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Molina D, Carrión–Olmedo JC, Jarrín–V P, Tenea GN. Genome characterization of a multi-drug resistant Escherichia coli strain, L1PEag1, isolated from commercial cape gooseberry fruits ( Physalis peruviana L.). Front Microbiol 2024; 15:1392333. [PMID: 39104589 PMCID: PMC11298459 DOI: 10.3389/fmicb.2024.1392333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/09/2024] [Indexed: 08/07/2024] Open
Abstract
Introduction Foodborne infections, which are frequently linked to bacterial contamination, are a serious concern to public health on a global scale. Whether agricultural farming practices help spread genes linked to antibiotic resistance in bacteria associated with humans or animals is a controversial question. Methods This study applied a long-read Oxford Nanopore MinION-based sequencing to obtain the complete genome sequence of a multi-drug resistant Escherichia coli strain (L1PEag1), isolated from commercial cape gooseberry fruits (Physalis peruviana L.) in Ecuador. Using different genome analysis tools, the serotype, Multi Locus Sequence Typing (MLST), virulence genes, and antimicrobial resistance (AMR) genes of the L1PEag1 isolate were determined. Additionally, in vitro assays were performed to demonstrate functional genes. Results The complete genome sequence of the L1PEag1 isolate was assembled into a circular chromosome of 4825.722 Kbp and one plasmid of 3.561 Kbp. The L1PEag1 isolate belongs to the B2 phylogroup, sequence type ST1170, and O1:H4 serotype based on in silico genome analysis. The genome contains 4,473 genes, 88 tRNA, 8 5S rRNA, 7 16S rRNA, and 7 23S rRNA. The average GC content is 50.58%. The specific annotation consisted of 4,439 and 3,723 genes annotated with KEEG and COG respectively, 3 intact prophage regions, 23 genomic islands (GIs), and 4 insertion sequences (ISs) of the ISAs1 and IS630 families. The L1PEag1 isolate carries 25 virulence genes, and 4 perfect and 51 strict antibiotic resistant gene (ARG) regions based on VirulenceFinder and RGI annotation. Besides, the in vitro antibiotic profile indicated resistance to kanamycin (K30), azithromycin (AZM15), clindamycin (DA2), novobiocin (NV30), amikacin (AMK30), and other antibiotics. The L1PEag1 isolate was predicted as a human pathogen, matching 464 protein families (0.934 likelihood). Conclusion Our work emphasizes the necessity of monitoring environmental antibiotic resistance, particularly in commercial settings to contribute to develop early mitigation techniques for dealing with resistance diffusion.
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Affiliation(s)
- Diana Molina
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad Técnica del Norte, Ibarra, Ecuador
| | - Julio C. Carrión–Olmedo
- Laboratorio de Secuenciamiento de Ácidos Nucleicos, Dirección de Innovación, Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador
| | - Pablo Jarrín–V
- Laboratorio de Secuenciamiento de Ácidos Nucleicos, Dirección de Innovación, Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador
| | - Gabriela N. Tenea
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad Técnica del Norte, Ibarra, Ecuador
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Fusaro C, Miranda-Madera V, Serrano-Silva N, Bernal JE, Ríos-Montes K, González-Jiménez FE, Ojeda-Juárez D, Sarria-Guzmán Y. Antibiotic-Resistant Bacteria Isolated from Street Foods: A Systematic Review. Antibiotics (Basel) 2024; 13:481. [PMID: 38927148 PMCID: PMC11201236 DOI: 10.3390/antibiotics13060481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Street food may be a vehicle of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) to humans. Foods contaminated with ARB entail serious problems or challenges in the fields of medical care, animal husbandry, food industry, and public health worldwide. The objectives of this systematic review were to identify and evaluate scientific reports associated with ARB isolated from various street foods. "Preferred reporting items for systematic reviews and meta-analysis" (PRISMA) guidelines were followed. The bibliographic material covers a period from January 2015 to April 2024. Six electronic scientific databases were searched individually for full-text articles; only those papers that met the inclusion and exclusion criteria were selected. Seventeen papers were included in this systematic review. This study highlighted the wide distribution of ARB resistant to β-lactams and other antibiotics, posing significant health risks to consumers. High resistance levels were observed for antibiotics such as ampicillin, ceftriaxone, and tetracycline, while some antibiotics, such as ceftazidime, clavulanic acid, cefoperazone, cotrimoxazole, doxycycline, doripenem, fosfomycin, vancomycin, and piperacillin-tazobactam, demonstrated 100% susceptibility. The prevalence of ARB in street foods varied between 5.2% and 70.8% among different countries. The multiple resistance of various bacteria, including Escherichia coli, Staphylococcus, Salmonella, and Klebsiella, to multiple classes of antibiotics, as well as environmental factors contributing to the spread of antibiotic resistance (AR), emphasize the urgent need for comprehensive approaches and coordinated efforts to confront antimicrobial resistance (AMR) under the "One Health" paradigm.
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Affiliation(s)
- Carmine Fusaro
- Facultad de Ingenierías, Universidad de San Buenaventura, Cartagena de Indias, Bolivar 130010, Colombia;
| | - Valentina Miranda-Madera
- Facultad de Ingenierías, Universidad de Cartagena, Cartagena de Indias, Bolivar 130015, Colombia
| | - Nancy Serrano-Silva
- Consejo Nacional de Humanidades Ciencias y Tecnologías (CONAHCYT), Mexico City 03940, Mexico
| | - Jaime E. Bernal
- Facultad de Medicina, Universidad del Sinú, Cartagena de Indias, Bolivar 130001, Colombia
| | - Karina Ríos-Montes
- Facultad de Ciencias de la Salud, Universidad de San Buenaventura, Cartagena de Indias, Bolivar 130010, Colombia
| | | | - Dennys Ojeda-Juárez
- Facultad de Ciencias Químicas, Universidad Veracruzana, Orizaba, Veracruz 9430, Mexico
| | - Yohanna Sarria-Guzmán
- Facultad de Ingenierías, Universidad de Cartagena, Cartagena de Indias, Bolivar 130015, Colombia
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Solis MN, Loaiza K, Torres-Elizalde L, Mina I, Šefcová MA, Larrea-Álvarez M. Detecting Class 1 Integrons and Their Variable Regions in Escherichia coli Whole-Genome Sequences Reported from Andean Community Countries. Antibiotics (Basel) 2024; 13:394. [PMID: 38786123 PMCID: PMC11117327 DOI: 10.3390/antibiotics13050394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Various genetic elements, including integrons, are known to contribute to the development of antimicrobial resistance. Class 1 integrons have been identified in E. coli isolates and are associated with multidrug resistance in countries of the Andean Community. However, detailed information on the gene cassettes located on the variable regions of integrons is lacking. Here, we investigated the presence and diversity of class 1 integrons, using an in silico approach, in 2533 whole-genome sequences obtained from EnteroBase. IntFinder v1.0 revealed that almost one-third of isolates contained these platforms. Integron-bearing isolates were associated with environmental, food, human, and animal origins reported from all countries under scrutiny. Moreover, they were identified in clones known for their pathogenicity or multidrug resistance. Integrons carried cassettes associated with aminoglycoside (aadA), trimethoprim (dfrA), cephalosporin (blaOXA; blaDHA), and fluoroquinolone (aac(6')-Ib-cr; qnrB) resistance. These platforms showed higher diversity and larger numbers than previously reported. Moreover, integrons carrying more than three cassettes in their variable regions were determined. Monitoring the prevalence and diversity of genetic elements is necessary for recognizing emergent patterns of resistance in pathogenic bacteria, especially in countries where various factors are recognized to favor the selection of resistant microorganisms.
