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Rheman S, Hossain S, Sarker MS, Akter F, Khor L, Gan HM, Powell A, Card RM, Hounmanou YMG, Dalsgaard A, Mohan CV, Bupasha ZB, Samad MA, Verner-Jeffreys DW, Delamare-Deboutteville J. Nanopore sequencing for identification and characterization of antimicrobial-resistant Escherichia coli and Salmonella spp. from tilapia and shrimp sold at wet markets in Dhaka, Bangladesh. Front Microbiol 2024; 15:1329620. [PMID: 38516018 PMCID: PMC10956512 DOI: 10.3389/fmicb.2024.1329620] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/09/2024] [Indexed: 03/23/2024] Open
Abstract
Wet markets in low-and middle-income countries are often reported to have inadequate sanitation resulting in fecal contamination of sold produce. Consumption of contaminated wet market-sourced foods has been linked to individual illness and disease outbreaks. This pilot study, conducted in two major wet markets in Dhaka city, Bangladesh during a 4-month period in 2021 aimed to assess the occurrence and characteristics of Escherichia coli and non-typhoidal Salmonella spp. (NTS) from tilapia (Oreochromis niloticus) and shrimp (Penaeus monodon). Fifty-four individuals of each species were collected. The identity of the bacterial isolates was confirmed by PCR and their susceptibility toward 15 antimicrobials was tested by disk diffusion. The whole genome of 15 E. coli and nine Salmonella spp. were sequenced using Oxford Nanopore Technology. E. coli was present in 60-74% of tilapia muscle tissue and 41-44% of shrimp muscle tissue. Salmonella spp. was found in skin (29%) and gills (26%) of tilapia, and occasionally in muscle and intestinal samples of shrimp. The E. coli had several Multilocus sequence typing and serotypes and limited antimicrobial resistance (AMR) determinants, such as point mutations on glpT and pmrB. One E. coli (BD17) from tilapia carried resistance genes for beta-lactams, quinolones, and tetracycline. All the E. coli belonged to commensal phylogroups B1 and A and showed no Shiga-toxin and other virulence genes, confirming their commensal non-pathogenic status. Among the Salmonella isolates, five belonged to Kentucky serovar and had similar AMR genes and phenotypic resistance patterns. Three strains of this serovar were ST198, often associated with human disease, carried the same resistance genes, and were genetically related to strains from the region. The two undetermined sequence types of S. Kentucky were distantly related and positioned in a separate phylogenetic clade. Two Brunei serovar isolates, one Augustenborg isolate, and one Hartford isolate showed different resistance profiles. This study revealed high fecal contamination levels in tilapia and shrimp sold at two main wet markets in Dhaka. Together with the occurrence of Salmonella spp., including S. Kentucky ST198, a well-known human pathogen, these results stress the need to improve hygienic practices and sanitation standards at markets to improve food safety and protect consumer health.
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Affiliation(s)
- Shafiq Rheman
- Laboratory Department of Sustainable Aquaculture, WorldFish, Dhaka, Bangladesh
| | - Sabrina Hossain
- Laboratory Department of Sustainable Aquaculture, WorldFish, Dhaka, Bangladesh
| | - Md Samun Sarker
- Antimicrobial Resistance Action Center (ARAC), Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Bangladesh
| | - Farhana Akter
- Laboratory Department of Sustainable Aquaculture, WorldFish, Dhaka, Bangladesh
| | - Laura Khor
- Department of Sustainable Aquaculture, WorldFish, Penang, Malaysia
| | - Han Ming Gan
- Patriot Biotech Sdn Bhd, Bandar Sunway, Malaysia
| | - Andy Powell
- Weymouth Laboratory, Cefas: Centre for Environment Fisheries and Aquaculture Science, Weymouth, United Kingdom
- Veterinary Medicines Directorate FAO Reference Centre for Antimicrobial Resistance, Weybridge, United Kingdom
| | - Roderick M. Card
- Bacteriology Department, Animal Plant Health Agency, Weybridge, United Kingdom
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Zamila Bueaza Bupasha
- Antimicrobial Resistance Action Center (ARAC), Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Bangladesh
| | - Mohammed A. Samad
- Antimicrobial Resistance Action Center (ARAC), Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Bangladesh
| | - David W. Verner-Jeffreys
- Weymouth Laboratory, Cefas: Centre for Environment Fisheries and Aquaculture Science, Weymouth, United Kingdom
- Veterinary Medicines Directorate FAO Reference Centre for Antimicrobial Resistance, Weybridge, United Kingdom
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Odih EE, Oaikhena AO, Underwood A, Hounmanou YMG, Oduyebo OO, Fadeyi A, Aboderin AO, Ogunleye VO, Argimón S, Akpunonu VN, Oshun PO, Egwuenu A, Okwor TJ, Ihekweazu C, Aanensen DM, Dalsgaard A, Okeke IN. Correction for Odih et al., "High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020". mSphere 2024; 9:e0065923. [PMID: 38126760 PMCID: PMC10826356 DOI: 10.1128/msphere.00659-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
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Odih EE, Sunmonu GT, Okeke IN, Dalsgaard A. NDM-1- and OXA-23-producing Acinetobacter baumannii in wastewater of a Nigerian hospital. Microbiol Spectr 2023; 11:e0238123. [PMID: 37796014 PMCID: PMC10714947 DOI: 10.1128/spectrum.02381-23] [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: 07/05/2023] [Accepted: 08/22/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Acinetobacter baumannii is a leading cause of hospital-associated infections globally. A. baumannii reservoirs outside hospital settings are still unknown, and their occurrence in the environment is linked to clinical and anthropogenic activities. Although the risk of transmission of A. baumannii from environmental sources to humans is not fully understood, these sources pose significant risks for the continued dissemination of A. baumannii and their resistance traits. This study provides evidence that diverse and clinically relevant A. baumannii strains, many of which are resistant to carbapenems, are constantly being discharged into the environment through inadequately treated hospital wastewater. We further elucidate potential transmission routes between the environment and clinical infections and demonstrate the high prevalence of carbapenem resistance genes on highly mobile transposons among these strains. Our findings highlight the pressing need to address hospital wastewater as a crucial factor in curtailing the spread of carbapenem-resistant A. baumannii.
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Affiliation(s)
- Erkison Ewomazino Odih
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Gabriel Temitope Sunmonu
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Erickson VI, Khoi LM, Hounmanou YMG, Dung TT, Phu TM, Dalsgaard A. Comparative genomic analysis of Aeromonas dhakensis and Aeromonas hydrophila from diseased striped catfish fingerlings cultured in Vietnam. Front Microbiol 2023; 14:1254781. [PMID: 37808293 PMCID: PMC10556525 DOI: 10.3389/fmicb.2023.1254781] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Motile Aeromonas septicemia (MAS) is a burden for striped catfish (Pangasius hypophthalmus) farmers in Vietnam. MAS can be caused by several species of Aeromonas but Aeromonas hydrophila is seen as the leading cause of MAS in aquaculture, but recent reports suggest that A. dhakensis is also causing MAS. Methods Here we investigated the bacterial etiology of MAS and compared the genomic features of A. hydrophila and A. dhakensis. We collected 86 isolates from diseased striped catfish fingerlings over 5 years from eight provinces in Vietnam. Species identification was done using PCR, MALDI-TOF and whole genome sequence (WGS). The MICs of commonly used antimicrobials was established. Thirty presumed A. hydrophila isolates were sequenced for species confirmation and genomic comparison. A phylogenetic analysis was conducted using publicly available sequences and sequences from this study. Results A total of 25/30 isolates were A. dhakensis sequence type (ST) 656 and 5/30 isolates were A. hydrophila ST 251. Our isolates and all publicly available A. hydrophila isolates from Vietnam belonged to ST 251 and differed with <200 single nucleotide polymorphisms (SNP). Similarly, all A. dhakensis isolates from Vietnam belonged to ST 656 and differed with <100 SNPs. The tet(A) gene was found in 1/5 A. hydrophila and 19/25 A. dhakensis. All A. hydrophila had an MIC ≤2 mg/L while 19/25 A. dhakensis had MIC ≥8 mg/L for oxytetracycline. The floR gene was only found in A. dhakensis (14/25) which showed a MIC ≥8 mg/L for florfenicol. Key virulence genes, i.e., aerA/act, ahh1 and hlyA were present in all genomes, while ast was only present in A. dhakensis. Discussion This study confirms previous findings where A. dhakensis was the dominating pathogen causing MAS and that the importance of A. hydrophila has likely been overestimated. The differences in antimicrobial susceptibility between the two species could indicate a need for targeted antimicrobial treatment plans. The lipopolysaccharide regions and outer membrane proteins did not significantly differ in their immunogenic potentials, but it remains to be determined with in vivo experiments whether there is a difference in the efficacy of available vaccines against A. hydrophila and A. dhakensis.
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Affiliation(s)
- Vera Irene Erickson
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Le Minh Khoi
- Department of Aquatic Pathology, Can Tho University, Can Tho, Vietnam
| | | | - Tu Thanh Dung
- Department of Aquatic Pathology, Can Tho University, Can Tho, Vietnam
| | - Tran Minh Phu
- Department of Aquatic Product Processing, Can Tho University, Can Tho, Vietnam
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
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Odih EE, Oaikhena AO, Underwood A, Hounmanou YMG, Oduyebo OO, Fadeyi A, Aboderin AO, Ogunleye VO, Argimón S, Akpunonu VN, Oshun PO, Egwuenu A, Okwor TJ, Ihekweazu C, Aanensen DM, Dalsgaard A, Okeke IN. High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020. mSphere 2023; 8:e0009823. [PMID: 37067411 PMCID: PMC10286719 DOI: 10.1128/msphere.00098-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
Acinetobacter baumannii causes difficult-to-treat infections mostly among immunocompromised patients. Clinically relevant A. baumannii lineages and their carbapenem resistance mechanisms are sparsely described in Nigeria. This study aimed to characterize the diversity and genetic mechanisms of carbapenem resistance among A. baumannii strains isolated from hospitals in southwestern Nigeria. We sequenced the genomes of all A. baumannii isolates submitted to Nigeria's antimicrobial resistance surveillance reference laboratory between 2016 and 2020 on an Illumina platform and performed in silico genomic characterization. Selected strains were sequenced using the Oxford Nanopore technology to characterize the genetic context of carbapenem resistance genes. The 86 A. baumannii isolates were phylogenetically diverse and belonged to 35 distinct Oxford sequence types (oxfSTs), 16 of which were novel, and 28 Institut Pasteur STs (pasSTs). Thirty-eight (44.2%) isolates belonged to none of the known international clones (ICs). Over 50% of the isolates were phenotypically resistant to 10 of 12 tested antimicrobials. The majority (n = 54) of the isolates were carbapenem resistant, particularly the IC7 (pasST25; 100%) and IC9 (pasST85; >91.7%) strains. blaOXA-23 (34.9%) and blaNDM-1 (27.9%) were the most common carbapenem resistance genes detected. All blaOXA-23 genes were carried on Tn2006 or Tn2006-like transposons. Our findings suggest that a 10-kb Tn125 composite transposon is the primary means of blaNDM-1 dissemination. Our findings highlight an increase in blaNDM-1 prevalence and the widespread transposon-facilitated dissemination of carbapenemase genes in diverse A. baumannii lineages in southwestern Nigeria. We make the case for improving surveillance of these pathogens in Nigeria and other understudied settings. IMPORTANCE Acinetobacter baumannii bacteria are increasingly clinically relevant due to their propensity to harbor genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing. Our study characterized the diversity and antimicrobial resistance profiles of clinical A. baumannii in southwestern Nigeria using whole-genome sequencing. We also identified the key genetic elements facilitating the dissemination of carbapenem resistance genes within this species. This study provides key insights into the clinical burden and population dynamics of A. baumannii in hospitals in Nigeria and highlights the importance of routine whole-genome sequencing-based surveillance of this and other previously understudied pathogens in Nigeria and other similar settings.
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Affiliation(s)
- Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anderson O. Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Anthony Underwood
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oyinlola O. Oduyebo
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Abayomi Fadeyi
- Department of Medical Microbiology and Parasitology, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Aaron O. Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Veronica O. Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Silvia Argimón
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | | | - Phillip O. Oshun
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | | | | | | | - David M. Aanensen
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
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Erickson VI, Alfifi A, Hounmanou YGM, Sana MJ, Christensen JP, Dalsgaard A. Genomic traits of Aeromonas veronii isolated from slaughtered Danish broilers. Vet Microbiol 2023; 283:109772. [PMID: 37207528 DOI: 10.1016/j.vetmic.2023.109772] [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: 08/31/2022] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/21/2023]
Abstract
Aeromonas veronii is a Gram-negative opportunistic bacterium found in fish, poultry and humans and has occasionally been associated with disease although not generally considered a poultry pathogen. A. veronii was recently isolated from both healthy and condemned broiler carcasses at a major Danish abattoir. In this study, we did a whole genomic analysis of 24A. veronii strains from the abattoir to determine their potential sources and relatedness as well as their pathogenic potential, antimicrobial resistance determinants and associated mobile elements. No strains were multi-drug resistant, but all strains carried the beta-lactam resistance genes cphA3 and blaOXA-12 without being phenotypically resistant to carbapenems. One strain carried an IncA plasmid with tet(A), tet(B) and tet(E) genes. A phylogenetic tree including public A. veronii sequences showed that our isolates were not clonal but were dispersed around the phylogenetic tree, suggesting a diffuse spread of A. veronii across human, aquatic and poultry samples. Strains carried different virulence factors known to be associated with pathogenesis and severity of disease in animals and humans, e.g. type II (aerolysin, amylases, proteases, and cytotoxic enterotoxin Act) and III secretion systems where the latter has been associated with mortality in hospitalized patients. Although our genomic analysis of A. veronii shows zoonotic potential, epidemiological studies of human gastro-enteritis cases of A. veronii associated with consumption of broiler meat are needed. It remains to be proven if A. veronii is a true poultry pathogen and part of the established microflora in abattoirs and the gut-intestinal microflora of poultry.
