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De Smet J, Boyen F, Croubels S, Rasschaert G, Haesebrouck F, De Backer P, Devreese M. Similar Gastro-Intestinal Exposure to Florfenicol After Oral or Intramuscular Administration in Pigs, Leading to Resistance Selection in Commensal Escherichia coli. Front Pharmacol 2018; 9:1265. [PMID: 30459619 PMCID: PMC6232271 DOI: 10.3389/fphar.2018.01265] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/17/2018] [Indexed: 12/24/2022] Open
Abstract
Florfenicol, which is licensed for veterinary use only, proves to be a potent antimicrobial for treatment of respiratory disease. However, the subsequent exposure of the gut microbiota to florfenicol is not well described. Hence, the effect of various administration protocols on both plasma and gastro-intestinal florfenicol concentrations in pigs was evaluated. In field situations were simulated by application of different administration routes and dosages [single oral bolus at 10 or 5 mg/kg body weight (BW), medicated feed at 10 or 5 mg/kg BW and intramuscular injections at 15 or 30 mg/kg BW]. After intramuscular administration of 30 mg florfenicol/kg BW, gastro-intestinal concentrations of florfenicol, quantified 10 h after the last administration, were significantly elevated in comparison with the other treatment groups and ranging between 31.5 and 285.8 μg/g over the different gut segments. For the other treatment groups, the influence of dose and administration route was not significantly different. Bacteriological analysis of the fecal samples from the animals at the start of the experiment, demonstrated the presence of both florfenicol susceptible (with minimal inhibitory concentration (MIC) values of 2-16 μg/mL) and florfenicol resistant (MIC ≥ 256 μg/mL) Escherichia coli isolates in all treatment groups. Following, at 10 h after the last administration the susceptible E. coli population was eradicated in all treatment groups due to the high intestinal florfenicol concentrations measured. Moreover, selection of the resistant E. coli strains during treatment occurred in all groups. This is likely related to the fact that the different treatment strategies led to high gastro-intestinal concentrations albeit not reaching the high magnitude of MIC values associated with florfenicol resistance (≥256 μg/mL). Conclusively, in our experimental setup the administration route and dose alterations studied, had no influence on monitored florfenicol resistance selection in E. coli from the microbiota.
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Affiliation(s)
- Joren De Smet
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Boyen
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Siska Croubels
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Geertrui Rasschaert
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Patrick De Backer
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Mathias Devreese
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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102
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Pornsukarom S, van Vliet AHM, Thakur S. Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources. BMC Genomics 2018; 19:801. [PMID: 30400810 PMCID: PMC6218967 DOI: 10.1186/s12864-018-5137-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/02/2018] [Indexed: 11/13/2022] Open
Abstract
Background Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology and AMR patterns within Salmonella isolates from two adjacent US states. Results WGS data of 200 S. enterica isolates recovered from human (n = 44), swine (n = 32), poultry (n = 22), and farm environment (n = 102) were used for in silico prediction of serovar, distribution of virulence genes, and phylogenetically clustered using core genome single nucleotide polymorphism (SNP) and feature frequency profiling (FFP). Furthermore, AMR was studied both by genotypic prediction using five curated AMR databases, and compared to phenotypic AMR using broth microdilution. Core genome SNP-based and FFP-based phylogenetic trees showed consistent clustering of isolates into the respective serovars, and suggested clustering of isolates based on the source of isolation. The overall correlation of phenotypic and genotypic AMR was 87.61% and 97.13% for sensitivity and specificity, respectively. AMR and virulence genes clustered with the Salmonella serovars, while there were also associations between the presence of virulence genes in both animal/environmental isolates and human clinical samples. Conclusions WGS is a helpful tool for Salmonella phylogenetic analysis, AMR and virulence gene predictions. The clinical isolates clustered closely with animal and environmental isolates, suggesting that animals and environment are potential sources for dissemination of AMR and virulence genes between Salmonella serovars. Electronic supplementary material The online version of this article (10.1186/s12864-018-5137-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suchawan Pornsukarom
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-ok, Chonburi, Thailand
| | - Arnoud H M van Vliet
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA. .,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.
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103
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Lu J, Zhang J, Xu L, Liu Y, Li P, Zhu T, Cheng C, Lu S, Xu T, Yi H, Li K, Zhou W, Li P, Ni L, Bao Q. Spread of the florfenicol resistance floR gene among clinical Klebsiella pneumoniae isolates in China. Antimicrob Resist Infect Control 2018; 7:127. [PMID: 30410748 PMCID: PMC6211440 DOI: 10.1186/s13756-018-0415-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 09/27/2018] [Indexed: 11/10/2022] Open
Abstract
Background Florfenicol is a derivative of chloramphenicol that is used only for the treatment of animal diseases. A key resistance gene for florfenicol, floR, can spread among bacteria of the same and different species or genera through horizontal gene transfer. To analyze the potential transmission of resistance genes between animal and human pathogens, we investigated floR in Klebsiella pneumoniae isolates from patient samples. floR in human pathogens may originate from animal pathogens and would reflect the risk to human health of using antimicrobial agents in animals. Methods PCR was used to identify floR-positive strains. The floR genes were cloned, and the minimum inhibitory concentrations (MICs) were determined to assess the relative resistance levels of the genes and strains. Sequencing and comparative genomics methods were used to analyze floR gene-related sequence structure as well as the molecular mechanism of resistance dissemination. Results Of the strains evaluated, 20.42% (67/328) were resistant to florfenicol, and 86.96% (20/23) of the floR-positive strains demonstrated high resistance to florfenicol with MICs ≥512 μg/mL. Conjugation experiments showed that transferrable plasmids carried the floR gene in three isolates. Sequencing analysis of a plasmid approximately 125 kb in size (pKP18-125) indicated that the floR gene was flanked by multiple copies of mobile genetic elements. Comparative genomics analysis of a 9-kb transposon-like fragment of pKP18-125 showed that an approximately 2-kb sequence encoding lysR-floR-virD2 was conserved in the majority (79.01%, 83/105) of floR sequences collected from NCBI nucleotide database. Interestingly, the most similar sequence was a 7-kb fragment of plasmid pEC012 from an Escherichia coli strain isolated from a chicken. Conclusions Identified on a transferable plasmid in the human pathogen K. pneumoniae, the floR gene may be disseminated through horizontal gene transfer from animal pathogens. Studies on the molecular mechanism of resistance gene dissemination in different bacterial species of animal origin could provide useful information for preventing or controlling the spread of resistance between animal and human pathogens.
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Affiliation(s)
- Junwan Lu
- School of Medicine and Health, Lishui University, Lishui, 323000 China
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Jinfang Zhang
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Lei Xu
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Yabo Liu
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Pingping Li
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Tingyuan Zhu
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Cong Cheng
- School of Medicine and Health, Lishui University, Lishui, 323000 China
| | - Shunfei Lu
- School of Medicine and Health, Lishui University, Lishui, 323000 China
| | - Teng Xu
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Huiguang Yi
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Kewei Li
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Wu Zhou
- School of Medicine and Health, Lishui University, Lishui, 323000 China
| | - Peizhen Li
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Liyan Ni
- The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325035 China
| | - Qiyu Bao
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
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Paudyal N, Pan H, Li X, Fang W, Yue M. Retracted: Antibiotic Resistance in Salmonella Enteritidis Isolates Recovered from Chicken, Chicken Breast, and Humans Through National Antimicrobial Resistance Monitoring System Between 1996 and 2014. Foodborne Pathog Dis 2018; 15:e814-e820. [PMID: 29927626 DOI: 10.1089/fpd.2017.2402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The online e-pub version of the article entitled, Antibiotic Resistance in Salmonella Enteritidis Isolates Recovered from Chicken, Chicken Breast, and Humans Through National Antimicrobial Resistance Monitoring System Between 1996 and 2014" by Paudyal N, Pan H, Li X. Fang W. Yue M., Foodborne Pathog Dis [Epub ahead of print]; DOI: 10.1089/fpd.2017.2402 is being officially retracted from Foodborne Pathogens and Disease (FPD) due to a significant number of errors in reporting and miscalculations of the National Antimicrobial Resistance Monitoring System (NARMS) datasets reported in the paper. Authors evaluated NARMS data, which are in the public domain, and analyzed a subset of NARMS data to address questions about a specific serotype of Salmonella in humans and chicken meat. Authors analyzed Salmonella Enteritidis isolates from humans, chicken and retail chicken meat, with their minimum inhibitory concentrations (MICs) to a range of commonly used antibiotics in the US collected over a period of 1996-2014 by NARMS, to segregate isolates based on their MIC value for a certain antimicrobial and evaluate their relationship along the foodborne transmission pathway. NARMS has data on more than 185,000 isolates that can be downloaded in an accessible format. To help make these large data sets more accessible, the NARMS teams continue to develop new tools to enable users to explore them according to their own interests. As a public health surveillance system, the goal is continuous improvement and open, transparent data sharing. The NARMS partners believe this is the best way to foster a collaborative effort to combat antibiotic resistance. After the online-ahead-of-print version of the paper, which used a subset of NARMS data, was published, a significant concern was brought to the attention of the Editor-in-Chief of FPD indicating that the article contained several significant errors which could potentially lead to a misunderstanding of the resistance situation in the United States. Of particular import is with regard to the authors of the paper reversing the poultry and human resistance data found in Figure 2, which displays the overall antimicrobial resistance data and is a central element of the article. The authors correctly state it in the text, but the figure is incorrect. Additionally, there appeared to be an accidental omission of a reference to a published article which shows a strong association between quinolone-resistant Salmonella Enteritidis infections in humans and international travel (O'Donnell et al., 2014) This appears to be a critical oversight given that the intention of the study was to analyze the NARMS data to help understand the dynamics of Salmonella transmission. The authors of the published article were notified of this communication by the Editor of FPD and were provided an opportunity to respond, which they quickly did. The corresponding author, Dr. Min Yue, agreed that after he and his team reanalyzed the data, there were indeed errors in the published paper and supplied revised versions of Figure 2 and supplemental Figure 3, as well as providing a significantly revised version of the manuscript, based upon the criticisms levied against the published paper. After giving the revised manuscript and figures very careful consideration, and after significant probing of his own, the Editor of FPD determined that the significantly revised manuscript, coupled with the multiple errors presented in the figures, is simply far too weighty for a correction statement to be issued, and determined a full retraction of the published article was warranted. It is important to note that there is no indication whatsoever that the errors or miscalculations were intentional, and that Dr. Yue and his team quickly and honestly replied to the concerns raised about their work. However, in the interest of upholding the proper protocols of peer review, and in accurate and truthful reporting in the scientific literature, the Editor of Foodborne Pathogens and Diseases is issuing this full and formal retraction of the article.
