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Giralt-Zúñiga M, Redondo-Solano M, Moura A, Tessaud-Rita N, Bracq-Dieye H, Vales G, Thouvenot P, Leclercq A, Chaves-Ulate C, Núñez-Montero K, Guillén-Watson R, Rivas-Solano O, Chanto-Chacón G, Duarte-Martínez F, Soto-Blanco V, Pizarro-Cerdá J, Lecuit M. Genome-Based Characterization of Listeria monocytogenes, Costa Rica. Emerg Infect Dis 2023; 29:2566-2569. [PMID: 37987595 PMCID: PMC10683821 DOI: 10.3201/eid2912.230774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Abstract
Genomic data on the foodborne pathogen Listeria monocytogenes from Central America are scarce. We analyzed 92 isolates collected during 2009-2019 from different regions in Costa Rica, compared those to publicly available genomes, and identified unrecognized outbreaks. Our findings suggest mandatory reporting of listeriosis in Costa Rica would improve pathogen surveillance.
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Rojas-Sánchez E, Jiménez-Soto M, Barquero-Calvo E, Duarte-Martínez F, Mollenkopf DF, Wittum TE, Muñoz-Vargas L. Prevalence Estimation, Antimicrobial Susceptibility, and Serotyping of Salmonella enterica Recovered from New World Non-Human Primates ( Platyrrhini), Feed, and Environmental Surfaces from Wildlife Centers in Costa Rica. Antibiotics (Basel) 2023; 12:antibiotics12050844. [PMID: 37237747 DOI: 10.3390/antibiotics12050844] [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: 03/31/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Concern about zoonoses and wildlife has increased. Few studies described the role of wild mammals and environments in the epidemiology of Salmonella. Antimicrobial resistance is a growing problem associated with Salmonella that threatens global health, food security, the economy, and development in the 21st century. The aim of this study is to estimate the prevalence and identify antibiotic susceptibility profiles and serotypes of non-typhoidal Salmonella enterica recovered from non-human primate feces, feed offered, and surfaces in wildlife centers in Costa Rica. A total of 180 fecal samples, 133 environmental, and 43 feed samples from 10 wildlife centers were evaluated. We recovered Salmonella from 13.9% of feces samples, 11.3% of environmental, and 2.3% of feed samples. Non-susceptibility profiles included six isolates from feces (14.6%): four non-susceptible isolates (9.8%) to ciprofloxacin, one (2.4%) to nitrofurantoin, and one to both ciprofloxacin and nitrofurantoin (2.4%). Regarding the environmental samples, one profile was non-susceptible to ciprofloxacin (2.4%) and two to nitrofurantoin (4.8%). The serotypes identified included Typhimurium/I4,[5],12:i:-, S. Braenderup/Ohio, S. Newport, S. Anatum/Saintpaul, and S. Westhampton. The epidemiological surveillance of Salmonella and antimicrobial resistance can serve in the creation of strategies for the prevention of the disease and its dissemination throughout the One Health approach.
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Affiliation(s)
- Ernesto Rojas-Sánchez
- Laboratorio de Salud Pública e Inocuidad de Alimentos, Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 40104, Costa Rica
- Hospital de Especies Menores y Silvestres, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 40104, Costa Rica
| | - Mauricio Jiménez-Soto
- Hospital de Especies Menores y Silvestres, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 40104, Costa Rica
| | - Elias Barquero-Calvo
- Laboratorio de Bacteriología, Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 40104, Costa Rica
| | - Francisco Duarte-Martínez
- Laboratorio de Genómica y Biología Molecular, Centro Nacional de Referencia de Inocuidad Microbiológica de Alimentos, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Cartago 30301, Costa Rica
| | - Dixie F Mollenkopf
- Department of Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine, Columbus, OH 43210, USA
| | - Thomas E Wittum
- Department of Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine, Columbus, OH 43210, USA
| | - Lohendy Muñoz-Vargas
- Laboratorio de Salud Pública e Inocuidad de Alimentos, Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 40104, Costa Rica
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Molina-Mora JA, Reales-González J, Camacho E, Duarte-Martínez F, Tsukayama P, Soto-Garita C, Brenes H, Cordero-Laurent E, Ribeiro dos Santos A, Guedes Salgado C, Santos Silva C, Santana de Souza J, Nunes G, Negri T, Vidal A, Oliveira R, Oliveira G, Muñoz-Medina JE, Salas-Lais AG, Mireles-Rivera G, Sosa E, Turjanski A, Monzani MC, Carobene MG, Remes Lenicov F, Schottlender G, Fernández Do Porto DA, Kreuze JF, Sacristán L, Guevara-Suarez M, Cristancho M, Campos-Sánchez R, Herrera-Estrella A. Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021. Front Public Health 2023; 11:1095202. [PMID: 36935725 PMCID: PMC10018007 DOI: 10.3389/fpubh.2023.1095202] [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: 11/11/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia, and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1,534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.
