.
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Affiliation(s)
- Sarah Rhodes
- Gillings School of Global Public Health, Department of Environmental Sciences & Engineering, University of North Carolina at Chapel Hill, 27599, USA
| | - Elizabeth Christenson
- Gillings School of Global Public Health, Department of Environmental Sciences & Engineering, University of North Carolina at Chapel Hill, 27599, USA.
| | - Allie Nguyen
- Gillings School of Global Public Health, Department of Environmental Sciences & Engineering, University of North Carolina at Chapel Hill, 27599, USA
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Lance B Price
- Milken Institute School of Public Health, Department of Environmental and Occupational Health, George Washington University, Washington DC, 20052, USA
| | - Jill Stewart
- Gillings School of Global Public Health, Department of Environmental Sciences & Engineering, University of North Carolina at Chapel Hill, 27599, USA
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14
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Martínez Arbas S, Narayanasamy S, Herold M, Lebrun LA, Hoopmann MR, Li S, Lam TJ, Kunath BJ, Hicks ND, Liu CM, Price LB, Laczny CC, Gillece JD, Schupp JM, Keim PS, Moritz RL, Faust K, Tang H, Ye Y, Skupin A, May P, Muller EEL, Wilmes P. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nat Microbiol 2021; 6:123-135. [PMID: 33139880 PMCID: PMC7752763 DOI: 10.1038/s41564-020-00794-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 09/11/2020] [Indexed: 02/07/2023]
Abstract
Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE-host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR-Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid-host and phage-host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant 'Candidatus Microthrix parvicella' population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.
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Affiliation(s)
- Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Megeno S.A., Esch-sur-Alzette, Luxembourg
| | - Malte Herold
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura A Lebrun
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Sujun Li
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Tony J Lam
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Benoît J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Nathan D Hicks
- TGen North, Flagstaff, AZ, USA
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Cindy M Liu
- TGen North, Flagstaff, AZ, USA
- Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Lance B Price
- TGen North, Flagstaff, AZ, USA
- Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Cedric C Laczny
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | | | - Paul S Keim
- TGen North, Flagstaff, AZ, USA
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Karoline Faust
- Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Haixu Tang
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Yuzhen Ye
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Neuroscience, University of California, La Jolla, CA, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Emilie E L Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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15
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Amato HK, Wong NM, Pelc C, Taylor K, Price LB, Altabet M, Jordan TE, Graham JP. Effects of concentrated poultry operations and cropland manure application on antibiotic resistant Escherichia coli and nutrient pollution in Chesapeake Bay watersheds. Sci Total Environ 2020; 735:139401. [PMID: 32464410 PMCID: PMC7324218 DOI: 10.1016/j.scitotenv.2020.139401] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 05/27/2023]
Abstract
Manure from poultry operations is typically applied to nearby cropland and may affect nutrient loading and the spread of antibiotic resistance (ABR). We analyzed the concentrations of nitrogen and phosphorus and the occurrence of ABR in Escherichia coli (E. coli) and extra-intestinal pathogenic E. coli isolates from streams draining 15 small (<19 km2) watersheds of the Chesapeake Bay with contrasting levels of concentrated poultry operations. Total nitrogen and nitrate plus nitrite concentrations increased with poultry barn density with concentrations two and three times higher, respectively, in watersheds with the highest poultry barn densities compared to those without poultry barns. Analysis of N and O isotopes in nitrate by mass spectrometry showed an increase in the proportion of 15N associated with an increase in barn density, suggesting that the nitrate associated with poultry barns originated from manure. Phosphorus concentrations were not correlated with barn density. Antibiotic susceptibility testing of putative E. coli isolates was conducted using the disk diffusion method for twelve clinically important antibiotics. Of the isolates tested, most were completely susceptible (67%); 33% were resistant to at least one antibiotic, 24% were resistant to ampicillin, 13% were resistant to cefazolin, and 8% were multi-drug resistant. Resistance to three cephalosporin drugs was positively associated with an index of manure exposure estimated from poultry barn density and proportion of cropland in a watershed. The proportion of E. coli isolates resistant to cefoxitin, cefazolin, and ceftriaxone, broad-spectrum antibiotics important in human medicine, increased by 18.9%, 16.9%, and 6.2%, respectively, at the highest estimated level of manure exposure compared to watersheds without manure exposure. Our results suggest that comparisons of small watersheds could be used to identify geographic areas where remedial actions may be needed to reduce nutrient pollution and the public health risks of ABR bacteria.
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Affiliation(s)
- Heather K Amato
- Division of Environmental Health Sciences, University of California, Berkeley School of Public Health, 2121 Berkeley Way, Berkeley, CA 94704, United States of America
| | - Nora M Wong
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, 950 New Hampshire Ave NW, Washington, D.C. 20052, United States of America
| | - Carey Pelc
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD 21037, United States of America
| | - Kishana Taylor
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Ave, Davis, CA 95616, United States of America
| | - Lance B Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, 950 New Hampshire Ave NW, Washington, D.C. 20052, United States of America
| | - Mark Altabet
- Department of Estuarine and Ocean Sciences, School for Marine Science and Technology, University of Massachusetts Dartmouth, 836 S Rodney French Blvd, New Bedford, MA 02744, United States of America
| | - Thomas E Jordan
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD 21037, United States of America
| | - Jay P Graham
- Division of Environmental Health Sciences, University of California, Berkeley School of Public Health, 2121 Berkeley Way, Berkeley, CA 94704, United States of America.
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16
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Innes GK, Randad PR, Korinek A, Davis MF, Price LB, So AD, Heaney CD. External Societal Costs of Antimicrobial Resistance in Humans Attributable to Antimicrobial Use in Livestock. Annu Rev Public Health 2020; 41:141-157. [PMID: 31910712 PMCID: PMC7199423 DOI: 10.1146/annurev-publhealth-040218-043954] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antimicrobial use (AMU) in animal agriculture contributes to antimicrobial resistance (AMR) in humans, which imposes significant health and economic costs on society. Economists call these costs negative externalities, societal costs that are not properly reflected in market prices. We review the relevant literature and develop a model to quantify the external costs of AMU in animal agriculture on AMR in humans. Parameters required for this estimate include (a) the health and economic burden of AMR in humans,(b) the impact of AMU in animal agriculture on AMR in animals, (c) the fraction of AMR in humans attributable to animal agriculture, and (d) AMU in animals. We use a well-documented historic case to estimate an externality cost of about US$1,500 per kilogram of fluoroquinolones administered in US broiler chicken production. Enhanced data collection, particularly on the third and fourth parameters, is urgently needed to quantify more fully the externalities of AMU in animal agriculture.
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Affiliation(s)
- Gabriel K Innes
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA; , , ,
| | - Pranay R Randad
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA; , , ,
| | - Anton Korinek
- Department of Economics and Darden School of Business, University of Virginia, Charlottesville, Virginia 22904, USA;
- National Bureau of Economic Research, Cambridge, Massachusetts 02138, USA
| | - Meghan F Davis
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA; , , ,
- Department of Molecular and Comparative Pathobiology, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA;
| | - Lance B Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA;
| | - Anthony D So
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA; ,
| | - Christopher D Heaney
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA; , , ,
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA; ,
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA;
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17
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Johnson JR, Johnston BD, Porter S, Thuras P, Aziz M, Price LB. Accessory Traits and Phylogenetic Background Predict Escherichia coli Extraintestinal Virulence Better Than Does Ecological Source. J Infect Dis 2019; 219:121-132. [PMID: 30085181 DOI: 10.1093/infdis/jiy459] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 07/31/2018] [Indexed: 01/11/2023] Open
Abstract
Background The distinguishing characteristics of extraintestinal pathogenic Escherichia coli (ExPEC) strains are incompletely defined. Methods We characterized 292 diverse-source human Escherichia coli isolates (116 from fecal specimens, 79 from urine specimens [of which 39 were from patients with cystitis and 40 were from patients with pyelonephritis], and 97 from blood specimens) for phylogenetic group, sequence type complex (STc), and 49 putative extraintestinal pathogenic E. coli (ExPEC)-associated virulence genes. We then assessed these traits and ecological source as predictors of illness severity in a murine sepsis model. Results The study isolates exhibited a broad range of virulence in mice. Most of the studied bacterial characteristics corresponded significantly with experimental virulence, as did ecological source and established molecular definitions of ExPEC and uropathogenic E. coli (UPEC). Multivariable modeling identified the following bacterial traits as independent predictors of illness severity both overall and among the fecal and clinical (ie, urine and blood) isolates separately: fyuA (yersiniabactin receptor), kpsM K1 (K1 capsule), and kpsM II (group 2 capsules). Molecular UPEC status predicted virulence independently only among fecal isolates. Neither ecological source (ie, clinical vs fecal) nor molecular ExPEC status added predictive power to these traits, which accounted collectively for up to 49% of the observed variation in virulence. Conclusions Among human-source E. coli isolates, specific accessory traits and phylogenetic/clonal backgrounds predict experimental virulence in a murine sepsis model better than does ecological source.
