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Allegretti YH, Yamaji R, Adams-Sapper S, Riley LW. Genetic features of antimicrobial drug-susceptible extraintestinal pathogenic Escherichia coli pandemic sequence type 95. Microbiol Spectr 2024; 12:e0418922. [PMID: 38059630 PMCID: PMC10783064 DOI: 10.1128/spectrum.04189-22] [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: 10/16/2022] [Accepted: 11/13/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE Despite the increasing prevalence of antibiotic-resistant Escherichia coli strains that cause urinary tract and bloodstream infections, a major pandemic lineage of extraintestinal pathogenic E. coli (ExPEC) ST95 has a comparatively low frequency of drug resistance. We compared the genomes of 1,749 ST95 isolates to identify genetic features that may explain why most strains of ST95 resist becoming drug-resistant. Identification of such genomic features could contribute to the development of novel strategies to prevent the spread of antibiotic-resistant genes and devise new measures to control antibiotic-resistant infections.
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Affiliation(s)
| | | | | | - Lee W. Riley
- University of California Berkeley, Berkeley, California, USA
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Amato HK, Loayza F, Salinas L, Paredes D, Garcia D, Sarzosa S, Saraiva-Garcia C, Johnson TJ, Pickering AJ, Riley LW, Trueba G, Graham JP. Risk factors for extended-spectrum beta-lactamase (ESBL)-producing E. coli carriage among children in a food animal-producing region of Ecuador: A repeated measures observational study. PLoS Med 2023; 20:e1004299. [PMID: 37831716 PMCID: PMC10621961 DOI: 10.1371/journal.pmed.1004299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/02/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND The spread of antibiotic-resistant bacteria may be driven by human-animal-environment interactions, especially in regions with limited restrictions on antibiotic use, widespread food animal production, and free-roaming domestic animals. In this study, we aimed to identify risk factors related to commercial food animal production, small-scale or "backyard" food animal production, domestic animal ownership, and practices related to animal handling, waste disposal, and antibiotic use in Ecuadorian communities. METHODS AND FINDINGS We conducted a repeated measures study from 2018 to 2021 in 7 semirural parishes of Quito, Ecuador to identify determinants of third-generation cephalosporin-resistant E. coli (3GCR-EC) and extended-spectrum beta-lactamase E. coli (ESBL-EC) in children. We collected 1,699 fecal samples from 600 children and 1,871 domestic animal fecal samples from 376 of the same households at up to 5 time points per household over the 3-year study period. We used multivariable log-binomial regression models to estimate relative risks (RR) of 3GCR-EC and ESBL-EC carriage, adjusting for child sex and age, caregiver education, household wealth, and recent child antibiotic use. Risk factors for 3GCR-EC included living within 5 km of more than 5 commercial food animal operations (RR: 1.26; 95% confidence interval (CI): 1.10, 1.45; p-value: 0.001), household pig ownership (RR: 1.23; 95% CI: 1.02, 1.48; p-value: 0.030) and child pet contact (RR: 1.23; 95% CI: 1.09, 1.39; p-value: 0.001). Risk factors for ESBL-EC were dog ownership (RR: 1.35; 95% CI: 1.00, 1.83; p-value: 0.053), child pet contact (RR: 1.54; 95% CI: 1.10, 2.16; p-value: 0.012), and placing animal feces on household land/crops (RR: 1.63; 95% CI: 1.09, 2.46; p-value: 0.019). The primary limitations of this study are the use of proxy and self-reported exposure measures and the use of a single beta-lactamase drug (ceftazidime with clavulanic acid) in combination disk diffusion tests for ESBL confirmation, potentially underestimating phenotypic ESBL production among cephalosporin-resistant E. coli isolates. To improve ESBL determination, it is recommended to use 2 combination disk diffusion tests (ceftazidime with clavulanic acid and cefotaxime with clavulanic acid) for ESBL confirmatory testing. Future studies should also characterize transmission pathways by assessing antibiotic resistance in commercial food animals and environmental reservoirs. CONCLUSIONS In this study, we observed an increase in enteric colonization of antibiotic-resistant bacteria among children with exposures to domestic animals and their waste in the household environment and children living in areas with a higher density of commercial food animal production operations.
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Affiliation(s)
- Heather K. Amato
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, California, United States of America
| | - Fernanda Loayza
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Liseth Salinas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Diana Paredes
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Daniela Garcia
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Soledad Sarzosa
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Carlos Saraiva-Garcia
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, United States of America
- Mid Central Research & Outreach Center, Willmar, Minnesota, United States of America
| | - Amy J. Pickering
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, United States of America
- Blum Center for Developing Economies, University of California, Berkeley, California, United States of America
| | - Lee W. Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jay P. Graham
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, California, United States of America
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Amato HK, Loayza F, Salinas L, Paredes D, García D, Sarzosa S, Saraiva-Garcia C, Johnson TJ, Pickering AJ, Riley LW, Trueba G, Graham JP. Leveraging the COVID-19 pandemic as a natural experiment to assess changes in antibiotic use and antibiotic-resistant E. coli carriage in semi-rural Ecuador. Sci Rep 2023; 13:14854. [PMID: 37684276 PMCID: PMC10491794 DOI: 10.1038/s41598-023-39532-5] [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: 02/24/2023] [Accepted: 07/26/2023] [Indexed: 09/10/2023] Open
Abstract
The coronavirus 2019 (COVID-19) pandemic has had significant impacts on health systems, population dynamics, public health awareness, and antibiotic stewardship, which could affect antibiotic resistant bacteria (ARB) emergence and transmission. In this study, we aimed to compare knowledge, attitudes, and practices (KAP) of antibiotic use and ARB carriage in Ecuadorian communities before versus after the COVID-19 pandemic began. We leveraged data collected for a repeated measures observational study of third-generation cephalosporin-resistant E. coli (3GCR-EC) carriage among children in semi-rural communities in Quito, Ecuador between July 2018 and September 2021. We included 241 households that participated in surveys and child stool sample collection in 2019, before the pandemic, and in 2021, after the pandemic began. We estimated adjusted Prevalence Ratios (aPR) and 95% Confidence Intervals (CI) using logistic and Poisson regression models. Child antibiotic use in the last 3 months declined from 17% pre-pandemic to 5% in 2021 (aPR: 0.30; 95% CI 0.15, 0.61) and 3GCR-EC carriage among children declined from 40 to 23% (aPR: 0.48; 95% CI 0.32, 0.73). Multi-drug resistance declined from 86 to 70% (aPR: 0.32; 95% CI 0.13; 0.79), the average number of antibiotic resistance genes (ARGs) per 3GCR-EC isolate declined from 9.9 to 7.8 (aPR of 0.79; 95% CI 0.65, 0.96), and the diversity of ARGs was lower in 2021. In the context of Ecuador, where COVID-19 prevention and control measures were strictly enforced after its major cities experienced some of the world's the highest mortality rates from SARS-CoV-2 infections, antibiotic use and ARB carriage declined in semi-rural communities of Quito from 2019 to 2021.
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Affiliation(s)
- Heather K Amato
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, CA, USA.
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA.
| | - Fernanda Loayza
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Liseth Salinas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Diana Paredes
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Daniela García
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Soledad Sarzosa
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Carlos Saraiva-Garcia
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Amy J Pickering
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Blum Center for Developing Economies, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Jay P Graham
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, CA, USA
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Shankaregowda R, Allegretti YH, Sumana MN, Rao MR, Raphael E, Mahesh PA, Riley LW. Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates from Diabetic and Non-Diabetic Patients with Pulmonary Tuberculosis. Microorganisms 2023; 11:1881. [PMID: 37630441 PMCID: PMC10457832 DOI: 10.3390/microorganisms11081881] [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: 05/29/2023] [Revised: 07/08/2023] [Accepted: 07/14/2023] [Indexed: 08/27/2023] Open
Abstract
The association of tuberculosis and type 2 diabetes mellitus has been a recognized re-emerging challenge in management of the convergence of the two epidemics. Though much of the literature has studied this association, there is less knowledge in the field of genetic diversities that might occur in strains infecting tuberculosis patients with and without diabetes. Our study focused on determining the extent of diversity of genotypes of Mycobacterium tuberculosis in both these categories of patients. We subjected 55 M. tuberculosis isolates from patients diagnosed with pulmonary TB with and without type 2 diabetes mellitus to whole-genome sequencing on Illumina Hi Seq platform. The most common lineage identified was lineage 1, the Indo-Oceanic lineage (n = 22%), followed by lineage 4, the Euro-American lineage (n = 18, 33%); lineage 3, the East-African Indian lineage (n = 13, 24%); and lineage 2, the East-Asian lineage (n = 1, 2%). There were no significant differences in the distribution of lineages in both diabetics and non-diabetics in the South Indian population, and further studies involving computational analysis and comparative transcriptomics are needed to provide deeper insights.
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Affiliation(s)
- Ranjitha Shankaregowda
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, CA 94720, USA; (R.S.); (L.W.R.)
- Department of Microbiology, JSS Medical College and Hospital, JSS AHER, Mysore 570015, India; (M.N.S.); (M.R.R.)
| | - Yuan Hu Allegretti
- School of Public Health, Division of Epidemiology, University of California, Berkeley, CA 94720, USA;
| | | | - Morubagal Raghavendra Rao
- Department of Microbiology, JSS Medical College and Hospital, JSS AHER, Mysore 570015, India; (M.N.S.); (M.R.R.)
| | - Eva Raphael
- Division of Epidemiology and Biostatistics, School of Medicine, University of California, San Fransico, CA 94143, USA;
| | - Padukudru Anand Mahesh
- Department of Respiratory Medicine, JSS Medical College and Hospital, JSS AHER, Mysore 570015, India
| | - Lee W. Riley
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, CA 94720, USA; (R.S.); (L.W.R.)
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Lima FR, Simões MMR, da Costa Manso GM, Toro DM, Antunes VMG, Felisbino GC, Dias GF, Riley LW, Arruda S, de Paula NA, Lugão HB, Perecin FAMC, Foss NT, Frade MAC. Serological testing for Hansen’s disease diagnosis: Clinical significance and performance of IgA, IgM, and IgG antibodies against Mce1A protein. Front Med (Lausanne) 2023; 10:1048759. [PMID: 37007773 PMCID: PMC10062478 DOI: 10.3389/fmed.2023.1048759] [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] [Received: 09/21/2022] [Accepted: 02/24/2023] [Indexed: 03/18/2023] Open
Abstract
Hansen’s disease (HD) is an infectious, treatable, and chronic disease. It is the main cause of infectious peripheral neuropathy. Due to the current limitations of laboratory tests for the diagnosis of HD, early identification of infected contacts is an important factor that would allow us to control the magnitude of this disease in terms of world public health. Thus, a cross-sectional study was conducted in the Brazilian southeast with the objective of evaluating humoral immunity and describing the accuracy of the immunoassay based on IgA, IgM, and IgG antibodies against surface protein Mce1A of Mycobacterium, the predictive potential of these molecules, the clinical significance of positivity, and the ability to segregate new HD cases (NC; n = 200), contacts (HHC; n = 105), and healthy endemic controls (HEC; n = 100) as compared to α-PGL-I serology. α-Mce1A levels for all tested antibodies were significantly higher in NC and HHC than in HEC (p < 0.0001). The performance of the assay using IgA and IgM antibodies was rated as highly accurate (AUC > 0.85) for screening HD patients. Among HD patients (NC), positivity was 77.5% for IgA α-Mce1A ELISA, 76.5% for IgM, and 61.5% for IgG, while α-PGL-I serology showed only 28.0% positivity. Multivariate PLS-DA showed two defined clusters for the HEC and NC groups [accuracy = 0.95 (SD = 0.008)] and the HEC and HHC groups [accuracy = 0.93 (SD = 0.011)]. IgA was the antibody most responsible for clustering HHC as compared to NC and HEC, evidencing its usefulness for host mucosal immunity and as an immunological marker in laboratory tests. IgM is the key antibody for the clustering of NC patients. Positive results with high antibody levels indicate priority for screening, new clinical and laboratory evaluations, and monitoring of contacts, mainly with antibody indexes ≥2.0. In light of recent developments, the incorporation of new diagnostic technologies permits to eliminate the main gaps in the laboratory diagnosis of HD, with the implementation of tools of greater sensitivity and accuracy while maintaining satisfactory specificity.
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Affiliation(s)
- Filipe Rocha Lima
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Mateus Mendonça Ramos Simões
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Gabriel Martins da Costa Manso
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Diana Mota Toro
- Department of Clinical, Toxicological and, Bromatological Analyses, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Vanderson Mayron Granemann Antunes
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Giovani Cesar Felisbino
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Gabriela Ferreira Dias
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Lee W. Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Sérgio Arruda
- Advanced Public Health Laboratory, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil
| | - Natália Aparecida de Paula
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Helena Barbosa Lugão
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Fernanda André Martins Cruz Perecin
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Norma Tiraboschi Foss
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Marco Andrey Cipriani Frade
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- *Correspondence: Marco Andrey Cipriani Frade,
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Pinheiro FR, Rozza-de-Menezes RE, Blum MC, Pereira RFA, Rocha JA, Guedes Pinto MCF, Penna BA, Riley LW, Aguiar-Alves F. Evaluation of changes in antimicrobial susceptibility in bacteria infecting children and their mothers in pediatric, neonatal-intensive care unit, and gynecology/obstetrics wards of a quaternary referral hospital during the COVID-19 pandemic. Front Microbiol 2023; 14:1096223. [PMID: 36891399 PMCID: PMC9986255 DOI: 10.3389/fmicb.2023.1096223] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/24/2023] [Indexed: 02/22/2023] Open
Abstract
The World Health Organization released a statement warning of increased risk for the incidence of multidrug resistant microorganisms and the absence of new drugs to control such infections soon. Since the beginning of the COVID-19 pandemic, the prescription of antimicrobial agents has increased and may have accelerated the emergence of multidrug resistant (MDR) bacteria. This study aimed to evaluate maternal and pediatric infections within a hospital from January 2019 to December 2021. An observational retrospective cohort study was performed at a quaternary referral hospital in a metropolitan area of Niteroi city, Rio de Janeiro state, Brazil. A total of 196 patients' medical records were analyzed. The data from 90 (45.9%) patients were collected before the SARS-CoV-2 pandemic, 29 (14.8%) from the 2020 pandemic period, and 77 (39.3%) from the 2021 pandemic period. A total of 256 microorganisms were identified during this period. Out of those, 101 (39.5%) were isolated in 2019, 51 (19.9%) in 2020, and 104 (40.6%) in 2021. Antimicrobial susceptibility tests were performed on 196 (76.6%) clinical isolates. The exact binomial test showed that the distribution of Gram-negative bacteria was predominant. The most common microorganism was Escherichia coli (23%; n = 45), followed by Staphylococcus aureus (17.9%, n = 35), Klebsiella pneumoniae (12.8%, n = 25), Enterococcus faecalis (7.7%, n = 15), Staphylococcus epidermidis (6.6%, n = 13) and Pseudomonas aeruginosa (5.6%, n = 11). Staphylococcus aureus was the predominant species among resistant bacteria. Among the antimicrobial agents tested, the following were resistant, presented on a descending scale: penicillin (72.7%, p = 0.001, Binomial test), oxacillin (68.3%, p = 0.006, Binomial test), ampicillin (64.3%, p = 0.003, Binomial test), and ampicillin/sulbactam (54.9%, p = 0.57, Binomial test). Infections with S. aureus were 3.1 times greater in pediatrics and maternal units than in other hospital wards. Despite the global reduction in the incidence of MRSA, we observed an increase in MDR S. aureus in this study. No changes were observed in the frequency of resistance profiles of the clinical isolates after the establishment of the global SARS-CoV-2 pandemic. More comprehensive studies are needed to understand the impact of the global SARS-CoV-2 pandemic on the resistance levels of bacteria associated with neonate and pediatric patients.