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Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- *Correspondence: Jose Arturo Molina-Mora
| | | | - Erwin Camacho
- Investigaciones Biomédicas, Universidad de Sucre, Sincelejo, Colombia
| | - Francisco Duarte-Martínez
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Pablo Tsukayama
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Claudio Soto-Garita
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Hebleen Brenes
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Estela Cordero-Laurent
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | | | | | - Caio Santos Silva
- Instituto de Ciências Biológica, Universidade Federal do Pará, Belém, Brazil
| | | | - Gisele Nunes
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Tatianne Negri
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Amanda Vidal
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Renato Oliveira
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Guilherme Oliveira
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Guadalupe Mireles-Rivera
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Ezequiel Sosa
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Adrián Turjanski
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Cecilia Monzani
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauricio G. Carobene
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico Remes Lenicov
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gustavo Schottlender
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Luisa Sacristán
- Vicerrectoria de Investigación y Creación, Universidad de Los Andes, Bogotá, Colombia
| | | | - Marco Cristancho
- Vicerrectoria de Investigación y Creación, Universidad de Los Andes, Bogotá, Colombia
| | - Rebeca Campos-Sánchez
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
- Alfredo Herrera-Estrella
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Molina-Mora JA, González A, Jiménez-Morgan S, Cordero-Laurent E, Brenes H, Soto-Garita C, Sequeira-Soto J, Duarte-Martínez F. Clinical Profiles at the Time of Diagnosis of SARS-CoV-2 Infection in Costa Rica During the Pre-vaccination Period Using a Machine Learning Approach. Phenomics 2022; 2:312-322. [PMID: 35692458 PMCID: PMC9173838 DOI: 10.1007/s43657-022-00058-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 04/16/2023]
Abstract
UNLABELLED The clinical manifestations of COVID-19, caused by the SARS-CoV-2, define a large spectrum of symptoms that are mainly dependent on the human host conditions. In Costa Rica, more than 169,000 cases and 2185 deaths were reported during the year 2020, the pre-vaccination period. To describe the clinical presentations at the time of diagnosis of SARS-CoV-2 infection in Costa Rica during the pre-vaccination period, we implemented a symptom-based clustering using machine learning to identify clusters or clinical profiles at the population level among 18,974 records of positive cases. Profiles were compared based on symptoms, risk factors, viral load, and genomic features of the SARS-CoV-2 sequence. A total of 18 symptoms at time of diagnosis of SARS-CoV-2 infection were reported with a frequency > 1%, and those were used to identify seven clinical profiles with a specific composition of clinical manifestations. In the comparison between clusters, a lower viral load was found for the asymptomatic group, while the risk factors and the SARS-CoV-2 genomic features were distributed among all the clusters. No other distribution patterns were found for age, sex, vital status, and hospitalization. In conclusion, during the pre-vaccination time in Costa Rica, the symptoms at the time of diagnosis of SARS-CoV-2 infection were described in clinical profiles. The host co-morbidities and the SARS-CoV-2 genotypes are not specific of a particular profile, rather they are present in all the groups, including asymptomatic cases. In addition, this information can be used for decision-making by the local healthcare institutions (first point of contact with health professionals, case definition, or infrastructure). In further analyses, these results will be compared against the profiles of cases during the vaccination period. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s43657-022-00058-x.
