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Ferrari RG, Rosario DKA, Cunha-Neto A, Mano SB, Figueiredo EES, Conte-Junior CA. Worldwide Epidemiology of Salmonella Serovars in Animal-Based Foods: a Meta-analysis. Appl Environ Microbiol 2019; 85:e00591-19. [PMID: 31053586 PMCID: PMC6606869 DOI: 10.1128/aem.00591-19] [Citation(s) in RCA: 262] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/25/2019] [Indexed: 01/27/2023] Open
Abstract
Salmonella spp. are among the most important foodborne pathogens and the third leading cause of human death among diarrheal diseases worldwide. Animals are the primary source of this pathogen, and animal-based foods are the main transmission route to humans. Thus, understanding the global epidemiology of Salmonella serovars is key to controlling and monitoring this bacterium. In this context, this study aimed to evaluate the prevalence and diversity of Salmonella enterica serovars in animal-based foods (beef, pork, poultry, and seafood) throughout the five continents (Africa, the Americas [North and Latin America], Asia, Europe, and Oceania). The meta-analysis consisted of a chemometric assessment (hierarchical cluster analysis and principal component analysis) to identify the main epidemiological findings, including the prevalence and diversity of the Salmonella serovars in each matrix. Regarding the serovar distribution, S Typhimurium presented a cosmopolitan distribution, reported in all four assessed matrices and continents; poultry continues to play a central role in the dissemination of the Enteritidis serovar to humans, and Anatum and Weltevreden were the most frequently found in beef and seafood, respectively. Additionally, we recommended careful monitoring of certain serovars, such as Derby, Agona, Infantis, and Kentucky. Finally, given the scientific data regarding the most frequently reported serovars and which matrices constitute the main vehicles for the transmission of this pathogen, control programs may be improved, and specific interventions may be implemented in an attempt to reduce the risk of this pathogen reaching humans.IMPORTANCE Salmonellosis is caused by Salmonella spp. and is the third leading cause of death among food-transmitted diseases. This pathogen is commonly disseminated in domestic and wild animals, and the infection's symptoms are characterized by acute fever, nausea, abdominal pain, and diarrhea. The animals are the primary source of salmonellae, and animal-based foods are the main transmission route to humans. Therefore, data collected from these sources could contribute to future global interventions for effective control and surveillance of Salmonella along the food chain. In light of this, the importance of our research is in identifying the prevalence of Salmonella serovars in four animal-based food matrices (pork, poultry, beef, and seafood) and to evaluate the importance that each matrix has as the primary source of this pathogen to humans.
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Affiliation(s)
- Rafaela G Ferrari
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Federal Fluminense University, Niterói, Brazil
- Post Graduate Program in Food Science Program, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Denes K A Rosario
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Federal Fluminense University, Niterói, Brazil
- Post Graduate Program in Food Science Program, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adelino Cunha-Neto
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Federal Fluminense University, Niterói, Brazil
- Nutrition, Food and Metabolism Program, Nutrition Faculty, Federal University of Mato Grosso, Cuiabá, Brazil
| | - Sérgio B Mano
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Federal Fluminense University, Niterói, Brazil
| | - Eduardo E S Figueiredo
- Animal Science Program, Faculty of Agronomy and Animal Science, Federal University of Mato Grosso, Cuiabá, Brazil
- Nutrition, Food and Metabolism Program, Nutrition Faculty, Federal University of Mato Grosso, Cuiabá, Brazil
| | - Carlos A Conte-Junior
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Federal Fluminense University, Niterói, Brazil
- Post Graduate Program in Food Science Program, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- National Institute of Health Quality Control, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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Salunke RA, Shukla M, Kaul G, Bansal BR, Chopra S, Chhibber M. New fluoroquinolone compounds with
endo
‐nortropine derivatives at C‐7 position show antibacterial activity against fluoroquinolone‐resistant strains of
Staphylococcus aureus. Chem Biol Drug Des 2019; 94:1626-1633. [DOI: 10.1111/cbdd.13513] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/26/2018] [Accepted: 02/09/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Ramkrushna Ashok Salunke
- School of Chemistry and Biochemistry Thapar Institute of Engineering and Technology Patiala India
- Saurav Chemicals Limited Derabassi‐ Mohali India
| | - Manjulika Shukla
- CDRI - Division of Microbiology CSIR‐Central Drug Research Institute Lucknow India
| | - Grace Kaul
- CDRI - Division of Microbiology CSIR‐Central Drug Research Institute Lucknow India
| | | | - Sidharth Chopra
- CDRI - Division of Microbiology CSIR‐Central Drug Research Institute Lucknow India
| | - Manmohan Chhibber
- School of Chemistry and Biochemistry Thapar Institute of Engineering and Technology Patiala India
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Hassena AB, Siala M, Guermazi S, Zormati S, Gdoura R, Sellami H. Occurrence and Phenotypic and Molecular Characterization of Antimicrobial Resistance of Salmonella Isolates from Food in Tunisia. J Food Prot 2019; 82:1166-1175. [PMID: 31233356 DOI: 10.4315/0362-028x.jfp-18-607] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
HIGHLIGHTS Multidrug-resistant Salmonella isolates have been recovered from food in Tunisia. Salmonella isolates from food are resistant to fluoroquinolones and cephalosporins. Surveillance of the antimicrobial susceptibility of foodborne bacteria is needed in Tunisia.
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Affiliation(s)
- Amal Ben Hassena
- 1 Laboratoire de recherche Toxicologie Microbiologie Environnementale et Santé (LR17ES06), Département des Sciences de la vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
| | - Mariam Siala
- 1 Laboratoire de recherche Toxicologie Microbiologie Environnementale et Santé (LR17ES06), Département des Sciences de la vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
| | - Sonda Guermazi
- 1 Laboratoire de recherche Toxicologie Microbiologie Environnementale et Santé (LR17ES06), Département des Sciences de la vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
| | - Sonia Zormati
- 1 Laboratoire de recherche Toxicologie Microbiologie Environnementale et Santé (LR17ES06), Département des Sciences de la vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia.,2 Centre Régional de Recherches Vétérinaires de Sfax, Sfax, Tunisia
| | - Radhouane Gdoura
- 1 Laboratoire de recherche Toxicologie Microbiologie Environnementale et Santé (LR17ES06), Département des Sciences de la vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
| | - Hanen Sellami
- 1 Laboratoire de recherche Toxicologie Microbiologie Environnementale et Santé (LR17ES06), Département des Sciences de la vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia.,3 Laboratoire de Traitement et de Valorisation des Rejets Hydriques (LTVRH), Water Researches and Technologies Center (CERTE), University of Carthage, Tourist Road Soliman, BP 273-8020, Nabeul 8000, Tunisia
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54
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Cheng RA, Eade CR, Wiedmann M. Embracing Diversity: Differences in Virulence Mechanisms, Disease Severity, and Host Adaptations Contribute to the Success of Nontyphoidal Salmonella as a Foodborne Pathogen. Front Microbiol 2019; 10:1368. [PMID: 31316476 PMCID: PMC6611429 DOI: 10.3389/fmicb.2019.01368] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/31/2019] [Indexed: 12/19/2022] Open
Abstract
Not all Salmonella enterica serovars cause the same disease. S. enterica represents an incredibly diverse species comprising >2,600 unique serovars. While some S. enterica serovars are host-restricted, others infect a wide range of hosts. The diseases that nontyphoidal Salmonella (NTS) serovars cause vary considerably, with some serovars being significantly more likely to cause invasive disease in humans than others. Furthermore, while genomic analyses have advanced our understanding of the genetic diversity of these serovars, they have not been able to fully account for the observed clinical differences. One overarching challenge is that much of what is known about Salmonella's general biology and virulence strategies is concluded from studies examining a select few serovars, especially serovar Typhimurium. As targeted control strategies have been implemented to control select serovars, an increasing number of foodborne outbreaks involving serovars that are less frequently associated with human clinical illness are being detected. Harnessing what is known about the diversity of NTS serovars represents an important factor in achieving the ultimate goal of reducing salmonellosis-associated morbidity and mortality worldwide. In this review we summarize the current understanding of the differences and similarities among NTS serovars, highlighting the virulence mechanisms, genetic differences, and sources that characterize S. enterica diversity and contribute to its success as a foodborne pathogen.
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Affiliation(s)
- Rachel A. Cheng
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Colleen R. Eade
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, United States
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
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Hawkey J, Le Hello S, Doublet B, Granier SA, Hendriksen RS, Fricke WF, Ceyssens PJ, Gomart C, Billman-Jacobe H, Holt KE, Weill FX. Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198. Microb Genom 2019; 5. [PMID: 31107206 PMCID: PMC6700661 DOI: 10.1099/mgen.0.000269] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S.enterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S.enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylogeographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase (gyrA) and DNA topoisomerase IV (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. enterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions, which appear to have hampered previous attempts to trace the clone’s evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results indicate that most MDR S. enterica serotype Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials. This article contains data hosted by Microreact.