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Affiliation(s)
- Felipe Ramos Pinheiro
- Molecular Epidemiology and Biotechnology Laboratory, School of Pharmacy, Fluminense Federal University, Niteroi, Brazil.,Pathology Post Graduate Program, School of Medicine, Fluminense Federal University, Niteroi, Brazil
| | | | - Marina Camille Blum
- Division of Health and Social Behavior, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Renata Freire Alves Pereira
- Molecular Epidemiology and Biotechnology Laboratory, School of Pharmacy, Fluminense Federal University, Niteroi, Brazil.,Applied Microbiology and Parasitology Post Graduate Programs, Fluminense Federal University, Niteroi, Brazil
| | - Jaqueline Abel Rocha
- Epidemiological Surveillance Unit, Antonio Pedro University Hospital, Fluminense Federal University, Niteroi, Brazil
| | - Maria Cristina F Guedes Pinto
- Epidemiological Surveillance Unit, Antonio Pedro University Hospital, Fluminense Federal University, Niteroi, Brazil
| | - Bruno A Penna
- Gram-Positive Cocci Laboratory, Biomedical Institute Fluminense Federal University, Niteroi, Brazil
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Fabio Aguiar-Alves
- Pathology Post Graduate Program, School of Medicine, Fluminense Federal University, Niteroi, Brazil.,Applied Microbiology and Parasitology Post Graduate Programs, Fluminense Federal University, Niteroi, Brazil.,Department of Pharmaceutical Sciences, Lloyd L. Gregory School of Pharmacy, Palm Beach Atlantic University, West Palm Beach, FL, United States
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Reis-Santos B, Locatelli R, Oliosi J, Sales CM, do Prado TN, Shete PB, Riley LW, Maciel EL. A Matter of Inclusion: A Cluster-Randomized Trial to Access the Effect of Food Vouchers Versus Traditional Treatment on Tuberculosis Outcomes in Brazil. Am J Trop Med Hyg 2022; 107:1281-1287. [PMID: 36375455 PMCID: PMC9768270 DOI: 10.4269/ajtmh.21-1074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
We assessed the effectiveness of food vouchers as a social protection strategy to enhance the adherence to tuberculosis treatment in health-care facilities in Brazil between 2014 and 2017. A cluster-randomized controlled trial was performed in four Brazilian capital cities. A total of 774 adults with newly diagnosed pulmonary tuberculosis were included in this study. Eligible participants initiated standard tuberculosis treatment per National Tuberculosis Program guidelines. Health clinics were assigned randomly to intervention groups (food voucher or standard treatment). The food voucher was provided by researchers, which could be used by subjects only for buying food. Most people with tuberculosis were poor, did receive benefits of the Bolsa Familia Program, and were unemployed. By Poisson regression analysis, with the total number of subjects included in the study, we found that individuals with tuberculosis who received food vouchers had a 1.13 greater risk of cure (95% CI, 1.03-1.21) compared with those who did not receive food vouchers. The provision of food vouchers improved outcomes of tuberculosis treatment and it should be enhanced even further as social protection for people with tuberculosis.
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Affiliation(s)
- Barbara Reis-Santos
- Laboratory of Epidemiology of Federal University of Espírito Santo, Maruípe, Vitória, Espírito Santo, Brazil
| | - Rodrigo Locatelli
- Laboratory of Epidemiology of Federal University of Espírito Santo, Maruípe, Vitória, Espírito Santo, Brazil
| | - Janaína Oliosi
- Laboratory of Epidemiology of Federal University of Espírito Santo, Maruípe, Vitória, Espírito Santo, Brazil
| | - Carolina M. Sales
- Laboratory of Epidemiology of Federal University of Espírito Santo, Maruípe, Vitória, Espírito Santo, Brazil
| | - Thiago Nascimento do Prado
- Laboratory of Epidemiology of Federal University of Espírito Santo, Maruípe, Vitória, Espírito Santo, Brazil
| | - Priya B. Shete
- Division of Pulmonary and Critical Care Medicine and Center for Tuberculosis, San Francisco, California
- University of California, San Francisco, California
| | - Lee W. Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California
| | - Ethel L. Maciel
- Laboratory of Epidemiology of Federal University of Espírito Santo, Maruípe, Vitória, Espírito Santo, Brazil
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Parker AM, Jackson N, Awasthi S, Kim H, Alwan T, Wyllie AL, Baldwin AB, Brennick NB, Moehle EA, Giannikopoulos P, Kogut K, Holland N, Mora-Wyrobek A, Eskenazi B, Riley LW, Lewnard JA. Association of upper respiratory Streptococcus pneumoniae colonization with SARS-CoV-2 infection among adults. Clin Infect Dis 2022; 76:1209-1217. [PMID: 36401872 DOI: 10.1093/cid/ciac907] [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] [Received: 10/04/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022] Open
Abstract
ABSTRACT
Background
Streptococcus pneumoniae interacts with numerous viral respiratory pathogens in the upper airway. It is unclear whether similar interactions occur with SARS-CoV-2.
Methods
We collected saliva specimens from working-age adults receiving SARS-CoV-2 molecular testing at outpatient clinics and via mobile community-outreach testing between July and November 2020 in Monterey County, California. Following bacterial culture enrichment, we tested for pneumococci by quantitative polymerase chain reaction (qPCR) targeting the lytA and piaB genes, and measured associations with SARS-CoV-2 infection via conditional logistic regression.
Results
Analyses included 1,278 participants, with 564 enrolled in clinics and 714 enrolled through outreach-based testing. Prevalence of pneumococcal carriage was 9.2% (117/1,278) among all participants (11.2% [63/564] clinic-based testing; 7.6% [54/714] outreach testing). Prevalence of SARS-CoV-2 infection was 27.4% (32/117) among pneumococcal carriers and 9.6% (112/1,161) among non-carriers (adjusted odds ratio [aOR]: 2.73; 95% confidence interval: 1.58-4.69). Associations between SARS-CoV-2 infection and pneumococcal carriage were enhanced in the clinic-based sample (aOR = 4.01 [2.08-7.75]) and among symptomatic participants (aOR = 3.38 [1.35-8.40]), when compared to findings within the outreach-based sample and among asymptomatic participants. Adjusted odds of SARS-CoV-2 co-infection increased 1.24 (1.00-1.55)-fold for each 1-unit decrease in piaB qPCR CT value among pneumococcal carriers. Last, pneumococcal carriage modified the association of SARS-CoV-2 infection with recent exposure to a suspected COVID-19 case (aOR = 7.64 [1.91-30.7] and 3.29 [1.94-5.59]) among pneumococcal carriers and non-carriers, respectively).
Conclusions
Associations of pneumococcal carriage detection and density with SARS-CoV-2 suggest a synergistic relationship in the upper airway. Longitudinal studies are needed to determine interaction mechanisms between pneumococci and SARS-CoV-2.
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Affiliation(s)
- Anna M Parker
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Nicole Jackson
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Shevya Awasthi
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Hanna Kim
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Tess Alwan
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health , New Haven, Connecticut 06510 , United States
| | - Alisha B Baldwin
- Innovative Genomics Institute, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Nicole B Brennick
- Innovative Genomics Institute, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Erica A Moehle
- Innovative Genomics Institute, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Katherine Kogut
- Center for Environmental Research & Community Health, School of Public Health, University of California , Berkeley, Berkeley, California 94720 , United States
| | - Nina Holland
- Center for Environmental Research & Community Health, School of Public Health, University of California , Berkeley, Berkeley, California 94720 , United States
| | - Ana Mora-Wyrobek
- Center for Environmental Research & Community Health, School of Public Health, University of California , Berkeley, Berkeley, California 94720 , United States
| | - Brenda Eskenazi
- Center for Environmental Research & Community Health, School of Public Health, University of California , Berkeley, Berkeley, California 94720 , United States
| | - Lee W Riley
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
| | - Joseph A Lewnard
- Division of Infectious Diseases & Vaccinology, School of Public Health, University of California, Berkeley , Berkeley, California 94720 , United States
- Division of Epidemiology, School of Public Health, University of California , Berkeley, Berkeley, California 94720 , United States
- Center for Computational Biology, College of Engineering, University of California , Berkeley, Berkeley, California 94720 , United States
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Kaleem Ullah M, Malamardi S, Siddaiah JB, A T, Prashant A, Vishwanath P, Riley LW, Madhivanan P, Mahesh PA. Trends in the Bacterial Prevalence and Antibiotic Resistance Patterns in the Acute Exacerbation of Chronic Obstructive Pulmonary Disease in Hospitalized Patients in South India. Antibiotics (Basel) 2022; 11:antibiotics11111577. [PMID: 36358232 PMCID: PMC9686600 DOI: 10.3390/antibiotics11111577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 09/29/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Exacerbation due to antimicrobial-drug-resistant bacteria among chronic obstructive pulmonary disease (AECOPD) patients contributes to mortality and morbidity. We examined the prevalence of the bacterial organisms and trends in drug resistance in AECOPD. In this retrospective study, between January 2016 to December 2020, among 3027 AECOPD patients, 432 (14.3%) had bacteria isolated. The regression and generalized estimating equations (GEE) were used for trends in the resistance patterns over five years, adjusting for age, gender, and comorbidities. Klebsiella pneumoniae (32.4%), Pseudomonas aeruginosa (17.8%), Acinetobacter baumannii (14.4%), Escherichia coli (10.4%), and Staphylococcus aureus (2.5%) were common. We observed high levels of drug resistance in AECOPD patients admitted to ICU (87.8%) and non-ICU (86.5%). A Cox proportional hazard analysis, observed infection with Acinetobacter baumannii and female sex as independent predictors of mortality. Acinetobacter baumannii had 2.64 (95% confidence interval (CI): 1.08−6.43) higher odds of death, compared to Klebsiella pneumoniae. Females had 2.89 (95% CI: 1.47−5.70) higher odds of death, compared to males. A high proportion of bacterial AECOPD was due to drug-resistant bacteria. An increasing trend in drug resistance was observed among females.
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Affiliation(s)
- Mohammed Kaleem Ullah
- Centre for Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research, Mysore 570015, Karnataka, India
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Sowmya Malamardi
- Department of Respiratory Medicine, JSS Medical College, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
- School of Psychology & Public Health, College of Science Health and Engineering, La Trobe University, Melbourne 3086, Australia
| | - Jayaraj Biligere Siddaiah
- Department of Respiratory Medicine, JSS Medical College, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | - Tejashree A
- Department of Microbiology, JSS Medical College, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | - Akila Prashant
- Centre for Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research, Mysore 570015, Karnataka, India
| | - Prashant Vishwanath
- Centre for Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research, Mysore 570015, Karnataka, India
| | - Lee W. Riley
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720, USA
- Correspondence: (L.W.R.); (P.A.M.)
| | - Purnima Madhivanan
- Department of Health Promotion Sciences, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85724, USA
- Division of Infectious Diseases, College of Medicine, University of Arizona, Tucson, AZ 85724, USA
- Public Health Research Institute of India, Mysuru 570020, Karnataka, India
| | - Padukudru Anand Mahesh
- Department of Respiratory Medicine, JSS Medical College, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
- Correspondence: (L.W.R.); (P.A.M.)
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Parker AM, Jackson N, Awasthi S, Kim H, Alwan T, Wyllie AL, Baldwin AB, Brennick NB, Moehle EA, Giannikopoulos P, Kogut K, Holland N, Mora-Wyrobek A, Eskenazi B, Riley LW, Lewnard JA. Association of upper respiratory Streptococcus pneumoniae colonization with SARS-CoV-2 infection among adults. medRxiv 2022:2022.10.04.22280709. [PMID: 36238718 PMCID: PMC9558443 DOI: 10.1101/2022.10.04.22280709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Background Streptococcus pneumoniae interacts with numerous viral respiratory pathogens in the upper airway. It is unclear whether similar interactions occur with SARS-CoV-2. Methods We collected saliva specimens from working-age adults receiving SARS-CoV-2 molecular testing at outpatient clinics and via mobile community-outreach testing between July and November 2020 in Monterey County, California. Following bacterial culture enrichment, we tested for pneumococci by quantitative polymerase chain reaction (qPCR) targeting the lytA and piaB genes, and measured associations with SARS-CoV-2 infection via conditional logistic regression. Results Analyses included 1,278 participants, with 564 enrolled in clinics and 714 enrolled through outreach-based testing. Prevalence of pneumococcal carriage was 9.2% (117/1,278) among all participants (11.2% [63/564] clinic-based testing; 7.6% [54/714] outreach testing). Prevalence of SARS-CoV-2 infection was 27.4% (32/117) among pneumococcal carriers and 9.6% (112/1,161) among non-carriers (adjusted odds ratio [aOR]: 2.73; 95% confidence interval: 1.58-4.69). Associations between SARS-CoV-2 infection and pneumococcal carriage were enhanced in the clinic-based sample (aOR=4.01 [2.08-7.75]) and among symptomatic participants (aOR=3.38 [1.35-8.40]), when compared to findings within the outreach-based sample and among asymptomatic participants. Adjusted odds of SARS-CoV-2 co-infection increased 1.24 (1.00-1.55)-fold for each 1-unit decrease in piaB qPCR C T value among pneumococcal carriers. Last, pneumococcal carriage modified the association of SARS-CoV-2 infection with recent exposure to a suspected COVID-19 case (aOR=7.64 [1.91-30.7] and 3.29 [1.94-5.59]) among pneumococcal carriers and non-carriers, respectively). Conclusions Associations of pneumococcal carriage detection and density with SARS-CoV-2 suggest a synergistic relationship in the upper airway. Longitudinal studies are needed to determine interaction mechanisms between pneumococci and SARS-CoV-2. Key points In an adult ambulatory and community sample, SARS-CoV-2 infection was more prevalent among pneumococcal carriers than non-carriers.Associations between pneumococcal carriage and SARS-CoV-2 infection were strongest among adults reporting acute symptoms and receiving SARS-CoV-2 testing in a clinical setting.