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Affiliation(s)
- María Nicole Solis
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Samborondón 092301, Ecuador
| | - Karen Loaiza
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark
| | - Lilibeth Torres-Elizalde
- Graduate School Life Sciences and Health (GS LSH), Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Ivan Mina
- School of Biological Science and Engineering, Yachay-Tech University, Urcuquí 100650, Ecuador
| | - Miroslava Anna Šefcová
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Samborondón 092301, Ecuador
| | - Marco Larrea-Álvarez
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Samborondón 092301, Ecuador
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Tenea GN, Reyes P. Bacterial community changes in strawberry fruits ( Fragaria × ananassa variety "Monterey") from farm field to retail market stands, an indicator of postharvest contamination. Front Microbiol 2024; 15:1348316. [PMID: 38435684 PMCID: PMC10904649 DOI: 10.3389/fmicb.2024.1348316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024] Open
Abstract
Background Strawberry (Fragaria × ananassa) fruits are vulnerable to bacterial contamination; some species are pathogenic and can affect human health. Comprehending the bacterial composition and diversity at different ripe stages is a key determinant of the fruit health, productivity, and quality. Methodology An amplicon metagenomic approach on the 16S rRNA region was used to identify the bacterial diversity in exocarp of fruits collected from a farm field at two ripe stages: breaking (white, phase two) and ripe (red, phase four) and purchased from different retail market stands at ripe (red, phase four, ready-to-eat) stage. Besides, the fruit quality was assessed. Results Strawberries carries a high microorganisms diversity, with Pseudomonaceae, Yearsiniaceae, and Hafniaceae being the most abundant families across the samples. Among the groups, Pseudomonaceae and Clostridiaceae were the most abundant families at breaking (phase two) and ripe (phase four), whereas Yearsiniaceae, Hafniaceae, Aeromonadaceae, and Streptococcaceae were the most abundant families in the market group. Although samples from group four-field and market were at the same ripe stage, the bacterial species composition was divergent. Serratia spp. were prevalent (above 60%) in samples collected from the market group, and Pseudomonas (above 70%) species were mostly found in the samples collected from the field settings regardless of the phase. Besides, Escherichia coli and Salmonella enterica were detected in the ready-to-eat samples from both the field and the market, while Enterococcus gallinarum was detected in the samples that originated from the market. Interestingly, Shewanella putrefaciens and Shewanella profunda, two human opportunistic pathogens, were detected in the fruits from the market only. According to alpha and beta diversity analyses, strawberry fruits displayed significant differences (P < 0.05) in bacterial communities within the ripe group, with the samples from the market showing the most bacterial diversity. Although we do not directly correlate the quality attributes with bacterial diversity, the results indicated a clear separation between groups according with their ripe stage and origin. Conclusion This study provides a comprehensive framework of the bacterial diversity throughout the transition from unripe to ripe strawberries which may aid in the development of preventative measures to manage the postharvest contamination.
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Affiliation(s)
- Gabriela N. Tenea
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad Técnica del Norte, Ibarra, Ecuador
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Puljko A, Babić I, Rozman SD, Barišić I, Jelić M, Maravić A, Parać M, Petrić I, Udiković-Kolić N. Treated municipal wastewater as a source of high-risk and emerging multidrug-resistant clones of E. coli and other Enterobacterales producing extended-spectrum β-lactamases. ENVIRONMENTAL RESEARCH 2024; 243:117792. [PMID: 38048868 DOI: 10.1016/j.envres.2023.117792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023]
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales are a major public health problem, and wastewater from municipal wastewater treatment plants (WWTPs) is a potential means of spreading them into the environment and community. Our objective was to isolate ESBL-producing E. coli and other Enterobacterales from wastewater after treatment at Croatia's largest WWTP and to characterize these isolates by phenotypic and genotypic testing. Of the 200 bacterial isolates, 140 were confirmed as Enterobacterales by MALDI-TOF MS, with Escherichia coli and Klebsiella spp. predominating (69% and 7%, respectively). All 140 enterobacterial isolates were multidrug-resistant (MDR) and produced ESBLs. The most prevalent ESBL genes among the isolates tested were blaCTX-M-15 (60%), blaTEM-116 (44%), and blaCTX-M-3 (13%). Most isolates (94%) carried more than one ESBL gene in addition to blaCTX-M. Genes encoding plasmid-mediated AmpC, most notably blaEBC, were detected in 22% of isolates, whereas genes encoding carbapenemases (blaOXA-48, blaNDM-1, blaVIM-1) were less represented (10%). In E. coli, 9 different sequence types (ST) were found, with the emerging high-risk clones ST361 (serotype A-O9:H30) and pandemic ST131 (serotype B2-O25:H4) predominating (32% and 15%, respectively). Other high-risk E. coli clones included ST405 (3%), ST410 (3%), CC10 (3%), ST10 (3%), and ST38 (2%), and emerging clones included ST1193 (2%) and ST635 (2%). Whole-genome sequencing of three representative E. coli from two dominant clone groups (ST361 and ST131) and one extensively drug-resistant K. oxytoca revealed the presence of multiple plasmids and resistance genes to several other antibiotic classes, as well as association of the blaCTX-M-15 gene with transposons and insertion sequences. Our findings indicate that treated municipal wastewater contributes to the spread of emerging and pandemic MDR E. coli clones and other enterobacterial strains of clinical importance into the aquatic environment, with the risk of reintroduction into humans.