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Affiliation(s)
- Vera Irene Erickson
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark; Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, China.
| | - Ahmed Alfifi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark; Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, Al-Ahasa 31982, Saudi Arabia
| | | | - Mohammad Jafar Sana
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Jens Peter Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
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Saidenberg ABS, Franco LS, Reple JN, Hounmanou YMG, Casas MRT, Cardoso B, Esposito F, Lincopan N, Dalsgaard A, Stegger M, Knöbl T. Salmonella Heidelberg and Salmonella Minnesota in Brazilian broilers: Genomic characterization of third-generation cephalosporin and fluoroquinolone-resistant strains. Environ Microbiol Rep 2023; 15:119-128. [PMID: 36629129 PMCID: PMC10103857 DOI: 10.1111/1758-2229.13132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/12/2022] [Indexed: 05/20/2023]
Abstract
Salmonella serovars Heidelberg and Minnesota encoding antimicrobial resistance to third-generation cephalosporins and fluoroquinolones are often detected in poultry/poultry meat. We analysed the genomes of 10 Salmonella Heidelberg (SH) and 4 Salmonella Minnesota (SM) from faecal isolates of Brazilian poultry. These featured virulent and multidrug-resistant characteristics, with AmpC beta-lactamase (blaCMY-2 ) predominance (9/14), for all SM (4/4) and some SH (3/10) located on IncC plasmid replicons. IncC carrying blaCTX-M-2 was only detected among SH (3/10). Mutation in the gyrA/parC genes was present in all SH, whereas SM harboured parC mutation plus qnrB19 on ColRNAI plasmids (3/4). In silico resistance overall corroborated with phenotypic results. Core genome phylogenies showed close clustering and high similarities between the Brazilian and poultry meat/food isolates from Europe, and to human isolates from European countries with documented import of Brazilian poultry meat. Conjugation assays with SM successfully transferred blaCMY-2 , and qnrB19 to an Escherichia coli recipient. The findings reinforce the ongoing antimicrobial resistance acquisition of SH and Minnesota and the risks for disseminating resistant strains and/or mobile elements which may increasingly affect importing countries and the need for controlling AMR in major poultry-exporting countries like Brazil.
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Affiliation(s)
- Andre Becker Simoes Saidenberg
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
- Department of Veterinary and Animal Sciences, Section for Food Safety and ZoonosesInstitute for Veterinary and Companion Animal Science, Københavns UniversitetCopenhagenDenmark
- Department of Bacteria, Parasites and FungiStatens Serum InstitutCopenhagenDenmark
| | - Leticia Soares Franco
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
| | - Jessica Nacarato Reple
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Section for Food Safety and ZoonosesInstitute for Veterinary and Companion Animal Science, Københavns UniversitetCopenhagenDenmark
| | | | - Brenda Cardoso
- Department of MicrobiologyInstitute of Biomedical Science, University of São PauloSão PauloBrazil
| | - Fernanda Esposito
- Department of Clinical AnalysisSchool of Pharmaceutical Sciences, University of São PauloSão PauloBrazil
| | - Nilton Lincopan
- Department of MicrobiologyInstitute of Biomedical Science, University of São PauloSão PauloBrazil
- Department of Clinical AnalysisSchool of Pharmaceutical Sciences, University of São PauloSão PauloBrazil
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Section for Food Safety and ZoonosesInstitute for Veterinary and Companion Animal Science, Københavns UniversitetCopenhagenDenmark
| | - Marc Stegger
- Department of Bacteria, Parasites and FungiStatens Serum InstitutCopenhagenDenmark
| | - Terezinha Knöbl
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
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Khurana MP, Essack S, Zoubiane G, Sreenivasan N, Cordoba GC, Westwood E, Dalsgaard A, Mdegela RH, Mpundu M, Scotini R, Matondo AB, Mzula A, Chanishvili N, Gogebashvili D, Beruashvili M, Tsereteli M, Sooronbaev T, Kjærgaard J, Bloch J, Isaeva E, Mainda G, Muuka G, Mudenda NB, Goma FY, Chu DH, Chanda D, Chirwa U, Yamba K, Kapolowe K, Fwoloshi S, Mwenge L, Skov R. Mitigating antimicrobial resistance (AMR) using implementation research: a development funder’s approach. JAC Antimicrob Resist 2023; 5:dlad031. [PMID: 36994233 PMCID: PMC10041058 DOI: 10.1093/jacamr/dlad031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Despite the escalating burden of antimicrobial resistance (AMR), the global response has not sufficiently matched the scale and scope of the issue, especially in low- and middle-income countries (LMICs). While many countries have adopted national action plans to combat AMR, their implementation has lagged due to resource constraints, dysfunctional multisectoral coordination mechanisms and, importantly, an under-recognized lack of technical capacity to adapt evidence-based AMR mitigation interventions to local contexts. AMR interventions should be tailored, context-specific, cost-effective and sustainable. The implementation and subsequent scale-up of these interventions require multidisciplinary intervention-implementation research (IIR). IIR involves both quantitative and qualitative approaches, occurs across a three-phase continuum (proof of concept, proof of implementation and informing scale-up), and across four context domains (inner setting, outer setting, stakeholders and the implementation process). We describe the theoretical underpinnings of implementation research (IR), its various components, and how to construct different IR strategies to facilitate sustainable uptake of AMR interventions. Additionally, we provide real-world examples of AMR strategies and interventions to demonstrate these principles in practice. IR provides a practical framework to implement evidence-based and sustainable AMR mitigation interventions.
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Affiliation(s)
- Mark P Khurana
- Corresponding author. E-mail: ; @markkhurana, @EssackSabiha, @RskSkov
| | | | - Ghada Zoubiane
- ICARS, International Centre for Antimicrobial Resistance Solutions, Ørestads Boulevard 5, Copenhagen 2300, Denmark
| | - Nandini Sreenivasan
- ICARS, International Centre for Antimicrobial Resistance Solutions, Ørestads Boulevard 5, Copenhagen 2300, Denmark
| | - Gloria Cristina Cordoba
- ICARS, International Centre for Antimicrobial Resistance Solutions, Ørestads Boulevard 5, Copenhagen 2300, Denmark
| | - Erica Westwood
- ICARS, International Centre for Antimicrobial Resistance Solutions, Ørestads Boulevard 5, Copenhagen 2300, Denmark
| | - Anders Dalsgaard
- ICARS, International Centre for Antimicrobial Resistance Solutions, Ørestads Boulevard 5, Copenhagen 2300, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Robinson H Mdegela
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Mirfin Mpundu
- ICARS, International Centre for Antimicrobial Resistance Solutions, Ørestads Boulevard 5, Copenhagen 2300, Denmark
- ReAct Africa, Lusaka, Zambia
| | | | - Augustine B Matondo
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Alexanda Mzula
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Nina Chanishvili
- George Eliava Institute of Bacteriophage Microbiology and Virology, Gotua Street 3, Tbilisi 0160, Georgia
| | | | - Maia Beruashvili
- Ministry of Environmental Protection and Agriculture of Georgia, Marshal Gelovani 6, Tbilisi 0159, Georgia
- The Faculty of Veterinary Medicine, European University, Tbilisi, Georgia
| | - Marika Tsereteli
- Department of Communicable Diseases, National Center for Disease Control and Public Health, Kakheti Highway 99, Tbilisi 0198, Georgia
| | - Talant Sooronbaev
- National Center of Cardiology and Internal Medicine named after academician M. Mirrakhimov, Togolok Moldo Str, 3, Bishkek 720040, Kyrgyzstan
| | - Jesper Kjærgaard
- Department of Children and Adolescents, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Joakim Bloch
- Department of Children and Adolescents, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Elvira Isaeva
- National Center of Maternity and Childhood Care, Akhunbaev Str, 190, Bishkek 720038, Kyrgyzstan
- Department of Public Health, The Research Unit for General Practice and Section of General Practice, University of Copenhagen, Øster Farimagsgade 5, Copenhagen 1354, Denmark
| | - Geoffrey Mainda
- Department of Veterinary Services, Ministry of Fisheries and Livestock, PO Box 50060, Lusaka, Zambia
| | - Geoffrey Muuka
- Department of Veterinary Services, Ministry of Fisheries and Livestock, PO Box 50060, Lusaka, Zambia
| | - Ntombi B Mudenda
- School of Veterinary Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Fusya Y Goma
- Department of Veterinary Services, Ministry of Fisheries and Livestock, PO Box 50060, Lusaka, Zambia
| | - Duc-Huy Chu
- Department of Animal Health, Ministry of Agriculture and Rural Development, Ha Noi 115-19, Viet Nam
| | - Duncan Chanda
- University Teaching Hospital, Box 17, UTH Post Office, Nationalist Rd., Lusaka, Zambia
- Ministry of Health, Ndeke House, Haile Selassie Avenue, PO Box 30205, Lusaka, Zambia
| | - Uchizi Chirwa
- University Teaching Hospital, Box 17, UTH Post Office, Nationalist Rd., Lusaka, Zambia
- Ministry of Health, Ndeke House, Haile Selassie Avenue, PO Box 30205, Lusaka, Zambia
| | - Kaunda Yamba
- School of Veterinary Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
- University Teaching Hospital, Box 17, UTH Post Office, Nationalist Rd., Lusaka, Zambia
| | - Kenneth Kapolowe
- University Teaching Hospital, Box 17, UTH Post Office, Nationalist Rd., Lusaka, Zambia
| | - Sombo Fwoloshi
- University Teaching Hospital, Box 17, UTH Post Office, Nationalist Rd., Lusaka, Zambia
- Ministry of Health, Ndeke House, Haile Selassie Avenue, PO Box 30205, Lusaka, Zambia
| | | | - Robert Skov
- ICARS, International Centre for Antimicrobial Resistance Solutions, Ørestads Boulevard 5, Copenhagen 2300, Denmark
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9
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Chaula D, Jacobsen C, Laswai HS, Chove BE, Dalsgaard A, Mdegela R, Hyldig G. Changes in fatty acids during storage of artisanal‐processed freshwater sardines (
Rastrineobola argentea
). Food Sci Nutr 2023. [DOI: 10.1002/fsn3.3284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Affiliation(s)
- Davis Chaula
- Department of Food Sciences and Agro‐Processing Sokoine University of Agriculture Morogoro Tanzania
| | - Charlotte Jacobsen
- National Food Institute, Division for Food Technology Technical University of Denmark Lyngby Denmark
| | - Henry S. Laswai
- Department of Food Sciences and Agro‐Processing Sokoine University of Agriculture Morogoro Tanzania
| | - Bernard Elias Chove
- Department of Food Sciences and Agro‐Processing Sokoine University of Agriculture Morogoro Tanzania
| | - Anders Dalsgaard
- Faculty of Health and Medical Sciences, Section of Food Safety and Zoonoses, Department of Veterinary and Animal Sciences University of Copenhagen Frederiksberg C Denmark
| | - Robinson Mdegela
- College of Veterinary and Medical Sciences, Department of Veterinary Medicine and Public Health Sokoine University of Agriculture Morogoro Tanzania
| | - Grethe Hyldig
- National Food Institute, Division for Food Technology Technical University of Denmark Lyngby Denmark
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10
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Jibril AH, Okeke IN, Dalsgaard A, Olsen JE. Prevalence and whole genome phylogenetic analysis reveal genetic relatedness between antibiotic resistance Salmonella in hatchlings and older chickens from farms in Nigeria. Poult Sci 2023; 102:102427. [PMID: 36584420 PMCID: PMC9827064 DOI: 10.1016/j.psj.2022.102427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/07/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
The presence of Salmonella in hatchlings is the single most important risk factor for the introduction of Salmonella into poultry farms, and resistant strains are particularly worrisome, as they could affect treatment outcomes in humans infected through consumption of contaminated poultry products. This study estimated Salmonella prevalence, determined resistance profiles of strains recovered from hatchlings in Nigeria, and determined genetic relatedness between hatchling strains and strains from poultry farms. In this study, 300 fecal samples were collected. Salmonella was isolated by culture and confirmed by PCR, and isolates were tested for susceptibility to antimicrobials by the disk diffusion method. Strains were pair-end sequenced, and genomes were used to obtain serotypes and antibiotic resistance genes. Whole-genome based phylogenetic analysis was used to determine genetic relatedness between these isolates and strains from previously characterized older chicken within the same geographical area. A prevalence of 10.7% was obtained belonging to 13 Salmonella serovars. Resistance to kanamycin (30/32), ciprofloxacin (22/32), nalidixic acid (22/32), and sulfonamides (22/32) were the most commonly observed phenotypic resistances. Twenty-two (68.8%) isolates showed multidrug resistance. In silico predictions identified 36 antimicrobial resistance genes. Four (12.5%) and 22 (68.8%) strains showed point mutations in gyrA and parC. Commonly observed acquired resistance genes included sul1, sul2, sul3, and tet(A) as well as a variety of aminoglycoside-modifying genes. Eleven (34.4%) isolates were predicted to have genes that confer resistance to fosfomycin (fosA7, fosB). A strain of S. Stanleyville was predicted to have optrA, which confers resistance to furazolidone. Strains of S. Kentucky, S. Muenster, and S. Menston obtained from hatchlings showed close genetic relatedness by having less than 30 SNPs difference to strains recovered from chickens at farms previously receiving hatchlings from the same sources.