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Affiliation(s)
- Narayan Paudyal
- 1 CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Medicine, College of Animal Sciences of Zhejiang University , Hangzhou, China
| | - Hang Pan
- 1 CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Medicine, College of Animal Sciences of Zhejiang University , Hangzhou, China
| | - Xiaoliang Li
- 1 CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Medicine, College of Animal Sciences of Zhejiang University , Hangzhou, China
- 2 Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine , Hangzhou, China
| | - Weihuan Fang
- 1 CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Medicine, College of Animal Sciences of Zhejiang University , Hangzhou, China
- 2 Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine , Hangzhou, China
| | - Min Yue
- 1 CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Medicine, College of Animal Sciences of Zhejiang University , Hangzhou, China
- 2 Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine , Hangzhou, China
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105
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Hau SJ, Haan JS, Davies PR, Frana T, Nicholson TL. Antimicrobial Resistance Distribution Differs Among Methicillin Resistant Staphylococcus aureus Sequence Type (ST) 5 Isolates From Health Care and Agricultural Sources. Front Microbiol 2018; 9:2102. [PMID: 30258418 PMCID: PMC6143795 DOI: 10.3389/fmicb.2018.02102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/17/2018] [Indexed: 12/01/2022] Open
Abstract
Antimicrobial resistance (AMR) is an expanding public health concern and methicillin resistant Staphylococcus aureus (MRSA) is a notable example. Since the discovery of livestock associated MRSA (LA-MRSA), public health concerns have arisen surrounding the potential of LA-MRSA isolates to serve as a reservoir for AMR determinants. In this study, we compare swine associated LA-MRSA ST5 and human clinical MRSA ST5 isolates for phenotypic antimicrobial susceptibilities determined via broth microdilution and genotypic determinants of AMR using whole genome sequencing and comparative genomic analysis to identify AMR elements. Swine associated LA-MRSA ST5 isolates exhibited phenotypic resistance to fewer antibiotics than clinical MRSA ST5 isolates from humans with no swine contact. Distinct genomic AMR elements were harbored by each subgroup, with little overlap in shared AMR genes between swine associated LA-MRSA ST5 and clinical MRSA ST5 isolates. Our results demonstrate that phenotypic antimicrobial susceptibilities and genotypic determinants of AMR among swine associated LA-MRSA ST5 and clinical MRSA ST5 isolates are separate and distinct.
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Affiliation(s)
- Samantha J Hau
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Jisun S Haan
- Enterics Unit-Infectious Disease Lab, Public Health Laboratory Division, Minnesota Department of Health, Saint Paul, MN, United States
| | - Peter R Davies
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Timothy Frana
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Tracy L Nicholson
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
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106
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New Variant of Multidrug-Resistant Salmonella enterica Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam. mBio 2018; 9:mBio.01056-18. [PMID: 30181247 PMCID: PMC6123440 DOI: 10.1128/mbio.01056-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Salmonella Typhimurium is a major diarrheal pathogen and associated with invasive nontyphoid Salmonella (iNTS) disease in vulnerable populations. We present the first characterization of iNTS organisms in Southeast Asia and describe a different evolutionary trajectory from that of organisms causing iNTS in sub-Saharan Africa. In Vietnam, the globally distributed monophasic variant of Salmonella Typhimurium, the serovar I:4,[5],12:i:− ST34 clone, has reacquired a phase 2 flagellum and gained a multidrug-resistant plasmid to become associated with iNTS disease in HIV-infected patients. We document distinct communities of S. Typhimurium and I:4,[5],12:i:− in animals and humans in Vietnam, despite the greater mixing of these host populations here. These data highlight the importance of whole-genome sequencing surveillance in a One Health context in understanding the evolution and spread of resistant bacterial infections. Nontyphoidal Salmonella (NTS), particularly Salmonella enterica serovar Typhimurium, is among the leading etiologic agents of bacterial enterocolitis globally and a well-characterized cause of invasive disease (iNTS) in sub-Saharan Africa. In contrast, S. Typhimurium is poorly defined in Southeast Asia, a known hot spot for zoonotic disease with a recently described burden of iNTS disease. Here, we aimed to add insight into the epidemiology and potential impact of zoonotic transfer and antimicrobial resistance (AMR) in S. Typhimurium associated with iNTS and enterocolitis in Vietnam. We performed whole-genome sequencing and phylogenetic reconstruction on 85 human (enterocolitis, carriage, and iNTS) and 113 animal S. Typhimurium isolates isolated in Vietnam. We found limited evidence for the zoonotic transmission of S. Typhimurium. However, we describe a chain of events where a pandemic monophasic variant of S. Typhimurium (serovar I:4,[5],12:i:− sequence type 34 [ST34]) has been introduced into Vietnam, reacquired a phase 2 flagellum, and acquired an IncHI2 multidrug-resistant plasmid. Notably, these novel biphasic ST34 S. Typhimurium variants were significantly associated with iNTS in Vietnamese HIV-infected patients. Our study represents the first characterization of novel iNTS organisms isolated outside sub-Saharan Africa and outlines a new pathway for the emergence of alternative Salmonella variants into susceptible human populations.
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107
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Gori M, Ebranati E, Scaltriti E, Huedo P, Ciceri G, Tanzi E, Pontello M, Zehender G, Pongolini S, Bolzoni L. High-resolution diffusion pattern of human infections by Salmonella enterica serovar Napoli in Northern Italy explained through phylogeography. PLoS One 2018; 13:e0202573. [PMID: 30133519 PMCID: PMC6104998 DOI: 10.1371/journal.pone.0202573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/06/2018] [Indexed: 01/31/2023] Open
Abstract
Salmonella enterica serovar Napoli (serovar Napoli) is an emerging cause of human salmonellosis in Northern Italy. No specific reservoirs of serovar Napoli have been identified in Italy, so far. However, the environment, especially surface waters, has been hypothesized as an important source of infection based on the observation that genotypically different clusters of serovar Napoli are detected in different geographical macro-areas. To further support the hypothesis of a spatially-restricted pattern of serovar Napoli diffusion, a spatial segregation of serovar Napoli lineages should be observed also at smaller geographical scale. However, classical genotyping techniques used for Salmonella, such as pulsed-field gel electrophoresis (PFGE), did not possess enough discriminatory power to highlight spatial clustering of serovar Napoli within the macro-areas. To this purpose, we performed phylogeographical analyses based on genome-wide single nucleotide polymorphisms to test whether spatio-temporal evolution patterns of serovar Napoli in Northern Italy could be recognized with high geographical resolution, i.e. at local level. Specifically, we analyzed the local spread of the main PFGE clonal group, responsible for more than 60% of human infections in the study area, that did not show any geographical differentiation by PFGE within Northern Italy, i.e. the macro-area considered in the study. Both discrete and continuous phylogeography highlighted the existence of two main geographically-restricted clades: a Southern clade corresponding to the Po Valley and a Northern clade corresponding to the Pre-Alps area. Furthermore, the phylogeographical analyses suggested that the most probable site of origin of the clone was in an area of the Po Valley at the confluence of the Po and Ticino rivers, one of the most important Italian wetlands. These findings provide further support to the hypothesis that environmental transmission may play an important role in the ecology of serovar Napoli.
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Affiliation(s)
- Maria Gori
- Department of Health Sciences, University of Milan, Milano, Italy
| | - Erika Ebranati
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milano, Italy
| | - Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, Parma, Italy
| | - Pol Huedo
- Department of Health Sciences, University of Milan, Milano, Italy
| | - Giulia Ciceri
- Department of Biomedical Sciences for Health, University of Milan, Milano, Italy
| | - Elisabetta Tanzi
- Department of Biomedical Sciences for Health, University of Milan, Milano, Italy
- CRC-Coordinated Research Center “EpiSoMI”, University of Milan, Milano, Italy
| | - Mirella Pontello
- Department of Health Sciences, University of Milan, Milano, Italy
- CRC-Coordinated Research Center “EpiSoMI”, University of Milan, Milano, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milano, Italy
- CRC-Coordinated Research Center “EpiSoMI”, University of Milan, Milano, Italy
| | - Stefano Pongolini
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, Parma, Italy
| | - Luca Bolzoni
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, Parma, Italy
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108
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Kim DW, Thawng CN, Lee K, Cha CJ. Revisiting Polymorphic Diversity of Aminoglycoside N-Acetyltransferase AAC(6')-Ib Based on Bacterial Genomes of Human, Animal, and Environmental Origins. Front Microbiol 2018; 9:1831. [PMID: 30147681 PMCID: PMC6095969 DOI: 10.3389/fmicb.2018.01831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/23/2018] [Indexed: 12/20/2022] Open
Abstract
The prevalence of aac(6')-Ib variants has been demonstrated in numerous epidemiological studies. We revisited the polymorphic diversity of aminoglycoside 6'-N-acetyltransferase gene [aac(6')-Ib] in the bacterial genome databases based on One Health perspectives. aac(6')-Ib was searched against bacterial complete and draft genome databases of NCBI. Based on the major polymorphic residues 102, 117, and 179, taxonomy, ecology, and temporal emergence of bacterial isolates harboring variants of aac(6')-Ib gene were evaluated using whole-genome sequences available in the databases. A total of 3,964 aac(6')-Ib sequences were found to be present in the genomes of 34 bacterial genera, mostly found in Gammaproteobacteria. Among these, aac(6')-Ib-cr variant, known to confer fluoroquinolone resistance, were increasingly detected in bacterial genomes and most abundant in the genera Klebsiella and Escherichia, thereby suggesting that these genera were the major reservoirs of the plasmid-mediated quinolone resistance (PMQR) determinant. The proportions of the cr variant were higher in animal and environmental isolates than in human isolates, among which the variant was dominant (>50%) in the genomes of intestinal, rectal, and fecal origins. In addition, our study suggested that the prevalence of the cr variant was associated with the occurrence of a variant with the mutation L117 (IbL). An integrated surveillance system for antimicrobial resistance in human, animal, and environmental sectors, based on whole-genome sequencing, would provide a better insight into the evolution, ecology, and epidemiology of antimicrobial-resistant bacteria.
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Affiliation(s)
| | | | | | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
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Branchu P, Bawn M, Kingsley RA. Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants. Infect Immun 2018; 86:e00079-18. [PMID: 29784861 PMCID: PMC6056856 DOI: 10.1128/iai.00079-18] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Salmonella enterica serovar Typhimurium is one of approximately 2,500 distinct serovars of the genus Salmonella but is exceptional in its wide distribution in the environment, livestock, and wild animals. S Typhimurium causes a large proportion of nontyphoidal Salmonella (NTS) infections, accounting for a quarter of infections, second only to S. enterica serovar Enteritidis in incidence. S Typhimurium was once considered the archetypal broad-host-range Salmonella serovar due to its wide distribution in livestock and wild animals, and much of what we know of the interaction of Salmonella with the host comes from research using a small number of laboratory strains of the serovar (LT2, SL1344, and ATCC 14028). But it has become clear that these strains do not reflect the genotypic or phenotypic diversity of S Typhimurium. Here, we review the epidemiological record of S Typhimurium and studies of the host-pathogen interactions of diverse strains of S Typhimurium. We present the concept of distinct pathovariants of S Typhimurium that exhibit diversity of host range, distribution in the environment, pathogenicity, and risk to food safety. We review recent evidence from whole-genome sequencing that has revealed the extent of genomic diversity of S Typhimurium pathovariants, the genomic basis of differences in the level of risk to human and animal health, and the molecular epidemiology of prominent strains. An improved understanding of the impact of genome variation of bacterial pathogens on pathogen-host and pathogen-environment interactions has the potential to improve quantitative risk assessment and reveal how new pathogens evolve.