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Affiliation(s)
- Ana Puljko
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia
| | - Ivana Babić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia
| | - Svjetlana Dekić Rozman
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, Austrian Institute of Technology, Giefinggasse 4, 1210, Vienna, Austria
| | - Marko Jelić
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000, Zagreb, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21 000, Split, Croatia
| | - Marija Parać
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia
| | - Ines Petrić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002, Zagreb, Croatia.
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Guibert F, Espinoza K, Taboada-Blanco C, Alonso CA, Oporto R, Castillo AK, Rojo-Bezares B, López M, Sáenz Y, Pons MJ, Ruiz J. Traditional marketed meats as a reservoir of multidrug-resistant Escherichia coli. Int Microbiol 2023:10.1007/s10123-023-00445-y. [PMID: 37995017 DOI: 10.1007/s10123-023-00445-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/24/2023]
Abstract
This study aimed to analyze Escherichia coli from marketed meat samples in Peru. Sixty-six E. coli isolates were recovered from 21 meat samples (14 chicken, 7 beef), and antimicrobial resistance levels and the presence of mechanisms of antibiotic resistance, as well as clonal relationships and phylogeny of colistin-resistant isolates, were established. High levels of antimicrobial resistance were detected, with 93.9% of isolates being multi-drug resistant (MDR) and 76.2% of samples possessing colistin-resistant E. coli; of these, 6 samples from 6 chicken samples presenting mcr-1-producer E. coli. Colistin-resistant isolates were classified into 22 clonal groups, while phylogroup A (15 isolates) was the most common. Extended-spectrum β-lactamase- and pAmpC-producing E. coli were found in 18 and 8 samples respectively, with blaCTX-M-55 (28 isolates; 16 samples) and blaCIT (8 isolates; 7 samples) being the most common of each type. Additionally, blaCTX-M-15, blaCTX-M-65, blaSHV-27, blaOXA-5/10-like, blaDHA, blaEBC and narrow-spectrum blaTEM were detected. In addition, 5 blaCTX-M remained unidentified, and no sought ESBL-encoding gene was detected in other 6 ESBL-producer isolates. The tetA, tetE and tetX genes were found in tigecycline-resistant isolates. This study highlights the presence of MDR E. coli in Peruvian food-chain. The high relevance of CTX-M-55, the dissemination through the food-chain of pAmpC, as well as the high frequency of unrelated colistin-resistant isolates is reported.
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Affiliation(s)
- Fernando Guibert
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Kathya Espinoza
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Clara Taboada-Blanco
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - Carla A Alonso
- Servicio de Análisis Clínicos, Laboratorio de Microbiología, Hospital San Pedro, Logroño, Spain
| | - Rosario Oporto
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Angie K Castillo
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Beatriz Rojo-Bezares
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - María López
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - Maria J Pons
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru.
| | - Joaquim Ruiz
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru.
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Esemu SN, Njoh ST, Ndip LM, Keneh NK, Kfusi JA, Njukeng AP. Ready-to-Eat Foods: A Potential Vehicle for the Spread of Coagulase-Positive Staphylococci and Antimicrobial-Resistant Staphylococcus aureus in Buea Municipality, South West Cameroon. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:9735319. [PMID: 38023661 PMCID: PMC10681794 DOI: 10.1155/2023/9735319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/09/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023]
Abstract
The consumption of ready-to-eat (RTE) foods contaminated with coagulase-positive staphylococci (CoPS) and especially Staphylococcus aureus puts consumers at a potential risk of food-borne disease or colonization and subsequent infection. This cross-sectional study determined the levels of CoPS and the presence of S. aureus in RTE foods sold in Buea municipality. A total of 420 RTE food samples, comprising 70 each of cake, bread, fruit salad, meat hot-pot, suya, and boiled rice were randomly purchased from February to August 2020. The CoPS counts were determined by culturing on Baird-Parker agar, and S. aureus was identified by amplification of the nuc gene using the polymerase chain reaction. All S. aureus isolates were screened for the presence of classical staphylococcal enterotoxin genes. To determine antimicrobial resistance profiles, each isolate was tested against 11 antimicrobials. Oxacillin-resistant S. aureus strains were analyzed for the presence of the mecA gene. Overall, 161 (38.3%) samples had detectable levels of CoPS ranging from 2.0 to 5.81 log10 CFU/g. Based on CoPS levels, 37 (8.81%) of the 420 RTE food samples-only fruit salad and meat hot-pot, had unsatisfactory microbiological quality. A total of 72 S. aureus isolates, comprising 52.78% from fruit salad, 16.67% from meat hot-pot, 12.5% from boiled rice, 9.72% from suya, 5.56% from bread, and 4.17% from cake, were recovered. None of the S. aureus isolates possessed any of the classical enterotoxin genes. All the isolates were susceptible to vancomycin and ofloxacin, while 68 (94.44%) and 66 (91.67%) were susceptible to oxacillin and ciprofloxacin, respectively. Resistance to penicillin (93.06%) was highest, followed by amoxicillin (91.67%) and erythromycin (79.17%). Four isolates were identified as methicillin-resistant S. aureus, all of which carried the mecA gene. A total of 24 antibiotypes were identified. Our findings showed that RTE foods sold in the Buea municipality are likely vehicles for the transmission of CoPS and antimicrobial-resistant S. aureus.