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Affiliation(s)
- James R Johnson
- Veterans Affairs Medical Center, Minneapolis, Minnesota.,University of Minnesota, Minneapolis, Minnesota
| | - Brian D Johnston
- Veterans Affairs Medical Center, Minneapolis, Minnesota.,University of Minnesota, Minneapolis, Minnesota
| | - Stephen Porter
- Veterans Affairs Medical Center, Minneapolis, Minnesota.,University of Minnesota, Minneapolis, Minnesota
| | - Paul Thuras
- George Washington University, Washington, D. C
| | - Maliha Aziz
- George Washington University, Washington, D. C
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18
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Nadimpalli M, Delarocque-Astagneau E, Love DC, Price LB, Huynh BT, Collard JM, Lay KS, Borand L, Ndir A, Walsh TR, Guillemot D. Combating Global Antibiotic Resistance: Emerging One Health Concerns in Lower- and Middle-Income Countries. Clin Infect Dis 2019; 66:963-969. [PMID: 29346620 DOI: 10.1093/cid/cix879] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/09/2017] [Indexed: 01/07/2023] Open
Abstract
Antibiotic misuse in lower- and middle-income countries (LMICs) contributes to the development of antibiotic resistance that can disseminate globally. Strategies specific to LMICs that seek to reduce antibiotic misuse by humans, but simultaneously improve antibiotic access, have been proposed. However, most approaches to date have not considered the growing impact of animal and environmental reservoirs of antibiotic resistance, which threaten to exacerbate the antibiotic resistance crisis in LMICs. In particular, current strategies do not prioritize the impacts of increased antibiotic use for terrestrial food-animal and aquaculture production, inadequate food safety, and widespread environmental pollution. Here, we propose new approaches that address emerging, One Health challenges.
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Affiliation(s)
- Maya Nadimpalli
- Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases Unit (B2PHI), Inserm, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut Pasteur, Université Paris-Saclay, France
| | - Elisabeth Delarocque-Astagneau
- Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases Unit (B2PHI), Inserm, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut Pasteur, Université Paris-Saclay, France
| | - David C Love
- Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Lance B Price
- Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, Antananarivo
| | - Bich-Tram Huynh
- Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases Unit (B2PHI), Inserm, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut Pasteur, Université Paris-Saclay, France
| | - Jean-Marc Collard
- Experimental Bacteriology Unit, Institut Pasteur of Madagascar, Antananarivo
| | - Kruy Sun Lay
- Food Microbiology and Water Analysis Laboratory and Epidemiology and Public Health Unit, Institut Pasteur of Cambodia, Phnom Penh
| | - Laurence Borand
- Epidemiology and Public Health Unit, Institut Pasteur of Cambodia, Phnom Penh
| | - Awa Ndir
- Institut Pasteur of Senegal, Dakar
| | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Institute of Infection and Immunity, Heath Park Hospital, Cardiff, United Kingdom
| | - Didier Guillemot
- Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases Unit (B2PHI), Inserm, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut Pasteur, Université Paris-Saclay, France
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19
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Randad PR, Dillen CA, Ortines RV, Mohr D, Aziz M, Price LB, Kaya H, Larsen J, Carroll KC, Smith TC, Miller LS, Heaney CD. Author Correction: Comparison of livestock-associated and community-associated Staphylococcus aureus pathogenicity in a mouse model of skin and soft tissue infection. Sci Rep 2019; 9:12811. [PMID: 31474748 PMCID: PMC6717733 DOI: 10.1038/s41598-019-46940-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Pranay R Randad
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
| | - Carly A Dillen
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Roger V Ortines
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - David Mohr
- Genetic Resources Core Facility, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Maliha Aziz
- Department of Environmental and Occupational Health, George Washington University, Washington, D.C., USA.,Antibiotic Resistance Action Center, George Washington University, Washington, D.C., USA
| | - Lance B Price
- Department of Environmental and Occupational Health, George Washington University, Washington, D.C., USA.,Antibiotic Resistance Action Center, George Washington University, Washington, D.C., USA
| | - Hülya Kaya
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Karen C Carroll
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tara C Smith
- Department of Epidemiology and Biostatistics, Kent State University, Kent, Ohio, USA
| | - Lloyd S Miller
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
| | - Christopher D Heaney
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. .,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. .,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
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20
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Liu CM, Packman ZR, Abraham AG, Serwadda DM, Nalugoda F, Aziz M, Prodger JL, Kaul R, Kalibbala S, Gray RH, Price LB, Quinn TC, Tobian AA, Reynolds SJ. The Effect of Antiretroviral Therapy Initiation on the Vaginal Microbiome in HIV-Infected Women. Open Forum Infect Dis 2019; 6:ofz328. [PMID: 31660406 DOI: 10.1093/ofid/ofz328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/11/2019] [Indexed: 11/14/2022] Open
Abstract
Background The impact of antiretroviral therapy (ART) initiation on the vaginal microbiome is unknown. This is of particular importance among women living in sub-Saharan Africa. Understanding this relationship could help elucidate if and how the host immune system interacts with the vaginal microbiome. Methods The vaginal microbiome of HIV-1/HSV-2-coinfected women (n = 92) in Uganda was evaluated from self-collected vaginal swabs 1 month pre-ART and at 4 and 6 months post-ART initiation. The vaginal microbiome was characterized by 16S rRNA gene-based sequencing and quantitative polymerase chain reaction. Vaginal community state types (CSTs) were identified using proportional abundance data. Changes in microbiome composition were assessed with permutational analyses of variance (PerMANOVA). Results Five vaginal CSTs were identified, which varied significantly by bacterial load (P < .01): CST-1 was characterized by Lactobacillus iners, CST-2 by Gardnerella, CST-3 by Gardnerella and Prevotella, CST-4 by Lactobacillus crispatus, and CST-5 was highly diverse. Vaginal microbiome composition also did not change significantly after ART initiation (P = .985). Immune reconstitution after ART initiation did not affect vaginal microbiome CST assignment (P = .722) or individual-level changes in bacterial load (log response ratio [interquartile range], -0.50 [-2.75 to 0.38] vs -0.29 [-2.03 to 1.42]; P = .40). Conclusions The vaginal microbiome of HIV-infected women was not affected by the initiation of ART or immune reconstitution in this observational study. Further research is needed to explore the long-term effects of ART treatment on the vaginal microbiome.
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Affiliation(s)
- Cindy M Liu
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC
| | - Zoe R Packman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alison G Abraham
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Ophthalmology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | | | - Maliha Aziz
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Rupert Kaul
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Ronald H Gray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Rakai Health Sciences Program, Kalisizo, Uganda
| | - Lance B Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC
| | - Thomas C Quinn
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland.,Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Aaron Ar Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Rakai Health Sciences Program, Kalisizo, Uganda
| | - Steven J Reynolds
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland.,Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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21
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Larsen J, Petersen A, Larsen AR, Sieber RN, Stegger M, Koch A, Aarestrup FM, Price LB, Skov RL. Emergence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Bloodstream Infections in Denmark. Clin Infect Dis 2019; 65:1072-1076. [PMID: 28575216 PMCID: PMC5850567 DOI: 10.1093/cid/cix504] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/28/2017] [Indexed: 11/13/2022] Open
Abstract
Background Livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398 (LA-MRSA CC398) is causing an increasing number of skin and soft tissue infections (SSTIs) in Denmark and other European countries with industrial pig production. Yet, its impact on MRSA bloodstream infections (BSIs) has not been well studied. Methods We investigated the clinical epidemiology of all human cases of LA-MRSA CC398 BSI during 2010–2015. Cases of LA-MRSA CC398 BSI were compared to cases of BSI caused by other types of MRSA and cases of SSTI caused by LA-MRSA CC398. Whole-genome sequence analysis was used to assess the phylogenetic relationship among LA-MRSA CC398 isolates from Danish pigs and cases of BSI and SSTI. Results The number of LA-MRSA CC398 BSIs and SSTIs increased over the years, peaking in 2014, when LA-MRSA CC398 accounted for 16% (7/44) and 21% (211/985) of all MRSA BSIs and SSTIs, corresponding to 1.2 and 37.4 cases of BSI and SSTI per 1000000 person-years, respectively. Most patients with LA-MRSA CC398 BSI had no contact to livestock, although they tended to live in rural areas. LA-MRSA CC398 caused 24.3 BSIs per 1000 SSTIs among people with no livestock contact, which is similar to the ratio observed for other types of MRSA. Whole-genome sequence analysis showed that most of the BSI and SSTI isolates were closely related to Danish pig isolates. Conclusions This study demonstrates that the increasing number of LA-MRSA CC398 BSIs occurred in parallel with a much larger wave of LA-MRSA CC398 SSTIs and an expanding pig reservoir.