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Affiliation(s)
- Priscilla Branchu
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
- Earlham Institute, Norwich Research Park, Colney, Norwich, United Kingdom
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
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Petsong K, Uddin MJ, Vongkamjan K, Ahn J. Combined effect of bacteriophage and antibiotic on the inhibition of the development of antibiotic resistance in Salmonella typhimurium. Food Sci Biotechnol 2018; 27:1239-1244. [PMID: 30263855 PMCID: PMC6085247 DOI: 10.1007/s10068-018-0351-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/25/2018] [Accepted: 03/01/2018] [Indexed: 01/21/2023] Open
Abstract
This study was designed to evaluate the combined effects of bacteriophage and antibiotic on the reduction of the development of antibiotic-resistance in Salmonella typhimurium LT2. The susceptibilities of S. typhimurium to ciprofloxacin and erythromycin were increased when treated with bacteriophages, showing more than 10% increase in clear zone sizes and greater than twofold decrease in minimum inhibitory concentration values. The growth of S. typhimurium was effectively inhibited by the combination of bacteriophage P22 and ciprofloxacin. The combination treatment effectively reduced the development of antibiotic resistance in S. typhimurium. The relative expression levels of efflux pump-related genes (acrA, acrB, and tolC) and outer membrane-related genes (ompC, ompD, and ompF) were decreased at all treatments. This study provides useful information for designing new antibiotic therapy to control antibiotic-resistant bacteria.
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Affiliation(s)
- Kantiya Petsong
- Department of Food Science and Technology, Prince of Songkla University, Hat Yai, Songkhla 90112 Thailand
| | - Md Jalal Uddin
- Department of Medical Biomaterials Engineering and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
| | - Kitiya Vongkamjan
- Department of Food Science and Technology, Prince of Songkla University, Hat Yai, Songkhla 90112 Thailand
| | - Juhee Ahn
- Department of Medical Biomaterials Engineering and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
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111
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Baker S, Thomson N, Weill FX, Holt KE. Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. Science 2018; 360:733-738. [PMID: 29773743 PMCID: PMC6510332 DOI: 10.1126/science.aar3777] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Whole-genome sequencing (WGS) has been vital for revealing the rapid temporal and spatial evolution of antimicrobial resistance (AMR) in bacterial pathogens. Some antimicrobialresistant pathogens have outpaced us, with untreatable infections appearing in hospitals and the community. However,WGS has additionally provided us with enough knowledge to initiate countermeasures. Although we cannot stop bacterial adaptation, the predictability of many evolutionary processes in AMR bacteria offers us an opportunity to channel them using new control strategies. Furthermore, by usingWGS for coordinating surveillance and to create a more fundamental understanding of the outcome of antimicrobial treatment and AMR mechanisms, we can use current and future antimicrobials more effectively and aim to extend their longevity.
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Affiliation(s)
- Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. .,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.,The Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicholas Thomson
- The Wellcome Trust Sanger Institute, Cambridge, UK.,The London School of Hygiene and Tropical Medicine, London, UK
| | | | - Kathryn E Holt
- The London School of Hygiene and Tropical Medicine, London, UK.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
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112
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Mancin M, Barco L, Losasso C, Belluco S, Cibin V, Mazzucato M, Bilei S, Carullo MR, Decastelli L, Di Giannatale E, D'Incau M, Goffredo E, Lollai S, Piraino C, Scuota S, Staffolani M, Tagliabue S, Ricci A. Salmonella serovar distribution from non-human sources in Italy; results from the IT-Enter-Vet network. Vet Rec 2018; 183:69. [PMID: 29980593 DOI: 10.1136/vr.104907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/18/2018] [Accepted: 05/31/2018] [Indexed: 11/04/2022]
Abstract
The study summarises the results obtained over the period 2002-2013 by the Italian IT-Enter-Vet network, aimed at collecting data on Salmonella isolates from non-human sources. A total of 42,491 Salmonella isolates were reported with a progressive decrease over the years. S. Typhimurium was the most frequent serovar up to 2011, but then, it was overtaken by S. 4,[5],12,:i:-, S. Derby, S. Livingstone and S. Enteritidis alternated as the third most commonly isolated serovars. With regard to the sources of isolation, S. Typhimurium was distributed ubiquitously among the animal species. On the contrary, S. 4,[5],12,:i:- and S. Derby were strictly associated with pigs, whereas S. Livingstone, S. Enteritidis and S. Infantis were clearly related to poultry. Intriguingly, when the frequency of serovar distribution along the food chain was considered, it was evident that S. Typhimurium and S. Derby tended to persist along the chain, as they were isolated even more frequently from foods than from animals. A similar distribution was found for S. Enteritidis and S. Hadar. Despite limitations related to non-mandatory participation of laboratories in the network, the data presented are valuable to obtain a picture of the evolution of Salmonella from non-human sources over time in Italy.
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Affiliation(s)
- Marzia Mancin
- OIE and National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Lisa Barco
- OIE and National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Carmen Losasso
- OIE and National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Simone Belluco
- OIE and National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Veronica Cibin
- OIE and National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Matteo Mazzucato
- GIS Unit, Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Stefano Bilei
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Roma, Italy
| | | | - Lucia Decastelli
- Istituto Zooprofilattico Sperimentale del Piemonte e Valle D'Aosta, Torino, Italy
| | | | - Mario D'Incau
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Brescia, Italy
| | - Elisa Goffredo
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Foggia, Italy
| | - Stefano Lollai
- Istituto Zooprofilattico Speimentale delle Sardegna, Sassari, Italy
| | - Chiara Piraino
- Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy
| | - Stefania Scuota
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Perugia, Italy
| | - Monica Staffolani
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Perugia, Italy
| | - Silvia Tagliabue
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Brescia, Italy
| | - Antonia Ricci
- OIE and National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
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113
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Cuypers WL, Jacobs J, Wong V, Klemm EJ, Deborggraeve S, Van Puyvelde S. Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing. Microb Genom 2018; 4. [PMID: 29975627 PMCID: PMC6113872 DOI: 10.1099/mgen.0.000195] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Fluoroquinolone (FQ)-resistant Salmonella spp. were listed by the WHO in 2017 as priority pathogens for which new antibiotics were urgently needed. The overall global burden of Salmonella infections is high, but differs per region. Whereas typhoid fever is most prevalent in South and South-East Asia, non-typhoidal salmonellosis is prevalent across the globe and associated with a mild gastroenteritis. By contrast, invasive non-typhoidal Salmonella cause bloodstream infections associated with high mortality, particularly in sub-Saharan Africa. Most Salmonella strains from clinical sources are resistant to first-line antibiotics, with FQs now being the antibiotic of choice for treatment of invasive Salmonella infections. However, FQ resistance is increasingly being reported in Salmonella, and multiple molecular mechanisms are already described. Whole-genome sequencing (WGS) is becoming more frequently used to analyse bacterial genomes for antibiotic-resistance markers, and to understand the phylogeny of bacteria in relation to their antibiotic-resistance profiles. This mini-review provides an overview of FQ resistance in Salmonella, guided by WGS studies that demonstrate that WGS is a valuable tool for global surveillance.
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Affiliation(s)
- Wim L Cuypers
- 1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium.,2Department of Mathematics and Computer Science, University of Antwerp, Antwerpen, Belgium
| | - Jan Jacobs
- 3Department of Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium.,4Department of Microbiology and Immunology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Vanessa Wong
- 5Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,6Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Stijn Deborggraeve
- 1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Sandra Van Puyvelde
- 6Wellcome Trust Sanger Institute, Hinxton, UK.,1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
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114
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Xiong W, Sun Y, Zeng Z. Antimicrobial use and antimicrobial resistance in food animals. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:18377-18384. [PMID: 29802609 DOI: 10.1007/s11356-018-1852-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
Antimicrobials have been widely used in food animals for growth promotion since the 1950s. Antimicrobial resistance emerges in animal production settings and frequently spreads to humans through the food chain and direct contact. There have been international efforts to restrict or ban antimicrobials used for both humans and animals. Denmark has taken positive strides in the development of a comprehensive database DANMAP to track antimicrobial usage and resistance. Although food animals are sources of antimicrobial resistance, there is little evidence that antimicrobial resistance originates from food animals. This review comprehensively introduces the history and trends of antimicrobial use, the emergence and spread of antimicrobial resistance in food animals provides suggestions to tackle the problems of the spread of antimicrobial resistance.
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Affiliation(s)
- Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs and the Guangdong Provincial Key Laboratory of Veterinary Drugs Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs and the Guangdong Provincial Key Laboratory of Veterinary Drugs Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China.
| | - Zhenling Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs and the Guangdong Provincial Key Laboratory of Veterinary Drugs Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China.
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115
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Tanner JR, Kingsley RA. Evolution of Salmonella within Hosts. Trends Microbiol 2018; 26:986-998. [PMID: 29954653 PMCID: PMC6249985 DOI: 10.1016/j.tim.2018.06.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/22/2018] [Accepted: 06/01/2018] [Indexed: 11/18/2022]
Abstract
Within-host evolution has resulted in thousands of variants of Salmonella that exhibit remarkable diversity in host range and disease outcome, from broad host range to exquisite host restriction, causing gastroenteritis to disseminated disease such as typhoid fever. Within-host evolution is a continuing process driven by genomic variation that occurs during each infection, potentiating adaptation to a new niche resulting from changes in animal husbandry, the use of antimicrobials, and emergence of immune compromised populations. We discuss key advances in our understanding of the evolution of Salmonella within the host, inferred from (i) the process of host adaptation of Salmonella pathovars in the past, and (ii) direct observation of the generation of variation and selection of beneficial traits during single infections. Salmonella is a bacterial pathogen with remarkable diversity in its host range and pathogenicity due to past within-host evolution in vertebrate species that modified ancestral mechanisms of pathogenesis. Variation arising during infection includes point mutations, new genes acquired through horizontal gene transfer (HGT), deletions, and genomic rearrangements. Beneficial mutations increase in frequency within the host and, if they retain the ability to be transmitted to subsequent hosts, may become fixed in the population. Whole-genome sequencing of sequential isolates from clinical infections reveals within-host HGT and point mutations that impact therapy and clinical management. HGT is the primary mechanism for evolution in prokaryotes and is synergised by complex networks of transfer involving the microbiome. Within-host evolution of Salmonella, resulting in new pathovars, can proceed in the absence of HGT.
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Affiliation(s)
- Jennifer R Tanner
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, UK
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, UK.