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Affiliation(s)
- Abdurrahman Hassan Jibril
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Anders Dalsgaard
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, Sokoto, Nigeria
| | - John Elmerdahl Olsen
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, Sokoto, Nigeria
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11
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Gildas Hounmanou YM, Engberg J, Bjerre KD, Holt HM, Olesen B, Voldstedlund M, Dalsgaard A, Ethelberg S. Correlation of High Seawater Temperature with Vibrio and Shewanella Infections, Denmark, 2010-2018. Emerg Infect Dis 2023; 29:605-608. [PMID: 36823018 PMCID: PMC9973676 DOI: 10.3201/eid2903.221568] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
During 2010-2018 in Denmark, 638 patients had Vibrio infections diagnosed and 521 patients had Shewanella infections diagnosed. Most cases occurred in years with high seawater temperatures. The substantial increase in those infections, with some causing septicemia, calls for clinical awareness and mandatory notification policies.
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12
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Hounmanou YMG, Njamkepo E, Rauzier J, Gallandat K, Jeandron A, Kamwiziku G, Porten K, Luquero F, Abedi AA, Rumedeka BB, Miwanda B, Michael M, Okitayemba PW, Saidi JM, Piarroux R, Weill FX, Dalsgaard A, Quilici ML. Genomic Microevolution of Vibrio cholerae O1, Lake Tanganyika Basin, Africa. Emerg Infect Dis 2023; 29:149-153. [PMID: 36573719 PMCID: PMC9796204 DOI: 10.3201/eid2901.220641] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Africa's Lake Tanganyika basin is a cholera hotspot. During 2001-2020, Vibrio cholerae O1 isolates obtained from the Democratic Republic of the Congo side of the lake belonged to 2 of the 5 clades of the AFR10 sublineage. One clade became predominant after acquiring a parC mutation that decreased susceptibility to ciprofloxacin.
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13
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Roldan-Henao M, Dalsgaard A, Cardona-Castro N, Restrepo-Rivera L, Veloza-Angulo LC, Alban L. Pilot study of the productivity and Salmonella seroprevalence in pigs administered organic acids. Front Vet Sci 2023; 10:1123137. [PMID: 36937024 PMCID: PMC10020582 DOI: 10.3389/fvets.2023.1123137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Control of Salmonella in pig/pork production is important to protect public health because pork is one of the main sources of human infection. Moreover, antimicrobial use in pig farms should be kept low to minimize development and transmission of antimicrobial resistance. This pilot study evaluated the productivity and Salmonella seroprevalence in pigs administered organic acids (OA) compared to pigs given growth promoters in one farm in Antioquia, Colombia. Two groups each consisting of 60 pigs of 6-weeks of age were studied for 4 months. One group was provided feed and water with OA (Selko pH® and Selacid®), whereas the other group (control) received antimicrobial growth promoters according to routine feeding practices (tylosin and zinc bacitracin). Blood samples were taken three times (T1-T3) and pigs were weighted five times to calculate daily weight gain (DWG) and feed conversion ratio (FCR). Initially when the pigs were 6 weeks old (T1), the Salmonella seroprevalence was 1.7% in both groups. When the pigs were 11 weeks old (T2), the seroprevalence was significantly lower in pigs provided OA compared to the control group (19 vs. 47%, P < 0.001), whereas when the pigs were 23 weeks old (T3), the seroprevalence did not differ between the groups (62 vs. 77%; P = 0.075). The cumulative DWG was significantly higher in the intervention group than in the control group (713 vs. 667 g/day; P < 0.001). The cumulative FCR did not differ between groups (2.80 vs. 2.77; P = 0.144). The pilot study indicates that cleaning the water pipes and administrating OA improve productivity in pigs and delay exposure to Salmonella spp. when compared with growth promoters. Thus, OA could replace antimicrobial growth promoters and reduce antimicrobial use and resistance. However, the study should be repeated before firmer conclusions can be drawn.
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Affiliation(s)
- Manuela Roldan-Henao
- Department of Veterinary and Animal Sciences, CES University, Medellin, Colombia
- *Correspondence: Manuela Roldan-Henao
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nora Cardona-Castro
- Instituto Colombiano de Medicina Tropical, CES University, Medellin, Colombia
| | | | | | - Lis Alban
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- Department for Food Safety and Veterinary Issues, Danish Agriculture & Food Council, Copenhagen, Denmark
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14
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Alfifi A, Christensen JP, Hounmanou YMG, Sandberg M, Dalsgaard A. Characterization of Escherichia coli and other bacteria isolated from condemned broilers at a Danish abattoir. Front Microbiol 2022; 13:1020586. [PMID: 36439808 PMCID: PMC9686377 DOI: 10.3389/fmicb.2022.1020586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/19/2022] [Indexed: 10/17/2023] Open
Abstract
Meat inspection is important to ensure food safety and protect public health. Visual inspection of slaughtered carcasses for pathological changes should be supported by bacteriological analysis to determine whether the entire carcass or parts of it should be condemned. The aim of this study was to determine the bacterial species present in different sample types from condemned broiler carcasses. Furthermore, we investigated the genetic characteristics, zoonotic potential, and relatedness of Escherichia coli, the predominant bacterial species isolated from the carcasses. A total of 400 broiler carcasses condemned because of cellulitis (100), scratches (100), hepatitis (100), and healthy control carcasses (100) were selected. Samples of meat, pathological lesion, and bone marrow of each carcass were obtained for microbial analysis. From the analyzed samples, 469 bacterial isolates were recovered with E. coli accounting for 45.8%, followed by Aeromonas spp. (27.9%), in particular A. veronii. The highest rate of bacterial isolation was observed in carcasses condemned with cellulitis, whereas carcasses with hepatitis had the lowest rate of bacterial isolation. Forty-four E. coli isolates originating from different sample types were selected for whole genome sequencing. A clonal relationship was shown between E. coli from different sample types of the same carcass condemned with cellulitis and scratches. A major clade of E. coli was found in carcasses condemned with cellulitis with isolates containing mdf(A), tet(A), and bla TEM-1B genes that confer resistance to macrolides, tetracycline, and ampicillin, respectively. E. coli in this clade all belonged to ST117 and clustered with E. coli isolates previously collected from dead chickens and carcasses condemned due to cellulitis in Denmark, Finland, and the United Kingdom. Bacterial evaluation results of carcasses condemned with cellulitis, scratches (moderate to severe skin lesion), and acute hepatitis confirmed the need for total condemnation of carcasses with these pathological findings. A similar evaluation should be done for carcasses affected with chronic hepatitis, and minor scratches lesions.
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Affiliation(s)
- Ahmed Alfifi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
- Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Jens P. Christensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Marianne Sandberg
- National Food Institute, Danish Technical University, Lyngby, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
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15
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Ankar-Brewoo GM, Darko G, Abaidoo RC, Dalsgaard A, Johnson PN, Ellis WO, Brimer L. Dietary Risk Assessment Due to the Consumption of Polycyclic Aromatic Hydrocarbon in Two Commonly Consumed Street Vended Foods. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2020.1830128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Gloria Mathanda Ankar-Brewoo
- Department of Food Science and Technology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Godfred Darko
- Department of Chemistry, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Robert Clement Abaidoo
- Department of Theoretical and Applied Biology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Anders Dalsgaard
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Paa-Nii Johnson
- Department of Agro-processing Technology and Food Biosciences, CSIR-College of Science and Technology, Accra, Ghana
| | - William Otoo Ellis
- Department of Food Science and Technology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Leon Brimer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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16
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Hounmanou YMG, Baniga Z, García V, Dalsgaard A. Salmonella Salamae and S. Waycross isolated from Nile perch in Lake Victoria show limited human pathogenic potential. Sci Rep 2022; 12:4229. [PMID: 35273308 PMCID: PMC8913728 DOI: 10.1038/s41598-022-08200-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/03/2022] [Indexed: 12/22/2022] Open
Abstract
Non-enterica subspecies of Salmonella enterica are rarely associated with human infections. Paradoxically, food safety legislations consider the entire genus Salmonella as pathogenic to humans. Globally, large amounts of seafoods are rejected and wasted due to findings of Salmonella. To inform better food safety decisions, we investigated the pathogenicity of Salmonella Salamae 42:r- and Salmonella Waycross isolated from Nile perch from Lake Victoria. Genome-wide analysis revealed absence of significant virulence determinants including on key Salmonella pathogenicity islands in both serovars. In epithelial cells, S. Salamae showed a weak invasion ability that was lower than the invH mutant of S. Typhimiurium used as negative control. Similarly, S. Salamae could not replicate inside macrophages. Moreover, intracellular replication in S. Waycross strains was significantly lower compared to the wild type S. Typhimurium. Our findings suggest a low pathogenicity of S. Salamae reinforcing the existing literature that non-enterica subspecies are avirulent. We propose that food legislations and actions taken on findings of Salmonella are revisited to avoid wasting valuable sea- and other foods.
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Affiliation(s)
- Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark. .,Research Unit of Applied Microbiology and Pharmacology of Natural Substances, University of Abomey-Calavi, Godomey, Benin.
| | - Zebedayo Baniga
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Vanesa García
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.,Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Universidade de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
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17
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Odih EE, Irek EO, Obadare TO, Oaikhena AO, Afolayan AO, Underwood A, Adenekan AT, Ogunleye VO, Argimon S, Dalsgaard A, Aanensen DM, Okeke IN, Aboderin AO. Rectal Colonization and Nosocomial Transmission of Carbapenem-Resistant Acinetobacter baumannii in an Intensive Care Unit, Southwest Nigeria. Front Med (Lausanne) 2022; 9:846051. [PMID: 35321470 PMCID: PMC8936076 DOI: 10.3389/fmed.2022.846051] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Background Acinetobacter baumannii are of major human health importance because they cause life-threatening nosocomial infections and often are highly resistant to antimicrobials. Specific multidrug-resistant A. baumannii lineages are implicated in hospital outbreaks globally. We retrospectively investigated a suspected outbreak of carbapenem-resistant A. baumannii (CRAB) colonizing patients in an intensive care unit (ICU) of a tertiary hospital in Southwest Nigeria where genomic surveillance of Acinetobacter has hitherto not been conducted. Methods A prospective observational study was conducted among all patients admitted to the ICU between August 2017 and June 2018. Acinetobacter species were isolated from rectal swabs and verified phenotypically with the Biomerieux Vitek 2 system. Whole genome sequencing (WGS) was performed on the Illumina platform to characterize isolates from a suspected outbreak during the study period. Phylogenetic analysis, multilocus sequence typing, and antimicrobial resistance gene prediction were carried out in silico. Results Acinetobacter isolates belonging to the A. baumannii complex were recovered from 20 (18.5%) ICU patients. Single nucleotide polymorphism (SNP) analysis and epidemiological information revealed a putative outbreak clone comprising seven CRAB strains belonging to the globally disseminated international clone (IC) 2. These isolates had ≤2 SNP differences, identical antimicrobial resistance and virulence genes, and were all ST1114/1841. Conclusion We report a carbapenem-resistant IC2 A. baumannii clone causing an outbreak in an ICU in Nigeria. The study findings underscore the need to strengthen the capacity to detect A. baumannii in human clinical samples in Nigeria and assess which interventions can effectively mitigate CRAB transmission in Nigerian hospital settings.
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Affiliation(s)
- Erkison Ewomazino Odih
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, University of Ibadan, Oyo, Nigeria
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Erkison Ewomazino Odih,
| | - Emmanuel Oladayo Irek
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ife, Nigeria
| | - Temitope O. Obadare
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ife, Nigeria
| | - Anderson O. Oaikhena
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, University of Ibadan, Oyo, Nigeria
| | - Ayorinde O. Afolayan
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, University of Ibadan, Oyo, Nigeria
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Anthony T. Adenekan
- Department of Anaesthesia and Intensive Care, Obafemi Awolowo University, Ife, Nigeria
| | | | - Silvia Argimon
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Iruka N. Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, University of Ibadan, Oyo, Nigeria
| | - A. Oladipo Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University, Ife, Nigeria
- A. Oladipo Aboderin,
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18
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Hounmanou YMG, Sit B, Fakoya B, Waldor MK, Dalsgaard A. Genomic and Phenotypic Insights for Toxigenic Clinical Vibrio cholerae O141. Emerg Infect Dis 2022; 28:617-624. [PMID: 35202520 PMCID: PMC8888207 DOI: 10.3201/eid2803.210715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Vibrio cholerae remains a major public health threat worldwide, causing millions of cholera cases each year. Although much is known about the evolution and pathogenicity of the O1/O139 serogroups of V. cholerae, information is lacking on the molecular epidemiology of non‒O1/O139 strains isolated from patients who have diarrheal illnesses. We performed whole-genome sequence analysis and in vivo infections to investigate characteristics of V. cholerae O141 isolated from sporadic diarrheal cases in 4 countries. The strains formed a distinct phylogenetic clade distinguishable from other serogroups and a unique multilocus sequence type 42, but interstrain variation suggests that O141 isolates are not clonal. These isolates encode virulence factors including cholera toxin and the toxin-coregulated pilus, as well as a type 3 secretion system. They had widely variable capacities for intestinal colonization in the infant mouse model. We propose that O141 isolates comprise a distinct clade of V. cholerae non‒O1/O139, and their continued surveillance is warranted.