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11
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Islam MA, Islam MR, Khan R, Amin MB, Rahman M, Hossain MI, Ahmed D, Asaduzzaman M, Riley LW. Prevalence, etiology and antibiotic resistance patterns of community-acquired urinary tract infections in Dhaka, Bangladesh. PLoS One 2022; 17:e0274423. [PMID: 36107878 PMCID: PMC9477272 DOI: 10.1371/journal.pone.0274423] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 06/24/2022] [Accepted: 08/30/2022] [Indexed: 11/25/2022] Open
Abstract
Urinary tract infection (UTI) accounts for a significant morbidity and mortality across the world and is a leading cause for antibiotic prescriptions in the community especially in developing countries. Empirical choice of antibiotics for treatment of UTI is often discordant with the drug susceptibility of the etiologic agent. This study aimed to estimate the prevalence of community-acquired UTI caused by antibiotic resistant organisms. This was a cross-sectional study where urine samples were prospectively collected from 4,500 patients at the icddr,b diagnostic clinic in Dhaka, Bangladesh during 2016–2018. Urine samples were analyzed by standard culture method and the isolated bacteria were tested for antibiotic susceptibility by using disc diffusion method and VITEK-2. Descriptive statistics were used to estimate the prevalence of community acquired UTI (CA-UTI) by different age groups, sex, and etiology of infection. Relationship between the etiology of CA-UTI and age and sex of patients was analyzed using binary logistic regression analysis. Seasonal trends in the prevalence of CA-UTI, multi-drug resistant (MDR) pathogens and MDR Escherichia coli were also analyzed. Around 81% of patients were adults (≥18y). Of 3,200 (71%) urine samples with bacterial growth, 920 (29%) had a bacterial count of ≥1.0x105 CFU/ml indicating UTI. Women were more likely to have UTI compared to males (OR: 1.48, CI: 1.24–1.76). E. coli (51.6%) was the predominant causative pathogen followed by Streptococcus spp. (15.7%), Klebsiella spp. (12.1%), Enterococcus spp. (6.4%), Pseudomonas spp. (4.4%), coagulase-negative Staphylococcus spp. (2.0%), and other pathogens (7.8%). Both E. coli and Klebsiella spp. were predominantly resistant to penicillin (85%, 95%, respectively) followed by macrolide (70%, 76%), third-generation cephalosporins (69%, 58%), fluoroquinolones (69%, 53%) and carbapenem (5%, 9%). Around 65% of patients tested positive for multi-drug resistant (MDR) uropathogens. A higher number of male patients tested positive for MDR pathogens compared to the female patients (p = 0.015). Overall, 71% of Gram-negative and 46% of Gram-positive bacteria were MDR. The burden of community-acquired UTI caused by MDR organisms was high among the study population. The findings of the study will guide clinicians to be more selective about their antibiotic choice for empirical treatment of UTI and alleviate misuse/overuse of antibiotics in the community.
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Affiliation(s)
- Mohammad Aminul Islam
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- * E-mail:
| | - Md Rayhanul Islam
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rizwana Khan
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammed Badrul Amin
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mahdia Rahman
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Muhammed Iqbal Hossain
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Dilruba Ahmed
- Clinical Microbiology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Muhammad Asaduzzaman
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- Centre for Global Health, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Lee W. Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States of America
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Lima FR, Filho FB, Antunes VMG, Santana JM, de Almeida RCP, Toro DM, Bragagnollo VF, Manso GMDC, de Paula NA, Alves ES, Riley LW, Arruda S, Frade MAC. Serological Immunoassay for Hansen’s Disease Diagnosis and Monitoring Treatment: Anti-Mce1A Antibody Response Among Hansen’s Disease Patients and Their Household Contacts in Northeastern Brazil. Front Med (Lausanne) 2022; 9:855787. [PMID: 35755036 PMCID: PMC9218539 DOI: 10.3389/fmed.2022.855787] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022] Open
Abstract
Hansen’s disease (HD) is an ancient disease, but more than 200,000 new cases were reported worldwide in 2019. Currently, there are not many satisfactory immunoassay methods for its diagnosis. We evaluated antibodies against Mce1A as a promising new serological biomarker. We collected plasma from new cases, contacts, and endemic controls in the city of Parnaíba and treated patients at Carpina, a former HD colony in Piauí state, northeastern Brazil. Receiver operating characteristic (ROC) curves were used to assess the assay thresholds, specificity and sensitivity of the IgA, IgM, and IgG antibodies against α-Mce1A by indirect ELISA and compared it with IgM anti-PGL-I and molecular diagnosis by quantitative polymerase chain reaction (qPCR). Venn diagrams were generated to represent the overlap in the antibody positivity pattern. Multivariate analysis was performed to assess the potential predictor of antibodies for the outcome of having an HD diagnosis. IgA and IgG were positive in 92.3 and 84% of patients, respectively. IgM was negative for all treated patients. IgG had a sensitivity and specificity of 94.7 and 100%, respectively. IgM-positive individuals had a 3.6 chance of being diagnosed with HD [OR = 3.6 (95% CI = 1.1–11.6); p = 0.028], while IgA-positive individuals had a 2.3 chance [OR = 2.3 (95% CI = 1.2–4.3); p = 0.005] compared to endemic controls. We found that the Mce1A antibody profile can be an excellent diagnostic method of HD. IgA is an ideal biomarker for confirming contact with the bacillus. IgM has potential in the detection of active disease. IgG antibodies confirm the performance of these serological markers in diagnosis and therapeutic follow-up.
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Affiliation(s)
- Filipe Rocha Lima
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Fred Bernardes Filho
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Vanderson Mayron Granemann Antunes
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Jaci Maria Santana
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Regina Coeli Palma de Almeida
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Diana Mota Toro
- Department of Clinical, Toxicological, and Bromatological Analyses, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Vinicius Fozatti Bragagnollo
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Gabriel Martins da Costa Manso
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Natália Aparecida de Paula
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Eliracema Silva Alves
- Directorate of Unit and Health Care Surveillance, HD Control Program, State Department of Health, Piauí, Brazil
- Federal University of Piauí, Piauí, Brazil
| | - Lee W. Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Sérgio Arruda
- Advanced Public Health Laboratory, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil
| | - Marco Andrey Cipriani Frade
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- *Correspondence: Marco Andrey Cipriani Frade,
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Asthana P, Singh D, Pedersen JS, Hynönen MJ, Sulu R, Murthy AV, Laitaoja M, Jänis J, Riley LW, Venkatesan R. Structural insights into the substrate-binding proteins Mce1A and Mce4A from Mycobacterium tuberculosis. IUCrJ 2021; 8:757-774. [PMID: 34584737 PMCID: PMC8420772 DOI: 10.1107/s2052252521006199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/15/2021] [Indexed: 05/28/2023]
Abstract
Mycobacterium tuberculosis (Mtb), which is responsible for more than a million deaths annually, uses lipids as the source of carbon and energy for its survival in the latent phase of infection. Mtb cannot synthesize all of the lipid molecules required for its growth and pathogenicity. Therefore, it relies on transporters such as the mammalian cell entry (Mce) complexes to import lipids from the host across the cell wall. Despite their importance for the survival and pathogenicity of Mtb, information on the structural properties of these proteins is not yet available. Each of the four Mce complexes in Mtb (Mce1-4) comprises six substrate-binding proteins (SBPs; MceA-F), each of which contains four conserved domains (N-terminal transmembrane, MCE, helical and C-terminal unstructured tail domains). Here, the properties of the various domains of Mtb Mce1A and Mce4A, which are involved in the import of mycolic/fatty acids and cholesterol, respectively, are reported. In the crystal structure of the MCE domain of Mce4A (MtMce4A39-140) a domain-swapped conformation is observed, whereas solution studies, including small-angle X-ray scattering (SAXS), indicate that all Mce1A and Mce4A domains are predominantly monomeric. Further, structural comparisons show interesting differences from the bacterial homologs MlaD, PqiB and LetB, which form homohexamers when assembled as functional transporter complexes. These data, and the fact that there are six SBPs in each Mtb mce operon, suggest that the MceA-F SBPs from Mce1-4 may form heterohexamers. Also, interestingly, the purification and SAXS analysis showed that the helical domains interact with the detergent micelle, suggesting that when assembled the helical domains of MceA-F may form a hydrophobic pore for lipid transport, as observed in EcPqiB. Overall, these data highlight the unique structural properties of the Mtb Mce SBPs.
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Affiliation(s)
- Pooja Asthana
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Dhirendra Singh
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Mikko J. Hynönen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Ramita Sulu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Abhinandan V. Murthy
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Mikko Laitaoja
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Lee W. Riley
- School of Public Health, University of California, Berkeley, California, USA
| | - Rajaram Venkatesan
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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14
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Hu Y, Rubin J, Mussio K, Riley LW. Risk factors for faecal carriage of multidrug-resistant Escherichia coli in a college community: a penalised regression model. J Glob Antimicrob Resist 2021; 26:166-173. [PMID: 34051401 DOI: 10.1016/j.jgar.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 01/30/2021] [Revised: 04/02/2021] [Accepted: 05/16/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Bacterial antimicrobial resistance is a serious global public-health threat. Intestinal commensal drug-resistant bacteria have been suggested as an important reservoir of antimicrobial resistance genes (ARGs), which may be acquired via food. We aimed to identify risk factors associated with faecal carriage of drug-resistant commensal Escherichia coli among healthy adults focused on their dietary habits. METHODS We conducted a cross-sectional study targeting healthy adult volunteers in a college community. Faecal samples and questionnaires were obtained from 113 volunteers. We conducted backward elimination logistic regression and least absolute shrinkage and selection operator (LASSO) methods to identify risk factors. RESULTS We analysed responses from 81 of 113 volunteers who completed the questionnaire. The logistic regression and LASSO methods identified red meat consumption to be associated with an increased risk [OR = 6.13 (95% CI 1.83-24.2) and 1.82, respectively] and fish consumption with a reduced risk [OR = 0.27 (95% CI 0.08-0.85) and 0.81] for carriage of multidrug-resistant (MDR) E. coli, adjusted for biological sex, employment status, frequently used supermarket and previous travel. CONCLUSION Dietary habits are associated with risk of faecal carriage of MDR E. coli. This study supports the growing evidence that food may be an important source of ARGs present in human commensal E. coli.
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Affiliation(s)
- Yuan Hu
- Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Julia Rubin
- Division of Environmental Health Science, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Kaitlyn Mussio
- Division of Environmental Health Science, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Lee W Riley
- Division of Infectious Diseases and Immunology, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
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Abstract
Under the WHO plan, the global elimination of the HCV pandemic is scheduled for 2030. The burden of HCV infection in developed countries is largely borne by people who inject drugs (PWID): new infections and reinfections are related to their risky behaviour. Although safe and sensitive hepatitis C diagnostic tools and directly acting antiviral medication are widely used, major challenges to disease elimination still remain in developed countries, where the WHO plan is in progress. The challenge is in the involvement and engagement of infected PWID. There is a strong need to change our uptake and treatment strategies to address all patients from the risk groups, connect them with the healthcare system and cure them with the vision to eliminate this HCV pandemic.
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Affiliation(s)
- Laura Krekulova
- Remedis s.r.o., Prague, Czech Republic.,4th Department of Internal Medicine, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Radkin Honzák
- Remedis s.r.o., Prague, Czech Republic.,Institute of Clinical and Experimental Medicine, Prague, Czech Republic
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
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Martins-Sorenson N, Snesrud E, Xavier DE, Cacci LC, Iavarone AT, McGann P, Riley LW, Moreira BM. A novel plasmid-encoded mcr-4.3 gene in a colistin-resistant Acinetobacter baumannii clinical strain. J Antimicrob Chemother 2021; 75:60-64. [PMID: 31578567 DOI: 10.1093/jac/dkz413] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 08/05/2019] [Accepted: 09/03/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES To identify the molecular mechanism of colistin resistance in an MDR Acinetobacter baumannii clinical strain isolated in 2008 from a meningitis case in Brazil. METHODS Long- and short-read WGS was used to identify colistin resistance genes in A. baumannii strain 597A with a colistin MIC of 64 mg/L. MS was used to analyse lipid A content. mcr was cloned into pET-26b (+) and transformed into Escherichia coli BL21(λDE3)pLysS for analysis. RESULTS A novel plasmid (pAb-MCR4.3) harbouring mcr-4.3 within a Tn3-like transposon was identified. The A. baumannii 597A lipid A MS spectra showed a main molecular ion peak at m/z=2034, which indicated the addition of phosphoethanolamine to the lipid A structure. E. coli BL21 transformed with pET-26b-mcr-4.3 gained colistin resistance with a colistin MIC of 8 mg/L. CONCLUSIONS Colistin resistance in A. baumannii 597A was correlated with the presence of a novel plasmid-encoded mcr-4.3 gene.
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Affiliation(s)
| | - Erik Snesrud
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, CA, USA
| | - Patrick McGann
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lee W Riley
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
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17
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Jackson N, Borges CA, Tarlton NJ, Resendez A, Milton AK, de Boer TR, Butcher CR, Murthy N, Riley LW. A rapid, antibiotic susceptibility test for multidrug-resistant, Gram-negative bacterial uropathogens using the biochemical assay, DETECT. J Microbiol Methods 2021; 182:106160. [PMID: 33548393 DOI: 10.1016/j.mimet.2021.106160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/04/2021] [Accepted: 01/31/2021] [Indexed: 12/26/2022]
Abstract
The increasing prevalence of extended spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC (pAmpC) β-lactamases among Enterobacterales threatens our ability to treat urinary tract infections (UTIs). These organisms are resistant to most β-lactam antibiotics and are frequently multidrug-resistant (MDR). Consequently, they are often resistant to antibiotics used to empirically treat UTIs. The lack of rapid diagnostic and antibiotic susceptibility tests (AST) makes clinical management of UTIs caused by such organisms difficult, as standard culture and susceptibility assays require several days. We have adapted a biochemical detection assay, termed dual-enzyme trigger-enabled cascade technology (DETECT) for rapid detection of resistance (time-to-result of 3 h) to other antibiotics commonly used in treatment of UTIs. DETECT is activated by the presence of CTX-M and pAmpC β-lactamases. In this proof-of-concept study, the adapted DETECT assay (AST-DETECT) has been performed on pure-cultures of Klebsiella pneumoniae and Escherichia coli (48 isolates) expressing ESBL or pAmpC β-lactamases to perform AST for ciprofloxacin (sensitivity 96.9%, specificity 100%, accuracy 97.9%) nitrofurantoin (sensitivity 95.7%, specificity 91.7%, accuracy 94%) and trimethoprim/sulfamethoxazole (sensitivity 83.3%, specificity 100%, accuracy 89.4%). These results suggest that AST-DETECT may be adapted as a potential diagnostic platform to rapidly detect multidrug-resistant E. coli and K. pneumoniae that cause UTI.
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Affiliation(s)
- Nicole Jackson
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA.
| | - Clarissa A Borges
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA
| | - Nicole J Tarlton
- Department of Microbiology, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | - Angel Resendez
- Department of Chemistry, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | | | - Tara R de Boer
- Department of Chemistry, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | - Cheyenne R Butcher
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA
| | - Niren Murthy
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Lee W Riley
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA.
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18
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Abstract
Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.
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Affiliation(s)
- Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
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19
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Liao N, Borges CA, Rubin J, Hu Y, Ramirez HA, Chen J, Zhou B, Zhang Y, Zhang R, Jiang J, Riley LW. Prevalence of β-Lactam Drug-Resistance Genes in Escherichia coli Contaminating Ready-to-Eat Lettuce. Foodborne Pathog Dis 2020; 17:739-742. [PMID: 33112663 DOI: 10.1089/fpd.2020.2792] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Thirty-four Escherichia coli isolates from 91 ready-to-eat lettuce packages, obtained from local supermarkets in Northern California, were genotyped by multilocus sequence typing, tested for susceptibility to antimicrobial agents, and screened for β-lactamase genes. We found 15 distinct sequence types (STs). Six of these genotypes (ST1198, ST2625, ST2432, ST2819, ST4600, and ST5143) have been reported as pathogens found in human samples. Twenty-six (76%) E. coli isolates were resistant to ampicillin, 17 (50%) to ampicillin/sulbactam, 8 (23%) to cefoxitin, and 7 (20%) to cefuroxime. blaCTX-M was the most prevalent β-lactamase gene, identified in eight (23%) isolates. We identified a class A broad-spectrum β-lactamase SED-1 gene, blaSED, reported by others in Citrobacter sedlakii isolated from bile of a patient. This study found that fresh lettuce carries β-lactam drug-resistant E. coli, which might serve as a reservoir for drug-resistance genes that could potentially be transmitted to pathogens that cause human infections.