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116
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Carter DL, Docherty KM, Gill SA, Baker K, Teachout J, Vonhof MJ. Antibiotic resistant bacteria are widespread in songbirds across rural and urban environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1234-1241. [PMID: 30857088 DOI: 10.1016/j.scitotenv.2018.01.343] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 05/20/2023]
Abstract
The widespread use of antibiotics in human and veterinary medicine to treat pathogenic bacteria has resulted in the rapid emergence of antibiotic-resistant bacteria (ARB). Wild animals may enable the spread of pathogenic and non-pathogenic ARB when they are exposed to reservoirs (e.g., contaminated soil, water, or crops) and carry ARB in and on their bodies to other environments. We tested for the presence of ARB in four songbird species in southwest Michigan across a gradient of land use. Our specific objectives were to: 1) quantify the prevalence of ARB found in the gut microbiome of birds; 2) identify the specific bacteria exhibiting resistance; 3) assess whether ARB prevalence and identity varied among bird species; and 4) assess whether anthropogenic land use influenced the prevalence and identity of ARB found on birds. We sampled birds across a land use gradient consisting of urban, agricultural, and natural land covers using a randomized, spatially-balanced sampling design and cultured bacteria from fecal samples in the presence of three different antibiotics (amoxicillin, tetracycline, and ciprofloxacin). Overall prevalence of ARB was high, with 88% of total birds carrying ARB resistant to one of three antibiotics that we tested. Resistance to amoxicillin was more common (83% of sampled birds) than resistance to tetracycline (15%) or ciprofloxacin (1%). Identified ARB were diverse, and included 135 isolates representing 5 bacterial phyla and 22 genera. There was no effect of land use on ARB prevalence, with 90% of sampled birds captured in rural sites and 85% of sampled birds in urban sites carrying ARB. We provide the first analysis of ARB prevalence across multiple bird species and land uses utilizing a spatially-balanced, randomized study design. Our results demonstrate that nearly all sampled birds carried at least some ARB, and that they may serve as important dispersal agents of ARB across large spatial scales.
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Affiliation(s)
- Diana L Carter
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Sharon A Gill
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Kathleen Baker
- Department of Geography, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Jordan Teachout
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States
| | - Maarten J Vonhof
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, United States; Institute of the Environment and Sustainability, Western Michigan University, Kalamazoo, MI 49008, United States.
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117
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Gibson B, Wilson DJ, Feil E, Eyre-Walker A. The distribution of bacterial doubling times in the wild. Proc Biol Sci 2018; 285:20180789. [PMID: 29899074 PMCID: PMC6015860 DOI: 10.1098/rspb.2018.0789] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/18/2018] [Indexed: 12/16/2022] Open
Abstract
Generation time varies widely across organisms and is an important factor in the life cycle, life history and evolution of organisms. Although the doubling time (DT) has been estimated for many bacteria in the laboratory, it is nearly impossible to directly measure it in the natural environment. However, an estimate can be obtained by measuring the rate at which bacteria accumulate mutations per year in the wild and the rate at which they mutate per generation in the laboratory. If we assume the mutation rate per generation is the same in the wild and in the laboratory, and that all mutations in the wild are neutral, an assumption that we show is not very important, then an estimate of the DT can be obtained by dividing the latter by the former. We estimate the DT for five species of bacteria for which we have both an accumulation and a mutation rate estimate. We also infer the distribution of DTs across all bacteria from the distribution of the accumulation and mutation rates. Both analyses suggest that DTs for bacteria in the wild are substantially greater than those in the laboratory, that they vary by orders of magnitude between different species of bacteria and that a substantial fraction of bacteria double very slowly in the wild.
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Affiliation(s)
- Beth Gibson
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Daniel J Wilson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Edward Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
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118
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Bloomfield SJ, Benschop J, Biggs PJ, Marshall JC, Hayman DTS, Carter PE, Midwinter AC, Mather AE, French NP. Genomic Analysis of Salmonella enterica Serovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998-2012. Emerg Infect Dis 2018; 23:906-913. [PMID: 28516864 PMCID: PMC5443446 DOI: 10.3201/eid2306.161934] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During 1998-2012, an extended outbreak of Salmonella enterica serovar Typhimurium definitive type 160 (DT160) affected >3,000 humans and killed wild birds in New Zealand. However, the relationship between DT160 within these 2 host groups and the origin of the outbreak are unknown. Whole-genome sequencing was used to compare 109 Salmonella Typhimurium DT160 isolates from sources throughout New Zealand. We provide evidence that DT160 was introduced into New Zealand around 1997 and rapidly propagated throughout the country, becoming more genetically diverse over time. The genetic heterogeneity was evenly distributed across multiple predicted functional protein groups, and we found no evidence of host group differentiation between isolates collected from human, poultry, bovid, and wild bird sources, indicating ongoing transmission between these host groups. Our findings demonstrate how a comparative genomic approach can be used to gain insight into outbreaks, disease transmission, and the evolution of a multihost pathogen after a probable point-source introduction.
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119
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Draft Genome Sequences of Two Salmonella Strains Isolated from Wild Animals on the Eastern Shore of Virginia. GENOME ANNOUNCEMENTS 2018; 6:6/19/e00329-18. [PMID: 29748400 PMCID: PMC5946047 DOI: 10.1128/genomea.00329-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Antimicrobial-resistant (AMR) Salmonella infections pose a significant public health threat. Here, we announce two draft genomes of Salmonella strains isolated from wildlife harboring an alarming array of antibiotic resistance genes. Continued investigations of these genomes will provide insight into the possible attribution of AMR Salmonella infection of wild animals.
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120
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Liu W, Jiang Y, Sun J, Geng S, Pan Z, Prinz RA, Wang C, Sun J, Jiao X, Xu X. Activation of TGF-β-activated kinase 1 (TAK1) restricts Salmonella Typhimurium growth by inducing AMPK activation and autophagy. Cell Death Dis 2018; 9:570. [PMID: 29752434 PMCID: PMC5948208 DOI: 10.1038/s41419-018-0612-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/07/2018] [Accepted: 04/10/2018] [Indexed: 01/24/2023]
Abstract
Autophagy is a conserved cellular process that functions as a first-line defense to restrict the growth of invading parasitic bacteria. As an intracellular pathogen, Salmonella (S) Typhimurium invades host cells through two Type III secretion systems (T3SS) and resides in the Salmonella-containing vacuole (SCV). When the SCV membrane is perforated and ruptured by T3SS-1, a small portion of the Salmonella egresses from the SCV and replicates rapidly in the nutrient-rich cytosol. Cytosolic Salmonella and those residing in the membrane-damaged SCV are tagged by ubiquitination and marked for autophagy through the ubiquitin-binding adaptor proteins such as p62, NDP52, and optineurin. Prior studies suggest that transient intracellular amino-acid starvation and subsequent inactivation of the mechanistic target of rapamycin (mTOR), a key molecule that phosphorylates Unc-51 like autophagy activating kinase (ULK1) and inhibits its activity, can trigger autophagy in S. Typhimurium-infected cells. Other studies suggest that energy stress in S. Typhimurium-infected cells leads to AMP-activated protein kinase (AMPK) activation and autophagy. In the present study, we report that autophagy was rapidly induced in S. Typhimurium-infected cells, as evidenced by increased LC3 lipidation and decreased p62 levels. However, S. Typhimurium infection drastically increased AKT phosphorylation but decreased S6K1T389, 4E-BPT37/46, and ULK1S757 phosphorylation, suggesting that mTOR activation by AKT is subverted. Further studies showed that AMPK was activated in S. Typhimurium-infected cells, as evidenced by increased ULK1S317 and ACCS79 phosphorylation. AMPK activation was mediated by Toll-like receptor-activated TAK1. Functional studies revealed that AMPK and TAK1 inhibitors accelerated S. Typhimurium growth in HeLa cells. Our results strongly suggest that TAK1 activation leads to AMPK activation, which activates ULK1 by phosphorylating ULK1S317 and suppressing mTOR activity and ULK1S757 phosphorylation. Our study has unveiled a previously unrecognized pathway for S. Typhimurium-induced autophagy.
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Affiliation(s)
- Wei Liu
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - Yuanyuan Jiang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - Jing Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - Shizhong Geng
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, 225009, China
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, 225009, China
| | - Richard A Prinz
- Department of Surgery, NorthShore University Health System, Evanston, IL, 60201, USA
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, 36849, USA
| | - Jun Sun
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, 225009, China
| | - Xiulong Xu
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China.
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, 225009, China.
- Department of Cell and Molecular Medicine, Rush University Medical Center, Chicago, IL, 60612, USA.
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121
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Ngoi ST, Yap KP, Thong KL. Genomic characterization of endemic Salmonella enterica serovar Typhimurium and Salmonella enterica serovar I 4,[5],12:i:- isolated in Malaysia. INFECTION GENETICS AND EVOLUTION 2018; 62:109-121. [PMID: 29684710 DOI: 10.1016/j.meegid.2018.04.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/03/2018] [Accepted: 04/19/2018] [Indexed: 11/29/2022]
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) and the monophasic variant Salmonella I 4,[5],12:i:- are two clinically-important non-typhoidal Salmonella serovars worldwide. However, the genomic information of these two organisms, especially the monophasic variant, is still lacking in Malaysia. The objective of the study was to compare the genomic features of a monophasic variant and two endemic S. Typhimurium strains isolated from humans. All three strains were subjected to whole genome sequencing followed by comparative genomic and phylogenetic analyses. Extensive genomic deletion in the fljAB operon (from STM2757 to iroB) is responsible for the monophasic phenotype of STM032/04. The two S. Typhimurium genomes (STM001/70 and STM057/05) were essentially identical, despite being isolated 35 years apart. All three strains were of sequence type ST19. Both S. Typhimurium genomes shared unique prophage regions not identified in the monophasic STM032/04 genome. Core genome phylogenetic analyses showed that the monophasic STM032/04 was closely-related to the S. Typhimurium LT2, forming a distinctive clade separated from the two endemic S. Typhimurium strains in Malaysia. The presence of serovar Typhimurium-specific mdh gene, conserved Gifsy and Fels-1 prophages, and the close genomic resemblance with S. Typhimurium LT2 suggested that the monophasic STM032/04 was originated from an LT2-like S. Typhimurium ancestor in Malaysia, following an evolutionary path different from the S. Typhimurium strains. In conclusion, the monophasic Salmonella I 4,[5],12:i:- and the S. Typhimurium strains isolated in Malaysia descended from different phylogenetic lineages. The high genomic resemblance between the two S. Typhimurium strains isolated for at least 35 years apart indicated their successful evolutionary lineage. The identification of multiple virulence and antimicrobial resistance determinants in the Salmonella I 4,[5],12:i:- and S. Typhimurium genomes explained the pathogenic nature of the organisms.
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Affiliation(s)
- Soo Tein Ngoi
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kien-Pong Yap
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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122
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Abstract
For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.
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123
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Knetsch CW, Kumar N, Forster SC, Connor TR, Browne HP, Harmanus C, Sanders IM, Harris SR, Turner L, Morris T, Perry M, Miyajima F, Roberts P, Pirmohamed M, Songer JG, Weese JS, Indra A, Corver J, Rupnik M, Wren BW, Riley TV, Kuijper EJ, Lawley TD. Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans. J Clin Microbiol 2018; 56:e01384-17. [PMID: 29237792 PMCID: PMC5824051 DOI: 10.1128/jcm.01384-17] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/08/2017] [Indexed: 11/20/2022] Open
Abstract
The emergence of Clostridium difficile as a significant human diarrheal pathogen is associated with the production of highly transmissible spores and the acquisition of antimicrobial resistance genes (ARGs) and virulence factors. Unlike the hospital-associated C. difficile RT027 lineage, the community-associated C. difficile RT078 lineage is isolated from both humans and farm animals; however, the geographical population structure and transmission networks remain unknown. Here, we applied whole-genome phylogenetic analysis of 248 C. difficile RT078 strains from 22 countries. Our results demonstrate limited geographical clustering for C. difficile RT078 and extensive coclustering of human and animal strains, thereby revealing a highly linked intercontinental transmission network between humans and animals. Comparative whole-genome analysis reveals indistinguishable accessory genomes between human and animal strains and a variety of antimicrobial resistance genes in the pangenome of C. difficile RT078. Thus, bidirectional spread of C. difficile RT078 between farm animals and humans may represent an unappreciated route disseminating antimicrobial resistance genes between humans and animals. These results highlight the importance of the "One Health" concept to monitor infectious disease emergence and the dissemination of antimicrobial resistance genes.