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19
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Peng S, Zheng H, Herrero-Fresno A, Olsen JE, Dalsgaard A, Ding Z. Co-occurrence of antimicrobial and metal resistance genes in pig feces and agricultural fields fertilized with slurry. Sci Total Environ 2021; 792:148259. [PMID: 34147788 DOI: 10.1016/j.scitotenv.2021.148259] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/14/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Antimicrobial resistance constitutes a global challenge to public health. The common addition of Zn, Cu and other metals to animal feed and the widespread presence of metal ions in livestock and their receiving environments may be a factor that facilitates the proliferation of antimicrobial resistance via co-selection of antimicrobial resistance genes (ARGs) and metal resistance genes (MRGs). However, the extent of co-selection is not yet fully understood. In this study, we used a metagenomic approach to profile ARGs, MRGs and mobile genetic elements (MGEs) known to constitute potential ARG and MRG vectors of transmission, and we determined the concentration of metal ions to assess the interrelationships between the occurrence of ARGs, MRGs and metal concentrations in samples from pig farms in China. Samples analyzed included fresh pig feces, soils fertilized with treated slurry, and sediments from aquatic environments, where effluent from treated slurry was discharged. Resistance genes to tetracycline and zinc were the most commonly observed ARGs and MRGs for all three types of samples. Significant correlations were observed between the abundance of ARGs and MRGs, and between ARGs/MRGs and MGEs, and between metal and ARGs/MGEs as documented by Pearson's correlation analysis (r > 0.9, P < 0.001). Further network analysis revealed significant co-occurrence between specific ARGs and MRGs, between ARGs/MRGs and MGEs, and between specific metals (Zn, Cr, and Mn) and ARGs and MGEs. Collectively, our findings demonstrate a high level of co-occurrence of antimicrobial and metal resistance genes in slurry from pig farms and their surrounding environments. The results suggest that metals added to pig feed might facilitate co-selection of ARGs and MGEs in the pig production environments, thereby resulting in a bigger pool of mobile ARGs.
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Affiliation(s)
- Shifu Peng
- Department of Environment and Health, Jiangsu Center for Disease Control and Prevention, Nanjing 210009, China; Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Hao Zheng
- Department of Environment and Health, Jiangsu Center for Disease Control and Prevention, Nanjing 210009, China
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore.
| | - Zhen Ding
- Department of Environment and Health, Jiangsu Center for Disease Control and Prevention, Nanjing 210009, China.
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20
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Truong DTQ, Hounmanou YMG, Dang STT, Olsen JE, Truong GTH, Tran NT, Scheutz F, Dalsgaard A. Genetic Comparison of ESBL-Producing Escherichia coli from Workers and Pigs at Vietnamese Pig Farms. Antibiotics (Basel) 2021; 10:1165. [PMID: 34680746 PMCID: PMC8532784 DOI: 10.3390/antibiotics10101165] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
We analyzed and compared genomes of Extended Spectrum Beta-Lactamase (ESBL)-producing Escherichia coli from pigs and pig farm workers at 116 farms in Vietnam. Analyses revealed the presence of blaCTX-M-55, blaCTX-M-27, blaCTX-M-15, blaCTX-M-14, blaCTX-M-3, blaCTX-M-65, blaCTX-M-24, blaDHA-1, and blaCMY2 in both hosts. Most strains from pigs contained quinolones (qnr) and colistin resistance genes (mcr-1 and mcr-3). Isolates predominantly harbored more than one plasmid replicon and some harbored plasmid replicons on the same contigs as the ESBL genes. Five strains from farm workers of ST38 (2), ST69 (1), and ST1722 (2) were classified as either uropathogenic E. coli (UPECHM)/extraintestinal pathogenic E. coli (ExPECJJ) or UPECHM, and the remaining were genetically distinct commensals. A high heterogeneity was found among the ESBL-producing E. coli from pigs and workers, with most isolates belonging to unrelated phylogroups, serogroups, and sequence types with >4046 Single-Nucleotide Polymorphisms-(SNPs). In comparing the genomes of pig isolates to those from humans, it appeared that ESBL-producing E. coli in workers did not predominantly originate from pigs but were rather host-specific. Nevertheless, the occurrence of ESBL-producing E. coli carrying plasmid-mediated colistin and quinolone resistance genes in pigs could represent a potential source for horizontal transmission to humans through food rather than direct contact.
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Affiliation(s)
- Duong Thi Quy Truong
- National Institute of Veterinary Research, Hanoi 10000, Vietnam; (D.T.Q.T.); (S.T.T.D.); (G.T.H.T.); (N.T.T.)
| | | | - Son Thi Thanh Dang
- National Institute of Veterinary Research, Hanoi 10000, Vietnam; (D.T.Q.T.); (S.T.T.D.); (G.T.H.T.); (N.T.T.)
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark;
| | - Giang Thi Huong Truong
- National Institute of Veterinary Research, Hanoi 10000, Vietnam; (D.T.Q.T.); (S.T.T.D.); (G.T.H.T.); (N.T.T.)
| | - Nhat Thi Tran
- National Institute of Veterinary Research, Hanoi 10000, Vietnam; (D.T.Q.T.); (S.T.T.D.); (G.T.H.T.); (N.T.T.)
| | - Flemming Scheutz
- Department of Bacteria, Parasites and Fungi, Statens Serum Institute, 2300 Copenhagen S, Denmark;
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark;
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21
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Jibril AH, Okeke IN, Dalsgaard A, Olsen JE. Association between antimicrobial usage and resistance in Salmonella from poultry farms in Nigeria. BMC Vet Res 2021; 17:234. [PMID: 34215271 PMCID: PMC8254292 DOI: 10.1186/s12917-021-02938-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 06/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a global health threat affecting treatment outcome in animals and humans. A pre-requisite for development of AMR reduction strategies is knowledge of antimicrobial use patterns, and how these affect resistance development. The aim of this study was to determine antimicrobial usage (AMU) and whether such usage was associated with AMR in Salmonella from poultry farms in Northwest Nigeria. RESULTS Fifteen (37%) of antimicrobial products observed contained compounds that are of highest priority and critically important for human medicine. Broilers chicken consumed higher (28 ± 14 mg/kg active ingredients) amounts of antimicrobials compared to layers (13 ± 8 mg/kg) per week (p = 0.0009). Surprisingly, chickens raised under backyard system consumed higher amounts of antimicrobials (34 ± 7 mg/kg) than poultry in other systems (p = 0.02). High levels of resistance to tetracycline (58%), sulphonamides (65%), ciprofloxacin (46%) and gentamicin (42%) correlated with high farm level usage of these antimicrobials, and there was a strong correlation (r = 0.9) between farm usage and resistance of isolates to the same antimicrobials (p = 0.03). CONCLUSION High AMU, including use of highest priority critically important antimicrobials was observed at poultry farms in Northwest Nigeria. AMU correlated with high levels of resistance. Communication of prudent use of antimicrobials to farmers and regulation to obtain reduction in AMU should be a priority.
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Affiliation(s)
- Abdurrahman Hassan Jibril
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, Sokoto, Nigeria
| | - Iruka N. Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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22
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Hounmanou YMG, Bortolaia V, Dang STT, Truong D, Olsen JE, Dalsgaard A. ESBL and AmpC β-Lactamase Encoding Genes in E. coli From Pig and Pig Farm Workers in Vietnam and Their Association With Mobile Genetic Elements. Front Microbiol 2021; 12:629139. [PMID: 33776959 PMCID: PMC7991805 DOI: 10.3389/fmicb.2021.629139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/19/2021] [Indexed: 01/27/2023] Open
Abstract
Animals are considered important sources of ESBL/AmpC-producing bacteria in humans. We analyzed indications of transfer of ESBL/AmpC genes between pigs and pig farmers in Vietnam by analyzing whole genome sequences of 114 ESBL/AmpC-producing E. coli isolated from the two hosts, and performed conjugation experiments and plasmid profiling to confirm that such transfer could have happened. ESBL-encoding genes detected in pigs and pig farmers included bla CTX-M-55, bla CTX-M-27, bla CTX-M-65, bla CTX-M-15, bla CTX-M-14, bla CTX-M-3, bla CTX-M-24, and bla CARB-2, and AmpC β-lactamases included bla CMY-2, bla DHA-1, and bla CMY-42. The most frequent ESBL gene, bla CTX-M-55, was carried on plasmid with replicons types IncF, IncX, IncH, IncN, IncR, and IncP. The insertion transposases downstream of the bla CTX-M-55 gene were different in plasmids carried by different strains. The second most detected gene, bla CTX-M-27, is found in a stable genetic arrangement with the same flanking transposons seen across strains, and the gene was located on similar conjugal IncF plasmid types, suggesting a horizontal spread of these plasmids. In three strains, we observed a novel bla CTX-M-27 harboring IncF type of plasmid which had not been reported before. Its closest reference in NCBI was the non-ESBL Salmonella Typhimurium plasmid pB71 that might have experienced an insertion of bla CTX-M-27. Our data also point to an emergence of plasmids co-carrying ESBL genes, mcr genes, quinolones and other antimicrobials resistance determinants, and such plasmids require special attention. Plasmids phylogeny confirmed that the bla CTX-M-55 encoding plasmids varied considerably, while those encoding bla CTX-M-27 were closely related. Plasmids harboring both ESBL genes were confirmed to be conjugative and not to differ in transfer efficacy. The isolates carrying the plasmids, even those with plasmids of similar types, showed wide genetic variation with high number of SNPs, suggesting horizontal spread of plasmids into different clonal lines. Their virulence profiles did not confirm to known pathotypes, suggesting that unrelated commensals are a main reservoir for ESBL and AmpC β-lactamases in both humans and pigs. Overall, despite evidence of transferability of plasmids in the analyzed strains, our findings do not support that ESBL-producing E. coli from pigs or their ESBL/AmpC encoding plasmids are commonly spread to workers in close contact with the animals.
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Affiliation(s)
| | - Valeria Bortolaia
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Son Thi Thanh Dang
- Veterinary Hygiene Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Duong Truong
- Veterinary Hygiene Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - John E Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.,School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
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23
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Jibril AH, Okeke IN, Dalsgaard A, Menéndez VG, Olsen JE. Genomic Analysis of Antimicrobial Resistance and Resistance Plasmids in Salmonella Serovars from Poultry in Nigeria. Antibiotics (Basel) 2021; 10:99. [PMID: 33498344 PMCID: PMC7909428 DOI: 10.3390/antibiotics10020099] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/06/2021] [Accepted: 01/19/2021] [Indexed: 12/31/2022] Open
Abstract
Antimicrobial resistance is a global public health concern, and resistance genes in Salmonella, especially those located on mobile genetic elements, are part of the problem. This study used phenotypic and genomic methods to identify antimicrobial resistance and resistance genes, as well as the plasmids that bear them, in Salmonella isolates obtained from poultry in Nigeria. Seventy-four isolates were tested for susceptibility to eleven commonly used antimicrobials. Plasmid reconstruction and identification of resistance and virulence genes were performed with a draft genome using in silico approaches in parallel with plasmid extraction. Phenotypic resistance to ciprofloxacin (50.0%), gentamicin (48.6%), nalidixic acid (79.7%), sulphonamides (71.6%) and tetracycline (59.5%) was the most observed. Antibiotic resistance genes (ARGs) detected in genomes corresponded well with these observations. Commonly observed ARGs included sul1, sul2, sul3, tet (A), tet (M), qnrS1, qnrB19 and a variety of aminoglycoside-modifying genes, in addition to point mutations in the gyrA and parC genes. Multiple ARGs were predicted to be located on IncN and IncQ1 plasmids of S. Schwarzengrund and S. Muenster, and most qnrB19 genes were carried by Col (pHAD28) plasmids. Seventy-two percent (19/24) of S. Kentucky strains carried multidrug ARGs located in two distinct variants of Salmonella genomic island I. The majority of strains carried full SPI-1 and SPI-2 islands, suggesting full virulence potential.
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Affiliation(s)
- Abdurrahman Hassan Jibril
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, Sokoto 234840, Nigeria
| | - Iruka N. Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan 234200, Nigeria;
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
| | - Vanesa García Menéndez
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
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24
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Alfifi A, Dalsgaard A, Christensen JP, Larsen MH, Sandberg M. The association between meat inspection codes, footpad lesions and thinning of broiler flocks in the Danish broiler production. Prev Vet Med 2020; 185:105205. [PMID: 33202294 DOI: 10.1016/j.prevetmed.2020.105205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 11/16/2022]
Abstract
The foundation of the condemnation practices in Post-Mortem Inspection (PMI) of poultry should be based on up-to-date scientific evidence about the cause of infection and hence whether the lesions observed are of food safety, animal health or welfare concerns. This study aimed to investigate the association between meat inspection codes, footpad lesions, and thinning of flocks in Danish broiler production. The data set was based on the delivery of chicken flocks to one of the two larger chicken slaughterhouses in Denmark, representing 71 farms, 174 houses, and 4,068 flocks over three years from January 2016 to December 2018. Post-mortem condemnation data of slaughtered chickens recorded and stored in the Danish Quality Assurance System (KIK) database was used in the study. Five potentially causal models were developed to investigate whether there was an association between dermatitis, arthritis, systemic infection, emaciation, mortality and possible explaining factors` (footpad lesion, age at slaughter, scratches, ascites, systemic infection and thinning of the flock). These five ecological logistic regression models were analyzed with the three levels: farm, house, and flock. Data from a total number of 126,137,002 (N) slaughtered chickens recorded in KIK databases were used for modeling and analyses. The prevalence of condemned carcasses was 1.1 % (n = 1,420,812). Overall, 12 individual reasons for condemnation of carcasses were recorded. The most frequently observed reason for condemnation was skin disease (scratches and dermatitis) with a prevalence of 0.5 %. Prevalence of ascites was 0.2 %, discoloration 0.09 %, emaciation 0.09 %, hepatitis 0.09 % and arthritis 0.07 %. In the first model, dermatitis was shown to be positively associated with age at slaughter with an OR = 1.04 (CI95 %: 1.02-1.05), while arthritis was considered an intervening variable. Moreover, there was a small protective effect of thinning of the flock for first and second delivery. There was a positive association between arthritis and age at the time of slaughter with an OR = 1.13 (CI95 %: 1.12-1.15). Systemic infections were associated with scratches with an OR = 24.5 (CI95 %: 16.6-36.3) and footpad lesions with an OR = 1.007 (CI95 %: 1.006-1.008). Further modelling of emaciation and mortality was not considered because of unbalanced groups in the data probably caused by the fact that some condemnation codes were rare. We observed that the most common causal factors of condemnation in the systemic infection models were scratches and footpad lesion, therefore preventing and controlling such lesions could reduce losses. Specific management and environmental etiological factors of the main infections causing condemnation in Danish broilers should be determined.