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Affiliation(s)
- Ningbo Liao
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Clarissa A Borges
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Julia Rubin
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Yuan Hu
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, USA
| | - Hector A Ramirez
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Jiang Chen
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Biao Zhou
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yanjun Zhang
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Ronghua Zhang
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jianmin Jiang
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
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20
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Tarlton NJ, Petrovic DF, Frazee BW, Borges CA, Pham EM, Milton AK, Jackson N, deBoer TR, Murthy N, Riley LW. A Dual Enzyme-Based Biochemical Test Rapidly Detects Third-Generation Cephalosporin-Resistant CTX-M-Producing Uropathogens in Clinical Urine Samples. Microb Drug Resist 2020; 27:450-461. [PMID: 32830997 DOI: 10.1089/mdr.2020.0128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 11/12/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Gram-negative bacteria (GNB) are increasingly identified as the cause of both community and healthcare-associated urinary tract infections (UTIs), with CTX-Ms being the most common ESBLs identified. CTX-M-producing GNB are resistant to most β-lactam antibiotics and are frequently multidrug-resistant, which limits treatment options. Rapid diagnostic tests that can detect ESBL-producing GNB, particularly CTX-M producers, in the urine of patients with UTIs are needed. Results from such a test could direct the selection of appropriate antimicrobial therapy at the point-of-care (POC). In this study, we show that a chromogenic, dual enzyme-mediated amplification system (termed DETECT [dual-enzyme trigger-enabled cascade technology]) can identify CTX-M-producing GNB from unprocessed urine samples in 30 minutes. We first tested DETECT against a diverse set of recombinant β-lactamases and β-lactamase-producing clinical isolates to elucidate its selectivity. We then tested DETECT with 472 prospectively collected clinical urine samples submitted for urine culture to a hospital clinical microbiology laboratory. Of these, 118 (25%) were consistent with UTI, 13 (11%) of which contained ESBL-producing GNB. We compared DETECT results in urine against a standard phenotypic method to detect ESBLs, and polymerase chain reaction and sequencing for CTX-M genes. DETECT demonstrated 90.9% sensitivity and 97.6% specificity (AUC, 0.937; 95% confidence interval, 0.822-1.000), correctly identifying 10 of 11 urine samples containing a clinically significant concentration of CTX-M-producing GNB (including Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis). Our results demonstrate the clinical potential of DETECT to deliver diagnostic information at the POC, which could improve initial antibiotic selection.
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Affiliation(s)
- Nicole J Tarlton
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Danka-Florence Petrovic
- Department of Laboratory Medicine and Pathology, Highland Hospital, Alameda Health System, Oakland, California, USA
| | - Bradley W Frazee
- Department of Emergency Medicine, Highland Hospital, Alameda Health System, Oakland, California, USA
| | - Clarissa A Borges
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Emily M Pham
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Aubrianne K Milton
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Nicole Jackson
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Tara R deBoer
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
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21
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Petrilli JD, Müller I, Araújo LE, Cardoso TM, Carvalho LP, Barros BC, Teixeira M, Arruda S, Riley LW, Queiroz A. Differential Host Pro-Inflammatory Response to Mycobacterial Cell Wall Lipids Regulated by the Mce1 Operon. Front Immunol 2020; 11:1848. [PMID: 32973761 PMCID: PMC7461851 DOI: 10.3389/fimmu.2020.01848] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/09/2020] [Indexed: 11/17/2022] Open
Abstract
The cell wall of wild-type (WT) Mycobacterium tuberculosis (Mtb), an etiologic agent of tuberculosis (TB) and a Mtb strain disrupted in a 13-gene operon mce1 (Δmce1) varies by more than 400 lipid species. Here, we examined Mtb lipid-induced response in murine macrophage, as well as in human T-cell subpopulations in order to gain an insight into how changes in cell wall lipid composition may modulate host immune response. Relative to WT Mtb cell wall lipids, the non-polar lipid extracts from Δmce1 enhanced the mRNA expression of lipid-sense nuclear receptors TR4 and PPAR-γ and dampened the macrophage expression of genes encoding TNF-α, IL-6, and IL-1β. Relative to untreated control, WT lipid-pre-stimulated macrophages from healthy individuals induced a higher level of CD4−CD8− double negative T-cells (DN T-cells) producing TNF-α. Conversely, compared to WT, stimulation with Δmce1 lipids induced higher mean fluorescence intensity (MFI) in IL-10-producing DN T cells. Mononuclear cells from TB patients stimulated with WT Mtb lipids induced an increased production of TNF-α by CD8+ lymphocytes. Taken together, these observations suggest that changes in mce1 operon expression during a course of infection may serve as a strategy by Mtb to evade the host pro-inflammatory responses.
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Affiliation(s)
- Jéssica D Petrilli
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Igor Müller
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Luana E Araújo
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Thiago M Cardoso
- Laboratório de Pesquisa Clínica, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Lucas P Carvalho
- Laboratório de Pesquisa Clínica, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Bruna C Barros
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Maurício Teixeira
- Laboratório de Pesquisa Clínica, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Sérgio Arruda
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Adriano Queiroz
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
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22
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He M, Li J, Han H, Borges CA, Neiman G, Røise JJ, Hadaczek P, Mendonsa R, Holm VR, Wilson RC, Bankiewicz K, Zhang Y, Sadlowski CM, Healy K, Riley LW, Murthy N. A traceless linker for aliphatic amines that rapidly and quantitatively fragments after reduction. Chem Sci 2020; 11:8973-8980. [PMID: 34123152 PMCID: PMC8163433 DOI: 10.1039/d0sc00929f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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] [Indexed: 12/13/2022] Open
Abstract
Reduction sensitive linkers (RSLs) have the potential to transform the field of drug delivery due to their ease of use and selective cleavage in intracellular environments. However, despite their compelling attributes, developing reduction sensitive self-immolative linkers for aliphatic amines has been challenging due to their poor leaving group ability and high pKa values. Here a traceless self-immolative linker composed of a dithiol-ethyl carbonate connected to a benzyl carbamate (DEC) is presented, which can modify aliphatic amines and release them rapidly and quantitatively after disulfide reduction. DEC was able to reversibly modify the lysine residues on CRISPR–Cas9 with either PEG, the cell penetrating peptide Arg10, or donor DNA, and generated Cas9 conjugates with significantly improved biological properties. In particular, Cas9–DEC–PEG was able to diffuse through brain tissue significantly better than unmodified Cas9, making it a more suitable candidate for genome editing in animals. Furthermore, conjugation of Arg10 to Cas9 with DEC was able to generate a self-delivering Cas9 RNP that could edit cells without transfection reagents. Finally, conjugation of donor DNA to Cas9 with DEC increased the homology directed DNA repair (HDR) rate of the Cas9 RNP by 50% in HEK 293T cell line. We anticipate that DEC will have numerous applications in biotechnology, given the ubiquitous presence of aliphatic amines on small molecule and protein therapeutics. Reduction sensitive linkers (RSLs) have the potential to transform the field of drug delivery due to their ease of use and selective cleavage in intracellular environments.![]()
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Affiliation(s)
- Maomao He
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Jie Li
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Hesong Han
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Clarissa Araujo Borges
- Department of Public Health, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Gabriel Neiman
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Joachim Justad Røise
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA .,Department of Chemistry, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Piotr Hadaczek
- Department of Neurological Surgery, The Ohio State University Columbus OH 43210 USA
| | - Rima Mendonsa
- Innovative Genomics Institute, University of California Berkeley CA 94704 USA
| | - Victoria R Holm
- Innovative Genomics Institute, University of California Berkeley CA 94704 USA
| | - Ross C Wilson
- Innovative Genomics Institute, University of California Berkeley CA 94704 USA
| | - Krystof Bankiewicz
- Department of Neurological Surgery, The Ohio State University Columbus OH 43210 USA
| | - Yumiao Zhang
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA .,School of Chemical Engineering and Technology, Tianjin University 300350 China
| | - Corinne M Sadlowski
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Kevin Healy
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Lee W Riley
- Department of Public Health, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Niren Murthy
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA .,Innovative Genomics Institute, University of California Berkeley CA 94704 USA
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23
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Dos Santos DCM, Lovero KL, Schmidt CM, Barros ACMW, Quintanilha AP, Barbosa AP, Pone MVS, Pone SM, Araujo JM, de Paula Martins C, Cosme EM, Dourado de Oliveira TR, Miceli AL, Vieira ML, Queiroz A, Coca Velarde LG, Kritski A, de Fátima Pombo March M, Maria de Azevedo Sias S, SantÀAnna CC, Riley LW, Araújo Cardoso CA. Serological biomarkers for monitoring response to treatment of pulmonary and extrapulmonary tuberculosis in children and adolescents. Tuberculosis (Edinb) 2020; 123:101960. [PMID: 32741536 PMCID: PMC7436889 DOI: 10.1016/j.tube.2020.101960] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/17/2020] [Accepted: 05/26/2020] [Indexed: 01/19/2023]
Abstract
Key measures to halt the spread of tuberculosis (TB) include early diagnosis, effective treatment, and monitoring disease management. We sought to evaluate the use of serum immunoglobulin levels against antigens present in cell envelope of Mycobacterium tuberculosis to monitor TB treatment response in children and adolescents with pulmonary (PTB) or extrapulmonary TB (EPTB). Blood samples were collected prior to and one, two, and six months following treatment initiation. Serum immunoglobulin levels against cardiolipin, sulfatide, mycolic acid and Mce1A protein were measured by ELISA. Serum from 53 TB patients and 12 healthy participants were analyzed. After six months of successful treatment, there was a significant decrease (p < 0.0001) in IgM levels against cardiolipin, sulfatide, mycolic acid and Mce1A protein and IgG levels against Mce1A protein when compared to baseline immunoglobulin levels. There was no significant variation in antibody levels during follow-up between participants with PTB and EPTB, confirmed and unconfirmed TB diagnosis, and HIV infection status. Antibody levels in control participants without TB did not decrease during follow-up. These results suggest that immunoglobulin responses to mycobacterial cell wall products may be a useful tool to monitor treatment response in children and adolescents with PTB or EPTB.
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Affiliation(s)
- Danielle C M Dos Santos
- Departamento de Patologia, Faculdade de Medicina, Universidade Federal Fluminense, Niterói, Brazil; Laboratório Multiusuário de Apoio à Pesquisa Em Nefrologia e Ciências Médicas, Faculdade de Medicina, Universidade Federal Fluminense, Niterói, Brazil
| | - Kathryn L Lovero
- New York State Psychiatric Institute, Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, 1051 Riverside Drive #24, New York, NY, 10032, USA
| | - Christiane M Schmidt
- Laboratório Multiusuário de Apoio à Pesquisa Em Nefrologia e Ciências Médicas, Faculdade de Medicina, Universidade Federal Fluminense, Niterói, Brazil; Departamento Materno-Infantil, Faculdade de Medicina, Universidade Federal Fluminense, Niterói, Brazil
| | - Ana Cláudia M W Barros
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fiocruz, Rio de Janeiro, Brazil
| | | | - Ana Paula Barbosa
- Programa de Controle de Tuberculose da Secretária de Saúde de São Gonçalo, RJ, Brazil
| | - Marcos V S Pone
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fiocruz, Rio de Janeiro, Brazil
| | - Sheila M Pone
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fiocruz, Rio de Janeiro, Brazil
| | | | - Camila de Paula Martins
- Laboratório Multiusuário de Apoio à Pesquisa Em Nefrologia e Ciências Médicas, Faculdade de Medicina, Universidade Federal Fluminense, Niterói, Brazil
| | - Estela Magalhães Cosme
- Departamento Materno-Infantil, Faculdade de Medicina, Universidade Federal Fluminense, Niterói, Brazil
| | | | - Ana Lúcia Miceli
- Programa de Controle de Tuberculose da Secretária de Saúde de Duque de Caxias, RJ, Brazil
| | - Maria Luíza Vieira
- Programa de Controle de Tuberculose da Secretária de Saúde de Duque de Caxias, RJ, Brazil
| | | | | | - Afranio Kritski
- Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria de Fátima Pombo March
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Clemax C SantÀAnna
- Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, United States
| | - Claudete A Araújo Cardoso
- Laboratório Multiusuário de Apoio à Pesquisa Em Nefrologia e Ciências Médicas, Faculdade de Medicina, Universidade Federal Fluminense, Niterói, Brazil; Departamento Materno-Infantil, Faculdade de Medicina, Universidade Federal Fluminense, Niterói, Brazil.
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24
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Neto EDA, Guerrero J, Snyder RE, Pereira RFA, de Fátima Nogueira de Freitas M, Silva-Santana G, Riley LW, Aguiar-Alves F. Genotypic distribution of Staphylococcus aureus colonizing children and adolescents in daycare centers, an outpatient clinic, and hospitals in a major Brazilian urban setting. Diagn Microbiol Infect Dis 2020; 97:115058. [PMID: 32380359 DOI: 10.1016/j.diagmicrobio.2020.115058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 12/13/2022]
Abstract
Staphylococcus aureus nasal colonization is a major risk factor for infection. Studies have suggested an epidemiologic shift in the methicillin-resistant S. aureus (MRSA) strains that circulate in Brazil. We conducted cross-sectional studies of MRSA carriage among 1) children and adolescents in community daycare centers, 2) an outpatient clinic, and 3) hospitals in a large Brazilian metropolitan setting. There were 1.500 study subjects, 500 from each locale: 768 (51.2%) carried S. aureus whereas 150 (10%) of these were colonized with MRSA. The most common lineages were the Southwest Pacific (SWP) and the Pediatric clones in all three groups. Roughly 50% of SWP carried Panton-Valentine leukocidin (PVL) (p < 0.01) genes while 63.3% of the Pediatric clones were resistant or intermediately resistant to erythromycin (p < 0.01). This study describes a clonal change of the Brazilian epidemic clone (BEC) to the Pediatric and SWP lineages in Brazil. This finding has implications for clinical management of MRSA infections.