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Affiliation(s)
- Seraphine Nkie Esemu
- Laboratory for Emerging Infectious Diseases, University of Buea, PO Box 63, Buea, Cameroon
- Department of Microbiology and Parasitology, University of Buea, PO Box 63, Buea, Cameroon
| | - Sally Tabe Njoh
- Department of Microbiology and Parasitology, University of Buea, PO Box 63, Buea, Cameroon
| | - Lucy Mande Ndip
- Laboratory for Emerging Infectious Diseases, University of Buea, PO Box 63, Buea, Cameroon
- Department of Microbiology and Parasitology, University of Buea, PO Box 63, Buea, Cameroon
| | - Nene Kaah Keneh
- Laboratory for Emerging Infectious Diseases, University of Buea, PO Box 63, Buea, Cameroon
- Department of Microbiology and Parasitology, University of Buea, PO Box 63, Buea, Cameroon
| | - Jerome Achah Kfusi
- Laboratory for Emerging Infectious Diseases, University of Buea, PO Box 63, Buea, Cameroon
- Department of Microbiology and Parasitology, University of Buea, PO Box 63, Buea, Cameroon
| | - Achiangia Patrick Njukeng
- Department of Microbiology and Parasitology, University of Buea, PO Box 63, Buea, Cameroon
- Global Health Systems Solutions, SONARA Road, Limbe, Cameroon
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Zurita J, Sevillano G, Paz Y Miño A, Haro N, Larrea-Álvarez M, Alcocer I, Ortega-Paredes D. Dominance of ST131, B2, blaCTX-M-15, and papA-papC-kpsMII-uitA among ESBL Escherichia coli isolated from bloodstream infections in Quito, Ecuador: a 10-year surveillance study (2009-2019). J Appl Microbiol 2023; 134:lxad269. [PMID: 37974051 DOI: 10.1093/jambio/lxad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/21/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
AIMS This study aimed to examine antibiotic resistance and the epidemiology of extended-spectrum β-lactamases (ESBL)-producing Escherichia coli associated with bloodstream infections over a period of 10 years. METHODS AND RESULTS Isolates were collected from January 2009 to December 2019 and those testing for E. coli were included. Antibiotic susceptibility was tested using the VITEK® system. Selected isolates were further characterized by amplification of marker genes (virulence traits, phylogroups, and sequence types). A total of 166 ESBL-producing E. coli were recovered. The blaCTX-M-15 allele was the most abundant. Most of the isolates were resistant to ceftriaxone, cefepime, ceftazidime, ampicillin/sulbactam, piperacillin/tazobactam, and ciprofloxacin. No resistance to carbapenems was registered. More than 80% of bacteria were classified as extraintestinal pathogenic E. coli (ExPEC), and the combination of virulence traits:papA-papC-kpsMII-uitA was the most common. Phylogroup B2 was the most prevalent, and bacteria predominantly belonged to ST131. CONCLUSIONS There was an increase in the ExPEC ESBL-E coli in bloodstream infections and the relationship between the isolates found in these infections during these 10 years.
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Affiliation(s)
- Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito 170525, Ecuador
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
- Servicio de Microbiología y Tuberculosis, Hospital Vozandes, Quito 170521, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Ariane Paz Y Miño
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Nathalí Haro
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Marco Larrea-Álvarez
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Km 2.5 vía a Samborondón 0901952, Ecuador
| | - Iliana Alcocer
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito 170525, Ecuador
| | - David Ortega-Paredes
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Km 2.5 vía a Samborondón 0901952, Ecuador
- Unidad de Investigación en Enfermedades Transmitidas por Alimentos y Resistencia a los, Antimicrobianos (UNIETAR), Facultad de Veterinaria, Universidad Central del Ecuador, Quito 170129, Ecuador
- Laboratorio de Referencia de E. coli, Department of Microbiology and Parasitology, Veterinary Faculty, University of Santiago de Compostela, Lugo 15782, Spain
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Andrade AA, Paiva AD, Machado ABF. Microbiology of street food: understanding risks to improve safety. J Appl Microbiol 2023; 134:lxad167. [PMID: 37516449 DOI: 10.1093/jambio/lxad167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 07/31/2023]
Abstract
Street foods play important socioeconomic and cultural roles and are popular worldwide. In addition to providing convenient and low-cost meals for urban populations, street food offers an essential source of income for vendors, especially women, and it can reflect traditional local culture, which is an important attraction for tourists. Despite these benefits, the microbiological safety of street food has become a worldwide concern because it is often prepared and sold under inadequate safety conditions, without legal control and sanitary surveillance. Consequently, high counts of fecal indicator bacteria and several foodborne pathogens have been detected in street foods. This review provides insight into the microbiology of street food, focus on the associated microbiological safety aspects and main pathogens, and the global status of this important economic activity. Furthermore, the need to apply molecular detection rather than traditional culture-based methods is discussed to better understand the actual risks of microbial infection associated with street foods. Recognition is always the first step toward addressing a problem.
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Affiliation(s)
- Anderson Assunção Andrade
- Microbiology Research Laboratory, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, Minas Gerais 38025-015, Brazil
| | - Aline Dias Paiva
- Microbiology Research Laboratory, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, Minas Gerais 38025-015, Brazil
| | - Alessandra Barbosa Ferreira Machado
- Laboratory of Bacterial Physiology and Molecular Genetics, Center for Studies in Microbiology, Department of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora (UFJF), Juiz de Fora 36036-330, Brazil
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10
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Bastidas-Caldes C, Cisneros-Vásquez E, Zambrano A, Mosquera-Maza A, Calero-Cáceres W, Rey J, Yamamoto Y, Yamamoto M, Calvopiña M, de Waard JH. Co-Harboring of Beta-Lactamases and mcr-1 Genes in Escherichia coli and Klebsiella pneumoniae from Healthy Carriers and Backyard Animals in Rural Communities in Ecuador. Antibiotics (Basel) 2023; 12:antibiotics12050856. [PMID: 37237759 DOI: 10.3390/antibiotics12050856] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Few studies have addressed drug resistance of Enterobacterales in rural communities in developing countries. This study aimed to determine the coexistence of extended-spectrum β-lactamase (ESBL) and carbapenemase genes in Escherichia coli and Klebsiella pneumoniae strains carrying the mcr-1 gene in rural communities in Ecuador from healthy humans and their backyard animals. Sixty-two strains, thirty E. coli and thirty-two K. pneumoniae strains carrying the mcr-1 gene were selected from a previous study. PCR were performed for the presence of ESBLs and carbapenemase genes. The strains were further characterized, and the genetic relationship was studied with multi-locus sequencing typing (MLST) of seven housekeeping genes. Fifty-nine of the sixty-two mcr-1 isolates (95%) harbored at least on β-lactam resistance gene. The most prevalent ESBL genes were the blaTEM genes (present in in 80% of the E. coli strains) and the blaSHV gene (present in 84% of the K. pneumoniae strains). MSLT analysis revealed 28 different sequence types (ST); 15 for E. coli and 12 for K. pneumoniae, with most ST never described in humans and animals. The coexistence of mcr-1 and β-lactams resistant genes in E. coli and K. pneumoniae strains is alarming and threatens the efficacy of last-resort antibiotics. Our findings highlight backyard animals as a reservoir of mcr-1/β-lactams resistant genes.