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Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San José, 2060 Costa Rica
| | - Alejandra González
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
| | | | - Estela Cordero-Laurent
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
| | - Hebleen Brenes
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
| | - Claudio Soto-Garita
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
| | - Jorge Sequeira-Soto
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
| | - Francisco Duarte-Martínez
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, 30301 Costa Rica
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Lazo-Láscarez S, Gutiérrez LZ, Duarte-Martínez F, Romero Zúñiga JJ, Arias Echandi ML, Muñoz-Vargas L. Antimicrobial Resistance and Genetic Diversity of Campylobacter spp. Isolated from Broiler Chicken at Three Levels of the Poultry Production Chain in Costa Rica. J Food Prot 2021; 84:2143-2150. [PMID: 34324670 DOI: 10.4315/jfp-21-111] [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: 03/15/2021] [Revised: 07/29/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Campylobacter spp. are considered the most common bacterial cause of human gastroenteritis, one of the four main causes of diarrheal disease worldwide, and they are one of the main foodborne pathogens causing hospitalizations and deaths. Here, 148 strains of Campylobacter spp. isolated from poultry at farms, processing plants, and retail stores in Costa Rica were examined for resistance to six antibiotics. An agar dilution test was used to determine the MIC and susceptibility profiles against doxycycline, ciprofloxacin, nalidixic acid, enrofloxacin, chloramphenicol, and erythromycin. In addition, a pulsed-field gel electrophoresis analysis was carried out to determine the genotype relatedness of a representative subset of the isolates. Approximately 136 (92%) of the 148 analyzed isolates showed resistance to the tested drugs. Nalidixic acid, ciprofloxacin, and enrofloxacin were the antibiotics for which resistance occurred most frequently (91.2, 85.8, and 85.8%, respectively), followed by doxycycline (25.0%), chloramphenicol (5.4%), and erythromycin (2.7%). The profile conferring only resistance to quinolones was the most frequently found, and only 2.0% of the isolates showed resistance to quinolones and macrolides simultaneously. Results showed a high frequency of resistant Campylobacter spp. strains and evidenced the distribution, selection, and circulation of resistant strains along the poultry chain from farms to consumers. Cross-contamination and resistance seem to play important roles in the dissemination of these strains at specific points of the poultry chain, even when control measures are being taken. The establishment of effective surveillance and control strategies represents an essential tool for foodborne diseases mitigation. The rational use of antibiotics, especially those still showing efficacy, should be a priority in both human and veterinary medicine to contain the progress of this phenomenon and its consequences. HIGHLIGHTS
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Affiliation(s)
| | | | - Francisco Duarte-Martínez
- National Reference Centre for Microbiological Food Safety, Costa Rican Institute for Research and Education in Nutrition and Health (INCIENSA), Tres Ríos, Cartago, Costa Rica
| | | | - María Laura Arias Echandi
- Food and Water Microbiology Laboratory, Faculty of Microbiology and Tropical Disease Research Center, University of Costa Rica, San José 2060, Costa Rica
| | - Lohendy Muñoz-Vargas
- Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 86-3000, Costa Rica
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Molina-Mora JA, Cordero-Laurent E, Godínez A, Calderón-Osorno M, Brenes H, Soto-Garita C, Pérez-Corrales C, Drexler JF, Moreira-Soto A, Corrales-Aguilar E, Duarte-Martínez F. SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Infect Genet Evol 2021; 92:104872. [PMID: 33905892 PMCID: PMC8065237 DOI: 10.1016/j.meegid.2021.104872] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 02/07/2023]
Abstract
Genome sequencing is a key strategy in the surveillance of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Latin America is the hardest-hit region of the world, accumulating almost 20% of COVID-19 cases worldwide. In Costa Rica, from the first detected case on March 6th to December 31st almost 170,000 cases have been reported. We analyzed the genomic variability during the SARS-CoV-2 pandemic in Costa Rica using 185 sequences, 52 from the first months of the pandemic, and 133 from the current wave. Three GISAID clades (G, GH, and GR) and three PANGOLIN lineages (B.1, B.1.1, and B.1.291) were predominant, suggesting multiple re-introductions from other regions. The whole-genome variant calling analysis identified a total of 283 distinct nucleotide variants, following a power-law distribution with 190 single nucleotide mutations in a single sequence, and only 16 mutations were found in >5% sequences. These mutations were distributed through the whole genome. The prevalence of worldwide-found variant D614G in the Spike (98.9% in Costa Rica), ORF8 L84S (1.1%) is similar to what is found elsewhere. Interestingly, the frequency of mutation T1117I in the Spike has increased during the current pandemic wave beginning in May 2020 in Costa Rica, reaching 29.2% detection in the full genome analyses in November 2020. This variant has been observed in less than 1% of the GISAID reported sequences worldwide in 2020. Structural modeling of the Spike protein with the T1117I mutation suggests a potential effect on the viral oligomerization needed for cell infection, but no differences with other genomes on transmissibility, severity nor vaccine effectiveness are predicted. In conclusion, genome analyses of the SARS-CoV-2 sequences over the course of the COVID-19 pandemic in Costa Rica suggest the introduction of lineages from other countries and the detection of mutations in line with other studies, but pointing out the local increase in the detection of Spike-T1117I variant. The genomic features of this virus need to be monitored and studied in further analyses as part of the surveillance program during the pandemic.