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Affiliation(s)
- C W Knetsch
- Section Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - N Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - S C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
| | - T R Connor
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff, United Kingdom
| | - H P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - C Harmanus
- Section Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - I M Sanders
- Section Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - S R Harris
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - L Turner
- Public Health Wales, Microbiology, Wales, United Kingdom
| | - T Morris
- Public Health Wales, Microbiology, Wales, United Kingdom
| | - M Perry
- Public Health Wales, Microbiology, Wales, United Kingdom
| | - F Miyajima
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - P Roberts
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - M Pirmohamed
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - J G Songer
- Department of Veterinary Science and Microbiology, The University of Arizona, Tucson, Arizona, USA
| | - J S Weese
- Department of Pathobiology, Canada Veterinary College, University of Guelph, Guelph, Canada
| | - A Indra
- Institute of Medical Microbiology and Hygiene, Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Vienna, Austria
| | - J Corver
- Section Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - M Rupnik
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
- National Laboratory for Health, Environment and Food, Maribor, Slovenia
| | - B W Wren
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, University of London, London, United Kingdom
| | - T V Riley
- Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Western Australia, Australia
- Microbiology & Immunology, School of Pathology & Laboratory Medicine, The University of Western Australia, Western Australia, Australia
| | - E J Kuijper
- Section Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - T D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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124
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Distinct fermentation and antibiotic sensitivity profiles exist in salmonellae of canine and human origin. BMC Microbiol 2018; 18:15. [PMID: 29482521 PMCID: PMC5828451 DOI: 10.1186/s12866-018-1153-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 02/07/2018] [Indexed: 11/10/2022] Open
Abstract
Background Salmonella enterica is a recognised cause of diarrhoea in dogs and humans, yet the potential for transfer of salmonellosis between dogs and their owners is unclear, with reported evidence both for and against Salmonella as a zoonotic pathogen. A collection of 174 S. enterica isolates from clinical infections in humans and dogs were analysed for serotype distribution, carbon source utilisation, chemical and antimicrobial sensitivity profiles. The aim of the study was to understand the degree of conservation in phenotypic characteristics of isolates across host species. Results Serovar distribution across human and canine isolates demonstrated nine serovars common to both host species, 24 serovars present in only the canine collection and 39 solely represented within the human collection. Significant differences in carbon source utilisation profiles and ampicillin, amoxicillin and chloramphenicol sensitivity profiles were detected in isolates of human and canine origin. Differences between the human and canine Salmonella collections were suggestive of evolutionary separation, with canine isolates better able to utilise several simple sugars than their human counterparts. Generally higher minimum inhibitory concentrations of three broad-spectrum antimicrobials, commonly used in veterinary medicine, were also observed in canine S. enterica isolates. Conclusions Differential carbon source utilisation and antimicrobial sensitivity profiles in pathogenic Salmonella isolated from humans and dogs are suggestive of distinct reservoirs of infection for these hosts. Although these findings do not preclude zoonotic or anthroponotic potential in salmonellae, the separation of carbon utilisation and antibiotic profiles with isolate source is indicative that infectious isolates are not part of a common reservoir shared frequently between these host species.
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125
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Salmonella Typhimurium in livestock in Great Britain - trends observed over a 32-year period. Epidemiol Infect 2018; 146:409-422. [PMID: 29415790 DOI: 10.1017/s095026881800002x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In this retrospective study, we describe and analyse Salmonella data from four livestock species in Great Britain between 1983 and 2014, focusing on Salmonella Typhimurium. A total of 96 044 Salmonella isolates were obtained during the study period. S. Typhimurium was the predominant serovar isolated from cattle and pigs and represented 40.7% (18 455/45 336) and 58.3% (4495/7709) of isolates from these species respectively, while it only accounted for 6.7% (2114/31 492) of chicken isolates and 8.1% (926/11 507) of turkey isolates. Over the study period, DT104 was the most common phage type in all four species; however, DT104 peaked in occurrence between 1995 and 1999, but is currently rare. Monophasic strains of S. Typhimurium represented less than 3% of all Salmonella isolates in cattle and chickens in 2014, but accounted for 10.4% of all turkey isolates and 39.0% of all pig isolates in the same year. Salmonella isolates were tested for their in vitro susceptibility to 16 antimicrobials. Antimicrobial resistance of S. Typhimurium isolates is largely influenced by the dominance of specific phage types at a certain time, which are commonly associated with particular resistance patterns. Changes in resistance patterns over time were analysed and compared between species.
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126
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Lawson B, Franklinos LHV, Rodriguez-Ramos Fernandez J, Wend-Hansen C, Nair S, Macgregor SK, John SK, Pizzi R, Núñez A, Ashton PM, Cunningham AA, M de Pinna E. Salmonella Enteritidis ST183: emerging and endemic biotypes affecting western European hedgehogs (Erinaceus europaeus) and people in Great Britain. Sci Rep 2018; 8:2449. [PMID: 29402927 PMCID: PMC5799193 DOI: 10.1038/s41598-017-18667-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 12/07/2017] [Indexed: 12/30/2022] Open
Abstract
The impacts of hedgehog (Erinaceus europaeus) Salmonella infection on public health and on animal welfare and conservation are unknown. We isolated Salmonella Enteritidis multi-locus sequence-type (ST)183 from 46/170 (27%) hedgehog carcasses (27 S. Enteritidis phage type (PT)11, 18 of a novel PT66 biotype and one with co-infection of these PTs) and from 6/208 (3%) hedgehog faecal samples (4 PT11, 2 PT66) from across Great Britain, 2012–2015. Whole genome phylogenetic analysis of the hedgehog isolates and ST183 from people in England and Wales found that PT11 and PT66 form two divergent clades. Hedgehog and human isolates were interspersed throughout the phylogeny indicating that infections in both species originate from a common population. PT11 was recovered from hedgehogs across England and Scotland, consistent with endemic infection. PT66 was isolated from Scotland only, possibly indicating a recent emergence event. People infected with ST183 were four times more likely to be aged 0–4 years than people infected by the more common ST11 S. Enteritidis. Evidence for human ST183 infection being non-foodborne included stronger correlation between geographic and genetic distance, and significantly increased likelihood of infection in rural areas, than for ST11. These results are consistent with hedgehogs acting as a source of zoonotic infection.
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Affiliation(s)
- Becki Lawson
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom.
| | - Lydia H V Franklinos
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom.,University College London, Gower Street, London, WC1E 6BT, UK
| | - Julia Rodriguez-Ramos Fernandez
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom.,IDEXX Laboratories Limited, Grange House, Sandbeck Way, Wetherby, West Yorkshire, LS22 7DN, UK
| | - Clare Wend-Hansen
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, NW9 5EQ, United Kingdom
| | - Satheesh Nair
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, NW9 5EQ, United Kingdom
| | - Shaheed K Macgregor
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
| | - Shinto K John
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
| | - Romain Pizzi
- Scottish SPCA National Wildlife Rescue Centre, Fishcross, Alloa, FK10 3AN, & Royal Zoological Society of Scotland, Edinburgh, EH12 6TS, United Kingdom
| | - Alejandro Núñez
- Animal and Plant Health Agency (APHA), APHA Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Philip M Ashton
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, NW9 5EQ, United Kingdom.
| | - Andrew A Cunningham
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
| | - Elizabeth M de Pinna
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, NW9 5EQ, United Kingdom
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127
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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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128
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Uddin MJ, Ahn J. Characterization of β-lactamase- and efflux pump-mediated multiple antibiotic resistance in Salmonella Typhimurium. Food Sci Biotechnol 2018; 27:921-928. [PMID: 30263820 DOI: 10.1007/s10068-018-0317-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 10/18/2022] Open
Abstract
This study aimed to assess the β-lactamase- and efflux pump-mediated antibiotic resistance in Salmonella Typhimurium (WT-ST), ciprofloxacin-induced antibiotic-resistant S. Typhimurium (CI-ST), and clinically-acquired antibiotic-resistant S. Typhimurium (CA-ST). The β-lactamase activities were significantly increased up to 63 μmol/min/mL in CA-ST and 24 μmol/min/mL in CI-ST when compared to WT-ST (13 μmol/min/mL). The highest efflux pump activity was observed in CI-ST and CA-ST, showing more than 45%. The antibiotic susceptibilities of WT-ST, CI-ST, and CA-ST were increased in the presence of β-lactamase and efflux pump inhibitors. CA-ST showed the highest activity in AcrD, MdtABC, EmrAB, MdtK, and MacAB efflux pumps. The repressed ompF were responsible for the decreased susceptibility of CA-ST to ampicillin (MIC > 512 μg/mL). This study would provide useful information for better understating of the development of multidrug resistance in association with β-lactamase and efflux pump activities and designing new antibiotic chemotherapy in combination with inhibitors.
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Affiliation(s)
- Md Jalal Uddin
- Department of Medical Biomaterials Engineering and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
| | - Juhee Ahn
- Department of Medical Biomaterials Engineering and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
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Silk M, Drewe J, Delahay R, Weber N, Steward L, Wilson-Aggarwal J, Boots M, Hodgson D, Croft D, McDonald R. Quantifying direct and indirect contacts for the potential transmission of infection between species using a multilayer contact network. BEHAVIOUR 2018. [DOI: 10.1163/1568539x-00003493] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Detecting opportunities for between-species transmission of pathogens can be challenging, particularly if rare behaviours or environmental transmission are involved. We present a multilayer network framework to quantify transmission potential in multi-host systems, incorporating environmental transmission, by using empirical data on direct and indirect contacts between European badgers Meles meles and domestic cattle. We identify that indirect contacts via the environment at badger latrines on pasture are likely to be important for transmission within badger populations and between badgers and cattle. We also find a positive correlation between the role of individual badgers within the badger social network, and their role in the overall badger-cattle-environment network, suggesting that the same behavioural traits contribute to the role of individual badgers in within- and between-species transmission. These findings have implications for disease management interventions in this system, and our novel network approach can provide general insights into transmission in other multi-host disease systems.
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Affiliation(s)
- Matthew J. Silk
- aEnvironment and Sustainability Institute, University of Exeter, Penryn, Cornwall, UK
| | - Julian A. Drewe
- bThe Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, UK
| | - Richard J. Delahay
- cNational Wildlife Management Centre, Animal and Plant Health Agency, Gloucestershire, UK
| | - Nicola Weber
- dCentre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK
| | - Lucy C. Steward
- aEnvironment and Sustainability Institute, University of Exeter, Penryn, Cornwall, UK
| | - Jared Wilson-Aggarwal
- aEnvironment and Sustainability Institute, University of Exeter, Penryn, Cornwall, UK
| | - Mike Boots
- dCentre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK
- eIntegrative Biology, University of California, Berkeley, CA, USA
| | - David J. Hodgson
- dCentre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK
| | - Darren P. Croft
- fCentre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - Robbie A. McDonald
- aEnvironment and Sustainability Institute, University of Exeter, Penryn, Cornwall, UK
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130
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Abstract
This review examined the likely impact of climate change upon food-borne disease in the UK using Campylobacter and Salmonella as example organisms. Campylobacter is an important food-borne disease and an increasing public health threat. There is a reasonable evidence base that the environment and weather play a role in its transmission to humans. However, uncertainty as to the precise mechanisms through which weather affects disease, make it difficult to assess the likely impact of climate change. There are strong positive associations between Salmonella cases and ambient temperature, and a clear understanding of the mechanisms behind this. However, because the incidence of Salmonella disease is declining in the UK, any climate change increases are likely to be small. For both Salmonella and Campylobacter the disease incidence is greatest in older adults and young children. There are many pathways through which climate change may affect food but only a few of these have been rigorously examined. This provides a high degree of uncertainty as to what the impacts of climate change will be. Food is highly controlled at the National and EU level. This provides the UK with resilience to climate change as well as potential to adapt to its consequences but it is unknown whether these are sufficient in the context of a changing climate.