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Affiliation(s)
| | | | | | | | - Marc Stegger
- Statens Serum Institut, Copenhagen, Denmark.,Translational Genomics Research Institute, Flagstaff, Arizona
| | | | | | - Lance B Price
- Translational Genomics Research Institute, Flagstaff, Arizona.,George Washington University, District of Columbia
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22
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Randad PR, Dillen CA, Ortines RV, Mohr D, Aziz M, Price LB, Kaya H, Larsen J, Carroll KC, Smith TC, Miller LS, Heaney CD. Comparison of livestock-associated and community-associated Staphylococcus aureus pathogenicity in a mouse model of skin and soft tissue infection. Sci Rep 2019; 9:6774. [PMID: 31043631 PMCID: PMC6494861 DOI: 10.1038/s41598-019-42919-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/08/2019] [Indexed: 11/08/2022] Open
Abstract
Industrial hog operation (IHO) workers are at increased risk of carrying Staphylococcus aureus in their nares, particularly strains that are livestock-associated (LA) and multidrug-resistant. The pathogenicity of LA-S. aureus strains remains unclear, with some prior studies suggesting reduced transmission and virulence in humans compared to community-associated methicillin-resistant (CA-MRSA) S. aureus. The objective of this study was to determine the degree to which LA-S. aureus strains contracted by IHO workers cause disease relative to a representative CA-MRSA strain in a mouse model of skin and soft tissue infection (SSTI). Mice infected with CC398 LA-S. aureus strains (IHW398-1 and IHW398-2) developed larger lesion sizes with higher bacterial burden than mice infected with CA-MRSA (SF8300) (p < 0.05). The greatest lesion size and bacterial burden was seen with a CC398 strain that produced a recurrent SSTI in an IHO worker. The LA-S. aureus infected mice had decreased IL-1β protein levels compared with CA-MRSA-infected mice (p < 0.05), suggesting a suboptimal host response to LA-S. aureus SSTIs. WGSA revealed heterogeneity in virulence factor and antimicrobial resistance genes carried by LA-S. aureus and CA-MRSA strains. The observed pathogenicity suggest that more attention should be placed on preventing the spread of LA-S. aureus into human populations.
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Affiliation(s)
- Pranay R. Randad
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland USA
| | - Carly A. Dillen
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland USA
| | - Roger V. Ortines
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland USA
| | - David Mohr
- Genetic Resources Core Facility, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Maliha Aziz
- Department of Environmental and Occupational Health, George Washington University, Washington, D.C. USA
- Antibiotic Resistance Action Center, George Washington University, Washington, D.C. USA
| | - Lance B. Price
- Department of Environmental and Occupational Health, George Washington University, Washington, D.C. USA
- Antibiotic Resistance Action Center, George Washington University, Washington, D.C. USA
| | - Hülya Kaya
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Karen C. Carroll
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Tara C. Smith
- Department of Epidemiology and Biostatistics, Kent State University, Kent, Ohio, USA
| | - Lloyd S. Miller
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland USA
| | - Christopher D. Heaney
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland USA
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland USA
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23
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Davis GS, Waits K, Nordstrom L, Grande H, Weaver B, Papp K, Horwinski J, Koch B, Hungate BA, Liu CM, Price LB. Antibiotic-resistant Escherichia coli from retail poultry meat with different antibiotic use claims. BMC Microbiol 2018; 18:174. [PMID: 30390618 PMCID: PMC6215666 DOI: 10.1186/s12866-018-1322-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 10/21/2018] [Indexed: 11/23/2022] Open
Abstract
Background We sought to determine if the prevalence of antibiotic-resistant Escherichia coli differed across retail poultry products and among major production categories, including organic, “raised without antibiotics”, and conventional. Results We collected all available brands of retail chicken and turkey—including conventional, “raised without antibiotic”, and organic products—every two weeks from January to December 2012. In total, E. coli was recovered from 91% of 546 turkey products tested and 88% of 1367 chicken products tested. The proportion of samples contaminated with E. coli was similar across all three production categories. Resistance prevalence varied by meat type and was highest among E. coli isolates from turkey for the majority of antibiotics tested. In general, production category had little effect on resistance prevalence among E. coli isolates from chicken, although resistance to gentamicin and multidrug resistance did vary. In contrast, resistance prevalence was significantly higher for 6 of the antibiotics tested—and multidrug resistance—among isolates from conventional turkey products when compared to those labelled organic or “raised without antibiotics”. E. coli isolates from chicken varied strongly in resistance prevalence among different brands within each production category. Conclusion The high prevalence of resistance among E. coli isolates from conventionally-raised turkey meat suggests greater antimicrobial use in conventional turkey production as compared to “raised without antibiotics” and organic systems. However, among E. coli from chicken meat, resistance prevalence was more strongly linked to brand than to production category, which could be caused by brand-level differences during production and/or processing, including variations in antimicrobial use. Electronic supplementary material The online version of this article (10.1186/s12866-018-1322-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregg S Davis
- George Washington University Milken Institute School of Public Health, Washington, DC, USA.
| | - Kara Waits
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA.,The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Lora Nordstrom
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Heidi Grande
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Brett Weaver
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Katerina Papp
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA.,Department of Civil and Environmental Engineering and Construction, University of Las Vegas, Las Vegas, NV, USA.,Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Joseph Horwinski
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Benjamin Koch
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Cindy M Liu
- George Washington University Milken Institute School of Public Health, Washington, DC, USA.,Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Lance B Price
- George Washington University Milken Institute School of Public Health, Washington, DC, USA.,Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
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24
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Abstract
Staphylococcus aureus strain sequence type (ST) 398 has emerged during the last decade, largely among persons who have contact with swine or other livestock. Although colonization with ST398 is common in livestock workers, infections are not frequently documented. We report recurrent ST398-IIa infection in an Iowa farmer in contact with swine and cattle.
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25
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You Y, Song L, Nonyane BAS, Price LB, Silbergeld EK. Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities. PLoS One 2018; 13:e0193820. [PMID: 29509797 PMCID: PMC5839586 DOI: 10.1371/journal.pone.0193820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/20/2018] [Indexed: 01/31/2023] Open
Abstract
New human pathogens can emerge from the livestock-human interface and spread into human populations through many pathways including livestock products. Occupational contact with livestock is a risk factor for exposure to those pathogens and may cause further spreading of those pathogens in the community. The current study used whole genome sequencing to explore nasal Staphylococcus aureus obtained from hog slaughterhouse workers and their community members, all of whom resided in a livestock-dense region in rural North Carolina. Sequence data were analyzed for lineage distribution, pathogenicity-related genomic features, and mobile genetic elements. We observed evidence of nasal S. aureus differences between hog workers and non-workers. Nasal S. aureus from hog workers showed a greater lineage diversity than nasal S. aureus from community residents. Hog worker isolates were less likely to carry the φSa3 prophage and human-specific immune evasion cluster genes than community resident isolates (φSa3 prophage: 54.5% vs. 91.7%, Benjamini-Hochberg (BH) corrected p = 0.035; immune evasion cluster genes: 66.7% vs. 100%, BH p = 0.021). Hog worker isolates had a lower prevalence and diversity of enterotoxins than community resident isolates, particularly lacking the enterotoxin gene cluster (39.4% vs. 70.8%, BH p = 0.125). Moreover, hog worker isolates harbored more diverse antibiotic resistance genes, with a higher prevalence of carriage of multiple resistance genes, than community resident isolates (75.8% vs. 29.2%, BH p = 0.021). Phylogenetic analysis of all ST5 isolates, the most abundant lineage in the collection, further supported separation of isolates from hog workers and non-workers. Together, our observations suggest impact of occupational contact with livestock on nasal S. aureus colonization and highlight the need for further research on the complex epidemiology of S. aureus at the livestock-human interface.
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Affiliation(s)
- Yaqi You
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Li Song
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Bareng A. S. Nonyane
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Lance B. Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Ellen K. Silbergeld
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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26
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Affiliation(s)
- Alison Holmes
- Department of Infectious Diseases and the NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, UK
| | - Mark Holmes
- Department of Veterinary Medicine, University of Cambridge, UK
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital, Sydney, Australia
| | - Lance B Price
- Milken Institute School of Public Health, George Washington University, Washington DC, US
| | - Arnfinn Sundsfjord
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø -The Arctic University of Norway
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27
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Affiliation(s)
- Lance B. Price
- Milken Institute School of Public Health, George Washington University, Washington DC, United States of America
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- * E-mail:
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Benjamin J. Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Gregg S. Davis
- Milken Institute School of Public Health, George Washington University, Washington DC, United States of America
| | - Cindy M. Liu
- Milken Institute School of Public Health, George Washington University, Washington DC, United States of America
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28
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Davis GS, Price LB. Recent Research Examining Links Among Klebsiella pneumoniae from Food, Food Animals, and Human Extraintestinal Infections. Curr Environ Health Rep 2017; 3:128-35. [PMID: 27022987 DOI: 10.1007/s40572-016-0089-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Klebsiella pneumoniae is a colonizer of livestock, a contaminant of retail meats and vegetables, and a cause of extraintestinal infections in humans. Antibiotic-resistant strains of K. pneumoniae are becoming increasingly prevalent among hospital and community-acquired infections. Antibiotics are used extensively in conventional food-animal production, where they select for antibiotic-resistant bacteria. Antibiotic-resistant K. pneumoniae has been isolated from livestock as well as from a variety of retail meats, seafood, and vegetables. Furthermore, recent phylogenetic analyses suggest close relationships between K. pneumoniae from humans and livestock. Therefore, it is essential that we quantify the contribution of foodborne K. pneumoniae to antibiotic-resistant human infections.