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Affiliation(s)
- Jane Hawkey
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur, 75015 Paris, France
| | - Benoît Doublet
- ISP, Institut National de la Recherche Agronomique, Université François Rabelais de Tours, UMR 1282, Nouzilly, France
| | - Sophie A Granier
- Laboratoire de sécurité des aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Université PARIS-EST, 94701 Maisons-Alfort, France.,Laboratoire de Fougères, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), 35306 Fougères, France
| | - Rene S Hendriksen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - W Florian Fricke
- Department of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Camille Gomart
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur, 75015 Paris, France
| | - Helen Billman-Jacobe
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kathryn E Holt
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur, 75015 Paris, France
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56
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Haley BJ, Kim SW, Haendiges J, Keller E, Torpey D, Kim A, Crocker K, Myers RA, Van Kessel JAS. Salmonella enterica serovar Kentucky recovered from human clinical cases in Maryland, USA (2011-2015). Zoonoses Public Health 2019; 66:382-392. [PMID: 30891945 DOI: 10.1111/zph.12571] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/18/2018] [Accepted: 02/07/2019] [Indexed: 11/27/2022]
Abstract
Salmonella Kentucky is among the most frequently isolated S. enterica serovars from food animals in the United States. Recent research on isolates recovered from these animals suggests there may be geographic and host specificity signatures associated with S. Kentucky strains. However, the sources and genomic features of human clinical S. Kentucky isolated in the United States remain poorly described. To investigate the characteristics of clinical S. Kentucky and the possible sources of these infections, the genomes of all S. Kentucky isolates recovered from human clinical cases in the State of Maryland between 2011 and 2015 (n = 12) were sequenced and compared to a database of 525 previously sequenced S. Kentucky genomes representing 12 sequence types (ST) collected from multiple sources on several continents. Of the 12 human clinical S. Kentucky isolates from Maryland, nine were ST198, two were ST152, and one was ST314. Forty-one per cent of isolates were recovered from patients reporting recent international travel and 58% of isolates encoded genomic characteristics similar to those originating outside of the United States. Of the five isolates not associated with international travel, three encoded antibiotic resistance genes conferring resistance to tetracycline or aminoglycosides, while two others only encoded the cryptic aac(6')-Iaa gene. Five isolates recovered from individuals with international travel histories (ST198) and two for which travel was not recorded (ST198) encoded genes conferring resistance to between 4 and 7 classes of antibiotics. Seven ST198 genomes encoded the Salmonella Genomic Island 1 and substitutions in the gyrA and parC genes known to confer resistance to ciprofloxacin. Case report data on food consumption and travel were, for the most part, consistent with the inferred S. Kentucky phylogeny. Results of this study indicate that the majority of S. Kentucky infections in Maryland are caused by ST198 which may originate outside of North America.
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Affiliation(s)
- Bradd J Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland
| | | | - Eric Keller
- Maryland Department of Health, Baltimore, Maryland
| | - David Torpey
- Maryland Department of Health, Baltimore, Maryland
| | | | - Kia Crocker
- Maryland Department of Health, Baltimore, Maryland
| | | | - Jo Ann S Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland
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57
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The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2017. EFSA J 2019; 17:e05598. [PMID: 32626224 PMCID: PMC7009238 DOI: 10.2903/j.efsa.2019.5598] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The data on antimicrobial resistance in zoonotic and indicator bacteria in 2017, submitted by 28 EU Member States (MSs), were jointly analysed by EFSA and ECDC. Resistance in zoonotic Salmonella and Campylobacter from humans, animals and food, and resistance in indicator Escherichia coli as well as meticillin‐resistant Staphylococcus aureus in animals and food were addressed, and temporal trends assessed. ‘Microbiological’ resistance was assessed using epidemiological cut‐off (ECOFF) values; for some countries, qualitative data on human isolates were interpreted in a way which corresponds closely to the ECOFF‐defined ‘microbiological’ resistance. In Salmonella from humans, as well as in Salmonella and E. coli isolates from fattening pigs and calves of less than 1 year of age, high proportions of isolates were resistant to ampicillin, sulfonamides and tetracyclines, whereas resistance to third‐generation cephalosporins was uncommon. Varying occurrence/prevalence rates of presumptive extended‐spectrum beta‐lactamase (ESBL)/AmpC producers in Salmonella and E. coli monitored in meat (pork and beef), fattening pigs and calves, and Salmonella monitored in humans, were observed between countries. Carbapenemase‐producing E. coli were detected in one single
sample from fattening pigs in one MS. Resistance to colistin was observed at low levels in Salmonella and E. coli from fattening pigs and calves and meat thereof and in Salmonella from humans. In Campylobacter from humans, high to extremely high proportions of isolates were resistant to ciprofloxacin and tetracyclines, particularly in Campylobacter coli. In five countries, high to very high proportions of C. coli from humans were resistant also to erythromycin, leaving few options for treatment of severe Campylobacter infections. High resistance to ciprofloxacin and tetracyclines was observed in C. coli isolates from fattening pigs, whereas much lower levels were recorded for erythromycin. Combined resistance to critically important antimicrobials in both human and animal isolates was generally uncommon but very high to extremely high multidrug resistance levels were observed in S. Typhimurium and its monophasic variant in both humans and animals. S. Kentucky from humans exhibited high‐level resistance to ciprofloxacin, in addition to a high prevalence of ESBL.
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Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Dewulf J, Hald T, Michel V, Niskanen T, Ricci A, Snary E, Boelaert F, Messens W, Davies R. Salmonella control in poultry flocks and its public health impact. EFSA J 2019; 17:e05596. [PMID: 32626222 PMCID: PMC7009056 DOI: 10.2903/j.efsa.2019.5596] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
An increase in confirmed human salmonellosis cases in the EU after 2014 triggered investigation of contributory factors and control options in poultry production. Reconsideration of the five current target serovars for breeding hens showed that there is justification for retaining Salmonella Enteritidis, Salmonella Typhimurium (including monophasic variants) and Salmonella Infantis, while Salmonella Virchow and Salmonella Hadar could be replaced by Salmonella Kentucky and either Salmonella Heidelberg, Salmonella Thompson or a variable serovar in national prevalence targets. However, a target that incorporates all serovars is expected to be more effective as the most relevant serovars in breeding flocks vary between Member State (MS) and over time. Achievement of a 1% target for the current target serovars in laying hen flocks is estimated to be reduced by 254,400 CrI95[98,540; 602,700] compared to the situation in 2016. This translates to a reduction of 53.4% CrI95[39.1; 65.7] considering the layer-associated human salmonellosis true cases and 6.2% considering the overall human salmonellosis true cases in the 23 MSs included in attribution modelling. A review of risk factors for Salmonella in laying hens revealed that overall evidence points to a lower occurrence in non-cage compared to cage systems. A conclusion on the effect of outdoor access or impact of the shift from conventional to enriched cages could not be reached. A similar review for broiler chickens concluded that the evidence that outdoor access affects the occurrence of Salmonella is inconclusive. There is conclusive evidence that an increased stocking density, larger farms and stress result in increased occurrence, persistence and spread of Salmonella in laying hen flocks. Based on scientific evidence, an impact of Salmonella control programmes, apart from general hygiene procedures, on the prevalence of Campylobacter in broiler flocks at the holding and on broiler meat at the end of the slaughter process is not expected.
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Fall-Niang NK, Sambe-Ba B, Seck A, Deme SN, Wane AA, Bercion R, Alambedji-Bada R, Gassama-Sow A. Antimicrobial Resistance Profile of Salmonella Isolates in Chicken Carcasses in Dakar, Senegal. Foodborne Pathog Dis 2019; 16:130-136. [PMID: 30707626 DOI: 10.1089/fpd.2018.2459] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The incidence of the Salmonella contamination of poultry products in Senegal is unknown. Salmonella contamination and antimicrobial drug resistance profiles in chicken carcasses were investigated. Between July 2012 and July 2013, three types of chicken carcasses (broilers, laying hens, and premises chickens) obtained from retailers in the markets of Dakar and its suburbs were tested for Salmonella contamination. Salmonella strains were isolated from 300 chicken carcasses according to International Organization for Standardization ISO 6579 (2002) guidelines. In these samples, 273 isolates were obtained, belonging to 22 serovars, and 53% samples were contaminated with at least 1 serovar. Standardized techniques were used for the susceptibility testing and serotyping of isolates. Hygiene conditions, in terms of the cleanliness of stalls, the packing of chicken carcasses in bags, and the maintenance of the cold chain at the stall, were moderately poor. The three serovars most frequently identified were Salmonella Istanbul (28%), Salmonella Brancaster (19%), and Salmonella Kentucky (13%). Overall, 21% of isolates were resistant to quinolones and fluoroquinolones. Serovar Istanbul was resistant to tetracycline (TE) and trimethoprim + sulfamethoxazole (SXT). Serovars Brancaster and Kentucky were resistant to betalactams and to quinolones or fluoroquinolones. The uncommon serovar Senftenberg had the strongest resistance profile, displaying resistance to betalactams including imipenem (IMP). Large numbers of isolates were resistant to TE (66%) and SXT (47%). Resistance to cephalosporins (5%), chloramphenicol (2%), gentamicin (8%), and IMP (1%) was less frequent. A large proportion of the broilers sold in Dakar markets were contaminated with Salmonella. This situation probably resulted from poor hygiene conditions in chicken farms and slaughterhouses and from breaks in the cold chain at some point in the distribution of poultry products.