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Affiliation(s)
- Carlos Bastidas-Caldes
- One Health Research Group, Facultad de Ingeniería y Ciencias Aplicadas, Biotecnología, Universidad de las Américas, Quito 170124, Ecuador
| | - Emily Cisneros-Vásquez
- One Health Research Group, Facultad de Ingeniería y Ciencias Aplicadas, Biotecnología, Universidad de las Américas, Quito 170124, Ecuador
| | - Antonella Zambrano
- One Health Research Group, Facultad de Ingeniería y Ciencias Aplicadas, Biotecnología, Universidad de las Américas, Quito 170124, Ecuador
| | | | - William Calero-Cáceres
- UTA RAM One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato 180103, Ecuador
| | - Joaquín Rey
- Unidad de Patología Infecciosa y Epidemiología, Facultad de Veterinaria, Universidad de Extremadura, 10003 Cáceres, Spain
| | - Yoshimasa Yamamoto
- The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Mayumi Yamamoto
- Health Administration Center, Gifu University, Gifu 501-1193, Japan
| | - Manuel Calvopiña
- One Health Research Group, Facultad de Ciencias de la Salud, Universidad de las Américas, Quito 170124, Ecuador
| | - Jacobus H de Waard
- One Health Research Group, Facultad de Ciencias de la Salud, Universidad de las Américas, Quito 170124, Ecuador
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11
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Pilamala Rosales A, Linnemann AR, Luning PA. Food safety knowledge, self-reported hygiene practices, and street food vendors’ perceptions of current hygiene facilities and services - An Ecuadorean case. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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12
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Pathogenic Microorganisms Linked to Fresh Fruits and Juices Purchased at Low-Cost Markets in Ecuador, Potential Carriers of Antibiotic Resistance. Antibiotics (Basel) 2023; 12:antibiotics12020236. [PMID: 36830147 PMCID: PMC9952111 DOI: 10.3390/antibiotics12020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
The pathogenic microorganisms linked to fresh fruits and juices sold out in retail low-cost markets raise safety concerns as they may carry multidrug-resistant (MDR) genes. To evaluate the microbiological quality and safety of highly consumed fruits and derivatives in Imbabura Province, Ecuador, ready-to-eat strawberries (5 independent batches; n = 300 samples), and gooseberries (5 separate batches; n = 500 samples), purchased from a local fruit farm grower and low-cost retail market, along with 20 different natural fruit- and vegetables-based juices (3 independent batches; n = 60 samples) purchased from food courts located within the low-cost markets were analyzed. Bacteriological analysis showed that the microbial quality was lower as several indicators (n = 984) consisting of total coliforms (TCOL), total aerobes (AEROB), Enterobacter spp. (ENT), Shigella spp., (SHIGA), yeasts (YE), and molds (M) were detected. Staphylococcus spp. (STAPHY) was found in both fruits regardless of origin, while Escherichia coli (EC) isolates were found in strawberries but not gooseberries. Salmonella spp. (SALM) were detected in juices only. Antibiotic susceptibility testing showed multidrug resistance of several isolates. The hemolytic pattern revealed that 88.89% of EC and 61.11% of ENT isolates were beta-hemolytic. All STAPHY isolates were beta-hemolytic while SALM and SHIGA were alpha-hemolytic. Plasmid curing assay of MDR isolates (ENT, EC, SALM, and STAPHY) showed that the antibiotic resistance (AR) was highly indicative of being plasmid-borne. These results raise concerns about the consumption of MDR bacteria. However, good agricultural and industrial practices, behavioral change communication, and awareness-raising programs are necessary for all stakeholders along the food production and consumption supply chain.
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13
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Bastidas-Caldes C, Romero-Alvarez D, Valdez-Vélez V, Morales RD, Montalvo-Hernández A, Gomes-Dias C, Calvopiña M. Extended-Spectrum Beta-Lactamases Producing Escherichia coli in South America: A Systematic Review with a One Health Perspective. Infect Drug Resist 2022; 15:5759-5779. [PMID: 36204394 PMCID: PMC9531622 DOI: 10.2147/idr.s371845] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Carlos Bastidas-Caldes
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
- Doctoral Program in Public and Animal Health, Faculty of Veterinary Medicine, University of Extremadura, Cáceres, Spain
- Correspondence: Carlos Bastidas-Caldes, One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, 170124, Ecuador, Tel +593 983 174949, Email
| | - Daniel Romero-Alvarez
- One Health Reserch Group, Faculty of Medicine, Universidad de las Américas, Quito, Ecuador
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, The University of Kansas, Lawrence, KS, USA
| | - Victor Valdez-Vélez
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Roberto D Morales
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Andrés Montalvo-Hernández
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Cicero Gomes-Dias
- Department of Basic Health Sciences, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Manuel Calvopiña
- One Health Reserch Group, Faculty of Medicine, Universidad de las Américas, Quito, Ecuador
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14
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Bastidas-Caldes C, Ochoa J, Guerrero-Latorre L, Moyota-Tello C, Tapia W, Rey-Pérez JM, Baroja MI. Removal of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli, ST98, in Water for Human Consumption by Black Ceramic Water Filters in Low-Income Ecuadorian Highlands. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19084736. [PMID: 35457602 PMCID: PMC9028703 DOI: 10.3390/ijerph19084736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/25/2022] [Accepted: 04/06/2022] [Indexed: 02/04/2023]
Abstract
Fecal contamination in natural water sources is a common problem in low-income countries. Several health risks are associated with unprotected water sources, such as gastrointestinal infections caused by parasites, viruses, and bacteria. Moreover, antibiotic-resistant bacteria in water sources have become an increasing problem worldwide. This study aimed to evaluate the bacterial pathogens present in water within a rural context in Ecuador, along with the efficiency of black ceramic water filters (BCWFs) as a sustainable household water treatment. We monitored five natural water sources that were used for human consumption in the highlands of Ecuador and analyzed the total coliforms and E. coli before and after BCWF installation. The results indicated a variable bacterial contamination (29–300 colony-forming units/100mL) in all unfiltered samples, and they were considered as high risk for human consumption, but after filtration, no bacteria were present. Moreover, extended-spectrum beta-lactamase-producing E. coli with blaTEM, blaCTX-M9, and blaCTX-M1 genes, and two E. coli classified in the clonal complex ST10 (ST98) were detected in two of the locations sampled; these strains can severely impact public health. The clonal complex ST10, found in the E. coli isolates, possesses the potential to spread bacteria-resistant genes to humans and animals. The results of the use of BCWFs, however, argue for the filters’ potential impact within those contexts, as the BCWFs completely removed even antibiotic-resistant contaminants from the water.