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Affiliation(s)
- Ahmed Alfifi
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, 1870, Frederiksberg C, Denmark; Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, P.O Box: 400, Al-Ahasa, 31982, Saudi Arabia.
| | - Anders Dalsgaard
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, 1870, Frederiksberg C, Denmark; School of Biomedical Engineering, Nanyang Technological University, Singapore.
| | - Jens P Christensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, 1870, Frederiksberg C, Denmark.
| | - Marianne Halberg Larsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, 1870, Frederiksberg C, Denmark.
| | - Marianne Sandberg
- Food Safety, Veterinary Issues and Risk Analysis, Danish Agriculture and Food Council, 1609 DK, Copenhagen V, Denmark; National Food Institute, Danish Technical University, Lyngby, Denmark.
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25
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Petersen HH, Dalsgaard A, Vinneras B, Jensen LS, Le TTA, Petersen MA, Enemark HL, Forslund A. Inactivation of Cryptosporidium parvum oocysts and faecal indicator bacteria in cattle slurry by addition of ammonia. J Appl Microbiol 2020; 130:1745-1757. [PMID: 33012074 DOI: 10.1111/jam.14881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 08/27/2020] [Accepted: 09/29/2020] [Indexed: 11/30/2022]
Abstract
AIMS To determine inactivation of Cryptosporidium parvum oocysts and reduction of Escherichia coli and enterococci in cattle slurry added aqueous ammonia. METHODS AND RESULTS Escherichia coli, enterococci and nonviable C. parvum oocysts (DAPI+PI+) were enumerated every second day for 2 weeks in cattle slurry amended with 60 mmol l-1 aq. ammonia and compared with untreated slurry at three temperatures. Regardless of temperature, the proportion of nonviable C. parvum oocysts increased significantly faster over time in slurry with added ammonia than raw slurry (P = 0·021) corresponding to 62·0% higher inactivation (P = 0·001) at day 14. Additionally, 91·8% fewer E. coli and 27·3% fewer enterococci were observed in slurry added ammonia at day 14 compared to raw slurry. CONCLUSION The addition of aqueous ammonia to raw slurry significantly reduced the viability of C. parvum oocysts and numbers of bacterial indicators. Hence, ammonia is usable at lower pathogen concentrations in slurry before application to agricultural land. SIGNIFICANCE AND IMPACT OF THE STUDY Livestock waste is a valuable source of plant nutrients and organic matter, but may contain high concentrations of pathogens like E. coli and Cryptosporidium sp. that can be spread in the environment, and cause disease outbreaks. However, die-off rates of pathogens in organic waste can increase following increasing ammonia concentrations.
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Affiliation(s)
- H H Petersen
- National Veterinary Institute, Technical University of Denmark, Kgs.Lyngby, Denmark.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - A Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - B Vinneras
- Department of Energy and Technology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - L S Jensen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - T T A Le
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M A Petersen
- Department for Palliative Medicine, The Research Unit, Bispebjerg Hospital, Copenhagen NV, Denmark
| | - H L Enemark
- National Veterinary Institute, Technical University of Denmark, Kgs.Lyngby, Denmark.,Department of Animal Health and Food Safety, Norwegian Veterinary Institute, PO Box 750 Sentrum, Oslo, NO-0106, Norway
| | - A Forslund
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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26
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Kretchy JP, Dzodzomenyo M, Ayi I, Dwomoh D, Agyabeng K, Konradsen F, Dalsgaard A. Risk of faecal pollution among waste handlers in a resource-deprived coastal peri-urban settlement in Southern Ghana. PLoS One 2020; 15:e0239587. [PMID: 33006973 PMCID: PMC7531843 DOI: 10.1371/journal.pone.0239587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 09/10/2020] [Indexed: 11/19/2022] Open
Abstract
Resource-deprived coastal peri-urban settlements in Southern Ghana are characterized by indiscriminate solid waste disposal and open defecation practices. Persons engaged in waste handling in such communities perform their activities with little or no personal protective equipment. They are thus confronted with the risk of faecal pollution of the hands and other bodily parts. A mixed method approach was used to investigate 280 waste handlers performing different activities to estimate recent faecal pollution of their hands and to observe the utilization of personal protective equipment and sanitation/hygiene facilities during work. The log concentration of E. coli on hands of waste handlers after work (8.60 ± 4.20 CFU/hand, mean ± standard deviation) was significantly higher compared with the E. coli log concentration before work (2.95 ± 1.89 CFU/hand, mean ± standard deviation) (p<0.001). The odds of faecal pollution was significantly higher (aOR 4.2; 95% CI: 1.9-9.1) for workers aged 35 years and above compared with those less than 35 years; and for workers at public toilet facilities (aOR 3.0; 95% CI: 1.0-8.4) compared with those who worked for private waste handling companies. Female workers were, however, 60% less likely (aOR 0.4; 95% CI: 0.2-0.8) to experience faecal pollution of their hands compared with males. The workers had limited access to water and sanitation and hygiene facilities, and about one-fifth (n = 59; 21.1%) did not use personal protective equipment during work. Waste handlers should be provided and instructed in proper use of personal protective equipment, have access to sanitation facilities and adopt improved hygiene behaviour to avoid the risk of faecal pollution and associated disease risk.
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Affiliation(s)
- James-Paul Kretchy
- Department of Physician Assistantship Studies, School of Medicine and Health Sciences, Central University, Miotso, Accra, Ghana
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
- * E-mail: ,
| | - Mawuli Dzodzomenyo
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Irene Ayi
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Duah Dwomoh
- Department of Biostatistics, School of Public Health, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Kofi Agyabeng
- Department of Biostatistics, School of Public Health, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Flemming Konradsen
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
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27
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Dang STT, Truong DTQ, Olsen JE, Tran NT, Truong GTH, Vu HTK, Dalsgaard A. Research note: Occurrence of mcr-encoded colistin resistance in Escherichia coli from pigs and pig farm workers in Vietnam. FEMS Microbes 2020; 1:xtaa003. [PMID: 37333956 PMCID: PMC10117427 DOI: 10.1093/femsmc/xtaa003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/16/2020] [Indexed: 10/13/2023] Open
Abstract
WHO considers colistin as a highest priority critically important drug for human health, and occurrence of colistin-resistant bacteria in livestock is of health concern. The current study determined occurrence of colistin-resistant Escherichia coli in pigs and workers at pig farms in Vietnam, and investigated the genetic background for resistance. Colistin-resistant E. coli were detected from pigs in 53/116 (45.7%) farms, and from workers taking care of the pigs in 21/94 (22.3%) farms. Colistin-resistant isolates showed MIC to colistin between 4-16 mg/L, they were multidrug resistant (99%) and resistance was caused by the presence of mcr-1 genes in 97/102 (95.1%) E. coli from pigs and in 31/34 (91.1%) isolates from humans. mcr-1 is considered a plasmid-encoded gene, but this was not confirmed in the current investigation. In total, one pig isolate carried both mcr-1 and mcr-3 genes, whereas mcr-2, mcr-4 and mcr-5 genes were not detected. Shared resistance profiles between pig and human isolates on the same farm was only observed in four farms. The study showed that commensal E. coli from pigs in Vietnam constitute a reservoir for colistin-resitant E. coli, however, further studies are needed to confirm that mcr genes are associated with plasmids and their importance for human health.
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Affiliation(s)
- Son Thi Thanh Dang
- National Institute of Veterinary Research, 74 Truong Chinh, Phuong Dinh, Dong Da, Hanoi, Vietnam
| | - Duong Thi Quy Truong
- National Institute of Veterinary Research, 74 Truong Chinh, Phuong Dinh, Dong Da, Hanoi, Vietnam
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, Frederiksberg C 1870, Denmark
| | - Nhat Thi Tran
- National Institute of Veterinary Research, 74 Truong Chinh, Phuong Dinh, Dong Da, Hanoi, Vietnam
| | - Giang Thi Huong Truong
- National Institute of Veterinary Research, 74 Truong Chinh, Phuong Dinh, Dong Da, Hanoi, Vietnam
| | - Hue Thi Kim Vu
- National Institute of Veterinary Research, 74 Truong Chinh, Phuong Dinh, Dong Da, Hanoi, Vietnam
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, Frederiksberg C 1870, Denmark
- School of Chemical and Biomedical Engineering Nanyang Technological University, 62 Nanyang Drive Singapore 637459
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28
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Hounmanou YMG, Dalsgaard A, Sopacua TF, Uddin GMN, Leekitcharoenphon P, Hendriksen RS, Olsen JE, Larsen MH. Molecular Characteristics and Zoonotic Potential of Salmonella Weltevreden From Cultured Shrimp and Tilapia in Vietnam and China. Front Microbiol 2020; 11:1985. [PMID: 32983012 PMCID: PMC7477899 DOI: 10.3389/fmicb.2020.01985] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
Salmonella Weltevreden is increasingly reported from aquatic environments, seafood, and patients in several Southeast Asian countries. Using genome-wide analysis, we characterized S. Weltevreden isolated from cultured shrimp and tilapia from Vietnam and China to study their genetic characteristics and relatedness to clinical isolates of S. Weltevreden ST-365. The phylogenetic analysis revealed up to 312 single-nucleotide polymorphism (SNP) difference between tilapia isolates, whereas isolates from shrimp were genetically more closely related. Epidemiologically unrelated isolates from Vietnam were closely related to isolates from China, e.g., 20 SNPs differences between strains 28V and 75C. In comparison with strains from other parts of the world, our environmental isolates predominantly clustered within the continental South Asia lineage, constituted mostly of strains from human stool with as low as seven SNPs difference, e.g., 30V versus Cont_ERR495254. All sequenced isolates were MLST type ST-365 and contained the major virulence-related genes encoded by the Salmonella Pathogenicity Islands 1–5. Ten of the isolates harbored the IncFII(S) plasmid similar to the virulence genes-mediated plasmid pSPCV of S. Paratyphi C, and one isolate had the IncQ1 plasmid on the same contig with strA/B, sul2, and tetA resistance genes similar to the IncQ1 type, pNUC of S. Typhimurium. A pangenomic analysis yielded 7891 genes including a core genome of 4892 genes, with a closely related accessory genome content between clinical and environmental isolates (Benjamini p > 0.05). In a search for differences that could explain the higher prevalence of S. Weltevreden in aquatic samples, genomes were compared with those of other Salmonella enterica serovars. S. Weltevreden revealed specific regions harboring glpX (Fructose-1;6-bisphosphatase; class II), rfbC (dTDP-4-dehydrorhamnose 3;5-epimerase), and cmtB (PTS Mannitol-specific cryptic phosphotransferase enzyme IIA component) involved in carbohydrate biosynthesis pathways. Our study builds grounds for future experiments to determine genes or pathways that are essential when S. Weltevreden are in aquatic environments and microbial interactions providing survival advantages to S. Weltevreden in such environments.
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Affiliation(s)
- Yaovi M G Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,School of Chemical and Biological Engineering, Nanyang Technological University, Singapore, Singapore
| | - Tirzania Frannetta Sopacua
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gazi Md Noor Uddin
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rene S Hendriksen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Halberg Larsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Ellis-Iversen J, Seyfarth AM, Korsgaard H, Bortolaia V, Munck N, Dalsgaard A. Antimicrobial resistant E. coli and enterococci in pangasius fillets and prawns in Danish retail imported from Asia. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106958] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Li H, Tang T, Stegger M, Dalsgaard A, Liu T, Leisner JJ. Characterization of antimicrobial-resistant Staphylococcus aureus from retail foods in Beijing, China. Food Microbiol 2020; 93:103603. [PMID: 32912578 DOI: 10.1016/j.fm.2020.103603] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/01/2020] [Accepted: 07/21/2020] [Indexed: 02/05/2023]
Abstract
Staphylococcus aureus is an opportunistic pathogen leading to food poisoning as well as human infections. The present study examined the prevalence and characterization of antimicrobial-resistant S. aureus in sushi from 42 outlets and in pork products from eight outlets in Beijing, China. The total bacterial counts were between 3.0 and 8.9 log CFU/g (mean 5.5 ± 1.5 log CFU/g) in sushi products and 4.8 to 7.4 log CFU/g (mean 5.6 ± 0.8 log CFU/g) in pork products. The mean counts of coliforms were 2.7 and 2.9 log CFU/g in sushi and pork, respectively. Staphylococcus aureus was isolated from seven sushi outlets (13 isolates) and two pork outlets (2 isolates) with average counts below 2 log CFU/g in all cases. A total of 15 S. aureus isolates were further characterized. Six lineages of S. aureus were present, including ST398 (n = 5), ST25 (n = 4), ST15 (n = 2), ST59 (n = 2), ST8 (n = 1) and ST2631 (n = 1). Thirteen isolates contained the scn virulence marker, whereas four and eight isolates contained the virulence marker edinB and enterotoxin genes, respectively. Characterization of antimicrobial resistance profiles documented resistances to ampicillin (n = 15), penicillin (n = 14), ceftazidime (n = 6), erythromycin (n = 4), tetracycline (n = 3), clindamycin (n = 3), and gentamicin (n = 1). Three MRSA isolates were obtained, one from pork (ST398) and two from one sushi outlet (ST59). They were all resistant to at least three classes of antimicrobials and two of them contained the scn gene and enterotoxin genes. Twelve sushi isolates and one of the pork isolates contained the scn gene, indicating that they were of human origin. This emphasizes the potential importance of transmission through foods of antimicrobial-resistant S. aureus including MRSA. We also showed that S. aureus exhibited geographical variation with regards to ST profiles, antimicrobial-resistance and virulence genes when comparing isolates from sushi products sold in Beijing and Copenhagen, Denmark. Whereas food safety is not compromised by the presence of low amounts of S. aureus in sushi, this study shows that with regards to public health such foods may serve as vehicles for transmission of multidrug-resistant S. aureus and MRSA lineages.