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Affiliation(s)
| | - Bissoume Sambe-Ba
- 1 Experimental Bacteriology Unit, Pasteur Institute Dakar, Dakar, Senegal
| | - Abdoulaye Seck
- 2 Medical Biology Analysis Laboratory, Pasteur Institute Dakar, Dakar, Senegal
| | - Saidou Nourou Deme
- 3 Food Safeties and Environmental Hygiene Laboratory, Pasteur Institute Dakar, Dakar, Senegal
| | - Abdoul Aziz Wane
- 1 Experimental Bacteriology Unit, Pasteur Institute Dakar, Dakar, Senegal
| | - Raymond Bercion
- 2 Medical Biology Analysis Laboratory, Pasteur Institute Dakar, Dakar, Senegal
| | - Rianatou Alambedji-Bada
- 4 Microbiology-Immunology-Infectious Pathology Laboratory, Interstate School of Veterinary Science, UCAD, Dakar, Senegal
| | - Amy Gassama-Sow
- 1 Experimental Bacteriology Unit, Pasteur Institute Dakar, Dakar, Senegal.,3 Food Safeties and Environmental Hygiene Laboratory, Pasteur Institute Dakar, Dakar, Senegal.,5 Chemical Engineering and Applied Biology Department, Polytechnic School, UCAD, Dakar, Senegal
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60
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Thompson CP, Doak AN, Amirani N, Schroeder EA, Wright J, Kariyawasam S, Lamendella R, Shariat NW. High-Resolution Identification of Multiple Salmonella Serovars in a Single Sample by Using CRISPR-SeroSeq. Appl Environ Microbiol 2018; 84:e01859-18. [PMID: 30170999 PMCID: PMC6193385 DOI: 10.1128/aem.01859-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 08/21/2018] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica is represented by >2,600 serovars that can differ in routes of transmission, host colonization, and in resistance to antimicrobials. S. enterica is the leading bacterial cause of foodborne illness in the United States, with well-established detection methodology. Current surveillance protocols rely on the characterization of a few colonies to represent an entire sample; thus, minority serovars remain undetected. Salmonella contains two CRISPR loci, CRISPR1 and CRISPR2, and the spacer contents of these can be considered serovar specific. We exploited this property to develop an amplicon-based and multiplexed sequencing approach, CRISPR-SeroSeq (serotyping by sequencing of the CRISPR loci), to identify multiple serovars present in a single sample. Using mixed genomic DNA from two Salmonella serovars, we were able to confidently detect a serovar that constituted 0.01% of the sample. Poultry is a major reservoir of Salmonella spp., including serovars that are frequently associated with human illness, as well as those that are not. Numerous studies have examined the prevalence and diversity of Salmonella spp. in poultry, though these studies were limited to culture-based approaches and therefore only identified abundant serovars. CRISPR-SeroSeq was used to investigate samples from broiler houses and a processing facility. Ninety-one percent of samples harbored multiple serovars, and there was one sample in which four different serovars were detected. In another sample, reads for the minority serovar comprised 0.003% of the total number of Salmonella spacer reads. The most abundant serovars identified were Salmonella enterica serovars Montevideo, Kentucky, Enteritidis, and Typhimurium. CRISPR-SeroSeq also differentiated between multiple strains of some serovars. This high resolution of serovar populations has the potential to be utilized as a powerful tool in the surveillance of Salmonella species.IMPORTANCESalmonella enterica is the leading bacterial cause of foodborne illness in the United States and is represented by over 2,600 distinct serovars. Some of these serovars are pathogenic in humans, while others are not. Current surveillance for this pathogen is limited by the detection of only the most abundant serovars, due to the culture-based approaches that are used. Thus, pathogenic serovars that are present in a minority remain undetected. By exploiting serovar-specific differences in the CRISPR arrays of Salmonella spp., we have developed a high-throughput sequencing tool to be able to identify multiple serovars in a single sample and tested this in multiple poultry samples. This novel approach allows differences in the dynamics of individual Salmonella serovars to be measured and can have a significant impact on understanding the ecology of this pathogen with respect to zoonotic risk and public health.
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Affiliation(s)
- Cameron P Thompson
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Alexandra N Doak
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
- Department of Computer Science, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Naufa Amirani
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Erin A Schroeder
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Justin Wright
- Wright Labs, Juniata Center for Entrepreneurial Leadership, Huntingdon, Pennsylvania, USA
| | - Subhashinie Kariyawasam
- Department of Veterinary Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Regina Lamendella
- Wright Labs, Juniata Center for Entrepreneurial Leadership, Huntingdon, Pennsylvania, USA
- Biology Department, Juniata College, Huntingdon, Pennsylvania, USA
| | - Nikki W Shariat
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
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61
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Affiliation(s)
- D I Rendle
- Rainbow Equine Hospital, Malton, North Yorkshire, UK
| | - S W Page
- Advanced Veterinary Therapeutics, Newtown, Australia
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Elkenany RM, Eladl AH, El-Shafei RA. Genetic characterisation of class 1 integrons among multidrug-resistant Salmonella serotypes in broiler chicken farms. J Glob Antimicrob Resist 2018; 14:202-208. [DOI: 10.1016/j.jgar.2018.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022] Open
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Abstract
ABSTRACT
Non-typhoidal
Salmonella
is the most common foodborne bacterial pathogen in most countries. It is widely present in food animal species, and therefore blocking its transmission through the food supply is a prominent focus of food safety activities worldwide. Antibiotic resistance in non-typhoidal
Salmonella
arises in large part because of antibiotic use in animal husbandry. Tracking resistance in
Salmonella
is required to design targeted interventions to contain or diminish resistance and refine use practices in production. Many countries have established systems to monitor antibiotic resistance in
Salmonella
and other bacteria, the earliest ones appearing the Europe and the US. In this chapter, we compare recent
Salmonella
antibiotic susceptibility data from Europe and the US. In addition, we summarize the state of known resistance genes that have been identified in the genus. The advent of routine whole genome sequencing has made it possible to conduct genomic surveillance of resistance based on DNA sequences alone. This points to a new model of surveillance in the future that will provide more definitive information on the sources of resistant
Salmonella
, the specific types of resistance genes involved, and information on how resistance spreads.
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Rauch HE, Vosik D, Kariyawasam S, M'ikanatha N, Shariat NW. Prevalence of Group I Salmonella Kentucky in domestic food animals from Pennsylvania and overlap with human clinical CRISPR sequence types. Zoonoses Public Health 2018; 65:831-837. [PMID: 30014599 DOI: 10.1111/zph.12506] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 01/29/2023]
Abstract
Although infrequently associated with illness in humans, Salmonella enterica, subsp. enterica serovar Kentucky is the most common non-clinical, non-human serovar reported in the United States, being largely found in poultry and poultry products, as well as being associated with cattle. This serovar is polyphyletic and can be separated into two groups, Group I and II, based on CRISPR-typing analysis. In Salmonella Kentucky isolates from human clinical samples in Pennsylvania, both lineages are equally represented. The goal of this study was to determine whether both groups were also represented in domestic food animals in Pennsylvania. We analysed the CRISPR arrays from 67 Salmonella Kentucky isolates used PCR and sequencing of CRISPR arrays or analysis of whole genome sequences to analyse the CRISPR arrays and Across a collection of 67 Salmonella Kentucky isolates that includes those collected from farms, veterinary clinical samples as well as isolates from retail meats, we show that Group I Salmonella Kentucky are the exclusive lineage present. We reveal that the specific subtype of over a quarter of these animal isolates are also found to be responsible for causing human salmonellosis in the same region over the same time period.
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Affiliation(s)
- Hallie E Rauch
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania
| | - Dorothy Vosik
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania
| | - Subhashinie Kariyawasam
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, Pennsylvania
| | - Nkuchia M'ikanatha
- Division of Infectious Disease Epidemiology, Pennsylvania Department of Health, Harrisburg, Pennsylvania.,Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nikki W Shariat
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania
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65
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Mąka Ł, Maćkiw E, Stasiak M, Wołkowicz T, Kowalska J, Postupolski J, Popowska M. Ciprofloxacin and nalidixic acid resistance of Salmonella spp. isolated from retail food in Poland. Int J Food Microbiol 2018; 276:1-4. [DOI: 10.1016/j.ijfoodmicro.2018.03.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 11/16/2022]
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Complete Genome Sequence of a Ciprofloxacin-Resistant Salmonella enterica subsp. enterica Serovar Kentucky Sequence Type 198 Strain, PU131, Isolated from a Human Patient in Washington State. GENOME ANNOUNCEMENTS 2018; 6:6/9/e00125-18. [PMID: 29496839 PMCID: PMC5834327 DOI: 10.1128/genomea.00125-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Strains of the ciprofloxacin-resistant (Cipr) Salmonella enterica subsp. enterica serovar Kentucky sequence type 198 (ST198) have rapidly and extensively disseminated globally to become a major food safety and public health concern. Here, we report the complete genome sequence of a CiprS. Kentucky ST198 strain, PU131, isolated from a human patient in Washington State (USA).
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67
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Tadesse G, Tessema TS, Beyene G, Aseffa A. Molecular epidemiology of fluoroquinolone resistant Salmonella in Africa: A systematic review and meta-analysis. PLoS One 2018; 13:e0192575. [PMID: 29432492 PMCID: PMC5809059 DOI: 10.1371/journal.pone.0192575] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/25/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Wide-ranging evidence on the occurrence of fluoroquinolone (FQ) resistance genetic determinants in African Salmonella strains is not available. The main objectives of this study were to assess the heterogeneity, estimate pooled proportions and describe the preponderance of FQ-resistance determinants in typhoidal and non-typhoidal Salmonella (NTS) isolates of Africa. METHODS Genetic and phenotypic data on 6103 Salmonella isolates were considered. Meta- and frequency analyses were performed depending on the number of studies by category, number of isolates and risks of bias. A random effects model was used to assess heterogeneity and estimate pooled proportions. Relative and cumulative frequencies were calculated to describe the overall preponderance of FQ-resistance determinants in quinolone resistant isolates. RESULTS The pooled proportion of gyrA mutants (Salmonella enterica serovar Typhi, Salmonella enterica serovar Typhimurium, and Salmonella enterica serovar Enteritidis) was estimated at 5.7% (95% Confidence interval (CI) = 2.6, 9.8; Tau squared (T2) = 0.1105), and was higher in S. Typhi than in S. Typhimurium (odds ratio (OR) = 3.3, 95%CI = 2, 5.7). The proportions of each of gyrB and parC mutants, and strains with Plasmid Mediated Quinolone Resistance genes (qnrA, qnrB and qnrS) were low (≤ 0.3%). Overall, 23 mutant serotypes were identified, and most strains had mutations at codons encoding Ser83 and Asp87 of gyrA (82%, 95%CI = 78, 86). CONCLUSIONS Mutations at gyrA appear to account for ciprofloxacin non-susceptibility in most clinical Salmonella strains in Africa. The estimates could be harnessed to develop a mismatch-amplification mutation-assay for the detection of FQ-resistant strains in Africa.