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Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, Costa Rica.
| | - Estela Cordero-Laurent
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
| | - Adriana Godínez
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
| | - Melany Calderón-Osorno
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
| | - Hebleen Brenes
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
| | - Claudio Soto-Garita
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
| | - Cristian Pérez-Corrales
- Hospital Nacional De Niños Dr. Carlos Sáenz Herrera, Caja Costarricense de Seguro Social (CCSS), Costa Rica
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany.
| | - Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany.
| | - Eugenia Corrales-Aguilar
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, Costa Rica.
| | - Francisco Duarte-Martínez
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
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7
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Rojas-Jiménez J, Jiménez-Pearson MA, Duarte-Martínez F, Brenes-Mora E, Arguedas R, Barquero-Calvo E. First Report of a Multidrug-Resistant ST58 Escherichia coli Harboring Extended-Spectrum Beta-Lactamase of the CTX-M-1 Class in a Fecal Sample of a Captive Baird's Tapir ( Tapirus bairdii) in Costa Rica, Central America. Microb Drug Resist 2021; 28:143-148. [PMID: 34314636 DOI: 10.1089/mdr.2020.0339] [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] [Indexed: 11/13/2022] Open
Abstract
Objective: This study's main objective was to analyze the antibiotic susceptibility profile of Escherichia coli isolates obtained from a fecal sample of a captive Baird's tapir (Tapirus bairdii) in Costa Rica. Materials and Methods: The fecal sample was collected inside the enclosure on March 3, 2017, right after the animal defecated. Samples were cultured on MacConkey agar plates nonsupplemented and supplemented with 2 μg/mL of cefotaxime. Bacterial identification and antibiotic susceptibility were performed with the Vitek 2 Compact System and the Kirby Bauer disk diffusion method, respectively. Polymerase chain reaction amplification was performed to detect blaCTX-M beta-lactamase genes. Resistant isolates were subjected to whole-genome sequencing (WGS). Results: After evaluating several antibiotic classes, a multidrug-resistant E. coli strain with extended-spectrum beta-lactamase phenotype was isolated. Resistance to cefotaxime, cefepime, ampicillin, ampicillin/sulbactam, and tetracycline was detected. WGS analysis showed the presence of blaCTX-M-1, blaTEM-1B, and tet(B) genes. The presence of IncN plasmids and Col156 was also detected. Conclusion: Our findings are according with the notion that animals' high density enhances the spread of resistant determinants in a captive environment in a limited space, where the likelihood of direct or indirect contact with other animals and humans is more frequent.