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Affiliation(s)
- Heng Li
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870, Frederiksberg C, Denmark
| | - Taya Tang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, No. 2 West Road Yuanmingyuan, Beijing, PR China
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870, Frederiksberg C, Denmark; School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
| | - Tianlong Liu
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, No. 2 West Road Yuanmingyuan, Beijing, PR China
| | - Jørgen J Leisner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870, Frederiksberg C, Denmark.
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31
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Jensen C, Li H, Vestergaard M, Dalsgaard A, Frees D, Leisner JJ. Nisin Damages the Septal Membrane and Triggers DNA Condensation in Methicillin-Resistant Staphylococcus aureus. Front Microbiol 2020; 11:1007. [PMID: 32582052 PMCID: PMC7283504 DOI: 10.3389/fmicb.2020.01007] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 01/03/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
Nisin is applied as a food preservative in processed foods and has the potential to be used synergistically with antibiotics for treatment of patients infected by antibiotic-resistant bacteria, such as methicillin-resistant Staphylococcus aureus. The present study explores the antimicrobial effect of nisin on S. aureus viability and membrane integrity and, for the first time, used super-resolution microscopy to study morphological changes induced in S. aureus cells exposed to nisin. The exposure of S. aureus to nisin caused membrane depolarization and rapid killing. Super-resolution structured-illumination microscopy and transmission electron microscopy confirmed that nisin damages the cellular membrane and causes lysis of cells. Strikingly, condensation of chromosomal DNA was observed in all cells exposed to nisin, a phenotype not previously reported for this compound. Moreover, cells exposed to nisin were significantly smaller than non-exposed cells indicating the emergence of cell shrinkage. The strong association of DNA condensation with nisin exposure indicates that nisin interferes with chromosome replication or segregation in S. aureus.
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Affiliation(s)
- Camilla Jensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Heng Li
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Martin Vestergaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.,School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Dorte Frees
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jørgen J Leisner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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32
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Minh DK, Hounmanou YMG, Mai HBT, Olsen JE, Dalsgaard A. Prevalence and genomic characterization of Salmonella Weltevreden in commercial pig feed. Vet Microbiol 2020; 246:108725. [PMID: 32605745 DOI: 10.1016/j.vetmic.2020.108725] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
Viet Nam is the world's fifth largest producer of pork meat. Salmonella is frequently found at farm level; however, risk factors for Salmonella infection in pigs have not been thoroughly investigated in the production system. In the current study, 123 commercial feed samples were obtained from 103 small, medium and large-scale pig farms in Viet Nam and investigated for the presence of Salmonella in 25 g of feed using the ISO 6579:2002/Cor 1:2004 method. Salmonella was detected in five samples (4.1%; 95% CI 1.75-9.16%). All five samples were found to contain S. Weltevreden as the only serovar. The isolates were subjected to phenotypic and whole genome sequencing analysis for further characterization. They all belonged to ST365 and were sensitive to the 14 antimicrobials tested. Four strains were found to belong to the continental lineage of S. Weltevreden, while one isolate was of the island type. This isolate, contrary to the remaining four isolates contained a prophage homolog to the Vibrio prophage X-29. The findings of only S. Weltevreden, which is often isolated from fish and aquatic samples, suggests that fishmeal used in the feed preparation was a likely source of contamination.
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Affiliation(s)
- Duc Kieu Minh
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Food Microbiology and Molecular Biology, National Institute of Nutrition, Viet Nam
| | - Yaovi M Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Huong Bui Thi Mai
- Department of Food Microbiology and Molecular Biology, National Institute of Nutrition, Viet Nam
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore.
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33
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Baniga Z, Hounmanou YMG, Kudirkiene E, Kusiluka LJM, Mdegela RH, Dalsgaard A. Genome-Based Analysis of Extended-Spectrum β-Lactamase-Producing Escherichia coli in the Aquatic Environment and Nile Perch ( Lates niloticus) of Lake Victoria, Tanzania. Front Microbiol 2020; 11:108. [PMID: 32153519 PMCID: PMC7046833 DOI: 10.3389/fmicb.2020.00108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing bacteria constitute an emerging global health issue with food products being vehicles of transmission and the aquatic environments serving as potential reservoirs. This study aimed to characterize ESBL-producing Escherichia coli in Nile perch and water from Lake Victoria in Tanzania. A total of 180 samples of Nile perch and 60 water samples were screened for ESBL-producing E. coli on MacConkey agar supplemented with 2 μg/ml of cefotaxime and confirmed by blaCTX–M and blaTEM PCR. Antimicrobial resistance was determined by the disk diffusion method, and the ESBL-producing isolates were whole genome sequencing (WGS). ESBL-producing E. coli were detected in eight of the 180 analyzed Nile perch samples, and only one water sample was positive (1.7%, n = 60). Isolates were resistant to sulfamethoxazole–trimethoprim (100%), ampicillin/cloxacillin (100%), erythromycin 72.7% (8/11), tetracycline 90.9% (10/11), and nalidixic acid 63.6% (7/11). This mostly corroborates the resistance genes that they carried for sulfonamides (sul1 and sul2), trimethoprim (dfrA and dfrB), aminoglycosides [aac(3)-IId, strA, and strB], tetracycline [tet(B) and tet(D)], and fluoroquinolones (qepA4). They harbored plasmid replicon types IncF, IncX, IncQ, and Col and carried blaCTX–M–15 and blaTEM–1B genes generally found on the same contigs as the IncF plasmid replicon. Although epidemiologically unrelated, the strains formed three separate sequence type–phylogroup–serotype-specific clusters: C1, C2, and C3. Cluster C1 included five strains (3 to 13 SNPs) belonging to ST167, phylogroup A, and serotype O9:H21; the two C2 strains (11 SNPs) belong to ST156, phylogroup B1, and serotype ONT:H28; and C3 was made up of four strains (SNPs ranged from 4 to 17) of ST636, phylogroup B2, and serotype O45:H7. The common virulence gene gad was reported in all strains. In addition, strains in C2 and C3 possessed iss, lpfA, and nfaE virulence genes, and the vat gene was found only in C3. The present study reports the occurrence of multidrug-resistant ESBL-producing E. coli carrying plasmid-mediated ESBL genes in offshore water and Nile perch in Lake Victoria. Strains formed three clonal clusters of unknown origin. This study reveals that the Lake may serve as reservoir for ESBL-producing bacteria that can be transmitted by fish as a food chain hazard of One-Health concern.
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Affiliation(s)
- Zebedayo Baniga
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Fisheries Development, National Fish Quality Control Laboratory-Nyegezi, Mwanza, Tanzania
| | - Yaovi M Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Egle Kudirkiene
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lughano J M Kusiluka
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania.,Mzumbe University, Mzumbe, Tanzania
| | - Robinson H Mdegela
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
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34
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Hounmanou YMG, Leekitcharoenphon P, Hendriksen RS, Dougnon TV, Mdegela RH, Olsen JE, Dalsgaard A. Corrigendum: Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania. Front Microbiol 2020; 10:2974. [PMID: 31921095 PMCID: PMC6934033 DOI: 10.3389/fmicb.2019.02974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/10/2019] [Indexed: 11/28/2022] Open
Affiliation(s)
- Yaovi M Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pimlapas Leekitcharoenphon
- National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rene S Hendriksen
- National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tamegnon V Dougnon
- Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Laboratory of Research in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Cotonou, Benin
| | - Robinson H Mdegela
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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35
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Hounmanou YMG, Leekitcharoenphon P, Kudirkiene E, Mdegela RH, Hendriksen RS, Olsen JE, Dalsgaard A. Genomic insights into Vibrio cholerae O1 responsible for cholera epidemics in Tanzania between 1993 and 2017. PLoS Negl Trop Dis 2019; 13:e0007934. [PMID: 31869327 PMCID: PMC6927581 DOI: 10.1371/journal.pntd.0007934] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 11/18/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Tanzania is one of seven countries with the highest disease burden caused by cholera in Africa. We studied the evolution of Vibrio cholerae O1 isolated in Tanzania during the past three decades. METHODOLOGY/PRINCIPAL FINDINGS Genome-wide analysis was performed to characterize V. cholerae O1 responsible for the Tanzanian 2015-2017 outbreak along with strains causing outbreaks in the country for the past three decades. The genomes were further analyzed in a global context of 590 strains of the seventh cholera pandemic (7PET), as well as environmental isolates from Lake Victoria. All Tanzanian cholera outbreaks were caused by the 7PET lineage. The T5 sub-lineage (ctxB3) dominated outbreaks until 1997, followed by the T10 atypical El Tor (ctxB1) up to 2015, which were replaced by the T13 atypical El Tor of the current third wave (ctxB7) causing most cholera outbreaks until 2017 with T13 being phylogenetically related to strains from East African countries, Yemen and Lake Victoria. The strains were less drug resistant with approximate 10-kb deletions found in the SXT element, which encodes resistance to sulfamethoxazole and trimethoprim. Nucleotide deletions were observed in the CTX prophage of some strains, which warrants further virulence studies. Outbreak strains share 90% of core genes with V. cholerae O1 from Lake Victoria with as low as three SNPs difference and a significantly similar accessory genome, composed of genomic islands namely the CTX prophage, Vibrio Pathogenicity Islands; toxin co-regulated pilus biosynthesis proteins and the SXT-ICE element. CONCLUSION/SIGNIFICANCE Characterization of V. cholerae O1 from Tanzania reveals genetic diversity of the 7PET lineage composed of T5, T10 and T13 sub-lineages with introductions of new sequence types from neighboring countries. The presence of these sub-lineages in environmental isolates suggests that the African Great Lakes may serve as aquatic reservoirs for survival of V. cholerae O1 favoring continuous human exposure.
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Affiliation(s)
| | | | - Egle Kudirkiene
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Robinson H. Mdegela
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Rene S. Hendriksen
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore city, Singapore
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36
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Li H, Andersen PS, Stegger M, Sieber RN, Ingmer H, Staubrand N, Dalsgaard A, Leisner JJ. Antimicrobial Resistance and Virulence Gene Profiles of Methicillin-Resistant and -Susceptible Staphylococcus aureus From Food Products in Denmark. Front Microbiol 2019; 10:2681. [PMID: 31920996 PMCID: PMC6920630 DOI: 10.3389/fmicb.2019.02681] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 08/23/2019] [Accepted: 11/05/2019] [Indexed: 12/25/2022] Open
Abstract
Foods may potentially serve as vehicles for the transmission of antimicrobial-resistant variants of Staphylococcus aureus that are important in a human clinical context. Further, retail food products can be a cause of staphylococcal food poisoning. For these reasons and to account for source attribution and risk assessment, detailed information on the population structure, resistance, and virulence profiles of S. aureus originating from retail food products is necessary. In the current study, whole-genome sequences from 88 S. aureus isolates were subjected to bioinformatics analyses in relation to sequence types, antimicrobial resistance, and virulence profiles. The sequence types (ST) identified belonged to 13 clonal complexes (CC) with CC5 and CC398 being the most common. CC398 was identified as the dominant clone (n = 31). CC5 was identified as of avian origin, with the presence of φAVβ prophage genes (n = 13). In total, 39.8% of the isolates contained multiple resistance genes, and methicillin-resistant Staphylococcus aureus (MRSA) isolates were found in CC8, CC9, and CC398. Genes conferring resistance to the antimicrobial classes of β-lactams, tetracycline, and erythromycin were detected in this study, all of which are commonly used in Danish livestock production. The tst gene encoding the toxic shock syndrome toxin was for the first time identified in ST398 isolates, probably as a result of a single acquisition of a SaPI-like element. The sushi-CC398 isolates carrying the scn gene likely originated from a human reservoir, while the other isolates originated from livestock. Taken together, our results show that both human and animal reservoirs contribute to contamination in food products and that retail foods may serve as a vehicle of S. aureus between livestock and humans.
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Affiliation(s)
- Heng Li
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Paal Skytt Andersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicholas Staubrand
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jørgen J Leisner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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37
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Hounmanou YMG, Mølbak K, Kähler J, Mdegela RH, Olsen JE, Dalsgaard A. Cholera hotspots and surveillance constraints contributing to recurrent epidemics in Tanzania. BMC Res Notes 2019; 12:664. [PMID: 31639037 PMCID: PMC6805412 DOI: 10.1186/s13104-019-4731-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/14/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE We described the dynamics of cholera in Tanzania between 2007 and 2017 and assessed the weaknesses of the current surveillance system in providing necessary data in achieving the global roadmap to 2030 for cholera control. RESULTS The Poisson-based spatial scan identified cholera hotspots in mainland Tanzania. A zero-inflated Poisson regression investigated the relationship between the incidence of cholera and available demographic, socio-economic and climatic exposure variables. Four cholera hotspots were detected covering 17 regions, home to 28 million people, including the central regions and those surrounding the Lakes Victoria, Tanganyika and Nyaza. The risk of experiencing cholera in these regions was up to 2.9 times higher than elsewhere in the country. Regression analyses revealed that every 100 km of water perimeter in a region increased the cholera incidence by 1.5%. Due to the compilation of surveillance data at regional level rather than at district, we were unable to reliably identify any other significant risk factors and specific hotspots. Cholera high-risk populations in Tanzania include those living near lakes and central regions. Successful surveillance require disaggregated data available weekly and at district levels in order to serve as data for action to support the roadmap for cholera control.