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Affiliation(s)
- Egidio Domingos André Neto
- Laboratório de Epidemiologia Molecular e Biotecnologia (LEMB), Laboratório Universitário Rodolpho Albino (LURA), Universidade Federal Fluminense (UFF), Rua Mário Viana, 523 - Santa Rosa - Niteroi, , Rio de Janeiro, Brazil
| | - Jaclyn Guerrero
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California. 2121 Berkeley Way #5302, Berkeley, California, USA
| | - Robert E Snyder
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California. 2121 Berkeley Way #5302, Berkeley, California, USA
| | - Renata Freire Alves Pereira
- Laboratório de Epidemiologia Molecular e Biotecnologia (LEMB), Laboratório Universitário Rodolpho Albino (LURA), Universidade Federal Fluminense (UFF), Rua Mário Viana, 523 - Santa Rosa - Niteroi, , Rio de Janeiro, Brazil; Programa de Pós-Graduação em Patologia e Programa de Pós-Graduação em Microbiologia e Parasitologia aplicados, Universidade Federal Fluminense, Av. Marquês do Paraná, 303 - Centro, Niteroi, Rio de Janeiro, Brazil
| | - Maria de Fátima Nogueira de Freitas
- Laboratório de Epidemiologia Molecular e Biotecnologia (LEMB), Laboratório Universitário Rodolpho Albino (LURA), Universidade Federal Fluminense (UFF), Rua Mário Viana, 523 - Santa Rosa - Niteroi, , Rio de Janeiro, Brazil
| | - Giorgio Silva-Santana
- Laboratório de Epidemiologia Molecular e Biotecnologia (LEMB), Laboratório Universitário Rodolpho Albino (LURA), Universidade Federal Fluminense (UFF), Rua Mário Viana, 523 - Santa Rosa - Niteroi, , Rio de Janeiro, Brazil; Programa de Pós-Graduação em Patologia e Programa de Pós-Graduação em Microbiologia e Parasitologia aplicados, Universidade Federal Fluminense, Av. Marquês do Paraná, 303 - Centro, Niteroi, Rio de Janeiro, Brazil
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California. 2121 Berkeley Way #5302, Berkeley, California, USA
| | - Fábio Aguiar-Alves
- Laboratório de Epidemiologia Molecular e Biotecnologia (LEMB), Laboratório Universitário Rodolpho Albino (LURA), Universidade Federal Fluminense (UFF), Rua Mário Viana, 523 - Santa Rosa - Niteroi, , Rio de Janeiro, Brazil; Programa de Pós-Graduação em Patologia e Programa de Pós-Graduação em Microbiologia e Parasitologia aplicados, Universidade Federal Fluminense, Av. Marquês do Paraná, 303 - Centro, Niteroi, Rio de Janeiro, Brazil..
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Abstract
In general, foodborne diseases present themselves with gastrointestinal symptoms caused by bacterial, viral, and parasitic pathogens well established to be foodborne. These pathogens are also associated with extraintestinal clinical manifestations. Recent studies have suggested that Escherichia coli and Klebsiella pneumoniae, which both cause common extraintestinal infections such as urinary tract and bloodstream infections, may also be foodborne. The resolution and separation of these organisms into pathotypes versus commensals by modern genotyping methods have led to the identification of key lineages of these organisms causing outbreaks of extraintestinal infections. These epidemiologic observations suggested common- or point-source exposures, such as contaminated food. Here, we describe the spectrum of extraintestinal illnesses caused by recognized enteric pathogens and then review studies that demonstrate the potential role of extraintestinal pathogenic E. coli (ExPEC) and K. pneumoniae as foodborne pathogens. The impact of global food production and distribution systems on the possible foodborne spread of these pathogens is discussed.
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Affiliation(s)
- Lee W. Riley
- School of Public Health, University of California, Berkeley, California 94720, USA
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Maity S, Wang X, Das S, He M, Riley LW, Murthy N. A cephalosporin-chemiluminescent conjugate increases beta-lactamase detection sensitivity by four orders of magnitude. Chem Commun (Camb) 2020; 56:3516-3519. [PMID: 32101196 PMCID: PMC7666973 DOI: 10.1039/c9cc09498a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The expression of beta-lactamases in bacteria is a central cause of drug resistance. In this report, we present a beta-lactamase chemiluminescent probe, termed CCP, which can for the first time detect beta-lactamase activity via chemiluminescence and can detect beta lactamase with a sensitivity that is 4-orders of magnitude higher than the commercially available fluorescent lactamase substrate fluorocillin.
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Affiliation(s)
- Santanu Maity
- Department of Bioengineering, University of California, Berkeley, USA.
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Matsui Y, Hu Y, Rubin J, de Assis RS, Suh J, Riley LW. Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community. Microbiologyopen 2020; 9:1225-1233. [PMID: 32189451 PMCID: PMC7294302 DOI: 10.1002/mbo3.1032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 11/20/2019] [Revised: 02/14/2020] [Accepted: 03/06/2020] [Indexed: 11/10/2022] Open
Abstract
Community-acquired urinary tract infections (UTIs) are one of the most common bacterial infections worldwide. Escherichia coli is the most common cause of community-acquired UTI. In general, UTI results from E. coli in the intestine that enters the bladder via the urethra. However, whether these E. coli strains that cause UTI represent members of the intestinal commensal E. coli or a distinct subgroup of pathogenic E. coli remains unestablished. Here, we analyzed E. coli isolates from fecal samples of healthy volunteers and urine samples of UTI patients obtained from a university-affiliated health center. The E. coli isolates were genotyped by multilocus sequence typing (MLST). From May to October 2018, we analyzed 89 E. coli isolates from 76 (75%) rectal swabs from 113 unique healthy volunteers. We also analyzed 106 (27%) E. coli isolates from 398 unique urine samples collected between August and October 2018. Fecal and urine E. coli isolates each contained 31 distinct sequence types (STs). Nine STs were shared by fecal and urine E. coli isolates, which accounted for approximately 50% of urine isolates typed by MLST. Among the shared genotypes, ST10 and ST131 were significantly more frequently found in fecal samples, whereas ST95 and ST127 were significantly more frequently recovered from UTI samples. ST73 was found only among urine samples. These E. coli genotypes clustered and fluctuated over time. These observations suggest that E. coli genotypes found to cause UTI transiently colonize the intestine and that their primary reservoir may reside outside of the human intestine.
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Affiliation(s)
- Yusuke Matsui
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Yuan Hu
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Julia Rubin
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Reginara Souza de Assis
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Joy Suh
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
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Rubin J, Mussio K, Xu Y, Suh J, Riley LW. Prevalence of Antimicrobial Resistance Genes and Integrons in Commensal Gram-Negative Bacteria in a College Community. Microb Drug Resist 2020; 26:1227-1235. [PMID: 31985343 DOI: 10.1089/mdr.2019.0279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 11/13/2022] Open
Abstract
Although the human intestinal microbiome has been shown to harbor antimicrobial drug resistance genes (ARGs), the prevalence of such genes in a healthy population and their impact on extraintestinal infections that occur in that community are not well established. This study sought to identify ARG prevalence and their mobile elements in the intestines of a healthy community population at a California University, and compared these genes to those previously identified among uropathogenic Escherichia coli isolated from patients with urinary tract infection from the same community. We isolated Gram-negative bacteria (GNB) from fecal samples of healthy volunteers and screened them by polymerase chain reaction for class 1 integron cassette sequences and ARGs encoding resistance against ampicillin, trimethoprim-sulfamethoxazole, gentamicin, and colistin. We found antimicrobial-resistant GNB from 83 (81%) of 102 nonredundant rectal swab samples. Seventy-four (72%) of these samples contained β-lactamase genes (blaTEM, blaSHV, blaCTX-M, blaOXA, and blaOXY), dihydrofolate reductase (DHFR) genes (dhfr-A17, dhfr-A12, dhfr-A7, dhfr-A5, dhfr-A21, dhfr-A1, dhfr-A13, and dhfr-7), and aminoglycoside resistance genes (aadA5, aadA2, aadA1, and aadB). Integron sequences were found in 37 (36%) fecal samples. These genes were found in 11 different GNB species. The high prevalence of clinically common ARGs and integrons harbored by GNB in the intestine of a healthy population suggest that human intestines may serve as a major reservoir of these mobile ARGs that appear in E. coli strains causing extraintestinal infections in the same community.
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Affiliation(s)
- Julia Rubin
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Kaitlyn Mussio
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Yuqi Xu
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Peking University, Beijing, China
| | - Joy Suh
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
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29
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Rayasam SDG, Ray I, Smith KR, Riley LW. Extraintestinal Pathogenic Escherichia coli and Antimicrobial Drug Resistance in a Maharashtrian Drinking Water System. Am J Trop Med Hyg 2020; 100:1101-1104. [PMID: 30834880 DOI: 10.4269/ajtmh.18-0542] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Although access to piped drinking water continues to increase globally, information on the prevalence and clonal composition of coliforms found in piped water systems in low-resource settings remains limited. From June to July 2016, we examined Escherichia coli isolates in domestic water from the distribution system in Alibag, a small town in India. We analyzed the isolates for drug resistance and genotyped them by multilocus sequence typing. Of 147 water samples, 51 contained coliforms, and 19 (37%) of the 51 were biochemically confirmed to contain E. coli. These samples contained 104 E. coli isolates-all resistant to ampicillin. Resistance to ceftazidime was observed in 52 (50%) isolates, cefotaxime in 59 (57%), sulfamethoxazole-trimethoprim in 46 (44%), ciprofloxacin in 30 (29%), and gentamicin in two (2%). Thirty-eight (36%) belonged to sequence types recognized as extraintestinal pathogenic E. coli (ExPEC); 19 (50%) of these 38 ExPEC belonged to known uropathogenic E. coli lineages. This exploratory field research shows the extent to which "improved" drinking water is a potential source of E. coli strains capable of causing extraintestinal infections.
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Affiliation(s)
- Swati D G Rayasam
- Environmental Health Sciences Department, School of Public Health, University of California, Berkeley, California
| | - Isha Ray
- Energy and Resources Group, University of California, Berkeley, California
| | - Kirk R Smith
- Environmental Health Sciences Department, School of Public Health, University of California, Berkeley, California
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California
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30
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Cho B, Lee SH, Song J, Bhattacharjee S, Feng J, Hong S, Song M, Kim W, Lee J, Bang D, Wang B, Riley LW, Lee LP. Nanophotonic Cell Lysis and Polymerase Chain Reaction with Gravity-Driven Cell Enrichment for Rapid Detection of Pathogens. ACS Nano 2019; 13:13866-13874. [PMID: 31756079 DOI: 10.1021/acsnano.9b04685] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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] [Indexed: 06/10/2023]
Abstract
Rapid and precise detection of pathogens is a critical step in the prevention and identification of emergencies related to health and biosafety as well as the clinical management of community-acquired urinary tract infections or sexually transmitted diseases. However, a conventional culture-based pathogen diagnostic method is time-consuming, permitting physicians to use antibiotics without ample clinical data. Here, we present a nanophotonic Light-driven Integrated cell lysis and polymerase chain reaction (PCR) on a chip with Gravity-driven cell enrichment Health Technology (LIGHT) for rapid precision detection of pathogens (<20 min). We created the LIGHT, which has the three functions of (1) selective enrichment of pathogens, (2) photothermal cell lysis, and (3) photonic PCR on a chip. We designed the gravity-driven cell enrichment via a nanoporous membrane on a chip that allows an effective bacterial enrichment of 40 000-fold from a 1 mL sample in 2 min. We established a light-driven photothermal lysis of preconcentrated bacteria within 1 min by designing the network of nanoplasmonic optical antenna on a chip for ultrafast light-to-heat conversion, created the nanoplasmonic optical antenna network-based ultrafast photonic PCR on a chip, and identified Escherichia coli. Finally, we demonstrated the end-point detection of up to 103 CFU/mL of E. coli in 10 min. We believe that our nanophotonic LIGHT will provide rapid and precise identification of pathogens in both developing and developed countries.
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Affiliation(s)
- Byungrae Cho
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- UC Berkeley and UCSF Joint Graduate Program in Bioengineering , University of California , Berkeley , California 94720 , United States
- Berkeley Sensor and Actuator Center , University of California , Berkeley , California 94720 , United States
| | - Sang Hun Lee
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- Berkeley Sensor and Actuator Center , University of California , Berkeley , California 94720 , United States
| | - Jihwan Song
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
| | - Saptati Bhattacharjee
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
| | - Jeffrey Feng
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
| | - SoonGweon Hong
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- Berkeley Sensor and Actuator Center , University of California , Berkeley , California 94720 , United States
| | - Minsun Song
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- UC Berkeley and UCSF Joint Graduate Program in Bioengineering , University of California , Berkeley , California 94720 , United States
- Berkeley Sensor and Actuator Center , University of California , Berkeley , California 94720 , United States
| | - Wonseok Kim
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- Berkeley Sensor and Actuator Center , University of California , Berkeley , California 94720 , United States
| | - Jonghwan Lee
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- Berkeley Sensor and Actuator Center , University of California , Berkeley , California 94720 , United States
| | - Doyeon Bang
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- Berkeley Sensor and Actuator Center , University of California , Berkeley , California 94720 , United States
| | - Bowen Wang
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
| | - Lee W Riley
- Division of Infectious Disease and Vaccinology, School of Public Health , University of California , Berkeley , California 94720 , United States
| | - Luke P Lee
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- UC Berkeley and UCSF Joint Graduate Program in Bioengineering , University of California , Berkeley , California 94720 , United States
- Berkeley Sensor and Actuator Center , University of California , Berkeley , California 94720 , United States
- Department of Electrical Engineering and Computer Science , University of California , Berkeley , California 94720 , United States
- Biophysics Graduate Program , University of California , Berkeley , California 94720 , United States
- Biomedical Institute for Global Health Research and Technology (BIGHEART), Yong Loo Lin School of Medicine and Faculty of Engineering , National University of Singapore , Singapore 119077
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31
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Mocelin HJS, do Prado TN, Freitas PDSS, Bertolde AI, Perez F, Riley LW, Maciel ELN. [Variations in the detection of congenital Zika syndrome associated with changes in protocolsVariación de la detección del síndrome congénito por el virus del Zika en función de los cambios de los protocolos]. Rev Panam Salud Publica 2019; 43:e79. [PMID: 31579398 PMCID: PMC6752177 DOI: 10.26633/rpsp.2019.79] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/01/2019] [Indexed: 11/24/2022] Open
Abstract
Em 2015, o Brasil enfrentou uma epidemia de infecção pelo vírus Zika que se propagou por países do mundo. Posteriormente, recomendações acerca dos critérios de notificação de casos de síndrome congênita do Zika (SCZ) foram divulgadas através de protocolos. As mudanças frequentes nessas recomendações podem ter afetado o gerenciamento clínico e o acesso a suporte pós-diagnóstico por crianças afetadas mas não identificadas. No presente estudo, 39 casos de SCZ notificados no estado do Espírito Santo no período de 2015 a 2016 foram reclassificados quanto ao seu diagnóstico de acordo com o protocolo atualmente vigente, diferente daquele que vigorava em 2015. Pela reclassificação, apenas oito dos 36 casos seriam confirmados, respeitando o critério de dois ou mais sinais ou sintomas da SCZ com ou sem microcefalia e confirmação sorológica. Ainda, pela diminuição no perímetro cefálico que define microcefalia, 17 casos passaram a não se enquadrar nessa condição. Apesar de o protocolo vigente não utilizar somente o perímetro cefálico como critério para notificação e confirmação da SCZ, cabe ressaltar que este achado ainda é o maior sinalizador para as equipes de saúde, indicando um risco da não detecção precoce da SCZ. Seria prudente uma revisão dos casos “descartados” no momento de transição entre protocolos, a fim de avaliar se foram corretamente classificados.