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Affiliation(s)
- Iain R Lake
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
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131
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Hurtado-Barroso S, Tresserra-Rimbau A, Vallverdú-Queralt A, Lamuela-Raventós RM. Organic food and the impact on human health. Crit Rev Food Sci Nutr 2017; 59:704-714. [PMID: 29190113 DOI: 10.1080/10408398.2017.1394815] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In the last decade, the production and consumption of organic food have increased steadily worldwide, despite the lower productivity of organic crops. Indeed, the population attributes healthier properties to organic food. Although scientific evidence is still scarce, organic agriculture seems to contribute to maintaining an optimal health status and decreases the risk of developing chronic diseases. This may be due to the higher content of bioactive compounds and lower content of unhealthy substances such as cadmium and synthetic fertilizers and pesticides in organic foods of plant origin compared to conventional agricultural products. Thus, large long-term intervention studies are needed to determine whether an organic diet is healthier than a diet including conventionally grown food products. This review provides an update of the present knowledge of the impact of an organic versus a conventional food diet on health.
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Affiliation(s)
- Sara Hurtado-Barroso
- a Department of Nutrition, Food Sciences and Gastronomy, School of Pharmacy and Food Sciences , University of Barcelona , Barcelona , Spain.,b CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III , Spain.,c INSA-UB, Nutrition and Food Safety Research Institute, University of Barcelona , Barcelona , Spain
| | - Anna Tresserra-Rimbau
- a Department of Nutrition, Food Sciences and Gastronomy, School of Pharmacy and Food Sciences , University of Barcelona , Barcelona , Spain.,b CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III , Spain.,c INSA-UB, Nutrition and Food Safety Research Institute, University of Barcelona , Barcelona , Spain
| | - Anna Vallverdú-Queralt
- a Department of Nutrition, Food Sciences and Gastronomy, School of Pharmacy and Food Sciences , University of Barcelona , Barcelona , Spain.,b CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III , Spain
| | - Rosa María Lamuela-Raventós
- a Department of Nutrition, Food Sciences and Gastronomy, School of Pharmacy and Food Sciences , University of Barcelona , Barcelona , Spain.,b CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III , Spain.,c INSA-UB, Nutrition and Food Safety Research Institute, University of Barcelona , Barcelona , Spain
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132
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Tran-Dien A, Le Hello S, Bouchier C, Weill FX. Early transmissible ampicillin resistance in zoonotic Salmonella enterica serotype Typhimurium in the late 1950s: a retrospective, whole-genome sequencing study. THE LANCET. INFECTIOUS DISEASES 2017; 18:207-214. [PMID: 29198740 DOI: 10.1016/s1473-3099(17)30705-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/02/2017] [Accepted: 10/09/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Ampicillin, the first semi-synthetic penicillin active against Enterobacteriaceae, was released onto the market in 1961. The first outbreaks of disease caused by ampicillin-resistant strains of Salmonella enterica serotype Typhimurium were identified in the UK in 1962 and 1964. We aimed to date the emergence of this resistance in historical isolates of S enterica serotype Typhimurium. METHODS In this retrospective, whole-genome sequencing study, we analysed 288 S enterica serotype Typhimurium isolates collected between 1911 and 1969 from 31 countries on four continents and from various sources including human beings, animals, feed, and food. All isolates were tested for antimicrobial drug susceptibility with the disc diffusion method, and isolates shown to be resistant to ampicillin underwent resistance-transfer experiments. To provide insights into population structure and mechanisms of ampicillin resistance, we did whole-genome sequencing on a subset of 225 isolates, selected to maximise source, spatiotemporal, and genetic diversity. FINDINGS 11 (4%) of 288 isolates were resistant to ampicillin because of acquisition of various β lactamase genes, including blaTEM-1, carried by various plasmids, including the virulence plasmid of S enterica serotype Typhimurium. These 11 isolates were from three phylogenomic groups. One isolate producing TEM-1 β lactamase was isolated in France in 1959 and two isolates producing TEM-1 β lactamase were isolated in Tunisia in 1960, before ampicillin went on sale. The vectors for ampicillin resistance were different from those reported in the strains responsible for the outbreaks in the UK in the 1960s. INTERPRETATION The association between antibiotic use and selection of resistance determinants is not as direct as often presumed. Our results suggest that the non-clinical use of narrow-spectrum penicillins (eg, benzylpenicillin) might have favoured the diffusion of plasmids carrying the blaTEM-1 gene in S enterica serotype Typhimurium in the late 1950s. FUNDING Institut Pasteur, Santé publique France, the French Government's Investissement d'Avenir programme, the Fondation Le Roch-Les Mousquetaires.
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Affiliation(s)
- Alicia Tran-Dien
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | | | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France.
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133
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Mie A, Andersen HR, Gunnarsson S, Kahl J, Kesse-Guyot E, Rembiałkowska E, Quaglio G, Grandjean P. Human health implications of organic food and organic agriculture: a comprehensive review. Environ Health 2017; 16:111. [PMID: 29073935 PMCID: PMC5658984 DOI: 10.1186/s12940-017-0315-4] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 10/02/2017] [Indexed: 05/08/2023]
Abstract
This review summarises existing evidence on the impact of organic food on human health. It compares organic vs. conventional food production with respect to parameters important to human health and discusses the potential impact of organic management practices with an emphasis on EU conditions. Organic food consumption may reduce the risk of allergic disease and of overweight and obesity, but the evidence is not conclusive due to likely residual confounding, as consumers of organic food tend to have healthier lifestyles overall. However, animal experiments suggest that identically composed feed from organic or conventional production impacts in different ways on growth and development. In organic agriculture, the use of pesticides is restricted, while residues in conventional fruits and vegetables constitute the main source of human pesticide exposures. Epidemiological studies have reported adverse effects of certain pesticides on children's cognitive development at current levels of exposure, but these data have so far not been applied in formal risk assessments of individual pesticides. Differences in the composition between organic and conventional crops are limited, such as a modestly higher content of phenolic compounds in organic fruit and vegetables, and likely also a lower content of cadmium in organic cereal crops. Organic dairy products, and perhaps also meats, have a higher content of omega-3 fatty acids compared to conventional products. However, these differences are likely of marginal nutritional significance. Of greater concern is the prevalent use of antibiotics in conventional animal production as a key driver of antibiotic resistance in society; antibiotic use is less intensive in organic production. Overall, this review emphasises several documented and likely human health benefits associated with organic food production, and application of such production methods is likely to be beneficial within conventional agriculture, e.g., in integrated pest management.
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Affiliation(s)
- Axel Mie
- Karolinska Institutet, Department of Clinical Science and Education, Södersjukhuset, 11883 Stockholm, Sweden
- Swedish University of Agricultural Sciences (SLU), Centre for Organic Food and Farming (EPOK), Ultuna, Sweden
| | - Helle Raun Andersen
- University of Southern Denmark, Department of Public Health, Odense, Denmark
| | - Stefan Gunnarsson
- Swedish University of Agricultural Sciences (SLU), Department of Animal Environment and Health, Skara, Sweden
| | - Johannes Kahl
- University of Copenhagen, Department of Nutrition, Exercise and Sports, Frederiksberg, Denmark
| | - Emmanuelle Kesse-Guyot
- Research Unit on Nutritional Epidemiology (U1153 Inserm, U1125 INRA, CNAM, Université Paris 13), Centre of Research in Epidemiology and Statistics Sorbonne Paris Cité, Bobigny, France
| | - Ewa Rembiałkowska
- Warsaw University of Life Sciences, Department of Functional & Organic Food & Commodities, Warsaw, Poland
| | - Gianluca Quaglio
- Scientific Foresight Unit (Science and Technology Options Assessment [STOA]), Directorate-General for Parliamentary Research Services (EPRS), European Parliament, Brussels, Belgium
| | - Philippe Grandjean
- University of Southern Denmark, Department of Public Health, Odense, Denmark
- Harvard T.H. Chan School of Public Health, Department of Environmental Health, Boston, USA
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Noyes NR, Weinroth ME, Parker JK, Dean CJ, Lakin SM, Raymond RA, Rovira P, Doster E, Abdo Z, Martin JN, Jones KL, Ruiz J, Boucher CA, Belk KE, Morley PS. Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing. MICROBIOME 2017; 5:142. [PMID: 29041965 PMCID: PMC5645900 DOI: 10.1186/s40168-017-0361-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/05/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. RESULTS The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. CONCLUSIONS These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.
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Affiliation(s)
- Noelle R Noyes
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Maggie E Weinroth
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jennifer K Parker
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Chris J Dean
- Department of Computer Sciences, Colorado State University, Fort Collins, CO, USA
| | - Steven M Lakin
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Robert A Raymond
- Department of Computer Sciences, Colorado State University, Fort Collins, CO, USA
| | - Pablo Rovira
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Enrique Doster
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer N Martin
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, Section of Hematology Oncology and Bone Marrow Transplant, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jaime Ruiz
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Christina A Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Keith E Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Paul S Morley
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA.
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135
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Polymorphism of antibiotic-inactivating enzyme driven by ecology expands the environmental resistome. ISME JOURNAL 2017; 12:267-276. [PMID: 29028006 DOI: 10.1038/ismej.2017.168] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/10/2017] [Accepted: 08/14/2017] [Indexed: 12/15/2022]
Abstract
The environmental resistome has been recognized as the origin and reservoir of antibiotic resistance genes and considered to be dynamic and ever expanding. In this study, a targeted gene sequencing approach revealed that the polymorphic diversity of the aminoglycoside-inactivating enzyme AAC(6')-Ib was ecological niche-specific. AAC(6')-Ib-cr, previously known as a clinical variant, was prevalent in various soils and the intestines of chickens and humans, suggesting that this variant might not have arisen from adaptive mutations in the clinic but instead originated from the environment. Furthermore, ecologically dominant polymorphic variants of AAC(6')-Ib were characterized and found to display different substrate specificities for quinolones and aminoglycosides, conferring the altered resistance spectra. Interestingly, a novel variant with the D179Y substitution showed an extended resistance spectrum to the recently developed fluoroquinolone gemifloxacin. Our results suggest that soil and animal microbiomes could be major reservoirs of antibiotic resistance; polymorphic diversity expands the antibiotic resistome in the environment, resulting in the potential emergence of novel resistance.