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Affiliation(s)
- Getachew Tadesse
- Department of Biomedical Sciences, College of Veterinary Medicine and Agriculture, Addis Ababa University, Debre Zeit, Ethiopia
| | - Tesfaye S. Tessema
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Getenet Beyene
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute (AHRI), ALERT Campus, Addis Ababa, Ethiopia
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Vosik D, Tewari D, Dettinger L, M'ikanatha NM, Shariat NW. CRISPR Typing and Antibiotic Resistance Correlates with Polyphyletic Distribution in Human Isolates of Salmonella Kentucky. Foodborne Pathog Dis 2018; 15:101-108. [PMID: 29394097 DOI: 10.1089/fpd.2017.2298] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although infrequently associated with reported salmonellosis in humans, Salmonella enterica, subsp. enterica serovar Kentucky (ser. Kentucky) is the most common nonclinical, nonhuman serovar reported in the United States. The goal of this study was to use Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-multi-virulence-locus sequence typing (MVLST) to subtype a collection of human clinical isolates of ser. Kentucky submitted to the Pennsylvania Department of Health and to determine the extent of antibiotic resistance in these strains. This analysis highlighted the polyphyletic nature of ser. Kentucky, and separated our isolates into two groups, Group I and Group II, which were equally represented in our collection. Furthermore, antimicrobial susceptibility testing on all isolates using a National Antimicrobial Resistance Monitoring System (NARMS) panel of antibiotics demonstrated that resistance profiles could be divided into two groups. Group I isolates were resistant to cephems and penicillins, whereas Group II isolates were resistant to quinolones, gentamicin, and sulfisoxazole. Collectively, 50% of isolates were resistant to three or more classes of antibiotics and 30% were resistant to five or more classes. The correlation of antibiotic resistance with the two different lineages may reflect adaptation within two distinct reservoirs of ser. Kentucky, with differential exposure to antimicrobials.
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Affiliation(s)
- Dorothy Vosik
- 1 Department of Biology, Gettysburg College , Gettysburg, Pennsylvania
| | - Deepanker Tewari
- 2 Pennsylvania Veterinary Laboratory , Pennsylvania Department of Agriculture, Harrisburg, Pennsylvania
| | - Lisa Dettinger
- 3 Bureau of Laboratories , Pennsylvania Department of Health, Exton, Pennsylvania
| | - Nkuchia M M'ikanatha
- 4 Division of Infectious Disease Epidemiology , Pennsylvania Department of Health, Harrisburg, Pennsylvania.,5 Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Nikki W Shariat
- 1 Department of Biology, Gettysburg College , Gettysburg, Pennsylvania
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69
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Nhung NT, Van NTB, Cuong NV, Duong TTQ, Nhat TT, Hang TTT, Nhi NTH, Kiet BT, Hien VB, Ngoc PT, Campbell J, Thwaites G, Carrique-Mas J. Antimicrobial residues and resistance against critically important antimicrobials in non-typhoidal Salmonella from meat sold at wet markets and supermarkets in Vietnam. Int J Food Microbiol 2018; 266:301-309. [PMID: 29275223 PMCID: PMC5783717 DOI: 10.1016/j.ijfoodmicro.2017.12.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/01/2017] [Accepted: 12/15/2017] [Indexed: 12/14/2022]
Abstract
Excessive antimicrobial usage and deficiencies in hygiene in meat production systems may result in undesirable human health hazards, such as the presence of antimicrobial drug residues and non-typhoidal Salmonella (NTS), including antimicrobial resistant (AMR) NTS. Recently, Vietnam has witnessed the emergence of integrated intensive animal production systems, coexisting with more traditional, locally-sourced wet markets. To date no systematic studies have been carried out to compare health hazards in beef, pork and chicken in different production systems. We aimed to: (1) estimate the prevalence of antimicrobial residues in beef, pork and chicken meat; (2) investigate the prevalence and levels of NTS contamination; and (3) investigate serovar distribution and AMR against critically important antimicrobials by animal species and type of retail (wet market vs. supermarket) in Vietnam. Fresh pork, beef and chicken meat samples (N=357) sourced from wet markets and supermarkets in Ho Chi Minh City (HCMC), Hanoi and Dong Thap were screened for antimicrobial residues by PremiTest, and were further investigated by Charm II. Samples from HCMC (N=113) were cultured using ISO 6579:2002/Amd 1:2007. NTS bacteria were quantified using a minimum probable number (MPN) technique. NTS isolates were assigned to serovar by Multilocus Sequence Typing (MLST), and were investigated for their phenotypic susceptibility against 32 antimicrobials. A total of 26 (7.3%) samples tested positive by PremiTest (9.5% beef, 4.1% pork and 8.4% chicken meat). Sulfonamides, tetracyclines and macrolides were detected by Charm in 3.1%, 2.8% and 2.0% samples, respectively. Overall, meat samples from wet markets had a higher prevalence of residues than those from supermarkets (9.6% vs. 2.6%) (p=0.016). NTS were isolated from 68.4% samples from HCMC. Chicken samples from wet markets had by far the highest NTS counts (median 3.2 logMPN/g). NTS isolates displayed high levels of resistance against quinolones (52.2%) and β-lactams (49.6%), but low levels against 3rd generation cephalosporins (4.4%) and aminoglycosides (0.8%). The highest adjusted prevalence of multidrug resistance (MDR) corresponded to isolates from chicken meat and pork (OR 8.3 and 1.8, respectively) (baseline=beef). S. Kentucky was the most common serovar identified (11 from chicken, 1 from beef) and 91.7% isolates was MDR. 11/12 isolates corresponded to ST198, a worldwide-disseminated multi-resistant NTS clone. We recommend stepping up policy measures to promote responsible antimicrobial use in animal production, as well as awareness about withdrawal periods to limit the hazard of residues in animal products, and improving slaughtering/hygiene procedures to limit cross-contamination with NTS, particularly in poultry wet markets.
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Affiliation(s)
- Nguyen Thi Nhung
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam.
| | - Nguyen Thi Bich Van
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
| | | | - Tran Thi Nhat
- National Institute of Veterinary Research, Hanoi, Viet Nam
| | | | - Nguyen Thi Hong Nhi
- Sub-Department of Animal Health and Production, Dong Thap Province, Viet Nam
| | - Bach Tuan Kiet
- Sub-Department of Animal Health and Production, Dong Thap Province, Viet Nam
| | - Vo Be Hien
- Sub-Department of Animal Health and Production, Dong Thap Province, Viet Nam
| | - Pham Thi Ngoc
- National Institute of Veterinary Research, Hanoi, Viet Nam
| | - James Campbell
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, United Kingdom
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, United Kingdom
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, United Kingdom
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70
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Williamson DA, Lane CR, Easton M, Valcanis M, Strachan J, Veitch MG, Kirk MD, Howden BP. Increasing Antimicrobial Resistance in Nontyphoidal Salmonella Isolates in Australia from 1979 to 2015. Antimicrob Agents Chemother 2018; 62:e02012-17. [PMID: 29180525 PMCID: PMC5786757 DOI: 10.1128/aac.02012-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/13/2017] [Indexed: 12/28/2022] Open
Abstract
Australia has high and increasing rates of salmonellosis. To date, the serovar distribution and associated antimicrobial resistance (AMR) patterns of nontyphoidal Salmonella enterica (NTS) in Australia have not been assessed. Such information provides critical knowledge about AMR in the food chain and informs decisions about public health. We reviewed longitudinal data on NTS in two Australian states over a 37-year period, between 1979 and 2015, and antimicrobial resistance since 1984. Overall, 17% of isolates were nonsusceptible to at least one antimicrobial, 4.9% were nonsusceptible to ciprofloxacin, and 0.6% were nonsusceptible to cefotaxime. In total, 2.5% of isolates were from invasive infections, with no significant difference in AMR profiles between invasive and noninvasive isolates. Most isolates with clinically relevant AMR profiles were associated with travel, particularly to Southeast Asia, with multiple "incursions" of virulent and resistant clones into Australia. Our findings represent the largest longitudinal surveillance system for NTS in Australia and provide valuable public health knowledge on the trends and distribution of AMR in NTS. Ongoing surveillance is critical to identify local emergence of resistant isolates.