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Affiliation(s)
- Helaine Jacinta Salvador Mocelin
- Universidade Federal do Espírito Santo (UFES) Laboratório de Epidemiologia (Lab-Epi) Vitória (ES) Brasil Universidade Federal do Espírito Santo (UFES), Laboratório de Epidemiologia (Lab-Epi), Vitória (ES), Brasil
| | - Thiago Nascimento do Prado
- Universidade Federal do Espírito Santo (UFES) Laboratório de Epidemiologia (Lab-Epi) Vitória (ES) Brasil Universidade Federal do Espírito Santo (UFES), Laboratório de Epidemiologia (Lab-Epi), Vitória (ES), Brasil
| | - Paula de Souza Silva Freitas
- Universidade Federal do Espírito Santo (UFES) Laboratório de Epidemiologia (Lab-Epi) Vitória (ES) Brasil Universidade Federal do Espírito Santo (UFES), Laboratório de Epidemiologia (Lab-Epi), Vitória (ES), Brasil
| | - Adelmo Inácio Bertolde
- Universidade Federal do Espírito Santo (UFES) Departamento de Estatística Vitória (ES) Brasil Universidade Federal do Espírito Santo (UFES), Departamento de Estatística, Vitória (ES), Brasil
| | - Freddy Perez
- Organização Pan-Americana da Saúde (OPAS) Departamentos de Doenças Transmissíveis e Determinantes Ambientais da Saúde Washington (DC) Estados Unidos Organização Pan-Americana da Saúde (OPAS), Departamentos de Doenças Transmissíveis e Determinantes Ambientais da Saúde, Washington (DC), Estados Unidos
| | - Lee W Riley
- Universidade da Califórnia, Escola de Saúde Pública Divisão de Doenças Infecciosas e Vacinologia Berkeley (CA) Estados Unidos Universidade da Califórnia, Escola de Saúde Pública, Divisão de Doenças Infecciosas e Vacinologia, Berkeley (CA), Estados Unidos
| | - Ethel Leonor Noia Maciel
- Universidade Federal do Espírito Santo (UFES) Laboratório de Epidemiologia (Lab-Epi) Vitória (ES) Brasil Universidade Federal do Espírito Santo (UFES), Laboratório de Epidemiologia (Lab-Epi), Vitória (ES), Brasil
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Takenami I, de Oliveira CC, Petrilli JD, Machado A, Riley LW, Arruda S. Serum antiphospholipid antibody levels as biomarkers for diagnosis of pulmonary tuberculosis patients. Int J Tuberc Lung Dis 2019; 22:1063-1070. [PMID: 30092873 DOI: 10.5588/ijtld.17.0874] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING Salvador, Bahia, Brazil. OBJECTIVE To evaluate the immunoglobulin (Ig)M and total IgG antibody response to cardiolipin (CL), phosphatidylcholine (PTC), phosphatidylethanolamine (PE), phosphatidylinositol (PI) and sulfatide (SL-I) as biosignatures that can be used to diagnose pulmonary tuberculosis (TB) and its applicability for monitoring the efficacy of anti-tuberculosis treatment. DESIGN Serum samples from 37 adult pulmonary TB patients and 48 controls (16 healthy household contacts, 19 household contacts with latent tuberculous infection [LTBI] and 13 non-TB patients with lung disease) were screened using enzyme-linked immunosorbent assays (ELISAs) for IgM and total IgG against phospholipids. RESULTS Levels of IgM response to CL, PE and PI, and IgG response to CL, PE, PI and PTC were significantly higher in TB patients than in control groups. Anti-CL IgG had the best performance characteristics, with a sensitivity and specificity of respectively 86.5% and 87.2%. This IgG anti-CL ELISA test detected 86.5% (32/37) of the TB patients, whereas the number detected using sputum smear was only 65.9% (24/37). After anti-tuberculosis treatment, the median value for all anti-phospholipid antibodies decreased significantly compared with baseline values (P < 0.05). CONCLUSION Our results suggest that the total IgG anti-CL level could be useful to complement conventional bacteriological tests for the rapid diagnosis of adult pulmonary TB.
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Affiliation(s)
- I Takenami
- Laboratório Avançado de Saúde Pública, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia
| | - C C de Oliveira
- Laboratório Avançado de Saúde Pública, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia
| | - J D Petrilli
- Laboratório Avançado de Saúde Pública, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia
| | - A Machado
- Departamiento de Ciências da Vida, Universidade Estadual de Bahia, Salvador, Bahia, Hospital Especializado Octávio Mangabeira, Secretaria da Saúde do Estado da Bahia, Salvador, Bahia, Brazil
| | - L W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - S Arruda
- Laboratório Avançado de Saúde Pública, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Departamiento de Ciências da Vida, Universidade Estadual de Bahia, Salvador, Bahia
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Borges CA, Tarlton NJ, Riley LW. Escherichia coli from Commercial Broiler and Backyard Chickens Share Sequence Types, Antimicrobial Resistance Profiles, and Resistance Genes with Human Extraintestinal Pathogenic Escherichia coli. Foodborne Pathog Dis 2019; 16:813-822. [PMID: 31411497 DOI: 10.1089/fpd.2019.2680] [Citation(s) in RCA: 37] [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: 01/01/2023] Open
Abstract
Escherichia coli recovered from poultry, and extraintestinal pathogenic E. coli (ExPEC), responsible for most cases of urinary tract infection (UTI) and bloodstream infection (BSI) in humans, may share genetic characteristics, suggesting that poultry are a potential source of ExPEC. Here, we compared E. coli isolated from commercial broiler and backyard chickens (n = 111) with ExPEC isolated from patients with community- or hospital-acquired UTI or BSI (n = 149) from Southeast Brazil. Isolates were genotyped by multilocus sequence typing, tested for susceptibility to antimicrobial agents, and screened for β-lactamase genes. We found that 10 genotypes were shared among poultry and human isolates: sequence type (ST) 10, ST48, ST58, ST88, ST90, ST93, ST131, ST602, ST617, and ST1018. Thirty-five (23%) ExPEC and 35 (31%) poultry E. coli isolates belonged to the shared STs. ST58 and ST88 isolates from human and poultry sources shared identical antimicrobial resistance profiles. blaTEM-1 was the most prevalent β-lactamase gene, identified in 65 (92%) of 71 ExPEC and 29 (67%) of 43 poultry E. coli that tested positive for β-lactamase genes. Commercial broiler chicken isolates shared the extended-spectrum β-lactamase (ESBL) genes blaCTX-M-2, blaCTX-M-8, and blaSHV-2 with human isolates; backyard chicken isolates lacked ESBL genes. In conclusion, several genotypic and phenotypic characteristics were shared between human and poultry E. coli; this suggests that there is potential for transmission of E. coli and antimicrobial resistance genes from poultry to humans, perhaps through environmental contamination, direct contact, or consumption. Additional research is needed to understand the potential direction and pathways of transmission.
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Affiliation(s)
- Clarissa A Borges
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California
| | - Nicole J Tarlton
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California
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Neves FPG, Cardoso NT, Cardoso CAA, Teixeira LM, Riley LW. Direct effect of the 13-valent pneumococcal conjugate vaccine use on pneumococcal colonization among children in Brazil. Vaccine 2019; 37:5265-5269. [PMID: 31337592 DOI: 10.1016/j.vaccine.2019.07.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 10/08/2018] [Revised: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 01/17/2023]
Abstract
BACKGROUND The 13-valent pneumococcal conjugate vaccine (PCV13) has been commercially available in Brazil since 2010. We investigated the carriage prevalence, capsular types, and antimicrobial resistance among pneumococci isolated from children immunized with PCV13 in Brazil. METHODS We analyzed 500 children < 6 years old attending public (n = 270) and private (n = 230) clinics in Niterói/RJ, Brazil, in 2014. We determined the antimicrobial susceptibility and capsular types for all isolates. RESULTS Thirty-eight (7.6%) of 500 children had received at least one PCV13 dose. Since only two (0.7%) of 270 children at the public clinic were vaccinated with PCV13, major analyses focused on 36 (15.7%) of 230 children attending private clinics. Nine (25%) of 36 children were pneumococcal carriers. Characteristics associated with carriage were age ≥ 2 years, cough/expectoration, and childcare center attendance (p ≤ 0.01). The capsular types found were 15B/C (n = 2), 6C, 11A/D, 16F, 23A, and 23F. Two isolates were non-typeable (NT). Three (33.3%) isolates were multidrug resistant. We found four (44.4%) penicillin non-susceptible pneumococci, with penicillin and ceftriaxone MICs ranging from 0.12 to 4.0 µg/ml and 0.023-0.5 µg/ml, respectively. We also detected two (22.2%) erythromycin-resistant isolates (MICs of 3.0 and 256 µg/ml). CONCLUSIONS Colonization with PCV13 serotype was rare among the vaccinated children. Increasing PCV13 coverage might help reduce the frequency of major serotypes currently associated with invasive pneumococcal diseases in Brazil, such as 3 and 19A. The isolation of multidrug-resistant serotype 6C and NT isolates in carriage, however, requires close monitoring.
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Affiliation(s)
- Felipe P G Neves
- Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, 101. São Domingos, Niterói, RJ 24210-130, Brazil.
| | - Nayara T Cardoso
- Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, 101. São Domingos, Niterói, RJ 24210-130, Brazil
| | - Claudete A A Cardoso
- Faculdade de Medicina, Universidade Federal Fluminense, Av. Marquês do Paraná, 303. Centro, Niterói, RJ 24033-900, Brazil.
| | - Lúcia M Teixeira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - bloco I, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA.
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Neves FPG, Cardoso NT, Souza ARV, Snyder RE, Marlow MM, Pinto TCA, Teixeira LM, Riley LW. Population structure of Streptococcus pneumoniae colonizing children before and after universal use of pneumococcal conjugate vaccines in Brazil: emergence and expansion of the MDR serotype 6C-CC386 lineage. J Antimicrob Chemother 2019; 73:1206-1212. [PMID: 29401243 DOI: 10.1093/jac/dky001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/28/2017] [Indexed: 01/06/2023] Open
Abstract
Objectives To determine the population structure and change in drug resistance of pneumococci colonizing children before and after the introduction of the 10-valent and 13-valent pneumococcal conjugate vaccines (PCV10/13) in Brazil. Methods We used MLST to analyse 256 pneumococcal isolates obtained from children aged <6 years before (2009-10; n = 125) and after (2014; n = 131) the introduction of the PCV10 and PCV13. Antimicrobial susceptibility and capsular types were previously determined. Results We identified 97 different STs. Ninety (35.2%) isolates were related to international clones. The most frequent lineages were serogroup 6-CC724 (where CC stands for clonal complex) and the MDR serotype 6C-CC386 in the pre- and post-PCV10/13 periods, respectively. Penicillin-non-susceptible pneumococci (PNSP) formed 24% and 38.9% of the pre- and post-PCV10/13 isolates, respectively (P = 0.01). In the pre-PCV10/13 period, serotype 14-ST156 was the predominant penicillin-non-susceptible lineage, but it was not detected in the post-PCV10/13 period. Serotype 14-ST156 and serotype 19A-ST320 complex isolates had the highest penicillin and ceftriaxone MICs in the pre- and post-PCV10/13 periods, respectively. In turn, serotype 6C-CC386 comprised almost 30% of the PNSP and over 40% of the erythromycin-resistant isolates (MIC >256 mg/L) in the post-PCV10/13 period. Conclusions Although PNSP strains were polyclonal, most resistant isolates belonged to a single genotype from each period. Higher erythromycin resistance prevalence (42%) in the post-PCV10/13 period was mainly attributed to MDR serotype 6C-CC386. Ongoing surveillance of pneumococcal clonal composition is important to evaluate PCV use outcomes and to identify factors other than PCVs that drive pneumococcal drug resistance evolution.
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Affiliation(s)
- Felipe P G Neves
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA.,Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, 101 São Domingos, Niterói, RJ 24210-130, Brazil
| | - Nayara T Cardoso
- Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, 101 São Domingos, Niterói, RJ 24210-130, Brazil
| | - Aline R V Souza
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Robert E Snyder
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA
| | - Mariel M Marlow
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA
| | - Tatiana C A Pinto
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lúcia M Teixeira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA
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Jackson N, Wu TZ, Adams-Sapper S, Satoorian T, Geisberg M, Murthy N, Lee L, Riley LW. A multiplexed, indirect enzyme-linked immunoassay for the detection and differentiation of E. coli from other Enterobacteriaceae and P. aeruginosa from other glucose non-fermenters. J Microbiol Methods 2019; 158:52-58. [PMID: 30708086 DOI: 10.1016/j.mimet.2019.01.014] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/19/2019] [Accepted: 01/28/2019] [Indexed: 10/27/2022]
Abstract
Gram-negative bacteria (GNB) are important causes of community (CA) and hospital (HA)- associated infections. Here we describe the development of an indirect ELISA (I-ELISA), which can be used to detect and differentiate the Enterobacteriaceae Escherichia coli, and glucose non-fermenter Pseudomonas aeruginosa from other GNB species. The I-ELISA utilizes six antibodies for bacterial speciation, which were grouped according to their bacterial targets; Enterobacteriaceae (SL-EntA and CH1810 mAb), Escherichia coli (SL-EcA and 6103-46 mAb), Pseudomonas aeruginosa (SL-PaA and SL-PaB). The six, anti-GNB antibodies were first screened against a panel of well-characterized clinical GNB isolates to optimize assay conditions and to determine individual antibody sensitivity and specificity. When tested against a diverse, blinded panel of 94 GNB clinical isolates, the I-ELISA exhibited the following sensitivity/specificity for each target: Enterobacteriaceae (94.4%/95%), E. coli (82.6%/88.7%), P. aeruginosa (83.3%/96%). An I-ELISA to detect and differentiate the most common GNB pathogens offers advantage in terms of simplicity over diagnostic tests currently used in most clinical settings.
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Affiliation(s)
- N Jackson
- School of Public Health, Division of Infectious Disease and Vaccinology, University of California, Berkeley, CA 94720, USA
| | - T Z Wu
- School of Public Health, Division of Infectious Disease and Vaccinology, University of California, Berkeley, CA 94720, USA
| | - S Adams-Sapper
- School of Public Health, Division of Infectious Disease and Vaccinology, University of California, Berkeley, CA 94720, USA
| | - T Satoorian
- Silver Lake Research Corporation, Azusa, CA 91702, USA
| | - M Geisberg
- Silver Lake Research Corporation, Azusa, CA 91702, USA
| | - N Murthy
- School of Public Health, Division of Infectious Disease and Vaccinology, University of California, Berkeley, CA 94720, USA
| | - L Lee
- School of Public Health, Division of Infectious Disease and Vaccinology, University of California, Berkeley, CA 94720, USA
| | - L W Riley
- School of Public Health, Division of Infectious Disease and Vaccinology, University of California, Berkeley, CA 94720, USA.