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Affiliation(s)
- Gregg S Davis
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, 950 New Hampshire Ave NW, Washington, DC, 20052, USA. .,Antibiotic Resistance Action Center, Milken Institute School of Public Health, 950 New Hampshire Ave, NW, Washington, DC, 20052, USA.
| | - Lance B Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, 950 New Hampshire Ave NW, Washington, DC, 20052, USA.,Antibiotic Resistance Action Center, Milken Institute School of Public Health, 950 New Hampshire Ave, NW, Washington, DC, 20052, USA
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Larsen J, Stegger M, Andersen PS, Petersen A, Larsen AR, Westh H, Agersø Y, Fetsch A, Kraushaar B, Käsbohrer A, Feβler AT, Schwarz S, Cuny C, Witte W, Butaye P, Denis O, Haenni M, Madec JY, Jouy E, Laurent F, Battisti A, Franco A, Alba P, Mammina C, Pantosti A, Monaco M, Wagenaar JA, de Boer E, van Duijkeren E, Heck M, Domínguez L, Torres C, Zarazaga M, Price LB, Skov RL. Evidence for Human Adaptation and Foodborne Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus. Clin Infect Dis 2016; 63:1349-1352. [PMID: 27655995 PMCID: PMC5091345 DOI: 10.1093/cid/ciw532] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/27/2016] [Indexed: 12/03/2022] Open
Abstract
We investigated the evolution and epidemiology of a novel livestock-associated methicillin-resistant Staphylococcus aureus strain, which colonizes and infects urban-dwelling Danes even without a Danish animal reservoir. Genetic evidence suggests both poultry and human adaptation, with poultry meat implicated as a probable source.
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Affiliation(s)
| | - Marc Stegger
- Statens Serum Institut, Copenhagen.,Translational Genomics Research Institute, Flagstaff, Arizona
| | - Paal S Andersen
- Statens Serum Institut, Copenhagen.,University of Copenhagen, Frederiksberg
| | | | | | - Henrik Westh
- University of Copenhagen, Frederiksberg.,Hvidovre Hospital
| | | | | | | | | | | | | | | | | | - Patrick Butaye
- Ghent University.,Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | | | - Marisa Haenni
- French Agency for Food, Environmental and Occupational Health and Safety, Lyon
| | - Jean-Yves Madec
- French Agency for Food, Environmental and Occupational Health and Safety, Lyon
| | - Eric Jouy
- French Agency for Food, Environmental and Occupational Health and Safety, Ploufragan, France
| | | | - Antonio Battisti
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana
| | - Alessia Franco
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana
| | - Patricia Alba
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana
| | | | | | | | | | - Enne de Boer
- Netherlands Food and Consumer Product Safety Authority, Utrecht
| | | | - Max Heck
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | | | | | - Lance B Price
- Translational Genomics Research Institute, Flagstaff, Arizona.,George Washington University, Washington D.C
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Johnson JR, Davis G, Clabots C, Johnston BD, Porter S, DebRoy C, Pomputius W, Ender PT, Cooperstock M, Slater BS, Banerjee R, Miller S, Kisiela D, Sokurenko EV, Aziz M, Price LB. Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis. Open Forum Infect Dis 2016; 3:ofw129. [PMID: 27703993 PMCID: PMC5047392 DOI: 10.1093/ofid/ofw129] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/14/2016] [Indexed: 01/08/2023] Open
Abstract
In a whole genome-based phylogeny, clinical and fecal isolates of Escherichia coli sequence type 131 (H30R1 and H30Rx subclones) from six households formed household-specific clusters, interspersed among reference ST131 genomes. This supported the fecal-urethral hypothesis and confirmed within-household strain sharing. Background. Within-household sharing of strains from the resistance-associated H30R1 and H30Rx subclones of Escherichia coli sequence type 131 (ST131) has been inferred based on conventional typing data, but it has been assessed minimally using whole genome sequence (WGS) analysis. Methods. Thirty-three clinical and fecal isolates of ST131-H30R1 and ST131-H30Rx, from 20 humans and pets in 6 households, underwent WGS analysis for comparison with 52 published ST131 genomes. Phylogenetic relationships were inferred using a bootstrapped maximum likelihood tree based on core genome sequence polymorphisms. Accessory traits were compared between phylogenetically similar isolates. Results. In the WGS-based phylogeny, isolates clustered strictly by household, in clades that were distributed widely across the phylogeny, interspersed between H30R1 and H30Rx comparison genomes. For only 1 household did the core genome phylogeny place epidemiologically unlinked isolates together with household isolates, but even there multiple differences in accessory genome content clearly differentiated these 2 groups. The core genome phylogeny supported within-household strain sharing, fecal-urethral urinary tract infection pathogenesis (with the entire household potentially providing the fecal reservoir), and instances of host-specific microevolution. In 1 instance, the household's index strain persisted for 6 years before causing a new infection in a different household member. Conclusions. Within-household sharing of E coli ST131 strains was confirmed extensively at the genome level, as was long-term colonization and repeated infections due to an ST131-H30Rx strain. Future efforts toward surveillance and decolonization may need to address not just the affected patient but also other human and animal household members.
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Affiliation(s)
- James R Johnson
- Minneapolis Veterans Affairs Health Care System, Minnesota; University of Minnesota, Minneapolis
| | - Gregg Davis
- George Washington University , Washington, District of Columbia
| | - Connie Clabots
- Minneapolis Veterans Affairs Health Care System , Minnesota
| | - Brian D Johnston
- Minneapolis Veterans Affairs Health Care System, Minnesota; University of Minnesota, Minneapolis
| | - Stephen Porter
- Minneapolis Veterans Affairs Health Care System , Minnesota
| | | | | | - Peter T Ender
- St. Luke's University Hospital and Health Network , Bethlehem, Pennsylvania
| | | | | | | | | | | | | | - Maliha Aziz
- George Washington University , Washington, District of Columbia
| | - Lance B Price
- George Washington University , Washington, District of Columbia
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32
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Liu CM, Prodger JL, Tobian AAR, Serwadda D, Galiwango RM, Nalugoda F, Kighoma N, Mwinike J, Anyokorit M, Price LB, Wawer MJ, Kigozi G, Gray RH. Genital Anaerobic Bacterial Overgrowth and the PrePex Male Circumcision Device, Rakai, Uganda. J Infect Dis 2016; 214:595-8. [PMID: 27190185 DOI: 10.1093/infdis/jiw182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/28/2016] [Indexed: 12/28/2022] Open
Abstract
The PrePex circumcision device causes ischemic necrosis of the foreskin, raising concerns of anaerobic overgrowth. We compared the subpreputial microbiome of 2 men 7 days after PrePex device placement to that of 145 uncircumcised men in Rakai, Uganda, using 16S ribosomal (rRNA) RNA gene-based quantitative polymerase chain reaction analysis and sequencing. PrePex users had higher absolute abundance of all bacteria than uncircumcised men (P = .001), largely due to increased numbers of the following anaerobes: Porphyromonas (5.2 × 10(7) 16S rRNA gene copies/swab in the PrePex group and 1.1 × 10(6) 16S rRNA gene copies/swab in uncircumcised men; P = .002), Peptoniphilus (1.0 × 10(7) and 1.8 × 10(6) 16S rRNA gene copies/swab, respectively; P < .05), Anaerococcus (1.0 × 10(7) and 1.1 × 10(6) 16S rRNA gene copies/swab, respectively; P < .001), and Campylobacter ureolyticus (1.7 × 10(5) and 1.6 × 10(7)16S rRNA gene copies/swab, respectively; P < .001). The PrePex-associated increase in anaerobes may account for unpleasant odor and a possible heightened risk of tetanus.
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Affiliation(s)
- Cindy M Liu
- Department of Pathology, School of Medicine Center for Microbial Genetics and Genomics, Northern Arizona University Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona
| | - Jessica L Prodger
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Aaron A R Tobian
- Department of Pathology, School of Medicine Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland Rakai Health Sciences Program, Entebbe, Uganda
| | | | | | | | | | | | | | - Lance B Price
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University
| | - Maria J Wawer
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland Rakai Health Sciences Program, Entebbe, Uganda
| | | | - Ronald H Gray
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland Rakai Health Sciences Program, Entebbe, Uganda
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Wymore AS, Liu CM, Hungate BA, Schwartz E, Price LB, Whitham TG, Marks JC. The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem. Microb Ecol 2016; 71:825-834. [PMID: 26879940 DOI: 10.1007/s00248-016-0735-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 01/31/2016] [Indexed: 06/05/2023]
Abstract
Foliar chemistry influences leaf decomposition, but little is known about how litter chemistry affects the assemblage of bacterial communities during decomposition. Here we examined relationships between initial litter chemistry and the composition of the bacterial community in a stream ecosystem. We incubated replicated genotypes of Populus fremontii and P. angustifolia leaf litter that differ in percent tannin and lignin, then followed changes in bacterial community composition during 28 days of decomposition using 16S rRNA gene-based pyrosequencing. Using a nested experimental design, the majority of variation in bacterial community composition was explained by time (i.e., harvest day) (R(2) = 0.50). Plant species, nested within harvest date, explained a significant but smaller proportion of the variation (R(2) = 0.03). Significant differences in community composition between leaf species were apparent at day 14, but no significant differences existed among genotypes. Foliar chemistry correlated significantly with community composition at day 14 (r = 0.46) indicating that leaf litter with more similar phytochemistry harbor bacterial communities that are alike. Bacteroidetes and β-proteobacteria dominated the bacterial assemblage on decomposing leaves, and Verrucomicrobia and α- and δ-proteobacteria became more abundant over time. After 14 days, bacterial diversity diverged significantly between leaf litter types with fast-decomposing P. fremontii hosting greater richness than slowly decomposing P. angustifolia; however, differences were no longer present after 28 days in the stream. Leaf litter tannin, lignin, and lignin: N ratios all correlated negatively with diversity. This work shows that the bacterial community on decomposing leaves in streams changes rapidly over time, influenced by leaf species via differences in genotype-level foliar chemistry.