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Affiliation(s)
- Jorge Rojas-Jiménez
- Warnell School of Forestry and Natural Resources, The University of Georgia, Athens, Georgia, USA.,Costa Rica Wildlife Foundation, San José, Costa Rica
| | | | | | | | | | - Elías Barquero-Calvo
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Lagunilla, Costa Rica
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8
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Baker KS, Campos J, Pichel M, Della Gaspera A, Duarte-Martínez F, Campos-Chacón E, Bolaños-Acuña HM, Guzmán-Verri C, Mather AE, Diaz Velasco S, Zamudio Rojas ML, Forbester JL, Connor TR, Keddy KH, Smith AM, López de Delgado EA, Angiolillo G, Cuaical N, Fernández J, Aguayo C, Morales Aguilar M, Valenzuela C, Morales Medrano AJ, Sirok A, Weiler Gustafson N, Diaz Guevara PL, Montaño LA, Perez E, Thomson NR. Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses. Clin Microbiol Infect 2017; 23:845-853. [PMID: 28389276 PMCID: PMC5667938 DOI: 10.1016/j.cmi.2017.03.021] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/16/2017] [Accepted: 03/27/2017] [Indexed: 12/31/2022]
Abstract
Objectives Shigella sonnei is a globally important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed to demonstrate the possibility and advantages of transitioning to whole genome sequencing (WGS) for surveillance within existing networks across a continent where S. sonnei is endemic. Methods We applied WGS to representative archive isolates of S. sonnei (n = 323) from laboratories in nine PNLA&C countries to generate a regional phylogenomic reference for S. sonnei and put this in the global context. We used this reference to contextualise 16 S. sonnei from three Argentinian outbreaks, using locally generated sequence data. Assembled genome sequences were used to predict antimicrobial resistance (AMR) phenotypes and identify AMR determinants. Results S. sonnei isolates clustered in five Latin American sublineages in the global phylogeny, with many (46%, 149 of 323) belonging to previously undescribed sublineages. Predicted multidrug resistance was common (77%, 249 of 323), and clinically relevant differences in AMR were found among sublineages. The regional overview showed that Argentinian outbreak isolates belonged to distinct sublineages and had different epidemiologic origins. Conclusions Latin America contains novel genetic diversity of S. sonnei that is relevant on a global scale and commonly exhibits multidrug resistance. Retrospective passive surveillance with WGS has utility for informing treatment, identifying regionally epidemic sublineages and providing a framework for interpretation of prospective, locally sequenced outbreaks.
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Affiliation(s)
- K S Baker
- University of Liverpool, Department of Functional and Comparative Genomics, Liverpool, England, United Kingdom; Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom.
| | - J Campos
- Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
| | - M Pichel
- Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
| | - A Della Gaspera
- Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
| | - F Duarte-Martínez
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Costa Rica
| | - E Campos-Chacón
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Costa Rica
| | - H M Bolaños-Acuña
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Costa Rica
| | - C Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica; Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - A E Mather
- Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom; University of Cambridge, Department of Veterinary Medicine, Cambridge, England, United Kingdom
| | | | | | - J L Forbester
- Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom
| | - T R Connor
- Organisms and Environment Division, Cardiff University School of Biosciences, Sir Martin Evans Building, Cardiff, Wales, United Kingdom
| | - K H Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - E A López de Delgado
- Department of Bacteriology, National Institute of Hygiene 'Rafael Rangel', Ciudad University, Los Chaguaramos, Venezuela
| | - G Angiolillo
- Department of Bacteriology, National Institute of Hygiene 'Rafael Rangel', Ciudad University, Los Chaguaramos, Venezuela
| | - N Cuaical
- Department of Bacteriology, National Institute of Hygiene 'Rafael Rangel', Ciudad University, Los Chaguaramos, Venezuela
| | - J Fernández
- Molecular Genetics Laboratory, Institute of Public Health of Chile, Santiago, Chile
| | - C Aguayo
- Molecular Genetics Laboratory, Institute of Public Health of Chile, Santiago, Chile
| | - M Morales Aguilar
- Department of Foodborne Diseases, National Health Laboratory of Guatemala, Laboratorio Nacional de Salud, Barcenas, Guatemala
| | - C Valenzuela
- Department of Foodborne Diseases, National Health Laboratory of Guatemala, Laboratorio Nacional de Salud, Barcenas, Guatemala
| | - A J Morales Medrano
- Department of Foodborne Diseases, National Health Laboratory of Guatemala, Laboratorio Nacional de Salud, Barcenas, Guatemala
| | - A Sirok
- Bacteriology Laboratory, Departamento de Laboratorios de Salud Pública (DLSP), Ministerio de Salud Pública (MSP), Montevideo, Uruguay
| | - N Weiler Gustafson
- Department of Bacteriology, Laboratorio Central de Salud Pública, Asuncion, Paraguay
| | - P L Diaz Guevara
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - L A Montaño
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - E Perez
- Pan American Health Organization/World Health Organization, Department of Health Emergencies, Washington, DC, United States
| | - N R Thomson
- Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom; London School of Hygiene and Tropical Medicine, London, England, United Kingdom.
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