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Affiliation(s)
- Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Marion Easton
- Department of Health and Human Services, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Janet Strachan
- Department of Health and Human Services, Victoria, Australia
| | - Mark G Veitch
- Department of Health and Human Services, Tasmania, Australia
| | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
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71
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The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2016. EFSA J 2018; 16:e05182. [PMID: 32625816 PMCID: PMC7009656 DOI: 10.2903/j.efsa.2018.5182] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The data on antimicrobial resistance in zoonotic and indicator bacteria in 2016, submitted by 28 EU Member States (MSs), were jointly analysed by the EFSA and ECDC. Resistance in bacterial isolates of zoonotic Salmonella and Campylobacter from humans, animals and food, and resistance in indicator Escherichia coli as well as in meticillin-resistant Staphylococcus aureus from animals and food were addressed. 'Microbiological' resistance was assessed using epidemiological cut-off (ECOFF) values; for some countries, qualitative data on isolates from humans were interpreted in a way that corresponds closely to ECOFF-defined 'microbiological' resistance. In Salmonella from humans, the occurrence of resistance to ampicillin, sulfonamides and tetracyclines was high, whereas resistance to third-generation cephalosporins was low. In Salmonella and E. coli isolates from broilers, fattening turkeys and their meat, resistance to ampicillin, (fluoro)quinolones, tetracyclines and sulfonamides was frequently high, whereas resistance to third-generation cephalosporins was rare. The occurrence of ESBL-/AmpC producers was low in Salmonella and E. coli from poultry and in Salmonella from humans. The prevalence of ESBL-/AmpC-producing E. coli, assessed in poultry and its meat for the first time, showed marked variations among MSs. Fourteen presumptive carbapenemase-producing E. coli were detected from broilers and its meat in two MSs. Resistance to colistin was observed at low levels in Salmonella and E. coli from poultry and meat thereof and in Salmonella from humans. In Campylobacter from humans, broilers and broiler meat, resistance to ciprofloxacin and tetracyclines was high to extremely high, whereas resistance to erythromycin was low to moderate. Combined resistance to critically important antimicrobials in isolates from both humans and animals was generally uncommon, but very high to extremely high multidrug resistance levels were observed in certain Salmonella serovars. Specific serovars of Salmonella (notably Kentucky) from both humans and animals exhibited high-level resistance to ciprofloxacin, in addition to findings of ESBL.
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Abstract
Carrion's disease (CD) is a neglected biphasic vector-borne illness related to Bartonella bacilliformis. It is found in the Andean valleys and is transmitted mainly by members of the Lutzomyia genus but also by blood transfusions and from mother to child. The acute phase, Oroya fever, presents severe anemia and fever. The lethality is high in the absence of adequate treatment, despite the organism being susceptible to most antibiotics. Partial immunity is developed after infection by B. bacilliformis, resulting in high numbers of asymptomatic carriers. Following infection there is the chronic phase, Peruvian warts, involving abnormal proliferation of the endothelial cells. Despite potentially being eradicable, CD has been expanded due to human migration and geographical expansion of the vector. Moreover, in vitro studies have demonstrated the risk of the development of antimicrobial resistance. These findings, together with the description of new Bartonella species producing CD-like infections, the presence of undescribed potential vectors in new areas, the lack of adequate diagnostic tools and knowledge of the immunology and bacterial pathogenesis of CD, and poor international visibility, have led to the risk of increasing the potential expansion of resistant strains which will challenge current treatment schemes as well as the possible appearance of CD in areas where it is not endemic.
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Affiliation(s)
- Cláudia Gomes
- Institute for Global Health, Barcelona Centre for International Health Research, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Joaquim Ruiz
- Institute for Global Health, Barcelona Centre for International Health Research, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
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73
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Afroj S, Aldahami K, Reddy G, Guard J, Adesiyun A, Samuel T, Abdela W. Simultaneous Detection of Multiple Salmonella Serovars from Milk and Chicken Meat by Real-Time PCR Using Unique Genomic Target Regions. J Food Prot 2017; 80:1944-1957. [PMID: 29058479 DOI: 10.4315/0362-028x.jfp-17-133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/19/2017] [Indexed: 12/29/2022]
Abstract
A novel genomic and plasmid target-based PCR platform was developed for the detection of Salmonella serovars Heidelberg, Dublin, Hadar, Kentucky, and Enteritidis. Unique genome loci were obtained through extensive genome mining of protein databases and comparative genomic analysis of these serovars. Assays targeting Salmonella serovars Hadar, Heidelberg, Kentucky, and Dublin had 100% specificity and sensitivity, whereas those for Salmonella Enteritidis had 97% specificity and 88% sensitivity. The limits of detection for Salmonella serovars Heidelberg, Kentucky, Hadar, Enteritidis, and Dublin were 12, 9, 40, 13, and 5,280 CFU, respectively. A sensitivity assay was also performed by using milk artificially inoculated with pooled Salmonella serovars, yielding a detection limit of 1 to10 CFU/25 mL of milk samples after enrichment. The minimum DNA detected using the multiplexed TaqMan assay was 75.8 fg (1.53 × 101 genomic equivalents [GE]) for Salmonella Heidelberg, 140.8 fg (2.8 × 101 GE) for Salmonella Enteritidis, and 3.48 pg (6.96 × 102 GE) for Salmonella Dublin. PCR efficiencies were 89.8% for Salmonella Heidelberg, 94.5% for Salmonella Enteritidis, and 75.5% for Salmonella Dublin. Four types of 30 pasteurized milk samples were tested negative by culture techniques and with a genus-specific Salmonella invA gene PCR assay. Among 30 chicken samples similarly tested, 12 (40%) were positive by both culture and the invA PCR. Testing of these 12 samples with the serovar-specific PCR assay detected single and mixed contamination with Salmonella Kentucky, Salmonella Enteritidis, and Salmonella Heidelberg. Five unique primers were designed and tested by multiplex conventional PCR in conjunction with the use of the multiplex TaqMan assay with three of the primers. The diagnostic assays developed in this study could be used as tools for routine detection of these five Salmonella serovars and for epidemiological investigations of foodborne disease outbreaks.
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Affiliation(s)
- Sayma Afroj
- Department of Biology and.,Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.]).,Cellular and Molecular Biosciences Program, Auburn University, Auburn, Alabama 36849, USA
| | - Khaled Aldahami
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Gopal Reddy
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Jean Guard
- U.S. Department of Agriculture, Agricultural Research Service, Athens, Georgia 30602, USA
| | - Abiodun Adesiyun
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Temesgen Samuel
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Woubit Abdela
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
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Genome Sequences of Salmonella enterica subsp. enterica Serovar Kentucky Sequence Type 152 Isolated from Dairy Cows in the United States. GENOME ANNOUNCEMENTS 2017; 5:5/42/e01119-17. [PMID: 29051251 PMCID: PMC5646404 DOI: 10.1128/genomea.01119-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Salmonella enterica subsp. enterica serovar Kentucky (S. Kentucky) is frequently isolated from dairy cows in the United States, but is an infrequent cause of human salmonellosis. To investigate the genomic features of S Kentucky strains isolated from a single dairy farm, the genomes of eight isolates were sequenced and added to the public domain.
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75
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Tasmin R, Hasan NA, Grim CJ, Grant A, Choi SY, Alam MS, Bell R, Cavanaugh C, Balan KV, Babu US, Parveen S. Genotypic and phenotypic characterization of multidrug resistant Salmonella Typhimurium and Salmonella Kentucky strains recovered from chicken carcasses. PLoS One 2017; 12:e0176938. [PMID: 28481935 PMCID: PMC5421757 DOI: 10.1371/journal.pone.0176938] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/19/2017] [Indexed: 01/18/2023] Open
Abstract
Salmonella Typhimurium is the leading cause of human non-typhoidal gastroenteritis in the US. S. Kentucky is one the most commonly recovered serovars from commercially processed poultry carcasses. This study compared the genotypic and phenotypic properties of two Salmonella enterica strains Typhimurium (ST221_31B) and Kentucky (SK222_32B) recovered from commercially processed chicken carcasses using whole genome sequencing, phenotype characterizations and an intracellular killing assay. Illumina MiSeq platform was used for sequencing of two Salmonella genomes. Phylogenetic analysis employing homologous alignment of a 1,185 non-duplicated protein-coding gene in the Salmonella core genome demonstrated fully resolved bifurcating patterns with varying levels of diversity that separated ST221_31B and SK222_32B genomes into distinct monophyletic serovar clades. Single nucleotide polymorphism (SNP) analysis identified 2,432 (ST19) SNPs within 13 Typhimurium genomes including ST221_31B representing Sequence Type ST19 and 650 (ST152) SNPs were detected within 13 Kentucky genomes including SK222_32B representing Sequence Type ST152. In addition to serovar-specific conserved coding sequences, the genomes of ST221_31B and SK222_32B harbor several genomic regions with significant genetic differences. These included phage and phage-like elements, carbon utilization or transport operons, fimbriae operons, putative membrane associated protein-encoding genes, antibiotic resistance genes, siderophore operons, and numerous hypothetical protein-encoding genes. Phenotype microarray results demonstrated that ST221_31B is capable of utilizing certain carbon compounds more efficiently as compared to SK222_3B; namely, 1,2-propanediol, M-inositol, L-threonine, α-D-lactose, D-tagatose, adonitol, formic acid, acetoacetic acid, and L-tartaric acid. ST221_31B survived for 48 h in macrophages, while SK222_32B was mostly eliminated. Further, a 3-fold growth of ST221_31B was observed at 24 hours post-infection in chicken granulosa cells while SK222_32B was unable to replicate in these cells. These results suggest that Salmonella Typhimurium can survive host defenses better and could be more invasive than Salmonella Kentucky and provide some insights into the genomic determinants responsible for these differences.