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Affiliation(s)
- Adam S Wymore
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA.
| | - Cindy M Liu
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Lance B Price
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Public Health and Health Services, George Washington University, Washington, D.C., USA
| | - Thomas G Whitham
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Jane C Marks
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
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Morrissey EM, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, Koch BJ, Liu CM, Hayer M, McHugh TA, Marks JC, Price LB, Hungate BA. Phylogenetic organization of bacterial activity. ISME J 2016; 10:2336-40. [PMID: 26943624 PMCID: PMC4989319 DOI: 10.1038/ismej.2016.28] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 11/25/2022]
Abstract
Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with 13C and 18O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions.
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Affiliation(s)
- Ember M Morrissey
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - J Gregory Caporaso
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.,Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Natasja van Gestel
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Cindy M Liu
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.,Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, AZ, USA.,Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Theresa A McHugh
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Lance B Price
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, AZ, USA.,Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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Leibler JH, Jordan JA, Brownstein K, Lander L, Price LB, Perry MJ. Staphylococcus aureus Nasal Carriage among Beefpacking Workers in a Midwestern United States Slaughterhouse. PLoS One 2016; 11:e0148789. [PMID: 26866374 PMCID: PMC4750916 DOI: 10.1371/journal.pone.0148789] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/22/2016] [Indexed: 11/19/2022] Open
Abstract
Occupational contact with livestock is an established risk factor for exposure to livestock-associated methicillin-resistant Staphylococcus aureus (MRSA), particularly among industrial swine workers. While S. aureus is known to infect cattle, livestock-associated S. aureus carriage among workers in the beef production chain has received limited attention. Beefpacking workers, who slaughter, butcher and process cattle, have intensified exposure to potentially infectious animal materials and may be at risk of livestock-associated S. aureus exposure. We conducted a cross-sectional study of beefpacking workers (n = 137) at an industrial slaughterhouse in the Midwestern United States to evaluate prevalence and characteristics of S. aureus nasal colonization, specifically the absence of the scn gene to identify putative association with livestock, antibiotic susceptibility, presence of Panton-Valentin leukocidin (PVL) genes lukS-PV and lukF-PV, and spa type. Overall prevalence of S. aureus nasal carriage was 27.0%. No workers carried livestock-associated MRSA. Methicillin-sensitive S. aureus isolates (MSSA) recovered from five workers (3.6%) lacked the scn gene and were considered putative livestock-associated S. aureus (pLA-SA). Among pLA-SA isolates, spa types t338, t748, t1476 and t2379 were identified. To our knowledge, these spa types have not previously been identified as associated with livestock. Prevalence of human-adapted MRSA carriage in workers was 3.6%. MRSA isolates were identified as spa types t002, t008 and t024, and four of five MRSA isolates were PVL-positive. To date, this is the first study to indicate that industrial beefpacking workers in the United States may be exposed to livestock-associated S. aureus, notably MSSA, and to spa types not previously identified in livestock and livestock workers. Occupational exposure to livestock-associated S. aureus in the beef production chain requires further epidemiologic investigation.
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Affiliation(s)
- Jessica H. Leibler
- Department of Environmental Health, Boston University School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
| | - Jeanne A. Jordan
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, United States of America
| | - Kirsten Brownstein
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, United States of America
| | - Lina Lander
- Department of Epidemiology, College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Lance B. Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, United States of America
- Division of Pathogen Genomics, the Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Melissa J. Perry
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, United States of America
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Abstract
Industrial food animal production (IFAP) is a source of environmental microbial and chemical hazards. A growing body of literature suggests that populations living near these operations and manure-applied crop fields are at elevated risk for several health outcomes. We reviewed the literature published since 2000 and identified four health outcomes consistently and positively associated with living near IFAP: respiratory outcomes, methicillin-resistant Staphylococcus aureus (MRSA), Q fever, and stress/mood. We found moderate evidence of an association of IFAP with quality of life and limited evidence of an association with cognitive impairment, Clostridium difficile, Enterococcus, birth outcomes, and hypertension. Distance-based exposure metrics were used by 17/33 studies reviewed. Future work should investigate exposure through drinking water and must improve exposure assessment with direct environmental sampling, modeling, and high-resolution DNA typing methods. Investigators should not limit study to high-profile pathogens like MRSA but include a broader range of pathogens, as well as other disease outcomes.
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Affiliation(s)
- Joan A Casey
- Robert Wood Johnson Foundation Health and Society Scholars Program, UC San Francisco and UC Berkeley, 50 University Hall, Room 583, Berkeley, CA, 94720-7360, USA,
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Affiliation(s)
- Timothy P Robinson
- Livestock Systems and Environment, International Livestock Research Institute, 00100 Nairobi, Kenya.
| | - Heiman F L Wertheim
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi, Vietnam; Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK; Department of Medical Microbiology, Radboudumc, Nijmegen, Netherlands
| | | | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lance B Price
- Milken Institute School of Public Health, George Washington University, Washington DC, USA; Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, USA
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Tobin MR, Goldshear JL, Price LB, Graham JP, Leibler JH. A Framework to Reduce Infectious Disease Risk from Urban Poultry in the United States. Public Health Rep 2015; 130:380-91. [PMID: 26346104 DOI: 10.1177/003335491513000417] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Backyard poultry ownership is increasingly common in U.S. cities and is regulated at the local level. Human contact with live poultry is a well-known risk for infection with zoonotic pathogens, notably Salmonella, yet the ability of local jurisdictions to reduce the risk of infectious disease transmission from poultry to humans is unstudied. We reviewed urban poultry ordinances in the United States and reported Salmonella outbreaks from backyard poultry to identify regulatory gaps in preventing zoonotic pathogen transmission. Based on this analysis, we propose regulatory guidelines for U.S. cities to reduce infectious disease risk from backyard poultry ownership. METHODS We assessed local ordinances in the 150 most populous U.S. jurisdictions for content related to noncommercial poultry ownership using online resources and communications with government officials. We also performed a literature review using publicly available data sources to identify human infectious disease outbreaks caused by contact with backyard poultry. RESULTS Of the cities reviewed, 93% (n=139) permit poultry in some capacity. Most urban poultry ordinances share common characteristics focused on reducing nuisance to neighbors. Ordinances do not address many pathways of transmission relevant to poultry-to-human transmission of pathogens, such as manure management. CONCLUSIONS To reduce the risk of pathogen exposure from backyard poultry, urban ordinances should incorporate the following seven components: limited flock size, composting of manure in sealed containers, prohibition of slaughter, required veterinary care to sick birds, appropriate disposal of dead birds, annual permits linked to consumer education, and a registry of poultry owners.
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Affiliation(s)
| | | | - Lance B Price
- George Washington University, Milkin Institute School of Public Health, Department of Environmental and Occupational Health, Washington, DC ; Translational Genomics Research Institute, Center for Food Microbiology and Environmental Health, Flagstaff, AZ
| | - Jay P Graham
- George Washington University, Milkin Institute School of Public Health, Department of Environmental and Occupational Health, Washington, DC
| | - Jessica H Leibler
- Boston University School of Public Health, Department of Environmental Health, Boston, MA
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Davis GS, Waits K, Nordstrom L, Weaver B, Aziz M, Gauld L, Grande H, Bigler R, Horwinski J, Porter S, Stegger M, Johnson JR, Liu CM, Price LB. Intermingled Klebsiella pneumoniae Populations Between Retail Meats and Human Urinary Tract Infections. Clin Infect Dis 2015. [PMID: 26206847 PMCID: PMC4551003 DOI: 10.1093/cid/civ428] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a common colonizer of the gastrointestinal tract of humans, companion animals, and livestock. To better understand potential contributions of foodborne K. pneumoniae to human clinical infections, we compared K. pneumoniae isolates from retail meat products and human clinical specimens to assess their similarity based on antibiotic resistance, genetic relatedness, and virulence. METHODS Klebsiella pneumoniae was isolated from retail meats from Flagstaff grocery stores in 2012 and from urine and blood specimens from Flagstaff Medical Center in 2011-2012. Isolates underwent antibiotic susceptibility testing and whole-genome sequencing. Genetic relatedness of the isolates was assessed using multilocus sequence typing and phylogenetic analyses. Extraintestinal virulence of several closely related meat-source and urine isolates was assessed using a murine sepsis model. RESULTS Meat-source isolates were significantly more likely to be multidrug resistant and resistant to tetracycline and gentamicin than clinical isolates. Four sequence types occurred among both meat-source and clinical isolates. Phylogenetic analyses confirmed close relationships among meat-source and clinical isolates. Isolates from both sources showed similar virulence in the mouse sepsis model. CONCLUSIONS Meat-source K. pneumoniae isolates were more likely than clinical isolates to be antibiotic resistant, which could reflect selective pressures from antibiotic use in food-animal production. The close genetic relatedness of meat-source and clinical isolates, coupled with similarities in virulence, suggest that the barriers to transmission between these 2 sources are low. Taken together, our results suggest that retail meat is a potential vehicle for transmitting virulent, antibiotic-resistant K. pneumoniae from food animals to humans.