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Affiliation(s)
- Yaovi M G Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg C, Copenhagen, Denmark.
| | - Kåre Mølbak
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg C, Copenhagen, Denmark.,Division of Infectious Disease Preparedness, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Jonas Kähler
- Division of Infectious Disease Preparedness, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Robinson H Mdegela
- Department of Veterinary Medicine and Public Health, College of Veterinary and Biomedical Sciences, Sokoine University of Agriculture, PO Box: 3021, Morogoro, Tanzania
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg C, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg C, Copenhagen, Denmark.,School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
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38
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Li H, Stegger M, Dalsgaard A, Leisner JJ. Bacterial content and characterization of antibiotic resistant Staphylococcus aureus in Danish sushi products and association with food inspector rankings. Int J Food Microbiol 2019; 305:108244. [PMID: 31202150 DOI: 10.1016/j.ijfoodmicro.2019.108244] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 10/26/2022]
Abstract
This study examined the prevalence and phenotypic and genotypic antibiotic resistance patterns of Staphylococcus aureus in sushi from 20 Danish outlets. Microbial quality of sushi products and food inspector ranking of outlets were assessed and results for thirteen of the outlets were compared with findings from a previous study in 2012. Inspector rankings were similar in the two studies. The mesophilic aerobic counts were slightly lower (p = 0.0296) in 2017 than in 2012 with average values of the 13 shops of 5.2 log CFU/g and 5.7 log CFU/g, respectively. In both studies E. coli was only found in the products from outlets that did not have consistently superior rankings. On the other hand prevalence and average counts of Staphylococcus spp. were slightly higher in 2017 (p = 0.0286) but no methicillin-resistant S. aureus (MRSA) were observed in the present study. Methicillin-sensitive S. aureus (MSSA) were, however, isolated from 18.7% of sushi products with an average count below 2 log CFU/g. Based on spa and multilocus sequence typing (MLST), isolates belonged to clonal complex CC7 (t2016), CC20 (t7836), CC45 (t065, t127, t362), CC88 (t1998) and CC398 (t164, t331, t1451). The Panton-Valentine leukocidin (PVL)-encoding gene lukF was detected only in isolates of the t065 spa-type whereas the scn gene from the ΦSa3 prophage was detected in 76.5% of the isolates, supporting that the majority of isolates were of likely human origin. Thirty-six isolates (70.6%) were resistant to at least one of the antibiotic compounds tested. Antibiotic resistance genes that confer resistance to β-lactams (blaZ) and macrolides (ermC) were detected in 33.3% and 9.8% of isolates, respectively. The tet(K) gene that encode tetracycline resistance was only found in a t7836 strain. Overall, this study indicates that S. aureus in sushi products in Denmark do not represent a major food safety hazard due to, firstly, the low temperature and limited time of storage of product may prevent significant growth and production of toxic levels of enterotoxin of this species. Secondly, the S. aureus isolates obtained did not include MRSA variants and none of them encoded PVL that constitute one of the virulence factors in pathogenesis. Several MSSA isolates contained however genes encoding antibiotic resistance, which emphasize the potential role of foods as vehicles for transmission of such variants.
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Affiliation(s)
- Heng Li
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870 Frederiksberg C, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870 Frederiksberg C, Denmark; School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
| | - Jørgen J Leisner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870 Frederiksberg C, Denmark.
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Hounmanou YMG, Mdegela RH, Dougnon TV, Madsen H, Withey JH, Olsen JE, Dalsgaard A. Tilapia ( Oreochromis niloticus) as a Putative Reservoir Host for Survival and Transmission of Vibrio cholerae O1 Biotype El Tor in the Aquatic Environment. Front Microbiol 2019; 10:1215. [PMID: 31214149 PMCID: PMC6554700 DOI: 10.3389/fmicb.2019.01215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/15/2019] [Indexed: 12/17/2022] Open
Abstract
Studies have reported the occurrence of Vibrio cholerae in fish but little is known about the interaction between fish and toxigenic V. cholerae as opposed to phytoplankton, which are well-established aquatic reservoirs for V. cholerae. The present study determined the role of tilapia (Oreochromis niloticus) as a reservoir host for survival and transmission of V. cholerae in aquatic environments. Three experiments were performed with one repetition each, where O. niloticus (∼2 g) kept in beakers were inoculated with four V. cholerae strains (5 × 107 cfu/mL). Firstly, infected tilapia were kept in stagnant water and fed live brine shrimp (Artemia salina) larvae daily. Secondly, infected tilapia were kept without feeding and water was changed every 24 h. Thirdly, infected tilapia were fed and water was renewed daily. Infected tilapia and non-infected controls were sacrificed on days 1, 2, 3, 7, and 14 post-inoculation and V. cholerae were enumerated in intestinal content and water. Another experiment assessed the transmission of V. cholerae from infected to non-infected tilapia. The study revealed that El Tor biotype V. cholerae O1 and V. cholerae non-O1 colonized tilapia intestines and persisted at stable concentrations during the second week of the experiment whereas the Classical biotype was undetectable after 1 week. In stagnant water with feeding, V. cholerae counts dropped to 105 cfu/ml in water and from 107 to 104 cfu/intestine in fish after 14 days. When water was renewed, counts in water decreased from 107 to 103 cfu/ml and intestinal counts went from 106 to 102 cfu/intestine regardless of feeding. All strains were transmitted from infected to naïve fish after 24 h of cohabitation. Tilapia like other fish may play an essential role in the survival and dissemination of V. cholerae O1 in aquatic environments, e.g., the seventh pandemic strains mostly. In this study, tilapia were exposed to high concentrations of V. cholerae to ensure initial uptake and follow-up studies with lower doses resembling natural concentrations of V. cholerae in the aquatic environment are needed to confirm our findings.
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Affiliation(s)
- Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Robinson H Mdegela
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Tamegnon Victorien Dougnon
- Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Research Laboratory in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Henry Madsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeffrey H Withey
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, United States
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Anjum M, Madsen JS, Nesme J, Jana B, Wiese M, Jasinskytė D, Nielsen DS, Sørensen SJ, Dalsgaard A, Moodley A, Bortolaia V, Guardabassi L. Fate of CMY-2-Encoding Plasmids Introduced into the Human Fecal Microbiota by Exogenous Escherichia coli. Antimicrob Agents Chemother 2019; 63:e02528-18. [PMID: 30885897 PMCID: PMC6496067 DOI: 10.1128/aac.02528-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/19/2019] [Indexed: 11/20/2022] Open
Abstract
The gut is a hot spot for transfer of antibiotic resistance genes from ingested exogenous bacteria to the indigenous microbiota. The objective of this study was to determine the fate of two nearly identical blaCMY-2-harboring plasmids introduced into the human fecal microbiota by two Escherichia coli strains isolated from a human and from poultry meat. The chromosome and the CMY-2-encoding plasmid of both strains were labeled with distinct fluorescent markers (mCherry and green fluorescent protein [GFP]), allowing fluorescence-activated cell sorting (FACS)-based tracking of the strain and the resident bacteria that have acquired its plasmid. Each strain was introduced into an established in vitro gut model (CoMiniGut) inoculated with individual feces from ten healthy volunteers. Fecal samples collected 2, 6, and 24 h after strain inoculation were analyzed by FACS and plate counts. Although the human strain survived better than the poultry meat strain, both strains transferred their plasmids to the fecal microbiota at concentrations as low as 102 CFU/ml. Strain survival and plasmid transfer varied significantly depending on inoculum concentration and individual fecal microbiota. Identification of transconjugants by 16S rRNA gene sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) revealed that the plasmids were predominantly acquired by Enterobacteriaceae species, such as E. coli and Hafnia alvei Our experimental data demonstrate that exogenous E. coli of human or animal origin can readily transfer CMY-2-encoding IncI1 plasmids to the human fecal microbiota. Small amounts of the exogenous strain are sufficient to ensure plasmid transfer if the strain is able to survive the gastric environment.
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Affiliation(s)
- Mehreen Anjum
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Joseph Nesme
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bimal Jana
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Maria Wiese
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Džiuginta Jasinskytė
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Arshnee Moodley
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Luca Guardabassi
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom
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Hounmanou YMG, Leekitcharoenphon P, Hendriksen RS, Dougnon TV, Mdegela RH, Olsen JE, Dalsgaard A. Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania. Front Microbiol 2019; 10:901. [PMID: 31114556 PMCID: PMC6503148 DOI: 10.3389/fmicb.2019.00901] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/09/2019] [Indexed: 12/29/2022] Open
Abstract
The occurrence of toxigenic Vibrio cholerae O1 during a non- outbreak period in Lake Victoria was studied and genetic characteristics for environmental persistence and relatedness to pandemic strains were assessed. We analyzed 360 samples of carps, phytoplankton and water collected in 2017 during dry and rainy seasons in the Tanzanian basin of Lake Victoria. Samples were tested using PCR (ompW and ctxA) with DNA extracted from bacterial isolates and samples enriched in alkaline peptone water. Isolates were screened with polyvalent antiserum O1 followed by antimicrobial susceptibility testing. Whole genome sequencing and bioinformatics tools were employed to investigate the genomic characteristics of the isolates. More V. cholerae positive samples were recovered by PCR when DNA was obtained from enriched samples than from isolates (69.0% vs. 21.3%, p < 0.05), irrespectively of season. We identified ten V. cholerae O1 among 22 ctxA-positive isolates. Further studies are needed to serotype the remaining ctxA-positive non-O1 strains. Sequenced strains belonged to El Tor atypical biotype of V. cholerae O1 of MLST ST69 harboring the seventh pandemic gene. Major virulence genes, ctxA, ctxB, zot, ace, tcpA, hlyA, rtxA, ompU, toxR, T6SS, alsD, makA and pathogenicity islands VPI-1, VPI-2, VSP-1, and VSP-2 were found in all strains. The strains contained Vibrio polysaccharide biosynthesis enzymes, the mshA gene and two-component response regulator proteins involved in stress response and autoinducers for quorum sensing and biofilm formation. They carried the SXT integrative conjugative element with phenotypic and genotypic resistance to aminoglycoside, sulfamethoxazole, trimethoprim, phenicol, and quinolones. Strains contained a multidrug efflux pump component and were resistant to toxic compounds with copper homeostasis and cobalt-zinc-cadmium resistance proteins. The environmental strains belonged to the third wave of the seventh pandemic and most are genetically closely related to recent outbreak strains from Tanzania, Kenya, and Uganda with as low as three SNPs difference. Some strains have persisted longer in the environment and were more related to older outbreak strains in the region. V. cholerae O1 of outbreak potential seem to persist in Lake Victoria through interactions with fish and phytoplankton supported by the optimum water parameters and intrinsic genetic features enhancing survival in the aquatic environment.
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Affiliation(s)
- Yaovi M Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pimlapas Leekitcharoenphon
- National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rene S Hendriksen
- National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tamegnon V Dougnon
- Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Laboratory of Research in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Cotonou, Benin
| | - Robinson H Mdegela
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Owusu-Ansah EDGJ, Barnes B, Abaidoo R, Tine H, Dalsgaard A, Permin A, Schou TW. Probabilistic modeling for an integrated temporary acquired immunity with norovirus epidemiological data. Infect Dis Model 2019; 4:99-114. [PMID: 31080934 PMCID: PMC6503004 DOI: 10.1016/j.idm.2019.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/22/2019] [Indexed: 11/28/2022] Open
Abstract
Integration of acquired immunity into microbial risk assessment for illness incidence is of no doubt essential for the study of susceptibility to illness. In this study, a probabilistic model was set up as dose response for infection and a mathematical derivation was carried out by integrating immunity to obtain probability of illness models. Temporary acquire immunity from epidemiology studies which includes six different Norovirus transmission scenarios such as symptomatic individuals infectious, pre- and post-symptomatic infectiousness (low and high), innate genetic resistance, genogroup 2 type 4 and those with no immune boosting by asymptomatic infection were evaluated. Simulated results on illness inflation factor as a function of dose and exposure indicated that high frequency exposures had immense immunity build up even at high dose levels; hence minimized the probability of illness. Using Norovirus transmission dynamics data, results showed, and immunity included models had a reduction of 2-6 logs of magnitude difference in disease burden for both population and individual probable illness incidence. Additionally, the magnitude order of illness for each dose response remained largely the same for all transmission scenarios; symptomatic infectiousness and no immune boosting after asymptomatic infectiousness also remained the same throughout. With integration of epidemiological data on acquired immunity into the risk assessment, more realistic results were achieved signifying an overestimation of probable risk of illness when epidemiological immunity data are not included. This finding supported the call for rigorous integration of temporary acquired immunity in dose-response in all microbial risk assessments.
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Affiliation(s)
- Emmanuel de-Graft Johnson Owusu-Ansah
- Department of Mathematics, Faculty of Physical and Computational Science, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Laboratory of Integrated Statistical Applications (LISA), Faculty of Physical and Computational Sciences, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Regional Water and Environmental Sanitation Center-Kumasi, College of Engineering, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Benedict Barnes
- Department of Mathematics, Faculty of Physical and Computational Science, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Robert Abaidoo
- Department of Theoretical and Applied Biology, Faculty of Bio Science, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Hald Tine
- Research Group of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Anders Dalsgaard
- Food Safety and Zoonoses, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigböjlen 4, 1870 Frederiksberg C, Denmark
| | - Anders Permin
- Office for Innovation and Sector Services, Administration, Technical University of Denmark, Anker Engelunds Vej, 2800 Kgs Lyngby, Denmark
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Chaula D, Laswai H, Chove B, Dalsgaard A, Mdegela R, Jacobsen C, Hyldig G. Effect of clove ( Syzygium aromaticum) and seaweed ( Kappaphycus alvarezii) water extracts pretreatment on lipid oxidation in sun-dried sardines ( Rastrineobola argentea) from Lake Victoria, Tanzania. Food Sci Nutr 2019; 7:1406-1416. [PMID: 31024714 PMCID: PMC6475747 DOI: 10.1002/fsn3.975] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 01/02/2023] Open
Abstract
Small indigenous fish species play a significant role in food and nutritional security of poor communities in developing countries. Sardines (Rastrineobola argentea) are fish species of Lake Victoria known to be a good source of health-promoting omega-3 fatty acids. Open sun drying is a common and traditional sardine processing and preservation method. Sun-dried products suffer from characteristic off-flavor due to lipid oxidation which discourage product consumption and limit diversification. This study investigated the use of clove (Syzygium aromaticum) and seaweed (Kappaphycus alvarezii) water extracts as natural antioxidants to impede lipid oxidation in sun-dried sardines. Lipid oxidation was assessed by peroxide value, volatile secondary oxidation products, and fatty acid profiles. The antioxidant capacity of extracts was evaluated by total phenolic content, 1, 1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging, and iron (Fe2+) chelating ability. Results showed that 5, 10, and 20 g/L clove extracts significantly reduced peroxidation in sun-dried sardines by 38.7%, 54.6%, and 56%, respectively. Clove extracts resulted in higher retention of omega-3 fatty acids and lower concentrations of secondary lipid oxidation products as opposed to seaweed counterpart. This research has demonstrated feasibility of pretreating whole, omega-3-rich small sardines with natural antioxidants to avert lipid oxidation during sun drying.