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Affiliation(s)
- Carlos Bastidas-Caldes
- One Health Research Group, Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas (FICA), Universidad de las Américas (UDLA), Quito 170125, Ecuador
- Programa de Doctorado en Salud Pública y Animal, Universidad de Extremadura, 10003 Mérida, Spain
- Correspondence: (C.B.-C.); (M.I.B.); Tel.: +593-983174949 (C.B.-C.)
| | - Juan Ochoa
- Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas (FICA), Universidad de las Américas (UDLA), Quito 170125, Ecuador; (J.O.); (C.M.-T.); (W.T.)
| | - Laura Guerrero-Latorre
- Catalan Institute for Water Research (ICRA), Water Quality Area, Emili Grahit 101, 17003 Girona, Spain;
| | - Carlos Moyota-Tello
- Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas (FICA), Universidad de las Américas (UDLA), Quito 170125, Ecuador; (J.O.); (C.M.-T.); (W.T.)
| | - Wilson Tapia
- Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas (FICA), Universidad de las Américas (UDLA), Quito 170125, Ecuador; (J.O.); (C.M.-T.); (W.T.)
| | - Joaquín María Rey-Pérez
- Unidad de Patología Infecciosa, Facultad de Veterinaria, Universidad de Extremadura, 10003 Mérida, Spain;
| | - Maria Isabel Baroja
- Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas (FICA), Universidad de las Américas (UDLA), Quito 170125, Ecuador; (J.O.); (C.M.-T.); (W.T.)
- Programa de Doctorado en Biología Molecular y Celular, Biomedicina y Biotecnología, Universidad de Extremadura, 10003 Mérida, Spain
- Correspondence: (C.B.-C.); (M.I.B.); Tel.: +593-983174949 (C.B.-C.)
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15
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Peng Z, Maciel-Guerra A, Baker M, Zhang X, Hu Y, Wang W, Rong J, Zhang J, Xue N, Barrow P, Renney D, Stekel D, Williams P, Liu L, Chen J, Li F, Dottorini T. Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming. PLoS Comput Biol 2022; 18:e1010018. [PMID: 35333870 PMCID: PMC8986120 DOI: 10.1371/journal.pcbi.1010018] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/06/2022] [Accepted: 03/14/2022] [Indexed: 01/26/2023] Open
Abstract
Anthropogenic environments such as those created by intensive farming of livestock, have been proposed to provide ideal selection pressure for the emergence of antimicrobial-resistant Escherichia coli bacteria and antimicrobial resistance genes (ARGs) and spread to humans. Here, we performed a longitudinal study in a large-scale commercial poultry farm in China, collecting E. coli isolates from both farm and slaughterhouse; targeting animals, carcasses, workers and their households and environment. By using whole-genome phylogenetic analysis and network analysis based on single nucleotide polymorphisms (SNPs), we found highly interrelated non-pathogenic and pathogenic E. coli strains with phylogenetic intermixing, and a high prevalence of shared multidrug resistance profiles amongst livestock, human and environment. Through an original data processing pipeline which combines omics, machine learning, gene sharing network and mobile genetic elements analysis, we investigated the resistance to 26 different antimicrobials and identified 361 genes associated to antimicrobial resistance (AMR) phenotypes; 58 of these were known AMR-associated genes and 35 were associated to multidrug resistance. We uncovered an extensive network of genes, correlated to AMR phenotypes, shared among livestock, humans, farm and slaughterhouse environments. We also found several human, livestock and environmental isolates sharing closely related mobile genetic elements carrying ARGs across host species and environments. In a scenario where no consensus exists on how antibiotic use in the livestock may affect antibiotic resistance in the human population, our findings provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming. Moreover, our original data analysis method has the potential to uncover AMR transmission pathways when applied to the study of other pathogens active in other anthropogenic environments characterised by complex interconnections between host species. Livestock have been suggested as an important source of antimicrobial-resistant (AMR) Escherichia coli, capable of infecting humans and carrying resistance to drugs used in human medicine. China has a large intensive livestock farming industry, poultry being the second most important source of meat in the country, and is the largest user of antibiotics for food production in the world. Here we studied antimicrobial resistance gene overlap between E. coli isolates collected from humans, livestock and their shared environments in a large-scale Chinese poultry farm and associated slaughterhouse. By using a computational approach that integrates machine learning, whole-genome sequencing, gene sharing network and mobile genetic elements analysis we characterized the E. coli community structure, antimicrobial resistance phenotypes and the genetic relatedness of non-pathogenic and pathogenic E. coli strains. We uncovered the network of genes, associated with AMR, shared across host species (animals and workers) and environments (farm and slaughterhouse). Our approach opens up new avenues for the development of a fast, affordable and effective computational solutions that provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming.
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Affiliation(s)
- Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Alexandre Maciel-Guerra
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Xibin Zhang
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Jia Rong
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Jing Zhang
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Ning Xue
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Paul Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - David Renney
- Nimrod Veterinary Products Limited, Moreton-in-Marsh, United Kingdom
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
| | - Paul Williams
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Longhai Liu
- Qingdao Tian run Food Co., Ltd, New Hope, Beijing, People’s Republic of China
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, People’s Republic of China
- * E-mail: (FL); (TD)
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
- * E-mail: (FL); (TD)
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16
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Yoon S, Lee YJ. Molecular characteristics of ESBL-producing Escherichia coli isolated from chickens with colibacillosis. J Vet Sci 2022; 23:e37. [PMID: 35332711 PMCID: PMC9149503 DOI: 10.4142/jvs.21105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 12/31/2021] [Accepted: 02/03/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Sunghyun Yoon
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu 41566, Korea
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Young Ju Lee
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu 41566, Korea
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17
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Wang X, Zhao Y, Hua Q, Lu J, Tang F, Sun W, Luan F, Zhuang X, Tian C. An ultrasensitive electrochemiluminescence biosensor for the detection of total bacterial count in environmental and biological samples based on a novel sulfur quantum dot luminophore. Analyst 2022; 147:1716-1721. [DOI: 10.1039/d2an00153e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An electrochemiluminescence sensor for total bacterial count detection based on sulfur quantum dots with β-nicotinamide adenine dinucleotide as an important parameter.