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Affiliation(s)
- Gregg S Davis
- George Washington University Milken Institute School of Public Health, Washington D.C
| | - Kara Waits
- Translational Genomics Research Institute
| | | | | | - Maliha Aziz
- George Washington University Milken Institute School of Public Health, Washington D.C. Translational Genomics Research Institute
| | | | | | | | | | | | - Marc Stegger
- Translational Genomics Research Institute Statens Serum Institut, Copenhagen, Denmark
| | - James R Johnson
- VA Healthcare System Minneapolis, Minnesota Department of Medicine, University of Minnesota, Minneapolis
| | - Cindy M Liu
- Translational Genomics Research Institute Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Lance B Price
- George Washington University Milken Institute School of Public Health, Washington D.C. Translational Genomics Research Institute
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Driebe EM, Sahl JW, Roe C, Bowers JR, Schupp JM, Gillece JD, Kelley E, Price LB, Pearson TR, Hepp CM, Brzoska PM, Cummings CA, Furtado MR, Andersen PS, Stegger M, Engelthaler DM, Keim PS. Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus. PLoS One 2015; 10:e0130955. [PMID: 26161978 PMCID: PMC4498916 DOI: 10.1371/journal.pone.0130955] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 05/27/2015] [Indexed: 12/29/2022] Open
Abstract
Staphylococcus aureus is an important clinical pathogen worldwide and understanding this organism's phylogeny and, in particular, the role of recombination, is important both to understand the overall spread of virulent lineages and to characterize outbreaks. To further elucidate the phylogeny of S. aureus, 35 diverse strains were sequenced using whole genome sequencing. In addition, 29 publicly available whole genome sequences were included to create a single nucleotide polymorphism (SNP)-based phylogenetic tree encompassing 11 distinct lineages. All strains of a particular sequence type fell into the same clade with clear groupings of the major clonal complexes of CC8, CC5, CC30, CC45 and CC1. Using a novel analysis method, we plotted the homoplasy density and SNP density across the whole genome and found evidence of recombination throughout the entire chromosome, but when we examined individual clonal lineages we found very little recombination. However, when we analyzed three branches of multiple lineages, we saw intermediate and differing levels of recombination between them. These data demonstrate that in S. aureus, recombination occurs across major lineages that subsequently expand in a clonal manner. Estimated mutation rates for the CC8 and CC5 lineages were different from each other. While the CC8 lineage rate was similar to previous studies, the CC5 lineage was 100-fold greater. Fifty known virulence genes were screened in all genomes in silico to determine their distribution across major clades. Thirty-three genes were present variably across clades, most of which were not constrained by ancestry, indicating horizontal gene transfer or gene loss.
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Affiliation(s)
- Elizabeth M Driebe
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Jason W Sahl
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Chandler Roe
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Jolene R Bowers
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - James M Schupp
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - John D Gillece
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Erin Kelley
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Lance B Price
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Talima R Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Crystal M Hepp
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Pius M Brzoska
- Thermo Fisher Scientific, South San Francisco, California, United States of America
| | - Craig A Cummings
- Thermo Fisher Scientific, South San Francisco, California, United States of America
| | - Manohar R Furtado
- Thermo Fisher Scientific, South San Francisco, California, United States of America
| | - Paal S Andersen
- Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - David M Engelthaler
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Paul S Keim
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America; Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
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Liu CM, Price LB, Hungate BA, Abraham AG, Larsen LA, Christensen K, Stegger M, Skov R, Andersen PS. Staphylococcus aureus and the ecology of the nasal microbiome. Sci Adv 2015; 1:e1400216. [PMID: 26601194 PMCID: PMC4640600 DOI: 10.1126/sciadv.1400216] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/21/2015] [Indexed: 05/10/2023]
Abstract
The human microbiome can play a key role in host susceptibility to pathogens, including in the nasal cavity, a site favored by Staphylococcus aureus. However, what determines our resident nasal microbiota-the host or the environment-and can interactions among nasal bacteria determine S. aureus colonization? Our study of 46 monozygotic and 43 dizygotic twin pairs revealed that nasal microbiota is an environmentally derived trait, but the host's sex and genetics significantly influence nasal bacterial density. Although specific taxa, including lactic acid bacteria, can determine S. aureus colonization, their negative interactions depend on thresholds of absolute abundance. These findings demonstrate that nasal microbiota is not fixed by host genetics and opens the possibility that nasal microbiota may be manipulated to prevent or eliminate S. aureus colonization.
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Affiliation(s)
- Cindy M. Liu
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011, USA
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ 86001, USA
- Corresponding author. E-mail:
| | - Lance B. Price
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ 86001, USA
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Alison G. Abraham
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Lisbeth A. Larsen
- The Danish Twin Registry, University of Southern Denmark, Odense, Denmark
| | - Kaare Christensen
- The Danish Twin Registry, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics and Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Marc Stegger
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ 86001, USA
- Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Robert Skov
- Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Paal Skytt Andersen
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ 86001, USA
- Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
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Ahmed LN, Price LB, Graham JP. An exploratory study of dog park visits as a risk factor for exposure to drug-resistant extra-intestinal pathogenic E. coli (ExPEC). BMC Res Notes 2015; 8:137. [PMID: 25886556 PMCID: PMC4397871 DOI: 10.1186/s13104-015-1103-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 03/31/2015] [Indexed: 11/22/2022] Open
Abstract
Background Extraintestinal pathogenic E. coli (ExPEC) are common causative agents of urinary tract infections in humans. Dogs have been found to harbor ExPEC. This study tested stool samples from dogs (n = 16), the shoes of dog park visitors (n = 16) and the shoes of controls (n = 16) for ExPEC. Phenotypic resistance of isolates was characterized. Findings ExPEC were present in one-third of the dog stool samples, 9% of the samples from the shoes of dog park visitors and 6% of control samples. Half of the ExPEC isolates were multi-drug resistant. Discussion The findings suggest that dogs may be an important source of antibiotic resistant ExPEC. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1103-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lubna N Ahmed
- Department of Environmental & Occupational Health, Milken Institute School of Public Health, George Washington University, 950 New Hampshire Ave. NW, Washington, DC, 20052, USA.
| | - Lance B Price
- Department of Environmental & Occupational Health, Milken Institute School of Public Health, George Washington University, 950 New Hampshire Ave. NW, Washington, DC, 20052, USA.
| | - Jay P Graham
- Department of Environmental & Occupational Health, Milken Institute School of Public Health, George Washington University, 950 New Hampshire Ave. NW, Washington, DC, 20052, USA.
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Liu CM, Kohanski MA, Mendiola M, Soldanova K, Dwan MG, Lester R, Nordstrom L, Price LB, Lane AP. Impact of saline irrigation and topical corticosteroids on the postsurgical sinonasal microbiota. Int Forum Allergy Rhinol 2014; 5:185-90. [PMID: 25556553 DOI: 10.1002/alr.21467] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 11/01/2014] [Accepted: 11/07/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Topical treatments with nasal saline irrigation, topical steroid sprays, or corticosteroid rinses can improve sinonasal symptoms in chronic rhinosinusitis (CRS). However, the impact of these therapies on commensals (Corynebacterium) and on biofilm pathogens associated with CRS (Staphylococcus aureus and Pseudomonas) is not well characterized. METHODS Paired nasal and sinus swabs were collected endoscopically from 28 controls and 14 CRS patients with nasal polyposis (CRSwNP) who had not received systemic antibiotics or corticosteroids in the previous 8 weeks. Total DNA from swab eluents were extracted and analyzed by 16S rRNA gene-based pyrosequencing. A total of 359,077 reads were obtained and classified taxonomically. The association of use of topical therapies with sinonasal microbiota composition was assessed by factor/vector-fitting. The proportional abundances of sinonasal bacteria between topical therapy users and nonusers were further compared by 2-tailed Kolmogorov-Smirnov test among controls and among CRSwNP participants. RESULTS Nasal saline irrigation, with or without added budesonide, was not associated with significantly distinct sinonasal microbiota composition or significantly decreased Pseudomonas or S. aureus abundances among either controls or CRSwNP participants. Corynebacterium was slightly lower in controls that reported using saline irrigation than those who did not. No significant association was found between nasal saline irrigation and the proportional abundances of Pseudomonas, S. aureus, and Corynebacterium in CRSwNP participants. However, male CRSwNP patients were noted to have significantly higher Corynebacterium proportional abundances than their female counterparts. The use of topical steroid sprays was associated with a distinct microbiota in control subjects, characterized by higher proportional abundances of Dolosigranulum and Simonsiella and a lower proportional abundance of Campylobacter. CONCLUSION Nasal saline irrigation is not associated with a distinct alteration in the proportional abundance of commensal bacteria or biofilm-forming pathogens in CRSwNP patients. However, use of topical intranasal corticosteroid sprays in control subjects is associated with a distinct sinonasal microbiota.