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Affiliation(s)
- Rizwana Tasmin
- Agriculture, Food and Resource Sciences, University of Maryland, Eastern Shore, Princess Anne, Maryland, United States of America
| | - Nur A. Hasan
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, United States of America
- CosmosID Inc., Rockville, Maryland, United States of America
| | - Christopher J. Grim
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, United States of America
| | - Ar’Quette Grant
- Agriculture, Food and Resource Sciences, University of Maryland, Eastern Shore, Princess Anne, Maryland, United States of America
| | - Seon Young Choi
- CosmosID Inc., Rockville, Maryland, United States of America
| | - M. Samiul Alam
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, United States of America
| | - Rebecca Bell
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, United States of America
| | - Christopher Cavanaugh
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, United States of America
| | - Kannan V. Balan
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, United States of America
| | - Uma S. Babu
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, United States of America
| | - Salina Parveen
- Agriculture, Food and Resource Sciences, University of Maryland, Eastern Shore, Princess Anne, Maryland, United States of America
- * E-mail:
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76
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Yuan J, Guo W. Mechanisms of resistance to quinolones in Salmonella Typhimurium from patients with infectious diarrhea. Microbiol Immunol 2017; 61:138-143. [PMID: 28337780 DOI: 10.1111/1348-0421.12476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/20/2017] [Accepted: 03/22/2017] [Indexed: 11/28/2022]
Abstract
This study investigated the mechanisms of resistance of 36 quinolone-resistant Salmonella Typhimurium strains isolated from outpatients with infectious diarrhea in Beijing Tian Tan Hospital between 2013 and 2015. The resistance spectrum of the 36 strains was measured using a broth dilution method. Class 1 integrons harboring the β-lactamase gene and mutations in quinolone resistance determining regions were also investigated. All 36 quinolone-resistant Salmonella Typhimurium strains were found to be multidrug-resistant and the majority of these strains harbored Class 1 integrons. These findings study suggests that strategies for determining resistance spectrums should be implemented with greater urgency.
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Affiliation(s)
- Jing Yuan
- Emergency Department, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Wei Guo
- Emergency Department, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
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77
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Antimicrobial Resistance of Salmonella enterica Serovars Typhi and Paratyphi Isolates from a General Hospital in Karawaci, Tangerang, Indonesia: A Five-Year Review. Int J Microbiol 2017; 2017:6215136. [PMID: 28484494 PMCID: PMC5397621 DOI: 10.1155/2017/6215136] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/26/2017] [Accepted: 03/27/2017] [Indexed: 11/30/2022] Open
Abstract
Typhoid and paratyphoid fever known as enteric fever pose important global public health problem, with 21.6 million cases and approximately 250,000 deaths annually. It is a prevalent disease in Indonesia, but data on the antimicrobial resistance pattern is limited. This study aim was to provide data on the antimicrobial resistance pattern of S. Typhi and S. Paratyphi bloodstream isolates in a general hospital in Karawaci, Tangerang, Banten, Indonesia, during the period of January 2011 to December 2015. Susceptibility against antimicrobials was detected according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Out of a total of 168 isolates 55.4% were S. Typhi and 44.6% S. Paratyphi A. Most of the isolates, 92.9%, were from children aged 6–18 years and adult population. There was low resistance of S. Typhi against ampicillin, trimethoprim-sulfamethoxazole, ceftriaxone, ciprofloxacin, and levofloxacin, similar to previous studies in Indonesia. In the 2011–2015 period, resistance rates against most antimicrobials and MDR rate of S. Typhi and S. Paratyphi were low, emphasizing that there is a distinct epidemiological dynamic of the enteric fever in Indonesia.
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78
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Kim SW, Haley BJ, Roberson D, Allard M, Hammack TS, Brown EW, Van Kessel JAS. Genome Sequences of Four Nonhuman/Nonclinical Salmonella enterica Serovar Kentucky ST198 Isolates Recovered between 1972 and 1973. GENOME ANNOUNCEMENTS 2017; 5:e01699-16. [PMID: 28302786 PMCID: PMC5356063 DOI: 10.1128/genomea.01699-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/12/2017] [Indexed: 11/20/2022]
Abstract
Salmonella enterica serovar Kentucky is a polyphyletic member of S. enterica subclade A1 with multiple sequence types that often colonize the same hosts but in different frequencies on different continents. To evaluate the genomic features involved in S Kentucky host specificity, we sequenced the genomes of four isolates recovered in the 1970s.
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Affiliation(s)
- Seon-Woo Kim
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland, USA
| | - Bradd J Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland, USA
| | - Dwayne Roberson
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Marc Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Thomas S Hammack
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Eric W Brown
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Jo Ann S Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland, USA
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79
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Walther B, Tedin K, Lübke-Becker A. Multidrug-resistant opportunistic pathogens challenging veterinary infection control. Vet Microbiol 2017; 200:71-78. [DOI: 10.1016/j.vetmic.2016.05.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 12/23/2022]
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80
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Duchêne S, Holt KE, Weill FX, Le Hello S, Hawkey J, Edwards DJ, Fourment M, Holmes EC. Genome-scale rates of evolutionary change in bacteria. Microb Genom 2016; 2:e000094. [PMID: 28348834 PMCID: PMC5320706 DOI: 10.1099/mgen.0.000094] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 10/24/2016] [Indexed: 01/26/2023] Open
Abstract
Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host–pathogen associations and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with ‘ancient DNA’ data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from approximately 10−5 to 10−8 nucleotide substitutions per site year−1. This variation was negatively associated with sampling time, with this relationship best described by an exponential decay curve. To avoid potential estimation biases, such time-dependency should be considered when inferring evolutionary time-scales in bacteria.
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Affiliation(s)
- Sebastian Duchêne
- 1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.,2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kathryn E Holt
- 2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Simon Le Hello
- 4Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris 75015, France
| | - Jane Hawkey
- 2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David J Edwards
- 2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mathieu Fourment
- 1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- 1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
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81
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Genome Sequences of Two Salmonella enterica Serovar Kentucky Isolates Recovered from Poultry Carcasses in the United States. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01289-16. [PMID: 27856587 PMCID: PMC5114379 DOI: 10.1128/genomea.01289-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report here the draft genome sequences of two Salmonella enterica serovar Kentucky eBurstGroup 15 isolates collected from poultry carcasses in Georgia (USA).
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82
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Haley BJ, Kim SW, Pettengill J, Luo Y, Karns JS, Van Kessel JAS. Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America. PLoS One 2016; 11:e0161225. [PMID: 27695032 PMCID: PMC5047448 DOI: 10.1371/journal.pone.0161225] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 08/02/2016] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from healthy poultry and dairy cows and is occasionally isolated from people with clinical disease. A genomic analysis of 119 isolates collected in the United States from dairy cows, ground beef, poultry and poultry products, and human clinical cases was conducted. Results of the analysis demonstrated that the majority of poultry and bovine-associated S. Kentucky were sequence type (ST) 152. Several bovine-associated (n = 3) and food product isolates (n = 3) collected from the United States and the majority of human clinical isolates were ST198, a sequence type that is frequently isolated from poultry and occasionally from human clinical cases in Northern Africa, Europe and Southeast Asia. A phylogenetic analysis indicated that both STs are more closely related to other Salmonella serovars than they are to each other. Additionally, there was strong evidence of an evolutionary divergence between the poultry-associated and bovine-associated ST152 isolates that was due to polymorphisms in four core genome genes. The ST198 isolates recovered from dairy farms in the United States were phylogenetically distinct from those collected from human clinical cases with 66 core genome SNPs differentiating the two groups, but more isolates are needed to determine the significance of this distinction. Identification of S. Kentucky ST198 from dairy animals in the United States suggests that the presence of this pathogen should be monitored in food-producing animals.
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Affiliation(s)
- Bradd J. Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
| | - James Pettengill
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America
| | - Yan Luo
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America
| | - Jeffrey S. Karns
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Jo Ann S. Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
- * E-mail:
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83
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A toxin antitoxin system promotes the maintenance of the IncA/C-mobilizable Salmonella Genomic Island 1. Sci Rep 2016; 6:32285. [PMID: 27576575 PMCID: PMC5006074 DOI: 10.1038/srep32285] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/05/2016] [Indexed: 01/09/2023] Open
Abstract
The multidrug resistance Salmonella Genomic Island 1 (SGI1) is an integrative mobilizable element identified in several enterobacterial pathogens. This chromosomal island requires a conjugative IncA/C plasmid to be excised as a circular extrachromosomal form and conjugally mobilized in trans. Preliminary observations suggest stable maintenance of SGI1 in the host chromosome but paradoxically also incompatibility between SGI1 and IncA/C plasmids. Here, using a Salmonella enterica serovar Agona clonal bacterial population as model, we demonstrate that a Toxin-Antitoxin (TA) system encoded by SGI1 plays a critical role in its stable host maintenance when an IncA/C plasmid is concomitantly present. This system, designated sgiAT for Salmonella genomic island 1 Antitoxin and Toxin respectively, thus seems to play a stabilizing role in a situation where SGI1 is susceptible to be lost through plasmid IncA/C-mediated excision. Moreover and for the first time, the incompatibility between SGI1 and IncA/C plasmids was experimentally confirmed.
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84
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Fuzi M. Dissimilar Fitness Associated with Resistance to Fluoroquinolones Influences Clonal Dynamics of Various Multiresistant Bacteria. Front Microbiol 2016; 7:1017. [PMID: 27458434 PMCID: PMC4935693 DOI: 10.3389/fmicb.2016.01017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/15/2016] [Indexed: 01/24/2023] Open
Abstract
Fitness cost associated with resistance to fluoroquinolones was recently shown to vary across clones of methicillin-resistant Staphylococcus aureus and extended-spectrum β-lactamase-producing Klebsiella pneumoniae. The resulting dissimilar fitness should have influenced the clonal dynamics and thereby the rates of resistance for these pathogens. Moreover, a similar mechanism was recently proposed for the emergence of the H30 and H30R lineages of ESBL-producing E. coli and the major international clone (ribotype 027) of Clostridium difficile. Furthermore, several additional international clones of various multiresistant bacteria are suspect to have been selected by an analogous process. An ability to develop favorable mutations in the gyrase and topoisomerase IV genes seems to be a prerequisite for pathogens to retain fitness while showing high-level resistance to fluoroquinolones. Since, the consumption of other "non-fluoroquinolone" groups of antibiotics have also contributed to the rise in resistance rates a more judicious use of antibiotics in general and of fluoroquinolones in particular could ameliorate the international resistance situation.