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Affiliation(s)
- Xiaobin Wang
- College of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Yuqing Zhao
- College of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Qing Hua
- College of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Jiaojiao Lu
- College of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Feiyan Tang
- College of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Wenjie Sun
- College of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Feng Luan
- College of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Xuming Zhuang
- College of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Chunyuan Tian
- College of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
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18
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Zhang S, Huang Y, Yang G, Lei T, Chen M, Ye Q, Wang J, Gu Q, Wei X, Zhang J, Wu Q. High prevalence of multidrug-resistant Escherichia coli and first detection of IncHI2/IncX4-plasmid carrying mcr-1 E. coli in retail ready-to-eat foods in China. Int J Food Microbiol 2021; 355:109349. [PMID: 34371389 DOI: 10.1016/j.ijfoodmicro.2021.109349] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022]
Abstract
Antibiotic-resistant bacteria in food pose an important threat to public health. Multidrug-resistant strains in ready-to-eat (RTE) foods can be transferred to humans through diet, which increases their health risk. This study systematically investigated antibiotic resistance and antibiotic resistance genes in E. coli isolated from retail RTE foods and characterized plasmid-mediated colistin-resistant E. coli strains. A total of 1118 RTE food samples were collected from markets in 39 cities in China, and 126 E. coli strains, >95% of which were multidrug-resistant, were isolated. The isolates showed a high prevalence of resistance to tetracycline (95.24%), ampicillin (82.54%), trimethoprim-sulfamethoxazole (77.78%), nalidixic acid (74.60%), cephalothin (72.22%), chloramphenicol (66.67%), and streptomycin (53.97%). Twenty-two extended-spectrum β-lactamase (ESBL)-producing E. coli and four colistin-resistant E. coli were identified. The resistance genes TEM, CTX-M, tetA, sul2, strA/strB, aadA, and qnrS were the most frequently detected. CTX-M-55 and CTX-M-14 were the predominant CTX-M types. All the four colistin-resistant E. coli isolates were positive for mcr-1. The mcr-1 gene can be transferred to E. coli C600 through conjugation and transformation. Whole-genome sequencing revealed that the mcr-1 genes were found in IncX4 and IncHI2 plasmids. To the best of our knowledge, this is the first report of IncHI2/IncX4 plasmid-bearing mcr-1-positive E. coli strains in RTE foods sold in markets, and the first report of the isolation of the international epidemic E. coli clone ST101 and mcr-1-carrying ESBL-producing E. coli from RTE foods. These results provide valuable information for assessing antibiotic-resistant E. coli infections and controlling antibiotic-resistant E. coli.
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Affiliation(s)
- Shuhong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province 510070, China
| | - Yuanbin Huang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province 510070, China
| | - Guangzhu Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province 510070, China
| | - Tao Lei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province 510070, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province 510070, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province 510070, China
| | - Xianhu Wei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province 510070, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province 510070, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong Province 510070, China.
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19
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Leão C, Clemente L, Moura L, Seyfarth AM, Hansen IM, Hendriksen RS, Amaro A. Emergence and Clonal Spread of CTX-M-65-Producing Escherichia coli From Retail Meat in Portugal. Front Microbiol 2021; 12:653595. [PMID: 34354678 PMCID: PMC8329498 DOI: 10.3389/fmicb.2021.653595] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/10/2021] [Indexed: 12/24/2022] Open
Abstract
The emergence and dissemination of resistance to third- and fourth-generation cephalosporins among Enterobacteriaceae from different sources impose a global public health threat. Here, we characterized by whole-genome sequencing four Escherichia coli strains harboring the blaCTX–M–65 gene identified among 49 isolates from beef and pork collected at retail. The genomic content was determined using the Center for Genomic Epidemiology web tools. Additionally, the prediction and reconstruction of plasmids were conducted, the genetic platform of the blaCTX–M–65 genes was investigated, and phylogenetic analysis was carried out using 17 other genomes with the same sequence type and harboring the blaCTX–M–65 gene. All strains harbored blaCTX–M–65, blaOXA–1, and blaTEM–1B, and one also carried the blaSHV–12 gene. Other resistance genes, namely, qnrS2, aac(6′)-Ib-c, dfrA14, sul2, tetA, and mphA, were present in all the genomes; the mcr-1.1 gene was identified in the colistin-resistant strains. They belong to sequence type 2179, phylogenetic group B1, and serotype O9:H9 and carried plasmids IncI, IncFIC(FII), and IncFIB. All strains share an identical genetic environment with IS903 and ISEcp1 flanking the blaCTX–M–65 gene. It seems likely that the blaCTX–M–65 gene is located in the chromosome in all isolates based on deep in silico analysis. Our findings showed that the strains are clonally related and belong to two sub-lineages. This study reports the emergence of CTX-M-65-producing E. coli in Portugal in food products of animal origin. The chromosomal location of the blaCTX–M–65 gene may ensure a stable spread of resistance in the absence of selective pressure.
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Affiliation(s)
- Célia Leão
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal.,MED - Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal.,Faculty of Veterinary Science, CIISA- Centre for Interdisciplinary Research in Animal Health, Lisbon, Portugal
| | - Laura Moura
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal.,Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Anne Mette Seyfarth
- EURL-AR, European Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark (DTU), National Food Institute, Lyngby, Denmark
| | - Inge M Hansen
- EURL-AR, European Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark (DTU), National Food Institute, Lyngby, Denmark
| | - Rene S Hendriksen
- EURL-AR, European Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark (DTU), National Food Institute, Lyngby, Denmark
| | - Ana Amaro
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
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20
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Giri S, Kudva V, Shetty K, Shetty V. Prevalence and Characterization of Extended-Spectrum β-Lactamase-Producing Antibiotic-Resistant Escherichia coli and Klebsiella pneumoniae in Ready-to-Eat Street Foods. Antibiotics (Basel) 2021; 10:antibiotics10070850. [PMID: 34356771 PMCID: PMC8300707 DOI: 10.3390/antibiotics10070850] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/29/2021] [Accepted: 07/09/2021] [Indexed: 12/01/2022] Open
Abstract
As the global urban populations increase with rapid migration from rural areas, ready-to-eat (RTE) street foods are posing food safety challenges where street foods are prepared with less structured food safety guidelines in small and roadside outlets. The increased presence of extended-spectrum-β-lactamase (ESBL) producing bacteria in street foods is a significant risk for human health because of its epidemiological significance. Escherichia coli and Klebsiella pneumoniae have become important and dangerous foodborne pathogens globally for their relevance to antibiotic resistance. The present study was undertaken to evaluate the potential burden of antibiotic-resistant E. coli and K. pneumoniae contaminating RTE street foods and to assess the microbiological quality of foods in a typical emerging and growing urban suburb of India where RTE street foods are rapidly establishing with public health implications. A total of 100 RTE food samples were collected of which, 22.88% were E. coli and 27.12% K. pneumoniae. The prevalence of ESBL-producing E. coli and K. pneumoniae was 25.42%, isolated mostly from chutneys, salads, paani puri, and chicken. Antimicrobial resistance was observed towards cefepime (72.9%), imipenem (55.9%), cefotaxime (52.5%), and meropenem (16.9%) with 86.44% of the isolates with MAR index above 0.22. Among β-lactamase encoding genes, blaTEM (40.68%) was the most prevalent followed by blaCTX (32.20%) and blaSHV (10.17%). blaNDM gene was detected in 20.34% of the isolates. This study indicated that contaminated RTE street foods present health risks to consumers and there is a high potential of transferring multi-drug-resistant bacteria from foods to humans and from person to person as pathogens or as commensal residents of the human gut leading to challenges for subsequent therapeutic treatments.