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Delcroix M, Heydari K, Dodge R, Riley LW. Flow-cytometric analysis of human monocyte subsets targeted by Mycobacterium bovis BCG before granuloma formation. Pathog Dis 2018; 76:5185113. [PMID: 30445573 DOI: 10.1093/femspd/fty080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 11/09/2018] [Indexed: 11/14/2022] Open
Abstract
Infection with Mycobacterium tuberculosis (Mtb) is characterized by an inflammatory response resulting in the formation of granulomas. These tight aggregates of immune cells play an important role in bacterial containment and in the eventual outcome of infection. Monocytes are a major component of the early immune response to Mtb and contribute to the cellular matrix of the newly forming granuloma. Therefore, defining which monocyte subset is the target of mycobacterial infection is critical. Here, we describe a flow-cytometry-based assay to analyze infectivity in vitro of monocyte subsets by Mycobacterium bovis BCG before granuloma formation. We identified CD14+CD16- monocytes as the main target of infection in peripheral blood mononuclear cells from six healthy donors. CD14+CD16+ monocytes displayed the lowest infection rates and remained uninfected in some donors. We found that a longer infection time resulted in an increase of the percentage of monocytes infected and of the number of granulomas produced. We did not observe changes in monocyte cell death or subset expansion upon infection. Future experiments with our in vitro method could help define Mtb infectivity of monocyte subsets. Our study provides a platform to investigate how early infection of different monocyte subsets may alter granuloma formation and outcomes of Mtb infection.
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Affiliation(s)
- Melaine Delcroix
- Division of Infectious Disease and Vaccinology, 530E Li Ka Shing, School of Public Health, University of California, Berkeley, 94720, USA
| | - Kartoosh Heydari
- LKS Flow Cytometry Core, Cancer Research Laboratory, University of California, Berkeley, CA 94720, USA
| | - Ren Dodge
- Division of Infectious Disease and Vaccinology, 530E Li Ka Shing, School of Public Health, University of California, Berkeley, 94720, USA
| | - Lee W Riley
- Division of Infectious Disease and Vaccinology, 530E Li Ka Shing, School of Public Health, University of California, Berkeley, 94720, USA
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deBoer TR, Tarlton NJ, Yamaji R, Adams-Sapper S, Wu TZ, Maity S, Vesgesna GK, Sadlowski CM, DePaola P, Riley LW, Murthy N. Cover Feature: An Enzyme-Mediated Amplification Strategy Enables Detection of β-Lactamase Activity Directly in Unprocessed Clinical Samples for Phenotypic Detection of β-Lactam Resistance (ChemBioChem 20/2018). Chembiochem 2018. [DOI: 10.1002/cbic.201800571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Tara R. deBoer
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Nicole J. Tarlton
- Department of Public Health; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Reina Yamaji
- Department of Public Health; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Sheila Adams-Sapper
- Department of Public Health; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Tiffany Z. Wu
- Department of Public Health; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Santanu Maity
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Giri K. Vesgesna
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Corinne M. Sadlowski
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Peter DePaola
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Lee W. Riley
- Department of Public Health; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Niren Murthy
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
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deBoer TR, Tarlton NJ, Yamaji R, Adams-Sapper S, Wu TZ, Maity S, Vesgesna GK, Sadlowski CM, DePaola P, Riley LW, Murthy N. An Enzyme-Mediated Amplification Strategy Enables Detection of β-Lactamase Activity Directly in Unprocessed Clinical Samples for Phenotypic Detection of β-Lactam Resistance. Chembiochem 2018; 19:2173-2177. [PMID: 30079487 DOI: 10.1002/cbic.201800443] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 08/01/2018] [Indexed: 11/09/2022]
Abstract
Biochemical assays that can identify β-lactamase activity directly from patient samples have the potential to significantly improve the treatment of bacterial infections. However, current β-lactamase probes do not have the sensitivity needed to measure β-lactam resistance directly from patient samples. Here, we report the development of an instrument-free signal amplification technology, DETECT, that connects the activity of two enzymes in series to effectively amplify the activity of β-lactamase 40 000-fold, compared to the standard β-lactamase probe nitrocefin.
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Affiliation(s)
- Tara R deBoer
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Nicole J Tarlton
- Department of Public Health, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Reina Yamaji
- Department of Public Health, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Sheila Adams-Sapper
- Department of Public Health, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Tiffany Z Wu
- Department of Public Health, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Santanu Maity
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Giri K Vesgesna
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Corinne M Sadlowski
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Peter DePaola
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Lee W Riley
- Department of Public Health, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
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Rajan JV, Ferrazoli L, Waldman EA, Simonsen V, Ferreira P, Telles MA, Riley LW. Diabetes increases the risk of recent-transmission tuberculosis in household contacts in São Paulo, Brazil. Int J Tuberc Lung Dis 2018; 21:916-921. [PMID: 28786800 DOI: 10.5588/ijtld.16.0043] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING A cohort of household contacts of tuberculosis (TB) index cases from four public health clinics in São Paulo, Brazil. OBJECTIVE To measure the association between diabetes mellitus (DM) among household contacts and recent-transmission TB (RT TB). DESIGN Index TB cases (n = 263) identified from 2001 to 2002 in São Paulo, whose household contacts (n = 1383) were monitored for active TB until December 2010. RESULTS From 2001 to 2010, there were 29 cases of RT TB among household contacts (cumulative incidence 2.1%, 95%CI 1.4-2.9). DM in household contacts was associated with RT TB (OR 3.96, 95%CI 1.33-11.79) even after adjustment for human immunodeficiency virus (HIV) status, smoking and alcohol use (adjusted OR [aOR] 3.21, 95%CI 1.01-10.19). HIV infection was also associated with RT TB (OR 6.40, 95%CI 1.40-29.40; aOR 4.81, 95%CI 0.96-24.18). Household contact DM was not associated with non-RT TB (OR 1.27, 95%CI 0.30-5.40). The time to diagnosis of TB was shorter in household contacts with and without DM (P = 0.035) and in household contacts with and without HIV (P = 0.0002). CONCLUSION Household contact DM was associated with an increased risk of RT TB in a cohort in Brazil, lending support to the active screening of household contacts with DM for TB in Brazil.
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Affiliation(s)
- J V Rajan
- Department of Medicine, University of California, San Francisco, USA; Zuckerberg San Francisco General Hospital, San Francisco, California, USA
| | - L Ferrazoli
- Department of Public Health, Instituto Adolfo Lutz, São Paulo, São Paulo, Brazil
| | - E A Waldman
- School of Public Health, University of São Paulo, São Paulo, São Paulo, Brazil
| | - V Simonsen
- Department of Public Health, Instituto Adolfo Lutz, São Paulo, São Paulo, Brazil
| | - P Ferreira
- School of Public Health, University of São Paulo, São Paulo, São Paulo, Brazil
| | - M A Telles
- School of Public Health, University of São Paulo, São Paulo, São Paulo, Brazil
| | - L W Riley
- School of Public Health, University of California, Berkeley, Berkeley, California, USA
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Kim MW, Greenfield BK, Snyder RE, Steinmaus CM, Riley LW. The association between community-associated Staphylococcus aureus colonization and disease: a meta-analysis. BMC Infect Dis 2018; 18:86. [PMID: 29466953 PMCID: PMC5822478 DOI: 10.1186/s12879-018-2990-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 10/30/2017] [Accepted: 02/01/2018] [Indexed: 12/14/2022] Open
Abstract
Background Colonization with Staphylococcus aureus is a well-defined risk factor for disease in hospitals, which can range from minor skin infections to severe, systemic diseases. However, the generalizability of this finding has not been thoroughly investigated outside of the hospital environment. We aimed to assess the role of S. aureus colonization as a risk factor for disease in the community. Methods We performed a meta-analysis of observational studies and searched PubMed for articles published between December 1979 and May 23, 2016. We included cohort, cross-sectional, and case-control studies that reported quantitative estimates of both S. aureus colonization and disease statuses of all study subjects. We excluded studies on recently hospitalized subjects, long-term care facilities, surgery patients, dialysis patients, hospital staff, S. aureus outbreaks, and livestock-associated infections. Our meta-analysis was performed using random-effects analysis to obtain pooled odds ratios (ORs) to compare the odds of S. aureus disease with respect to S. aureus colonization status. Results We identified 3477 citations, of which 12 articles on 6998 subjects met the eligibility criteria. Overall, subjects colonized with S. aureus were more likely to progress to disease than those who were non-colonized: (OR 1.87, 95% CI 1.21–2.88, n = 7 studies). We observed a larger effect with methicillin-resistant S. aureus colonization (7.06, 4.60–10.84, n = 7 studies). However, the methicillin-sensitive S. aureus colonization was not associated with greater odds of disease (1.20, 0.69–2.06, n = 4 studies). Heterogeneity was present across studies in all of the subgroups: S. aureus (I2 = 95.0%, χ2 = 120.3, p < 0.001), MRSA (I2 = 92.8%, χ2 = 82.8, p = p < 0.001), and MSSA (I2 = 86.3%, χ2 = 21.8, p < 0.001). Conclusions While the majority of papers individually support the assumption that colonization is a risk factor for S. aureus disease in the general population, there is marked heterogeneity between studies and further investigation is needed to identify the major sources of this variance. There is a shortage of literature addressing this topic in the community setting and a need for further research on colonization as a focus for disease prevention. Electronic supplementary material The online version of this article (10.1186/s12879-018-2990-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina W Kim
- School of Public Health, University of California, Berkeley, CA, USA
| | - Ben K Greenfield
- Department of Environmental Sciences, Southern Illinois University, Edwardsville, IL, USA.
| | - Robert E Snyder
- School of Public Health, University of California, Berkeley, CA, USA
| | - Craig M Steinmaus
- School of Public Health, University of California, Berkeley, CA, USA
| | - Lee W Riley
- School of Public Health, University of California, Berkeley, CA, USA
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Lima FR, Takenami I, Cavalcanti MA, Riley LW, Arruda S. ELISA-based assay of immunoglobulin G antibodies against mammalian cell entry 1A (Mce1A) protein: a novel diagnostic approach for leprosy. Mem Inst Oswaldo Cruz 2017; 112:844-849. [PMID: 29211246 PMCID: PMC5719554 DOI: 10.1590/0074-02760160549] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 12/22/2016] [Accepted: 07/11/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Leprosy is a chronic infectious disease caused by the obligate intracellular
bacillus Mycobacterium leprae. Because leprosy diagnosis is
complex and requires professional expertise, new tools and methodologies are
needed to detect cases in early stages and prevent transmission. The
M. leprae genome contains mce1A, which
encodes a putative mammalian cell entry protein (Mce1A). We hypothesised
that the presence of Mce1A on the cell surface could be detected by the
host's immune system. OBJECTIVE The aim of this study was to evaluate antibody responses against the Mce1A
protein in leprosy patients, household contacts of patients, and the general
population to present an addition tool for leprosy diagnosis. METHODS A cross-sectional study involving 89 volunteers [55 leprosy cases, 12
household contacts (HHC) and 22 endemic controls (EC)] was conducted at
Couto Maia Hospital, in Salvador, Bahia (BA), Brazil. RESULTS The median anti-Mce1A IgA was significantly higher in multibacillary (MB) and
paucibacillary (PB) cases than in EC (p < 0.0001). A similar trend was
observed in IgM levels, which were significantly higher in both MB (p <
0.0001) and PB (p = 0.0006) groups compared to in EC individuals. The
greatest differences were observed for IgG class-specific antibodies against
Mce1A. The median levels of MB and PB were significantly higher compared to
both controls HHC and EC (MB or PB vs EC, MB vs HHC p < 0.0001; PB vs
HHC, p = 0.0013). Among leprosy cases, IgG enzyme-linked immunosorbent assay
sensitivity and specificity were 92.7% and 97.1%, respectively. IgG
positivity was confirmed in 92.1% and 94.1% of MB and PB patients,
respectively. CONCLUSION This novel diagnostic approach presents an easy, non-invasive, and
inexpensive method for leprosy screening, which may be applicable in endemic
areas.
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Affiliation(s)
- Filipe R Lima
- Fundação Oswaldo Cruz-Fiocruz, Centro de Pesquisas Gonçalo Moniz, Laboratório Avançado de Saúde Pública, Salvador, BA, Brasil.,Escola Bahiana de Medicina e Saúde Pública, Salvador, BA, Brasil
| | - Iukary Takenami
- Fundação Oswaldo Cruz-Fiocruz, Centro de Pesquisas Gonçalo Moniz, Laboratório Avançado de Saúde Pública, Salvador, BA, Brasil
| | | | - Lee W Riley
- University of California, School of Public Health, Division of Infectious Diseases and Vaccinology, Berkeley, CA, USA
| | - Sérgio Arruda
- Fundação Oswaldo Cruz-Fiocruz, Centro de Pesquisas Gonçalo Moniz, Laboratório Avançado de Saúde Pública, Salvador, BA, Brasil.,Escola Bahiana de Medicina e Saúde Pública, Salvador, BA, Brasil
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Prado TND, Riley LW, Sanchez M, Fregona G, Nóbrega RLP, Possuelo LG, Zandonade E, Locatelli RL, Souza FMD, Rajan JV, Maciel ELN. Prevalence and risk factors for latent tuberculosis infection among primary health care workers in Brazil. CAD SAUDE PUBLICA 2017; 33:e00154916. [PMID: 29267691 DOI: 10.1590/0102-311x00154916] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 04/03/2017] [Indexed: 02/06/2023] Open
Abstract
Health care workers (HCW) are at increased risk of latent tuberculosis infection (LTBI) from occupational exposure to Mycobacterium tuberculosis. The objective was to determine the prevalence of and risk factors for LTBI among primary HCW in five Brazilian cities. We conducted a cross-sectional study, from 2011 to 2013, among primary HCW, using a structured questionnaire and an evaluated for LTBI using the Quantiferon-TB Gold in-tube test. The magnitude of the associations was assessed using hierarchical logistic regression models. Among 708 HCW, the LTBI prevalence was 27% (n = 196; 95%CI: 24%-31%). We found that the following factors were positively associated with LTBI in primary HCW: age > 50 years (OR = 2.94; 95%CI: 1.44-5.99), absence of a BCG scar (OR = 2.10; 95%CI: 1.28-3.43), self-reported ex-smoker status (OR = 1.80; 95%CI: 1.04-3.11), being a nurse (OR = 2.97; 95%CI: 1.13-7.83), being a nurse technician (OR = 3.10; 95%CI: 1.26-7.60), being a community health agent (OR = 2.60; 95%CI: 1.06-6.40), and irregular use of N95 masks (OR = 2.51; 95%CI: 1.11-5.98). In contrast, HCWs who do not work in health care facilities with a TB control program were less likely to have LTBI (OR = 0.66; 95%CI: 0.45-0.97). This study demonstrated a substantial occupational risk of LTBI among primary HCW in Brazil. The Brazilian TB control program, as well as local programs, need to target these high-risk HCW with education, as well as with better personal protective equipment to prevent acquisition of new TB infection.