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Affiliation(s)
- Cindy M Liu
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD; Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ; Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ
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Mau RL, Liu CM, Aziz M, Schwartz E, Dijkstra P, Marks JC, Price LB, Keim P, Hungate BA. Linking soil bacterial biodiversity and soil carbon stability. ISME J 2014; 9:1477-80. [PMID: 25350158 DOI: 10.1038/ismej.2014.205] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 09/05/2014] [Accepted: 09/22/2014] [Indexed: 10/24/2022]
Abstract
Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this 'priming' effect. A single-substrate pulse suppressed native soil C loss and reduced bacterial diversity, whereas repeated substrate pulses stimulated native soil C loss and increased diversity. Increased diversity after repeated C amendments contrasts with resource competition theory, and may be explained by increased predation as evidenced by a decrease in bacterial 16S rRNA gene copies. Our results suggest that biodiversity and composition of the soil microbial community change in concert with its functioning, with consequences for native soil C stability.
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Affiliation(s)
- Rebecca L Mau
- 1] Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA [2] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA
| | - Cindy M Liu
- 1] Translational Genomics Research Institute (TGen North), Flagstaff, AZ, USA [2] Microbial Genetic and Genomics Center (MGGen), Northern Arizona University, Flagstaff, AZ, USA
| | - Maliha Aziz
- Translational Genomics Research Institute (TGen North), Flagstaff, AZ, USA
| | - Egbert Schwartz
- 1] Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA [2] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- 1] Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA [2] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA
| | - Jane C Marks
- 1] Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA [2] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA
| | - Lance B Price
- Translational Genomics Research Institute (TGen North), Flagstaff, AZ, USA
| | - Paul Keim
- 1] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA [2] Translational Genomics Research Institute (TGen North), Flagstaff, AZ, USA [3] Microbial Genetic and Genomics Center (MGGen), Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- 1] Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA [2] Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, USA
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Liu CM, Osborne BJW, Hungate BA, Shahabi K, Huibner S, Lester R, Dwan MG, Kovacs C, Contente-Cuomo TL, Benko E, Aziz M, Price LB, Kaul R. The semen microbiome and its relationship with local immunology and viral load in HIV infection. PLoS Pathog 2014; 10:e1004262. [PMID: 25058515 PMCID: PMC4110035 DOI: 10.1371/journal.ppat.1004262] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 06/06/2014] [Indexed: 12/02/2022] Open
Abstract
Semen is a major vector for HIV transmission, but the semen HIV RNA viral load (VL) only correlates moderately with the blood VL. Viral shedding can be enhanced by genital infections and associated inflammation, but it can also occur in the absence of classical pathogens. Thus, we hypothesized that a dysregulated semen microbiome correlates with local HIV shedding. We analyzed semen samples from 49 men who have sex with men (MSM), including 22 HIV-uninfected and 27 HIV-infected men, at baseline and after starting antiretroviral therapy (ART) using 16S rRNA gene-based pyrosequencing and quantitative PCR. We studied the relationship of semen bacteria with HIV infection, semen cytokine levels, and semen VL by linear regression, non-metric multidimensional scaling, and goodness-of-fit test. Streptococcus, Corynebacterium, and Staphylococcus were common semen bacteria, irrespective of HIV status. While Ureaplasma was the more abundant Mollicutes in HIV-uninfected men, Mycoplasma dominated after HIV infection. HIV infection was associated with decreased semen microbiome diversity and richness, which were restored after six months of ART. In HIV-infected men, semen bacterial load correlated with seven pro-inflammatory semen cytokines, including IL-6 (p = 0.024), TNF-α (p = 0.009), and IL-1b (p = 0.002). IL-1b in particular was associated with semen VL (r2 = 0.18, p = 0.02). Semen bacterial load was also directly linked to the semen HIV VL (r2 = 0.15, p = 0.02). HIV infection reshapes the relationship between semen bacteria and pro-inflammatory cytokines, and both are linked to semen VL, which supports a role of the semen microbiome in HIV sexual transmission. The classical paradigm of HIV infectivity centers on the blood HIV RNA viral load. However, while other fluid compartments such as semen and cerebrospinal fluid can have distinct viral loads from blood, the causes of localized HIV shedding are not fully understood. Since the semen viral load is an independent predictor of HIV transmission risk, it is critical to understand the local factors that trigger increased semen viral shedding in order to develop novel preventative strategies. Here, we evaluated the semen microbiome, bacterial load, and cytokine levels in 22 HIV-uninfected men who have sex with men (MSM) and in 27 HIV-infected MSM before and after initiation of antiretroviral therapy (ART). We found that HIV infection reduces semen microbiome biodiversity, which is restored with ART and immune reconstitution. We also found that semen bacterial load in untreated, HIV-infected men is associated with the levels of seven semen cytokines, relationships not seen in the uninfected controls. In particular, the cytokine IL-1b was uniquely correlated with both semen bacterial and viral load. Our findings support the interaction between semen microbiome and local immunology, and suggest that IL-1b could be a mechanism for semen microbiome to trigger semen viral shedding.
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Affiliation(s)
- Cindy M. Liu
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | | | - Bruce A. Hungate
- Department of Biology, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - Sanja Huibner
- Department of Medicine, University of Toronto, Toronto, Canada
| | - Richard Lester
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Michael G. Dwan
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Colin Kovacs
- Department of Medicine, University of Toronto, Toronto, Canada
- Maple Leaf Medical Centre, Toronto, Canada
| | - Tania L. Contente-Cuomo
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | | | - Maliha Aziz
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Department of Environmental and Occupational Health, George Washington University School of Public Health, Washington, D.C., United States of America
| | - Lance B. Price
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Department of Environmental and Occupational Health, George Washington University School of Public Health, Washington, D.C., United States of America
- * E-mail: (LBP); (RK)
| | - Rupert Kaul
- Department of Medicine, University of Toronto, Toronto, Canada
- Department of Medicine, University Health Network, Toronto, Canada
- * E-mail: (LBP); (RK)
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Schinasi L, Wing S, Augustino KL, Ramsey KM, Nobles DL, Richardson DB, Price LB, Aziz M, MacDonald PDM, Stewart JR. A case control study of environmental and occupational exposures associated with methicillin resistant Staphylococcus aureus nasal carriage in patients admitted to a rural tertiary care hospital in a high density swine region. Environ Health 2014; 13:54. [PMID: 24958086 PMCID: PMC4083368 DOI: 10.1186/1476-069x-13-54] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 06/10/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND Distinct strains of methicillin resistant Staphylococcus aureus (MRSA) have been identified on livestock and livestock workers. Industrial food animal production may be an important environmental reservoir for human carriage of these pathogenic bacteria. The objective of this study was to investigate environmental and occupational exposures associated with nasal carriage of MRSA in patients hospitalized at Vidant Medical Center, a tertiary hospital serving a region with intensive livestock production in eastern North Carolina. METHODS MRSA nasal carriage was identified via nasal swabs collected within 24 hours of hospital admission. MRSA carriers (cases) were gender and age matched to non-carriers (controls). Participants were interviewed about recent environmental and occupational exposures. Home addresses were geocoded and publicly available data were used to estimate the density of swine in residential census block groups of residence. Conditional logistic regression models were used to derive odds ratio (OR) estimates and 95% confidence intervals (CI). Presence of the scn gene in MRSA isolates was assessed. In addition, multi locus sequence typing (MLST) of the MRSA isolates was performed, and the Diversilab® system was used to match the isolates to USA pulsed field gel electrophoresis types. RESULTS From July - December 2011, 117 cases and 119 controls were enrolled. A higher proportion of controls than cases were current workforce members (41.2% vs. 31.6%) Cases had a higher odds of living in census block groups with medium densities of swine (OR: 4.76, 95% CI: 1.36-16.69) and of reporting the ability to smell odor from a farm with animals when they were home (OR: 1.51, 95% CI: 0.80-2.86). Of 49 culture positive MRSA isolates, all were scn positive. Twenty-two isolates belonged to clonal complex 5. CONCLUSIONS Absence of livestock workers in this study precluded evaluation of occupational exposures. Higher odds of MRSA in medium swine density areas could reflect environmental exposure to swine or poultry.