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Affiliation(s)
- Shobha Giri
- Department of Microbiology, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore 575018, India; (S.G.); (V.K.)
| | - Vaishnavi Kudva
- Department of Microbiology, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore 575018, India; (S.G.); (V.K.)
| | - Kalidas Shetty
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA;
| | - Veena Shetty
- Department of Microbiology, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore 575018, India; (S.G.); (V.K.)
- Correspondence:
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21
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Eger E, Heiden SE, Korolew K, Bayingana C, Ndoli JM, Sendegeya A, Gahutu JB, Kurz MSE, Mockenhaupt FP, Müller J, Simm S, Schaufler K. Circulation of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli of Pandemic Sequence Types 131, 648, and 410 Among Hospitalized Patients, Caregivers, and the Community in Rwanda. Front Microbiol 2021; 12:662575. [PMID: 34054764 PMCID: PMC8160302 DOI: 10.3389/fmicb.2021.662575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/20/2021] [Indexed: 11/13/2022] Open
Abstract
Multi-drug resistant (MDR), gram-negative Enterobacteriaceae, such as Escherichia coli (E. coli) limit therapeutic options and increase morbidity, mortality, and treatment costs worldwide. They pose a serious burden on healthcare systems, especially in developing countries like Rwanda. Several studies have shown the effects caused by the global spread of extended-spectrum beta-lactamase (ESBL)-producing E. coli. However, limited data is available on transmission dynamics of these pathogens and the mobile elements they carry in the context of clinical and community locations in Sub-Saharan Africa. Here, we examined 120 ESBL-producing E. coli strains from patients hospitalized in the University Teaching Hospital of Butare (Rwanda), their attending caregivers as well as associated community members and livestock. Based on whole-genome analysis, the genetic diversification and phylogenetics were assessed. Moreover, the content of carried plasmids was characterized and investigated for putative transmission among strains, and for their potential role as drivers for the spread of antibiotic resistance. We show that among the 30 different sequence types (ST) detected were the pandemic clonal lineages ST131, ST648 and ST410, which combine high-level antimicrobial resistance with virulence. In addition to the frequently found resistance genes blaCTX–M–15, tet(34), and aph(6)-Id, we identified csg genes, which are required for curli fiber synthesis and thus biofilm formation. Numerous strains harbored multiple virulence-associated genes (VAGs) including pap (P fimbriae adhesion cluster), fim (type I fimbriae) and chu (Chu heme uptake system). Furthermore, we found phylogenetic relationships among strains from patients and their caregivers or related community members and animals, which indicates transmission of pathogens. Also, we demonstrated the presence and potential transfer of identical/similar ESBL-plasmids in different strains from the Rwandan setting and when compared to an external plasmid. This study highlights the circulation of clinically relevant, pathogenic ESBL-producing E. coli among patients, caregivers and the community in Rwanda. Combining antimicrobial resistance with virulence in addition to the putative exchange of mobile genetic elements among bacterial pathogens poses a significant risk around the world.
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Affiliation(s)
- Elias Eger
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Stefan E Heiden
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Katja Korolew
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Claude Bayingana
- College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Jules M Ndoli
- College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.,University Teaching Hospital of Butare, Butare, Rwanda
| | - Augustin Sendegeya
- College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.,University Teaching Hospital of Butare, Butare, Rwanda
| | - Jean Bosco Gahutu
- College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.,University Teaching Hospital of Butare, Butare, Rwanda
| | - Mathis S E Kurz
- Institute of Tropical Medicine and International Health, Charité Medical University of Berlin, Berlin, Germany
| | - Frank P Mockenhaupt
- Institute of Tropical Medicine and International Health, Charité Medical University of Berlin, Berlin, Germany
| | - Julia Müller
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
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22
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Isler M, Wissmann R, Morach M, Zurfluh K, Stephan R, Nüesch-Inderbinen M. Animal petting zoos as sources of Shiga toxin-producing Escherichia coli, Salmonella and extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae. Zoonoses Public Health 2020; 68:79-87. [PMID: 33382208 DOI: 10.1111/zph.12798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/04/2020] [Accepted: 11/30/2020] [Indexed: 01/08/2023]
Abstract
Animal petting zoos and farm fairs provide the opportunity for children and adults to interact with animals, but contact with animals carries a risk of exposure to zoonotic pathogens and antimicrobial-resistant bacteria. The aim of this study was to assess the occurrence of Shiga toxin-producing Escherichia coli (STEC), Salmonella, extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae and methicillin-resistant Staphylococcus aureus (MRSA) in animal faeces from six animal petting zoos and one farm fair in Switzerland. Furthermore, hygiene facilities on the venues were evaluated. Of 163 faecal samples, 75 contained stx1, stx2 or stx1/stx2 genes, indicating the presence of STEC. Samples included faeces from sika deer (100%), sheep (92%), goats (88%), mouflons (80%), camels (62%), llamas (50%), yaks (50%), pigs (29%) and donkeys (6%), whereas no stx genes were isolated from faeces of calves, guinea pigs, hens, ostriches, ponies, zebras or zebus. Salmonella enterica subsp. enterica serovar Stourbridge (S. Stourbridge) was detected in faecal samples from camels. A total of four ESBL-producing E. coli strains were isolated from faeces of goats, camels and pigs. PCR and sequencing identified the presence of blaCTX-M-15 in three and blaCTX-M-65 in one E. coli. Antimicrobial resistance profiling using the disk diffusion method revealed two multidrug-resistant (MDR) E. coli with resistance to ciprofloxacin, gentamicin and azithromycin, all of which are critically important drugs for human medicine. Multilocus sequence typing identified E. coli ST162, E. coli ST2179, extraintestinal high-risk E. coli ST410 and E. coli ST4553, which belongs to the emerging extraintestinal clonal complex (CC) 648. No MRSA was detected. On all animal petting venues, there were inadequacies with regard to access to hygiene information and handwashing hygiene facilities. This study provides data that underscore the importance of hygiene measures to minimize the risk of transmission of zoonotic pathogens and MDR, ESBL-producing E. coli to visitors of animal petting venues.
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Affiliation(s)
- Meret Isler
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Ramona Wissmann
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Marina Morach
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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