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Affiliation(s)
| | - Lee W Riley
- School of Public Health, University of California, Berkeley, U.S.A
| | | | - Geisa Fregona
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brasil.,Hospital Universitário Cassiano Antonio Moraes, Universidade Federal do Espírito Santo, Vitória, Brasil
| | | | | | - Eliana Zandonade
- Departamento de Estatística, Universidade Federal do Espírito Santo, Vitória, Brasil
| | - Rodrigo Leite Locatelli
- Programa de Pós-graduação em Saúde Coletiva, Universidade Federal do Espírito Santo, Vitória, Brasil
| | | | - Jayant V Rajan
- School of Medicine, University of California, San Francisco, U.S.A
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Raphael E, Riley LW. Infections Caused by Antimicrobial Drug-Resistant Saprophytic Gram-Negative Bacteria in the Environment. Front Med (Lausanne) 2017; 4:183. [PMID: 29164118 PMCID: PMC5670356 DOI: 10.3389/fmed.2017.00183] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 09/04/2017] [Accepted: 10/12/2017] [Indexed: 11/25/2022] Open
Abstract
Background Drug-resistance genes found in human bacterial pathogens are increasingly recognized in saprophytic Gram-negative bacteria (GNB) from environmental sources. The clinical implication of such environmental GNBs is unknown. Objectives We conducted a systematic review to determine how often such saprophytic GNBs cause human infections. Methods We queried PubMed for articles published in English, Spanish, and French between January 2006 and July 2014 for 20 common environmental saprophytic GNB species, using search terms “infections,” “human infections,” “hospital infection.” We analyzed 251 of 1,275 non-duplicate publications that satisfied our selection criteria. Saprophytes implicated in blood stream infection (BSI), urinary tract infection (UTI), skin and soft tissue infection (SSTI), post-surgical infection (PSI), osteomyelitis (Osteo), and pneumonia (PNA) were quantitatively assessed. Results Thirteen of the 20 queried GNB saprophytic species were implicated in 674 distinct infection episodes from 45 countries. The most common species included Enterobacter aerogenes, Pantoea agglomerans, and Pseudomonas putida. Of these infections, 443 (66%) had BSI, 48 (7%) had SSTI, 36 (5%) had UTI, 28 (4%) had PSI, 21 (3%) had PNA, 16 (3%) had Osteo, and 82 (12%) had other infections. Nearly all infections occurred in subjects with comorbidities. Resistant strains harbored extended-spectrum beta-lactamase (ESBL), carbapenemase, and metallo-β-lactamase genes recognized in human pathogens. Conclusion These observations show that saprophytic GNB organisms that harbor recognized drug-resistance genes cause a wide spectrum of infections, especially as opportunistic pathogens. Such GNB saprophytes may become increasingly more common in healthcare settings, as has already been observed with other environmental GNBs such as Acinetobacter baumannii and Pseudomonas aeruginosa.
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Affiliation(s)
- Eva Raphael
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
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Tarlton NJ, Satoorian TS, Panchal A, Borges CA, Geisberg M, Riley LW. Monoclonal antibody-mediated detection of CTX-M β-lactamases in Gram-negative bacteria. J Microbiol Methods 2017; 144:37-43. [PMID: 28970054 DOI: 10.1016/j.mimet.2017.09.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 08/24/2017] [Revised: 09/27/2017] [Accepted: 09/29/2017] [Indexed: 11/30/2022]
Abstract
Gram-negative bacteria (GNB) that express CTX-M β-lactamases have become a serious threat to the clinical management of GNB infections. While antibody-based platforms have been successfully used in research settings to study and detect other β-lactamases-including SHV, CMY, and TEM enzymes-there is currently a lack of antibody-based tools to detect the CTX-M enzymes. Here we describe the development of an anti-CTX-M sandwich ELISA based on a pair of monoclonal antibodies (mAbs)-mAb 6101-33 and mAb 6101-19-used as the capture and detection antibody, respectively. This antibody pair detected CTX-M variants from group 1 (CTX-M-15), group 2 (CTX-M-2), group 8 (CTX-M-8), and group 9 (CTX-M-14) that were expressed by a training set of clinical GNB isolates. The limit of detection for this sandwich ELISA was 30ng of recombinant CTX-M-15, and CTX-Ms expressed by 106 lysed CFU of GNB. When tested against a blinded panel of 78 clinical isolates, the sandwich ELISA demonstrated a sensitivity of 96% and a specificity of 100%. The mAb pair did not cross-react with bacteria that contained other β-lactamases, including TEM, SHV, OXA, KPC, NDM, CMY, and DHA. In conclusion, we developed a highly sensitive and specific sandwich ELISA, capable of detecting CTX-M enzyme production in GNB pathogens.
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Affiliation(s)
- Nicole J Tarlton
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, CA 94720, USA
| | | | - Anand Panchal
- Silver Lake Research Corporation, Azusa, CA 91702, USA
| | - Clarissa A Borges
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, CA 94720, USA
| | - Mark Geisberg
- Silver Lake Research Corporation, Azusa, CA 91702, USA
| | - Lee W Riley
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, CA 94720, USA.
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Snyder RE, Rajan JV, Costa F, Lima HCAV, Calcagno JI, Couto RD, Riley LW, Reis MG, Ko AI, Ribeiro GS. Differences in the Prevalence of Non-Communicable Disease between Slum Dwellers and the General Population in a Large Urban Area in Brazil. Trop Med Infect Dis 2017; 2:E47. [PMID: 30270904 PMCID: PMC6082112 DOI: 10.3390/tropicalmed2030047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 12/13/2022] Open
Abstract
Residents of urban slums are at greater risk for disease than their non-slum dwelling urban counterparts. We sought to contrast the prevalences of selected non-communicable diseases (NCDs) between Brazilian adults living in a slum and the general population of the same city, by comparing the age and sex-standardized prevalences of selected NCDs from a 2010 survey in Pau da Lima, Salvador Brazil, with a 2010 national population-based telephone survey. NCD prevalences in both populations were similar for hypertension (23.6% (95% CI 20.9⁻26.4) and 22.9% (21.2⁻24.6), respectively) and for dyslipidemia (22.7% (19.8⁻25.5) and 21.5% (19.7⁻23.4)). Slum residents had higher prevalences of diabetes mellitus (10.1% (7.9⁻12.3)) and of overweight/obesity (46.5% (43.1⁻49.9)), compared to 5.2% (4.2⁻6.1) and 40.6% (38.5⁻42.8) of the general population in Salvador. Fourteen percent (14.5% (12.1⁻17.0)) of slum residents smoked cigarettes compared to 8.3% (7.1⁻9.5) of the general population in Salvador. The national telephone survey underestimated the prevalence of diabetes mellitus, overweight/obesity, and smoking in the slum population, likely in part due to differential sampling inside and outside of slums. Further research and targeted policies are needed to mitigate these inequalities, which could have significant economic and social impacts on slum residents and their communities.
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Affiliation(s)
- Robert E Snyder
- Division of Epidemiology, University of California, Berkeley, CA 94720, USA.
| | - Jayant V Rajan
- Department of Medicine, University of California, San Francisco, CA 94143, USA.
| | - Federico Costa
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Brazilian Ministry of Health, Salvador 40170-115, Bahia, Brazil.
- Institute of Collective Health, Federal University of Bahia, Salvador 40170-115, Bahia, Brazil.
| | - Helena C A V Lima
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Brazilian Ministry of Health, Salvador 40170-115, Bahia, Brazil.
| | - Juan I Calcagno
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Brazilian Ministry of Health, Salvador 40170-115, Bahia, Brazil.
| | - Ricardo D Couto
- Faculty of Pharmacy, Federal University of Bahia, Salvador 40170-115, Bahia, Brazil.
- School of Medicine, Federal University of Bahia, Salvador 40170-115, Bahia, Brazil.
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Mitermayer G Reis
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Brazilian Ministry of Health, Salvador 40170-115, Bahia, Brazil.
- School of Medicine, Federal University of Bahia, Salvador 40170-115, Bahia, Brazil.
| | - Albert I Ko
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Brazilian Ministry of Health, Salvador 40170-115, Bahia, Brazil.
- Department of the Epidemiology of Microbial Diseases, Yale University School of Public Health, New Haven, CT 06510, USA.
| | - Guilherme S Ribeiro
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Brazilian Ministry of Health, Salvador 40170-115, Bahia, Brazil.
- Institute of Collective Health, Federal University of Bahia, Salvador 40170-115, Bahia, Brazil.
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Neves FPG, Cardoso NT, Snyder RE, Marlow MA, Cardoso CAA, Teixeira LM, Riley LW. Pneumococcal carriage among children after four years of routine 10-valent pneumococcal conjugate vaccine use in Brazil: The emergence of multidrug resistant serotype 6C. Vaccine 2017; 35:2794-2800. [PMID: 28431817 DOI: 10.1016/j.vaccine.2017.04.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 11/18/2016] [Revised: 04/09/2017] [Accepted: 04/10/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND In 2010, the 10-valent pneumococcal conjugate vaccine (PCV10) was introduced free of charge in Brazil as part of the public immunization program. Here we investigated the carriage prevalence, colonization risk factors, capsular types, and antimicrobial resistance among pneumococcal isolates obtained from children in Brazil four years after routine PCV10 use. METHODS Between September and December 2014, we conducted a cross-sectional study among children<6years old who attended one public and two private clinics in Niterói, RJ, Brazil to evaluate pneumococcal nasopharyngeal carriage. Antimicrobial susceptibility and capsular types were determined for all isolates. RESULTS Of 522 children, 118 (22.6%) were pneumococcal carriers. Being≥2years old, attending childcare center, presenting with any symptoms, having acute or chronic respiratory disease, and residing in a slum were associated with pneumococcal carriage. The most prevalent capsular types were 6C (14.5%), 15B/C (11.5%), 11A/D (9.2%), and 6A (7.6%). PCV10 serotypes represented 2.5%. All isolates were susceptible to levofloxacin, rifampicin, and vancomycin. Penicillin non-susceptible pneumococci (PNSP) comprised 39%, with penicillin and ceftriaxone MICs ranging from 0.12-8.0μg/ml and 0.012-1.0μg/ml, respectively. The 33 (28%) erythromycin-resistant isolates (MICs of 1.5 to >256μg/ml) displayed the cMLSB (72.7%) or M (27.3%) phenotypes, harboring the erm(B) and/or mef(A/E) genes. High non-susceptibility rates (>20%) to clindamycin, erythromycin, penicillin, and tetracycline were largely explained by the prevalence of multidrug resistant (MDR) serotype 6C isolates. CONCLUSIONS Effects of universal childhood PCV10 use on carriage were evident, with the near elimination of PCV10 serotypes. The emergence of MDR serotype 6C isolates, however, is a concern. Ongoing surveillance to monitor serotype 6C increase in invasive diseases is warranted.
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Affiliation(s)
- Felipe P G Neves
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA; Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, 101 São Domingos, Niterói, RJ 24210-130, Brazil.
| | - Nayara T Cardoso
- Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, 101 São Domingos, Niterói, RJ 24210-130, Brazil.
| | - Robert E Snyder
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA.
| | - Mariel A Marlow
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA.
| | - Claudete A A Cardoso
- Faculdade de Medicina, Universidade Federal Fluminense, Av. Marquês do Paraná, 303 Centro, Niterói, RJ 24033-900, Brazil.
| | - Lúcia M Teixeira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - bloco I, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 530E Li Ka Shing Center, Berkeley, CA 94720, USA.
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Affiliation(s)
- Robert E. Snyder
- Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Claire E. Boone
- Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Claudete A. Araújo Cardoso
- Maternal and Child Department, School of Medicine, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Fabio Aguiar-Alves
- Pathology Program, Laboratório Universitário Rodolpho Albino, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Felipe P. G. Neves
- Department of Microbiology and Parasitology, Biomedical Institute, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Lee W. Riley
- Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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Pandya S, Ravi K, Srinivas V, Jadhav S, Khan A, Arun A, Riley LW, Madhivanan P. Comparison of culture-dependent and culture-independent molecular methods for characterization of vaginal microflora. J Med Microbiol 2017; 66:149-153. [PMID: 28260585 DOI: 10.1099/jmm.0.000407] [Citation(s) in RCA: 21] [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: 11/18/2022] Open
Abstract
PURPOSE To date, molecular methods that circumvent the limitations of traditional culture methods have not been used to describe the vaginal microflora in India. Here, we compared culture and culture-independent molecular methods in characterizing the vaginal microbiota in Indian women. METHODOLOGY Culture methods involved traditional cultivation on Rogosa and sheep blood agar, whereas culture-independent methods bypassed a culturing step by performing broadrange 16S rDNA PCR on DNA isolated directly from vaginal swabs. RESULTS A total of 13 women were included in the study, of which five were characterized as healthy, two were bacterial vaginosis intermediate and six were bacterial vaginosis positive according to Nugent scoring. Lactobacillus jensenii was detected most frequently when using culture methods. On the other hand, Lactobacillus iners, which was not detected by culture methods, was the most common Lactobacillus sp. detected using cultivation-independent methods. CONCLUSION We found little overlap between the species found using cultivation-dependent and cultivation-independent methods. Rather, culture-dependent and culture-independent methods were found to be complementary in describing the vaginal microflora among South Indian women. Culture-independent methods were found to be superior in detecting clinically relevant vaginal flora.
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Affiliation(s)
- Shirali Pandya
- Public Health Research Institute of India, Mysore, Karnataka, India.,Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kavitha Ravi
- Public Health Research Institute of India, Mysore, Karnataka, India
| | - Vijaya Srinivas
- Public Health Research Institute of India, Mysore, Karnataka, India
| | - Smitha Jadhav
- Public Health Research Institute of India, Mysore, Karnataka, India
| | - Anisa Khan
- Public Health Research Institute of India, Mysore, Karnataka, India
| | - Anjali Arun
- Public Health Research Institute of India, Mysore, Karnataka, India
| | - Lee W Riley
- College of Public Health, University of California, Berkeley, USA
| | - Purnima Madhivanan
- Public Health Research Institute of India, Mysore, Karnataka, India.,Department of Epidemiology, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, Florida, USA
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de Souza da-Silva AP, de Sousa VS, Martins N, da Silva Dias RC, Bonelli RR, Riley LW, Moreira BM. Escherichia coli sequence type 73 as a cause of community acquired urinary tract infection in men and women in Rio de Janeiro, Brazil. Diagn Microbiol Infect Dis 2017; 88:69-74. [PMID: 28214224 PMCID: PMC5392417 DOI: 10.1016/j.diagmicrobio.2017.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/25/2017] [Accepted: 01/31/2017] [Indexed: 12/22/2022]
Abstract
Escherichia coli clones ST131, ST69, ST95, and ST73 are frequent causes of urinary tract infections (UTI) and bloodstream infections. Specific clones and virulence profiles of E. coli causing UTI in men has been rarely described. The aim of this study was to characterize patient and clonal characteristics of community-acquired UTI caused by E. coli in men (n=12) and women (n=127) in Rio de Janeiro, Brazil, complementing a previous work. We characterized isolates in phylogenetic groups, ERIC2-PCR and PFGE types, MLST, genome similarity and virulence gene-profiles. UTI from men were more frequently caused by phylogenetic group B2 isolates (83% versus 42%, respectively, P = 0.01), a group with significantly higher virulence scores compared with women. ST73 was the predominant clone in men (50%) and the second most frequent in women (12%), with the highest virulence score (mean and median=9) among other clones. ST73 gnomes formed at least six clusters. E. coli from men carried significantly higher numbers of virulence genes, such as sfa/focDE (67% versus 27%), hlyA (58% versus 24%), cnf 1 (58% versus 16%), fyuA (100% versus 82%) and MalX (92% versus 44%), compared with isolates from women. These data suggest the predominance and spread of ST73 isolates likely relates to an abundance of virulence determinants.
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Affiliation(s)
| | - Viviane Santos de Sousa
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil
| | - Natacha Martins
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil
| | | | - Raquel Regina Bonelli
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil
| | - Lee W Riley
- School of Public Health, University of California, Berkeley, CA
| | - Beatriz Meurer Moreira
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil.
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