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Affiliation(s)
- Leah Schinasi
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Steve Wing
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kerri L Augustino
- Department of Infection Control, Vidant Medical Center, Greenville, NC, USA
- Division of Infectious Diseases, The Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Keith M Ramsey
- Department of Infection Control, Vidant Medical Center, Greenville, NC, USA
- Division of Infectious Diseases, The Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Delores L Nobles
- Department of Infection Control, Vidant Medical Center, Greenville, NC, USA
- Division of Infectious Diseases, The Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - David B Richardson
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lance B Price
- Division of Pathogen Genomics, The Translational Genomics Research Institute, Flagstaff, Arizona, USA
- Department of Occupational and Environmental Health, George Washington University, Washington, DC, USA
| | - Maliha Aziz
- Division of Pathogen Genomics, The Translational Genomics Research Institute, Flagstaff, Arizona, USA
- Department of Occupational and Environmental Health, George Washington University, Washington, DC, USA
| | - Pia DM MacDonald
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Social & Scientific Systems, Inc., Durham, NC, USA
| | - Jill R Stewart
- Department of Environmental Sciences and Engineering, The University of NC at Chapel Hill, Chapel Hill, NC, USA
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Neyra RC, Frisancho JA, Rinsky JL, Resnick C, Carroll KC, Rule AM, Ross T, You Y, Price LB, Silbergeld EK. Multidrug-resistant and methicillin-resistant Staphylococcus aureus (MRSA) in hog slaughter and processing plant workers and their community in North Carolina (USA). Environ Health Perspect 2014; 122:471-7. [PMID: 24508836 PMCID: PMC4014760 DOI: 10.1289/ehp.1306741] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 02/04/2014] [Indexed: 05/27/2023]
Abstract
BACKGROUND Use of antimicrobials in industrial food-animal production is associated with the presence of antimicrobial-resistant Staphylococcus aureus (S. aureus) among animals and humans. Hog slaughter/processing plants process large numbers of animals from industrial animal operations and are environments conducive to the exchange of bacteria between animals and workers. OBJECTIVES We compared the prevalence of multidrug-resistant S. aureus (MDRSA) and methicillin-resistant S. aureus (MRSA) carriage among processing plant workers, their household members, and community residents. METHODS We conducted a cross-sectional study of hog slaughter/processing plant workers, their household members, and community residents in North Carolina. Participants responded to a questionnaire and provided a nasal swab. Swabs were tested for S. aureus, and isolates were tested for antimicrobial susceptibility and subjected to multilocus sequence typing. RESULTS The prevalence of S. aureus was 21.6%, 30.2%, and 22.5% among 162 workers, 63 household members, and 111 community residents, respectively. The overall prevalence of MDRSA and MRSA tested by disk diffusion was 6.9% and 4.8%, respectively. The adjusted prevalence of MDRSA among workers was 1.96 times (95% CI: 0.71, 5.45) the prevalence in community residents. The adjusted average number of antimicrobial classes to which S. aureus isolates from workers were resistant was 2.54 times (95% CI: 1.16, 5.56) the number among isolates from community residents. We identified two MDRSA isolates and one MRSA isolate from workers as sequence type 398, a type associated with exposure to livestock. CONCLUSIONS Although the prevalence of S. aureus and MRSA was similar in hog slaughter/processing plant workers and their household and community members, S. aureus isolates from workers were resistant to a greater number of antimicrobial classes. These findings may be related to the nontherapeutic use of antimicrobials in food-animal production.
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Pearson T, Hornstra HM, Hilsabeck R, Gates LT, Olivas SM, Birdsell DM, Hall CM, German S, Cook JM, Seymour ML, Priestley RA, Kondas AV, Clark Friedman CL, Price EP, Schupp JM, Liu CM, Price LB, Massung RF, Kersh GJ, Keim P. High prevalence and two dominant host-specific genotypes of Coxiella burnetii in U.S. milk. BMC Microbiol 2014; 14:41. [PMID: 24533573 PMCID: PMC3936997 DOI: 10.1186/1471-2180-14-41] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/10/2014] [Indexed: 11/11/2022] Open
Abstract
Background Coxiella burnetii causes Q fever in humans and Coxiellosis in animals; symptoms range from general malaise to fever, pneumonia, endocarditis and death. Livestock are a significant source of human infection as they shed C. burnetii cells in birth tissues, milk, urine and feces. Although prevalence of C. burnetii is high, few Q fever cases are reported in the U.S. and we have a limited understanding of their connectedness due to difficulties in genotyping. Here, we develop canonical SNP genotyping assays to evaluate spatial and temporal relationships among C. burnetii environmental samples and compare them across studies. Given the genotypic diversity of historical collections, we hypothesized that the current enzootic of Coxiellosis is caused by multiple circulating genotypes. We collected A) 23 milk samples from a single bovine herd, B) 134 commercial bovine and caprine milk samples from across the U.S., and C) 400 bovine and caprine samples from six milk processing plants over three years. Results We detected C. burnetii DNA in 96% of samples with no variance over time. We genotyped 88.5% of positive samples; bovine milk contained only a single genotype (ST20) and caprine milk was dominated by a second type (mostly ST8). Conclusions The high prevalence and lack of genotypic diversity is consistent with a model of rapid spread and persistence. The segregation of genotypes between host species is indicative of species-specific adaptations or dissemination barriers and may offer insights into the relative lack of human cases and characterizing genotypes.
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Affiliation(s)
- Talima Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
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Leekitcharoenphon P, Friis C, Zankari E, Svendsen CA, Price LB, Rahmani M, Herrero-Fresno A, Fashae K, Vandenberg O, Aarestrup FM, Hendriksen RS. Genomics of an emerging clone of Salmonella serovar Typhimurium ST313 from Nigeria and the Democratic Republic of Congo. J Infect Dev Ctries 2013; 7:696-706. [DOI: 10.3855/jidc.3328] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/24/2013] [Accepted: 04/30/2013] [Indexed: 10/31/2022] Open
Abstract
Introduction: Salmonella enterica serovar Typhimurium ST313 is an invasive and phylogenetically distinct lineage present in sub-Saharan Africa. We report the presence of S. Typhimurium ST313 from patients in the Democratic Republic of Congo and Nigeria. Methodology: Eighteen S. Typhimurium ST313 isolates were characterized by antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Additionally, six of the isolates were characterized by whole genome sequence typing (WGST). The presence of a putative virulence determinant was examined in 177 Salmonella isolates belonging to 57 different serovars. Results: All S. Typhimurium ST313 isolates harbored resistant genes encoded by blaTEM1b, catA1, strA/B, sul1, and dfrA1. Additionally, aac(6’)1aa gene was detected. Phylogenetic analyses revealed close genetic relationships among Congolese and Nigerian isolates from both blood and stool. Comparative genomic analyses identified a putative virulence fragment (ST313-TD) unique to S. Typhimurium ST313 and S. Dublin. Conclusion: We showed in a limited number of isolates that S. Typhimurium ST313 is a prevalent sequence-type causing gastrointestinal diseases and septicemia in patients from Nigeria and DRC. We found three distinct phylogenetic clusters based on the origin of isolation suggesting some spatial evolution. Comparative genomics showed an interesting putative virulence fragment (ST313-TD) unique to S. Typhimurium ST313 and invasive S. Dublin.
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Millman JM, Waits K, Grande H, Marks AR, Marks JC, Price LB, Hungate BA. Prevalence of antibiotic-resistant E. coli in retail chicken: comparing conventional, organic, kosher, and raised without antibiotics. F1000Res 2013; 2:155. [PMID: 24555073 PMCID: PMC3901448 DOI: 10.12688/f1000research.2-155.v2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/29/2013] [Indexed: 01/24/2023] Open
Abstract
Retail poultry products are known sources of antibiotic-resistant Escherichia coli, a major human health concern. Consumers have a range of choices for poultry, including conventional, organic, kosher, and raised without antibiotics (RWA) - designations that are perceived to indicate differences in quality and safety. However, whether these categories vary in the frequency of contamination with antibiotic-resistant E. coli is unknown. We examined the occurrence of antibiotic-resistant E. coli on raw chicken marketed as conventional, organic, kosher and RWA. From April - June 2012, we purchased 213 samples of raw chicken from 15 locations in the New York City metropolitan area. We screened E. coli isolates from each sample for resistance to 12 common antibiotics. Although the organic and RWA labels restrict the use of antibiotics, the frequency of antibiotic-resistant E. coli tended to be only slightly lower for RWA, and organic chicken was statistically indistinguishable from conventional products that have no restrictions. Kosher chicken had the highest frequency of antibiotic-resistant E. coli, nearly twice that of conventional products, a result that belies the historical roots of kosher as a means to ensure food safety. These results indicate that production methods influence the frequency of antibiotic-resistant E. coli on poultry products available to consumers. Future research to identify the specific practices that cause the high frequency of antibiotic-resistant E. coli in kosher chicken could promote efforts to reduce consumer exposure to this potential pathogen.
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Affiliation(s)
| | - Kara Waits
- Translational Genomics Research Institute, Flagstaff AZ, 86001, USA
| | - Heidi Grande
- Translational Genomics Research Institute, Flagstaff AZ, 86001, USA
| | - Ann R Marks
- Horace Mann Bronx Campus, Bronx NY, 10471, USA
| | - Jane C Marks
- Department of Biological Sciences and Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff AZ, 86011, USA
| | - Lance B Price
- Department of Environmental and Occupational Health, George Washington University, Washington DC, 20037, USA
| | - Bruce A Hungate
- Department of Biological Sciences and Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff AZ, 86011, USA
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