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Affiliation(s)
- Davis Chaula
- Department of Food Technology, Nutrition and Consumer SciencesSokoine University of AgricultureMorogoroTanzania
| | - Henry Laswai
- Department of Food Technology, Nutrition and Consumer SciencesSokoine University of AgricultureMorogoroTanzania
| | - Bernard Chove
- Department of Food Technology, Nutrition and Consumer SciencesSokoine University of AgricultureMorogoroTanzania
| | - Anders Dalsgaard
- Department of Veterinary and Animal SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Robinson Mdegela
- Department of Veterinary Medicine and Public HealthSokoine University of AgricultureMorogoroTanzania
| | | | - Grethe Hyldig
- National Food InstituteTechnical University of Denmark LyngbyDenmark
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Chaula D, Laswai H, Chove B, Dalsgaard A, Mdegela R, Hyldig G. Fatty Acid Profiles and Lipid Oxidation Status of Sun Dried, Deep Fried, and Smoked Sardine (Rastrineobola argentea) from Lake Victoria, Tanzania. Journal of Aquatic Food Product Technology 2019. [DOI: 10.1080/10498850.2019.1570992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Davis Chaula
- Department of Food Technology, Nutrition and Consumer Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Henry Laswai
- Department of Food Technology, Nutrition and Consumer Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Bernard Chove
- Department of Food Technology, Nutrition and Consumer Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark
| | - Robinson Mdegela
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Grethe Hyldig
- National Food Institute, The Technical University of Denmark, Kgs. Lynby, Denmark
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45
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Dang STT, Bortolaia V, Tran NT, Le HQ, Dalsgaard A. Cephalosporin-resistant Escherichia coli isolated from farm workers and pigs in northern Vietnam. Trop Med Int Health 2019; 23:415-424. [PMID: 29575455 DOI: 10.1111/tmi.13054] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Antimicrobial-resistant bacteria may be transmitted between farm workers and livestock. This study aimed to determine and compare the prevalence and the genetic determinants of cefotaxime-resistant and ESBL-producing Escherichia coli in faecal isolates from workers and pigs at 100 farms in northern Vietnam. METHODS Farmers were interviewed about antimicrobial usage in livestock. Escherichia coli isolated on MacConkey agar containing 2 mg/l of cefotaxime (CTX) were tested for susceptibility to different cephalosporins by disc diffusion and screened for occurrence of ESBL-encoding genes by PCR. RESULTS Antimicrobial usage was widespread and included classes regarded of critical or high importance in human medicine. Dosages were 0.5-2 times higher than recommended, and antimicrobials were often administered right until slaughter. Prevalence of CTX-resistant E. coli was 86% in farm workers and 89% in pigs. In 76% of farms, CTX-resistant E. coli were shared by pigs and farm workers. ESBL-producing E. coli were detected from pigs and workers at 66 and 69 farms, respectively. The ESBL phenotype was mainly mediated by CTX-M and to a lesser extent by TEM. Occurrence of blaCTX-M was similar in E. coli from pigs (66.7%) and humans (68.5%). CONCLUSION The high occurrence of ESBL-producing E. coli in pig farmers and pigs could present a risk for spillover of these bacteria from pig farms into the community. Genomic studies are needed to elucidate reservoirs and transmission routes of ESBL-producing E. coli at livestock farms.
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Affiliation(s)
- Son T T Dang
- Veterinary Hygiene Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Valeria Bortolaia
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nhat T Tran
- Veterinary Hygiene Department, National Institute of Veterinary Research, Hanoi, Vietnam
| | - Huan Q Le
- Animal Cell Biotechnology Lab, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
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46
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Hossain ZZ, Leekitcharoenphon P, Dalsgaard A, Sultana R, Begum A, Jensen PKM, Hendriksen RS. Comparative genomics of Vibrio cholerae O1 isolated from cholera patients in Bangladesh. Lett Appl Microbiol 2018; 67:329-336. [PMID: 29981154 DOI: 10.1111/lam.13046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 06/23/2018] [Accepted: 07/04/2018] [Indexed: 01/08/2023]
Abstract
Whole genome sequencing was utilized to investigate the genomic profile of Vibrio cholerae O1 strains, isolated from symptomatic patients in a low-income urban area of Dhaka, Bangladesh. Comparative genomics using bioinformatics tools were applied to identify major virulence factors, biotype and antimicrobial resistance genes in three V. cholerae O1 strains (VC-1, 2 and 3) isolated from two case patients. A phylogenetic SNP (single nucleotide polymorphism)-based analysis was conducted to infer the relatedness to V. cholerae O1 strains isolated elsewhere. The V. cholerae strains were the El Tor variant carrying ctxB1 (standard classical genotype). SNP-based global phylogeny revealed that the three isolates were strictly clonal and the closest neighbouring genomes were epidemic clones of V. cholerae O1 isolated in 2010 from cholera patients in Pakistan. All strains harboured the integrase gene of the SXT element (intSXT ), antimicrobial resistance genes for aminoglycosides, phenicol, sulphonamide and trimethoprim except VC-1 that lacked sulphonamide resistance genes. The multilocus sequence typing (MLST) revealed that the strains belonged to sequence type, ST69. The study provides knowledge on current genetic traits of clinical V. cholerae O1 circulating in urban household clusters of Bangladesh which may help in predicting emergence of new pandemic strains in Bangladesh. SIGNIFICANCE AND IMPACT OF THE STUDY Vibrio cholerae has frequently experienced genetic changes with rapid evolution of pandemic clones in the Ganges Delta region. Whole genome sequencing can reveal genetic information of current pathogenic V. cholerae in Bangladesh which includes cefotaxime genotypes, virulence factors, altered antimicrobial resistance pattern as well as mobile genetic element compared to global pandemic strains. This study data could be used in planning future surveillance strategies in Ganges Delta region by informing new epidemiology of current outbreak strains.
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Affiliation(s)
- Z Z Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Institute of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - P Leekitcharoenphon
- National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens & Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - A Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - R Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - A Begum
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - P K M Jensen
- Institute of Public Health, University of Copenhagen, Copenhagen, Denmark.,Copenhagen Centre for Disaster Research, University of Copenhagen, Copenhagen, Denmark
| | - R S Hendriksen
- National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens & Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark
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47
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Sarajuddin J, Polcwiartek C, Tayal B, Kragholm K, Sogaard P, Dalsgaard A, Borup H, Arulanandam H, Aagaard J, Jensen S. P863Impact of the duration of schizophrenia in patients without known cardiac disease on myocardial function assessed by echocardiography. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy564.p863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- J Sarajuddin
- Aalborg University Hospital, Department of Cardiology, Aalborg, Denmark
| | - C Polcwiartek
- Aalborg University Hospital, Department of Cardiology, Aalborg, Denmark
| | - B Tayal
- Aalborg University Hospital, Department of Cardiology, Aalborg, Denmark
| | - K Kragholm
- Aalborg University Hospital, Department of Cardiology, Aalborg, Denmark
| | - P Sogaard
- Aalborg University Hospital, Department of Cardiology, Aalborg, Denmark
| | - A Dalsgaard
- Aalborg University Hospital, Department of Cardiology, Aalborg, Denmark
| | - H Borup
- Aalborg University Hospital, Department of Cardiology, Aalborg, Denmark
| | - H Arulanandam
- Aalborg University Hospital, Department of Cardiology, Aalborg, Denmark
| | - J Aagaard
- Aalborg University Hospital, Department of Psychiatry, Aalborg, Denmark
| | - S Jensen
- Aalborg University Hospital, Department of Cardiology, Aalborg, Denmark
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Kudirkiene E, Andoh LA, Ahmed S, Herrero-Fresno A, Dalsgaard A, Obiri-Danso K, Olsen JE. The Use of a Combined Bioinformatics Approach to Locate Antibiotic Resistance Genes on Plasmids From Whole Genome Sequences of Salmonella enterica Serovars From Humans in Ghana. Front Microbiol 2018; 9:1010. [PMID: 29867897 PMCID: PMC5966558 DOI: 10.3389/fmicb.2018.01010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 01/15/2018] [Accepted: 04/30/2018] [Indexed: 11/20/2022] Open
Abstract
In the current study, we identified plasmids carrying antimicrobial resistance genes in draft whole genome sequences of 16 selected Salmonella enterica isolates representing six different serovars from humans in Ghana. The plasmids and the location of resistance genes in the genomes were predicted using a combination of PlasmidFinder, ResFinder, plasmidSPAdes and BLAST genomic analysis tools. Subsequently, S1-PFGE was employed for analysis of plasmid profiles. Whole genome sequencing confirmed the presence of antimicrobial resistance genes in Salmonella isolates showing multidrug resistance phenotypically. ESBL, either blaTEM52-B or blaCTX-M15 were present in two cephalosporin resistant isolates of S. Virchow and S. Poona, respectively. The systematic genome analysis revealed the presence of different plasmids in different serovars, with or without insertion of antimicrobial resistance genes. In S. Enteritidis, resistance genes were carried predominantly on plasmids of IncN type, in S. Typhimurium on plasmids of IncFII(S)/IncFIB(S)/IncQ1 type. In S. Virchow and in S. Poona, resistance genes were detected on plasmids of IncX1 and TrfA/IncHI2/IncHI2A type, respectively. The latter two plasmids were described for the first time in these serovars. The combination of genomic analytical tools allowed nearly full mapping of the resistance plasmids in all Salmonella strains analyzed. The results suggest that the improved analytical approach used in the current study may be used to identify plasmids that are specifically associated with resistance phenotypes in whole genome sequences. Such knowledge would allow the development of rapid multidrug resistance tracking tools in Salmonella populations using WGS.
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Affiliation(s)
- Egle Kudirkiene
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Linda A. Andoh
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Shahana Ahmed
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kwasi Obiri-Danso
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Owusu-Ansah EDGJ, Sampson A, Amponsah SK, Abaidoo RC, Dalsgaard A, Hald T. Probabilistic quantitative microbial risk assessment model of norovirus from wastewater irrigated vegetables in Ghana using genome copies and fecal indicator ratio conversion for estimating exposure dose. Sci Total Environ 2017; 601-602:1712-1719. [PMID: 28618661 DOI: 10.1016/j.scitotenv.2017.05.168] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 05/19/2017] [Accepted: 05/19/2017] [Indexed: 05/22/2023]
Abstract
The need to replace the commonly applied fecal indicator conversions ratio (an assumption of 1:10-5 virus to fecal indicator organism) in Quantitative Microbial Risk Assessment (QMRA) with models based on quantitative data on the virus of interest has gained prominence due to the different physical and environmental factors that might influence the reliability of using indicator organisms in microbial risk assessment. The challenges facing analytical studies on virus enumeration (genome copies or particles) have contributed to the already existing lack of data in QMRA modelling. This study attempts to fit a QMRA model to genome copies of norovirus data. The model estimates the risk of norovirus infection from the intake of vegetables irrigated with wastewater from different sources. The results were compared to the results of a corresponding model using the fecal indicator conversion ratio to estimate the norovirus count. In all scenarios of using different water sources, the application of the fecal indicator conversion ratio underestimated the norovirus disease burden, measured by the Disability Adjusted Life Years (DALYs), when compared to results using the genome copies norovirus data. In some cases the difference was >2 orders of magnitude. All scenarios using genome copies met the 10-4 DALY per person per year for consumption of vegetables irrigated with wastewater, although these results are considered to be highly conservative risk estimates. The fecal indicator conversion ratio model of stream-water and drain-water sources of wastewater achieved the 10-6 DALY per person per year threshold, which tends to indicate an underestimation of health risk when compared to using genome copies for estimating the dose.
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Affiliation(s)
- Emmanuel de-Graft Johnson Owusu-Ansah
- Department of Mathematics, Faculty of Physical and Computational Sciences, SCB-SF 24/B6, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
| | - Angelina Sampson
- Department of Chemistry and Biochemistry, South Dakota State University, USA
| | - Samuel K Amponsah
- Department of Mathematics, Faculty of Physical and Computational Sciences, SCB-SF 24/B6, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Robert C Abaidoo
- Department of Theoretical and Applied Biology, Faculty of Bioscience, Biology Block, A 32, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Anders Dalsgaard
- Veterinary Diseases Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Tine Hald
- Genomic Epidemiology and Global Decision Support Initiative, National Food Institute, Soltofts Plads, Building 221 Room 250, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
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Baniga Z, Dalsgaard A, Mhongole OJ, Madsen H, Mdegela RH. Microbial quality and safety of fresh and dried Rastrineobola argentea from Lake Victoria, Tanzania. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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