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136
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Straight from the Horse's "Mouth": Genomic Epidemiology of an Icelandic Equine Epidemic. mBio 2017; 8:mBio.01613-17. [PMID: 29018124 PMCID: PMC5635694 DOI: 10.1128/mbio.01613-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite tight biosecurity measures, an outbreak of respiratory disease rapidly spread across the Icelandic equine population in 2010. Horse transportation was brought to a halt in order to contain the spread of the infectious agent. In a recent article, Björnsdóttir and colleagues (S. Björnsdóttir et al., mBio 8:e00826-17, 2017, https://doi.org/10.1128/mBio.00826-17) employ the power and resolution of “genomic epidemiology,” the combination of whole genomic sequencing and epidemiological approaches, to examine the source and spread of the outbreak. Intriguingly, the outbreak was not viral in origin, but linked to a bacterial “commensal” Streptococcus equi subsp. zooepidemicus infection. A national sampling strategy coupled with population genomics revealed that the outbreak was most likely driven by a S. equi subsp. zooepidemicus sequence type 209 (ST209) infection that spread nationally from a single source. This retrospective study demonstrates the power of genomics applied on a national scale to unravel the cause of a significant biosecurity threat.
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137
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Correia S, Hébraud M, Chafsey I, Chambon C, Viala D, Torres C, Caniça M, Capelo JL, Poeta P, Igrejas G. Subproteomic signature comparison of in vitro selected fluoroquinolone resistance and ciprofloxacin stress in Salmonella Typhimurium DT104B. Expert Rev Proteomics 2017; 14:941-961. [PMID: 28871888 DOI: 10.1080/14789450.2017.1375856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Fluoroquinolone resistance in nontyphoidal Salmonella is a situation of serious and international concern, particularly in S. Typhimurium DT104B multiresistant strains. Although known to be multifactorial, fluoroquinolone resistance is still far from a complete understanding. METHODS Subproteome changes between an experimentally selected fluoroquinolone-resistant strain (Se6-M) and its parent strain (Se6), and also in Se6-M under ciprofloxacin (CIP) stress, were evaluated in order to give new insights into the mechanisms involved. Proteomes were compared at the intracellular and membrane levels by a 2-DE~LC-MS/MS and a shotgun LC-MS/MS approach, respectively. RESULTS In total, 35 differentially abundant proteins were identified when comparing Se6 with Se6-M (25 more abundant in Se6 and 10 more abundant in Se6-M) and 82 were identified between Se6-M and Se6-M+CIP (51 more abundant in Se6-M and 31 more abundant under ciprofloxacin stress). CONCLUSION Several proteins with known and possible roles in quinolone resistance were identified which provide important information about mechanism-related differential protein expression, supporting the current knowledge and also leading to new testable hypotheses on the mechanism of action of fluoroquinolone drugs.
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Affiliation(s)
- Susana Correia
- a Functional Genomics and Proteomics Unit , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,b Department of Genetics and Biotechnology , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Veterinary Science Department , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal
| | - Michel Hébraud
- e UR454 Microbiology , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France.,f Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Ingrid Chafsey
- e UR454 Microbiology , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Christophe Chambon
- f Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Didier Viala
- f Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Carmen Torres
- g Área de Bioquímica y Biología Molecular , Universidad de La Rioja , Logroño , Spain
| | - Manuela Caniça
- h National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR-HAI), Department of Infectious Diseases , National Health Institute Doutor Ricardo Jorge (INSA) , Lisbon , Portugal
| | - José Luis Capelo
- d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal.,i Faculty of Sciences and Technology , ProteoMass Scientific Society , Caparica , Portugal
| | - Patrícia Poeta
- c Veterinary Science Department , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal
| | - Gilberto Igrejas
- a Functional Genomics and Proteomics Unit , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,b Department of Genetics and Biotechnology , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal
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138
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Abstract
Salmonella enterica subspecies enterica includes several serovars infecting both humans and other animals and leading to typhoid fever or gastroenteritis. The high prevalence of associated morbidity and mortality, together with an increased emergence of multidrug-resistant strains, is a current global health issue that has prompted the development of vaccination strategies that confer protection against most serovars. Currently available systemic vaccine approaches have major limitations, including a reduced effectiveness in young children and a lack of cross-protection among different strains. Having studied host-pathogen interactions, microbiologists and immunologists argue in favor of topical gastrointestinal administration for improvement in vaccine efficacy. Here, recent advances in this field are summarized, including mechanisms of bacterial uptake at the intestinal epithelium, the assessment of protective host immunity, and improved animal models that closely mimic infection in humans. The pros and cons of existing vaccines are presented, along with recent progress made with novel formulations. Finally, new candidate antigens and their relevance in the refined design of anti-Salmonella vaccines are discussed, along with antigen vectorization strategies such as nanoparticles or secretory immunoglobulins, with a focus on potentiating mucosal vaccine efficacy.
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139
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Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations. Appl Environ Microbiol 2017; 83:AEM.00140-17. [PMID: 28389536 DOI: 10.1128/aem.00140-17] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/27/2017] [Indexed: 01/09/2023] Open
Abstract
Multidrug-resistant (MDR) Salmonella enterica can be spread from cattle to humans through direct contact with animals shedding Salmonella as well as through the food chain, making MDR Salmonella a serious threat to human health. The objective of this study was to use whole-genome sequencing to compare antimicrobial-resistant (AMR) Salmonella enterica serovars Typhimurium, Newport, and Dublin isolated from dairy cattle and humans in Washington State and New York State at the genotypic and phenotypic levels. A total of 90 isolates were selected for the study (37 S Typhimurium, 32 S Newport, and 21 S Dublin isolates). All isolates were tested for phenotypic antibiotic resistance to 12 drugs using Kirby-Bauer disk diffusion. AMR genes were detected in the assembled genome of each isolate using nucleotide BLAST and ARG-ANNOT. Genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.2 and specificity of 85.2. Sulfamethoxazole-trimethoprim resistance was observed only in human isolates (P < 0.05), while resistance to quinolones and fluoroquinolones was observed only in 6 S Typhimurium isolates from humans in Washington State. S Newport isolates showed a high degree of AMR profile similarity, regardless of source. S Dublin isolates from New York State differed from those from Washington State based on the presence/absence of plasmid replicons, as well as phenotypic AMR susceptibility/nonsusceptibility (P < 0.05). The results of this study suggest that distinct factors may contribute to the emergence and dispersal of AMR S. enterica in humans and farm animals in different regions.IMPORTANCE The use of antibiotics in food-producing animals has been hypothesized to select for AMR Salmonella enterica and associated AMR determinants, which can be transferred to humans through different routes. Previous studies have sought to assess the degree to which AMR livestock- and human-associated Salmonella strains overlap, as well as the spatial distribution of Salmonella's associated AMR determinants, but have often been limited by the degree of resolution at which isolates can be compared. Here, a comparative genomics study of livestock- and human-associated Salmonella strains from different regions of the United States shows that while many AMR genes and phenotypes were confined to human isolates, overlaps between the resistomes of bovine and human-associated Salmonella isolates were observed on numerous occasions, particularly for S Newport. We have also shown that whole-genome sequencing can be used to reliably predict phenotypic resistance across Salmonella isolated from bovine sources.
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140
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Margos G, Hepner S, Mang C, Marosevic D, Reynolds SE, Krebs S, Sing A, Derdakova M, Reiter MA, Fingerle V. Lost in plasmids: next generation sequencing and the complex genome of the tick-borne pathogen Borrelia burgdorferi. BMC Genomics 2017; 18:422. [PMID: 28558786 PMCID: PMC5450258 DOI: 10.1186/s12864-017-3804-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/17/2017] [Indexed: 11/21/2022] Open
Abstract
Background Borrelia (B.) burgdorferi sensu lato, including the tick-transmitted agents of human Lyme borreliosis, have particularly complex genomes, consisting of a linear main chromosome and numerous linear and circular plasmids. The number and structure of plasmids is variable even in strains within a single genospecies. Genes on these plasmids are known to play essential roles in virulence and pathogenicity as well as host and vector associations. For this reason, it is essential to explore methods for rapid and reliable characterisation of molecular level changes on plasmids. In this study we used three strains: a low passage isolate of B. burgdorferi sensu stricto strain B31(−NRZ) and two closely related strains (PAli and PAbe) that were isolated from human patients. Sequences of these strains were compared to the previously sequenced reference strain B31 (available in GenBank) to obtain proof-of-principle information on the suitability of next generation sequencing (NGS) library construction and sequencing methods on the assembly of bacterial plasmids. We tested the effectiveness of different short read assemblers on Illumina sequences, and of long read generation methods on sequence data from Pacific Bioscience single-molecule real-time (SMRT) and nanopore (Oxford Nanopore Technologies) sequencing technology. Results Inclusion of mate pair library reads improved the assembly in some plasmids as did prior enrichment of plasmids. While cp32 plasmids remained refractory to assembly using only short reads they were effectively assembled by long read sequencing methods. The long read SMRT and nanopore sequences came, however, at the cost of indels (insertions or deletions) appearing in an unpredictable manner. Using long and short read technologies together allowed us to show that the three B. burgdorferi s.s. strains investigated here, whilst having similar plasmid structures to each other (apart from fusion of cp32 plasmids), differed significantly from the reference strain B31-GB, especially in the case of cp32 plasmids. Conclusion Short read methods are sufficient to assemble the main chromosome and many of the plasmids in B. burgdorferi. However, a combination of short and long read sequencing methods is essential for proper assembly of all plasmids including cp32 and thus, for gaining an understanding of host- or vector adaptations. An important conclusion from our work is that the evolution of Borrelia plasmids appears to be dynamic. This has important implications for the development of useful research strategies to monitor the risk of Lyme disease occurrence and how to medically manage it. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3804-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- G Margos
- German National Reference Centre for Borrelia (NRZ), Bavarian Health and Food Safety Authority (LGL), Veterinärstrasse 2, 85764, Oberschleissheim, Germany.
| | - S Hepner
- German National Reference Centre for Borrelia (NRZ), Bavarian Health and Food Safety Authority (LGL), Veterinärstrasse 2, 85764, Oberschleissheim, Germany
| | - C Mang
- German National Reference Centre for Borrelia (NRZ), Bavarian Health and Food Safety Authority (LGL), Veterinärstrasse 2, 85764, Oberschleissheim, Germany
| | - D Marosevic
- Bavarian Health and Food Safety Authority (LGL), Veterinärstrasse 2, 85764, Oberschleissheim, Germany.,European Programme for Public Health Microbiology Training, European Centre of Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - S E Reynolds
- Department of Biology and Biochemistry, University of Bath, Claverton Down, BA2 7AY, Bath, UK
| | - S Krebs
- Gene Centre, Laboratory for Functional Genome Analysis, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - A Sing
- German National Reference Centre for Borrelia (NRZ), Bavarian Health and Food Safety Authority (LGL), Veterinärstrasse 2, 85764, Oberschleissheim, Germany
| | - M Derdakova
- Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - M A Reiter
- Institut für Hygiene und Angewandte Immunologie, Medizinische Universität Wien, Kinderspitalgasse 15, A-1090, Wien, Austria
| | - V Fingerle
- German National Reference Centre for Borrelia (NRZ), Bavarian Health and Food Safety Authority (LGL), Veterinärstrasse 2, 85764, Oberschleissheim, Germany
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Shao YX, Lei Z, Wolf PG, Gao Y, Guo YM, Zhang BK. Zinc Supplementation, via GPR39, Upregulates PKCζ to Protect Intestinal Barrier Integrity in Caco-2 Cells Challenged bySalmonella entericaSerovar Typhimurium. J Nutr 2017; 147:1282-1289. [DOI: 10.3945/jn.116.243238] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/23/2016] [Accepted: 04/13/2017] [Indexed: 12/26/2022] Open
Affiliation(s)
- Yu-Xin Shao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhao Lei
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Patricia G Wolf
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Yan Gao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yu-Ming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Bing-Kun Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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142
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Antimicrobial resistance in human populations: challenges and opportunities. GLOBAL HEALTH EPIDEMIOLOGY AND GENOMICS 2017; 2:e4. [PMID: 29276617 PMCID: PMC5732576 DOI: 10.1017/gheg.2017.4] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 01/05/2017] [Accepted: 03/30/2017] [Indexed: 12/24/2022]
Abstract
Antimicrobial resistance (AMR) is a global public health threat. Emergence of AMR occurs naturally, but can also be selected for by antimicrobial exposure in clinical and veterinary medicine. Despite growing worldwide attention to AMR, there are substantial limitations in our understanding of the burden, distribution and determinants of AMR at the population level. We highlight the importance of population-based approaches to assess the association between antimicrobial use and AMR in humans and animals. Such approaches are needed to improve our understanding of the development and spread of AMR in order to inform strategies for the prevention, detection and management of AMR, and to support the sustainable use of antimicrobials in healthcare.