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Affiliation(s)
- Miklos Fuzi
- Institute of Medical Microbiology, Semmelweis UniversityBudapest, Hungary
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85
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Card R, Vaughan K, Bagnall M, Spiropoulos J, Cooley W, Strickland T, Davies R, Anjum MF. Virulence Characterisation of Salmonella enterica Isolates of Differing Antimicrobial Resistance Recovered from UK Livestock and Imported Meat Samples. Front Microbiol 2016; 7:640. [PMID: 27199965 PMCID: PMC4852480 DOI: 10.3389/fmicb.2016.00640] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/18/2016] [Indexed: 12/22/2022] Open
Abstract
Salmonella enterica is a foodborne zoonotic pathogen of significant public health concern. We have characterized the virulence and antimicrobial resistance gene content of 95 Salmonella isolates from 11 serovars by DNA microarray recovered from UK livestock or imported meat. Genes encoding resistance to sulphonamides (sul1, sul2), tetracycline [tet(A), tet(B)], streptomycin (strA, strB), aminoglycoside (aadA1, aadA2), beta-lactam (bla TEM), and trimethoprim (dfrA17) were common. Virulence gene content differed between serovars; S. Typhimurium formed two subclades based on virulence plasmid presence. Thirteen isolates were selected by their virulence profile for pathotyping using the Galleria mellonella pathogenesis model. Infection with a chicken invasive S. Enteritidis or S. Gallinarum isolate, a multidrug resistant S. Kentucky, or a S. Typhimurium DT104 isolate resulted in high mortality of the larvae; notably presence of the virulence plasmid in S. Typhimurium was not associated with increased larvae mortality. Histopathological examination showed that infection caused severe damage to the Galleria gut structure. Enumeration of intracellular bacteria in the larvae 24 h post-infection showed increases of up to 7 log above the initial inoculum and transmission electron microscopy (TEM) showed bacterial replication in the haemolymph. TEM also revealed the presence of vacuoles containing bacteria in the haemocytes, similar to Salmonella containing vacuoles observed in mammalian macrophages; although there was no evidence from our work of bacterial replication within vacuoles. This work shows that microarrays can be used for rapid virulence genotyping of S. enterica and that the Galleria animal model replicates some aspects of Salmonella infection in mammals. These procedures can be used to help inform on the pathogenicity of isolates that may be antibiotic resistant and have scope to aid the assessment of their potential public and animal health risk.
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Affiliation(s)
- Roderick Card
- Department of Bacteriology, Animal and Plant Health Agency Woking, UK
| | - Kelly Vaughan
- Department of Bacteriology, Animal and Plant Health Agency Woking, UK
| | - Mary Bagnall
- Department of Bacteriology, Animal and Plant Health Agency Woking, UK
| | - John Spiropoulos
- Department of Pathology, Animal and Plant Health Agency Woking, UK
| | - William Cooley
- Department of Bacteriology, Animal and Plant Health Agency Woking, UK
| | - Tony Strickland
- Department of Pathology, Animal and Plant Health Agency Woking, UK
| | - Rob Davies
- Department of Bacteriology, Animal and Plant Health Agency Woking, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency Woking, UK
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86
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Chattaway MA, Aboderin AO, Fashae K, Okoro CK, Opintan JA, Okeke IN. Fluoroquinolone-Resistant Enteric Bacteria in Sub-Saharan Africa: Clones, Implications and Research Needs. Front Microbiol 2016; 7:558. [PMID: 27148238 PMCID: PMC4841292 DOI: 10.3389/fmicb.2016.00558] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/04/2016] [Indexed: 11/13/2022] Open
Abstract
Fluoroquinolones came into widespread use in African countries in the early 2000s, after patents for the first generation of these drugs expired. By that time, quinolone antibacterial agents had been used intensively worldwide and resistant lineages of many bacterial species had evolved. We sought to understand which Gram negative enteric pandemic lineages have been reported from Africa, as well as the nature and transmission of any indigenous resistant clones. A systematic review of articles indexed in the Medline and AJOL literature databases was conducted. We report on the findings of 43 eligible studies documenting local or pandemic fluoroquinolone-resistant enteric clones in sub-Sahara African countries. Most reports are of invasive non-typhoidal Salmonella and Escherichia coli lineages and there have been three reports of cholera outbreaks caused by fluoroquinolone-resistant Vibrio cholerae O1. Fluoroquinolone-resistant clones have also been reported from commensals and animal isolates but there are few data for non-Enterobacteriaceae and almost none for difficult-to-culture Campylobacter spp. Fluoroquinolone-resistant lineages identified in African countries were universally resistant to multiple other classes of antibacterial agents. Although as many as 972 non-duplicate articles refer to fluoroquinolone resistance in enteric bacteria from Africa, most do not report on subtypes and therefore information on the epidemiology of fluoroquinolone-resistant clones is available from only a handful of countries in the subcontinent. When resistance is reported, resistance mechanisms and lineage information is rarely investigated. Insufficient attention has been given to molecular and sequence-based methods necessary for identifying and tracking resistant clones in Africa and more research is needed in this area.
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Affiliation(s)
- Marie A Chattaway
- Gastrointestinal Bacteria Reference Unit, Public Health England London, UK
| | - Aaron O Aboderin
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Obafemi Awolowo University Ile-Ife, Nigeria
| | - Kayode Fashae
- Department of Microbiology, University of Ibadan Ibadan, Nigeria
| | | | - Japheth A Opintan
- Department of Medical Microbiology, School of Biomedical and Allied Health Sciences, University of Ghana Accra, Ghana
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan Ibadan, Nigeria
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87
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Salmonellosis: the role of poultry meat. Clin Microbiol Infect 2015; 22:110-121. [PMID: 26708671 DOI: 10.1016/j.cmi.2015.12.004] [Citation(s) in RCA: 338] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/02/2015] [Accepted: 12/03/2015] [Indexed: 02/07/2023]
Abstract
Salmonellosis remains one of the most frequent food-borne zoonoses, constituting a worldwide major public health concern. Currently, at a global level, the main sources of infection for humans include meat products, including the consumption of contaminated poultry meat, in spite of the success of Salmonella control measures implemented in food-animal production of industrialized countries. In recent years, a shift in Salmonella serotypes related to poultry and poultry production has been reported in diverse geographical regions, being particularly associated with the spread of certain well-adapted clones. Moreover, antimicrobial resistance in non-typhoidal Salmonella is considered one of the major public health threats related with food-animal production, including the poultry production chain and poultry meat, which is an additional concern in the management of salmonellosis. The circulation of the same multidrug-resistant Salmonella clones and/or identical mobile genetic elements encoding antibiotic resistance genes from poultry to humans highlights this scenario. The purpose of this review was to provide an overview of the role of poultry meat on salmonellosis at a global scale and the main problems that could hinder the success of Salmonella control measures at animal production level. With the increasing globalization of foodstuffs like poultry meat, new problems and challenges might arise regarding salmonellosis control, making new integrated intervention strategies necessary along the food chain.
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88
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Ktari S, Le Hello S, Ksibi B, Courdavault L, Mnif B, Maalej S, Fabre L, Hammami A, Weill FX. Carbapenemase-producing Salmonella enterica serotype Kentucky ST198, North Africa. J Antimicrob Chemother 2015; 70:3405-7. [PMID: 26377865 DOI: 10.1093/jac/dkv276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sonia Ktari
- Faculté de médecine de Sfax, Centre Hospitalier Universitaire Habib Bourguiba, Sfax, Tunisia
| | - Simon Le Hello
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - Boutheina Ksibi
- Faculté de médecine de Sfax, Centre Hospitalier Universitaire Habib Bourguiba, Sfax, Tunisia
| | | | - Basma Mnif
- Faculté de médecine de Sfax, Centre Hospitalier Universitaire Habib Bourguiba, Sfax, Tunisia
| | - Sonda Maalej
- Faculté de médecine de Sfax, Centre Hospitalier Universitaire Habib Bourguiba, Sfax, Tunisia
| | - Laetitia Fabre
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - Adnene Hammami
- Faculté de médecine de Sfax, Centre Hospitalier Universitaire Habib Bourguiba, Sfax, Tunisia
| | - François-Xavier Weill
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France
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89
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Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ, Feasey NA, Kingsley RA, Thomson NR, Keane JA, Weill FX, Edwards DJ, Hawkey J, Harris SR, Mather AE, Cain AK, Hadfield J, Hart PJ, Thieu NTV, Klemm EJ, Glinos DA, Breiman RF, Watson CH, Kariuki S, Gordon MA, Heyderman RS, Okoro C, Jacobs J, Lunguya O, Edmunds WJ, Msefula C, Chabalgoity JA, Kama M, Jenkins K, Dutta S, Marks F, Campos J, Thompson C, Obaro S, MacLennan CA, Dolecek C, Keddy KH, Smith AM, Parry CM, Karkey A, Mulholland EK, Campbell JI, Dongol S, Basnyat B, Dufour M, Bandaranayake D, Naseri TT, Singh SP, Hatta M, Newton P, Onsare RS, Isaia L, Dance D, Davong V, Thwaites G, Wijedoru L, Crump JA, De Pinna E, Nair S, Nilles EJ, Thanh DP, Turner P, Soeng S, Valcanis M, Powling J, Dimovski K, Hogg G, Farrar J, Holt KE, Dougan G. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nat Genet 2015; 47:632-9. [PMID: 25961941 PMCID: PMC4921243 DOI: 10.1038/ng.3281] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/23/2015] [Indexed: 11/09/2022]
Abstract
The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.
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Affiliation(s)
- Vanessa K Wong
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Department of Microbiology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK
| | - Stephen Baker
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [3] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | | | | | - Robert A Kingsley
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Institute of Food Research, Norwich Research Park, Norwich, UK
| | - Nicholas R Thomson
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Jane Hawkey
- 1] Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia. [2] Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | | | | | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Peter J Hart
- Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nga Tran Vu Thieu
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Robert F Breiman
- 1] Kenya Medical Research Institute (KEMRI), Nairobi, Kenya. [2] Centers for Disease Control and Prevention, Atlanta, Georgia, USA. [3] Emory Global Health Institute, Atlanta, Georgia, USA
| | - Conall H Watson
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Samuel Kariuki
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Melita A Gordon
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Robert S Heyderman
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Jan Jacobs
- 1] Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium. [2] Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven, Belgium
| | - Octavie Lunguya
- 1] National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo. [2] University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Chisomo Msefula
- 1] Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi. [2] Microbiology Department, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Jose A Chabalgoity
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo, Uruguay
| | | | | | - Shanta Dutta
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Florian Marks
- International Vaccine Institute, Department of Epidemiology, Seoul, Republic of Korea
| | - Josefina Campos
- Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina
| | - Corinne Thompson
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Stephen Obaro
- 1] Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA. [2] University of Abuja Teaching Hospital, Abuja, Nigeria. [3] Bingham University, Karu, Nigeria
| | - Calman A MacLennan
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK. [3] Novartis Vaccines Institute for Global Health, Siena, Italy
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Karen H Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher M Parry
- 1] Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK. [2] Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Abhilasha Karkey
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - E Kim Mulholland
- 1] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. [2] Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - James I Campbell
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Sabina Dongol
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Buddha Basnyat
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Muriel Dufour
- Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua, New Zealand
| | - Don Bandaranayake
- National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua, New Zealand
| | | | - Shalini Pravin Singh
- National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva, Fiji
| | - Mochammad Hatta
- Department of Microbiology, Hasanuddin University, Makassar, Indonesia
| | - Paul Newton
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | | | | | - David Dance
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Viengmon Davong
- Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Guy Thwaites
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Lalith Wijedoru
- 1] Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. [2] Paediatric Emergency Medicine, Chelsea and Westminster Hospital, London, UK
| | - John A Crump
- Centre for International Health and Otago International Health Research Network, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Elizabeth De Pinna
- Salmonella Reference Service, Public Health England, Colindale, London, UK
| | - Satheesh Nair
- Salmonella Reference Service, Public Health England, Colindale, London, UK
| | - Eric J Nilles
- Emerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva, Fiji
| | - Duy Pham Thanh
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Paul Turner
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. [3] Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sona Soeng
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Mary Valcanis
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Joan Powling
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Karolina Dimovski
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Geoff Hogg
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jeremy Farrar
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
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90
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Wasyl D, Kern-Zdanowicz I, Domańska-Blicharz K, Zając M, Hoszowski A. High-level fluoroquinolone resistant Salmonella enterica serovar Kentucky ST198 epidemic clone with IncA/C conjugative plasmid carrying blaCTX-M-25 gene. Vet Microbiol 2015; 175:85-91. [DOI: 10.1016/j.vetmic.2014.10.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/03/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
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91
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Le Hello S. Salmonella : une bactérie multi-résistante aux antibiotiques dans nos assiettes. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.antinf.2014.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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92
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Tadesse G, Tessema TS. A meta-analysis of the prevalence of Salmonella in food animals in Ethiopia. BMC Microbiol 2014; 14:270. [PMID: 25398272 PMCID: PMC4234885 DOI: 10.1186/s12866-014-0270-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 10/15/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The globalization of the food supply and the increased movements of people, animals and goods have increased the threat of Salmonella infections in several countries. The objective of this study was to estimate the prevalence of Salmonella in food animals in Ethiopia by using meta-analytical methods. RESULTS The prevalence of Salmonella in slaughtered cattle, sheep, goats and pigs were 7.07%, 8.41%, 9.01% and 43.81% respectively. The occurrence of Salmonella was significantly higher in pigs than in slaughtered true ruminants (p <0.001) but not significantly different between cattle, sheep and goats (p >0. 05). S. Mishmarhaemek, S. Infantis and S. Hadar were the predominant isolates in cattle, small ruminants and pigs respectively. S. Typhimurium was isolated from all host species. CONCLUSIONS All food animals are considerable reservoirs of Salmonella and pose a significant risk to public health. Safety measures in slaughter houses and butcheries and education of the public could reduce the risk of transmission of Salmonella from animals to humans.
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Affiliation(s)
- Getachew Tadesse
- Department of Biomedical Sciences, College of Veterinary Medicine and Agriculture, Addis Ababa University, P.O. Box 34, Debra Zeit, Ethiopia.
| | - Tesfaye S Tessema
- Institute of Biotechnology, College of Natural and Computational Sciences, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
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93
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Wang C, Sui Z, Leclercq SO, Zhang G, Zhao M, Chen W, Feng J. Functional characterization and phylogenetic analysis of acquired and intrinsic macrolide phosphotransferases in theBacillus cereusgroup. Environ Microbiol 2014; 17:1560-73. [DOI: 10.1111/1462-2920.12578] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/21/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Chao Wang
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Zhihai Sui
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Sébastien Olivier Leclercq
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Gang Zhang
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Meilin Zhao
- School of Food and Biological Engineering; Jiangsu University; Zhenjiang Jiangsu 212013 China
| | - Weiqi Chen
- Department of Environmental and Biological Pharmaceutical; Beijing Industrial Technician College; Beijing 100023 China
| | - Jie Feng
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
- Beijing Key Laboratory of Microbial Drug Resistance and Resistome; Beijing 100101 China
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94
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Abgottspon H, Zurfluh K, Nüesch-Inderbinen M, Hächler H, Stephan R. Quinolone resistance mechanisms in Salmonella enterica serovars Hadar, Kentucky, Virchow, Schwarzengrund, and 4,5,12:i:-, isolated from humans in Switzerland, and identification of a novel qnrD variant, qnrD2, in S. Hadar. Antimicrob Agents Chemother 2014; 58:3560-3. [PMID: 24733466 PMCID: PMC4068464 DOI: 10.1128/aac.02404-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/06/2014] [Indexed: 11/20/2022] Open
Abstract
Human isolates of Salmonella enterica serovars Hadar, Kentucky, Virchow, Schwarzengrund, and the monophasic variant of S. Typhimurium, Salmonella enterica subsp. enterica serovar 4,5,12:i:- were examined for mutations within the quinolone resistance target genes gyrA, gyrB, parC, and parE and for plasmid-mediated resistance genes. Differences were observed among the serovars. A novel variant of qnrD, qnrD2, was detected in an S. Hadar isolate.
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Affiliation(s)
- Helga Abgottspon
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | | | - Herbert Hächler
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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95
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Redgrave LS, Sutton SB, Webber MA, Piddock LJV. Fluoroquinolone resistance: mechanisms, impact on bacteria, and role in evolutionary success. Trends Microbiol 2014; 22:438-45. [PMID: 24842194 DOI: 10.1016/j.tim.2014.04.007] [Citation(s) in RCA: 573] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/11/2014] [Accepted: 04/16/2014] [Indexed: 12/12/2022]
Abstract
Quinolone and fluoroquinolone antibiotics are potent, broad-spectrum agents commonly used to treat a range of infections. Resistance to these agents is multifactorial and can be via one or a combination of target-site gene mutations, increased production of multidrug-resistance (MDR) efflux pumps, modifying enzymes, and/or target-protection proteins. Fluoroquinolone-resistant clinical isolates of bacteria have emerged readily and recent data have shown that resistance to this class of antibiotics can have diverse, species-dependent impacts on host-strain fitness. Here we outline the impacts of quinolone-resistance mutations in relation to the fitness and evolutionary success of mutant strains.
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Affiliation(s)
- Liam S Redgrave
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Sam B Sutton
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark A Webber
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Laura J V Piddock
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK.
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96
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OXA-48 carbapenemase-producing Salmonella enterica serovar Kentucky isolate of sequence type 198 in a patient transferred from Libya to Switzerland. Antimicrob Agents Chemother 2014; 58:2446-9. [PMID: 24468781 DOI: 10.1128/aac.02417-13] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Here, we report a case of OXA-48-producing Salmonella enterica serovar Kentucky of sequence type 198 (ST198) from perianal screening cultures of a patient transferred from Libya to Switzerland. The blaOXA-48 gene was carried by Tn1999.2 and located on an ∼60-kb IncL/M plasmid. This Salmonella strain also possessed the blaVEB-8, aac(6)-Ib, tet(A), sul1, and mphA resistance genes and substitutions in GyrA (Ser83Phe and Asp87Asn) and ParC (Ser80Ile). This finding emphasizes that prompt screening strategies are essential to prevent the dissemination of carbapenemase producers imported from countries where they are endemic.
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