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143
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Correia S, Hébraud M, Chafsey I, Chambon C, Viala D, Sáenz Y, Capelo JL, Poeta P, Igrejas G. Comparative subproteomic analysis of clinically acquired fluoroquinolone resistance and ciprofloxacin stress in Salmonella Typhimurium DT104B. Proteomics Clin Appl 2017; 11. [PMID: 28314077 DOI: 10.1002/prca.201600107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 02/21/2017] [Accepted: 03/07/2017] [Indexed: 02/06/2023]
Abstract
PURPOSE Antimicrobial resistance is a worldwide public health threat and Salmonella enterica subsp. enterica serotype Typhimurium phage type DT104B multiresistant strains with additional quinolone resistance have been responsible for global outbreaks and high mortality. Quinolone resistance is known to be multifactorial but is still far from a complete understanding. To give new insights about the resistance mechanisms involved, this work aimed to evaluate subproteome changes between an S. Typhimurium DT104B clinical strain that acquired fluoroquinolone resistance after treatment (Se20) and its pretreatment parental strain (Se6), and also subproteome variations in Se20 under ciprofloxacin (CIP) stress (Se20+CIP). EXPERIMENTAL DESIGN The proteomes were compared at the intracellular and membrane levels by a 2-DE∼LC-MS/MS and a shotgun LC-MS/MS approach, respectively. RESULTS In total, 14 differentially abundant proteins were identified when comparing Se6 with Se20 and 91 were identified between Se20 and Se20+CIP. Several proteins with known and possible roles in quinolone resistance (AAC(6')-Ib-cr4, OmpD, OmpX, GlmS, GlmU, H-NS, etc.) were identified and discussed. CONCLUSIONS AND CLINICAL RELEVANCE The great number of proteins identified in this study provides important information about mechanism-related differential protein expression which supports the current knowledge and might lead to new testable hypotheses on the mechanism of action of fluoroquinolone drugs.
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Affiliation(s)
- Susana Correia
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
| | - Michel Hébraud
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne (UCA), UMR Microbiologie Environnement Digestif et Santé (MEDiS), site de Theix, France.,Institut National de la Recherche Agronomique (INRA), UR370 QuaPA, Plate-Forme d'Exploration du Métabolisme composante protéomique, site de Theix, France
| | - Ingrid Chafsey
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne (UCA), UMR Microbiologie Environnement Digestif et Santé (MEDiS), site de Theix, France
| | - Christophe Chambon
- Institut National de la Recherche Agronomique (INRA), UR370 QuaPA, Plate-Forme d'Exploration du Métabolisme composante protéomique, site de Theix, France
| | - Didier Viala
- Institut National de la Recherche Agronomique (INRA), UR370 QuaPA, Plate-Forme d'Exploration du Métabolisme composante protéomique, site de Theix, France
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logrono, Spain
| | - José Luis Capelo
- UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal.,ProteoMass Scientific Society, Faculty of Sciences and Technology, Caparica Campus, Caparica, Portugal
| | - Patrícia Poeta
- Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
| | - Gilberto Igrejas
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
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144
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McCann HC, Li L, Liu Y, Li D, Pan H, Zhong C, Rikkerink EH, Templeton MD, Straub C, Colombi E, Rainey PB, Huang H. Origin and Evolution of the Kiwifruit Canker Pandemic. Genome Biol Evol 2017; 9:932-944. [PMID: 28369338 PMCID: PMC5388287 DOI: 10.1093/gbe/evx055] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2017] [Indexed: 12/18/2022] Open
Abstract
Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa). In order to strengthen understanding of population structure, phylogeography, and evolutionary dynamics, we isolated Pseudomonas from cultivated and wild kiwifruit across six provinces in China. Based on the analysis of 80 sequenced Psa genomes, we show that China is the origin of the pandemic lineage but that strain diversity in China is confined to just a single clade. In contrast, Korea and Japan harbor strains from multiple clades. Distinct independent transmission events marked introduction of the pandemic lineage into New Zealand, Chile, Europe, Korea, and Japan. Despite high similarity within the core genome and minimal impact of within-clade recombination, we observed extensive variation even within the single clade from which the global pandemic arose.
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Affiliation(s)
- Honour C. McCann
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Li Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yifei Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Hui Pan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Erik H.A. Rikkerink
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Matthew D. Templeton
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, New Zealand
| | - Christina Straub
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Elena Colombi
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231 PSL Research University, Paris, France
| | - Hongwen Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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145
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Helke KL, McCrackin MA, Galloway AM, Poole AZ, Salgado CD, Marriott BP. Effects of antimicrobial use in agricultural animals on drug-resistant foodborne salmonellosis in humans: A systematic literature review. Crit Rev Food Sci Nutr 2017; 57:472-488. [PMID: 27602884 DOI: 10.1080/10408398.2016.1230088] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Controversy continues concerning antimicrobial use in food animals and its relationship to drug-resistant infections in humans. We systematically reviewed published literature for evidence of a relationship between antimicrobial use in agricultural animals and drug-resistant meat or dairy-borne non-typhoidal salmonellosis in humans. Based on publications from the United States (U.S.), Canada, and Denmark from January 2010 to July 2014, 858 articles received title and abstract review, 104 met study criteria for full article review with 68 retained for which data are presented. Antibiotic exposure in both cattle and humans found an increased likelihood of Salmonella colonization, whereas in chickens, animals not exposed to antibiotics (organic) were more likely to be Salmonella positive and those that had antibiotic exposure were more likely to harbor antimicrobial resistant Salmonella organisms. In swine literature, only tylosin exposure was examined and no correlation was found among exposure, Salmonella colonization, or antimicrobial resistance. No studies that identified farm antimicrobial use also traced antimicrobial-resistant Salmonella from farm to fork.
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Affiliation(s)
- Kristi L Helke
- a Department of Comparative Medicine , Medical University of South Carolina , Charleston , South Carolina , USA
| | - M A McCrackin
- a Department of Comparative Medicine , Medical University of South Carolina , Charleston , South Carolina , USA.,b Ralph H. Johnson VA Medical Center Department of Research Service , Charleston , South Carolina , USA
| | - Ashley M Galloway
- c Department of Medicine , Nutrition Section, Division of Gastroenterology, Medical University of South Carolina , Charleston , South Carolina , USA
| | - Ann Z Poole
- c Department of Medicine , Nutrition Section, Division of Gastroenterology, Medical University of South Carolina , Charleston , South Carolina , USA
| | - Cassandra D Salgado
- d Department of Medicine , Infectious Disease Division, Medical University of South Carolina , Charleston , South Carolina , USA
| | - Bernadette P Marriott
- c Department of Medicine , Nutrition Section, Division of Gastroenterology, Medical University of South Carolina , Charleston , South Carolina , USA.,e Department of Psychiatry , Nutrition Section, Division of Gastroenterology, Medical University of South Carolina , Charleston , South Carolina , USA
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146
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Abstract
Increasing evidence indicates that many, if not all, small genes encoding proteins ≤100 aa are missing in annotations of bacterial genomes currently available. To uncover unannotated small genes in the model bacterium Salmonella enterica Typhimurium 14028s, we used the genomic technique ribosome profiling, which provides a snapshot of all mRNAs being translated (translatome) in a given growth condition. For comprehensive identification of unannotated small genes, we obtained Salmonella translatomes from four different growth conditions: LB, MOPS rich defined medium, and two infection-relevant conditions low Mg2+ (10 µM) and low pH (5.8). To facilitate the identification of small genes, ribosome profiling data were analyzed in combination with in silico predicted putative open reading frames and transcriptome profiles. As a result, we uncovered 130 unannotated ORFs. Of them, 98% were small ORFs putatively encoding peptides/proteins ≤100 aa, and some of them were only expressed in the infection-relevant low Mg2+ and/or low pH condition. We validated the expression of 25 of these ORFs by western blot, including the smallest, which encodes a peptide of 7 aa residues. Our results suggest that many sequenced bacterial genomes are underannotated with regard to small genes and their gene annotations need to be revised.
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147
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Yu H, Hasan NM, In JG, Estes MK, Kovbasnjuk O, Zachos NC, Donowitz M. The Contributions of Human Mini-Intestines to the Study of Intestinal Physiology and Pathophysiology. Annu Rev Physiol 2017; 79:291-312. [PMID: 28192061 PMCID: PMC5549102 DOI: 10.1146/annurev-physiol-021115-105211] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lack of accessibility to normal and diseased human intestine and the inability to separate the different functional compartments of the intestine even when tissue could be obtained have held back the understanding of human intestinal physiology. Clevers and his associates identified intestinal stem cells and established conditions to grow "mini-intestines" ex vivo in differentiated and undifferentiated conditions. This pioneering work has made a new model of the human intestine available and has begun making contributions to the understanding of human intestinal transport in normal physiologic conditions and the pathophysiology of intestinal diseases. However, this model is reductionist and lacks many of the complexities of normal intestine. Consequently, it is not yet possible to predict how great the advances using this model will be for understanding human physiology and pathophysiology, nor how the model will be modified to include multiple other intestinal cell types and physical forces necessary to more closely approximate normal intestine. This review describes recent studies using mini-intestines, which have readdressed previously established models of normal intestinal transport physiology and newly examined intestinal pathophysiology. The emphasis is on studies with human enteroids grown either as three-dimensional spheroids or two-dimensional monolayers. In addition, comments are provided on mouse studies in cases when human studies have not yet been described.
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Affiliation(s)
- Huimin Yu
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Nesrin M Hasan
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Julie G In
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Olga Kovbasnjuk
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Nicholas C Zachos
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
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148
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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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149
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Baele G, Suchard MA, Rambaut A, Lemey P. Emerging Concepts of Data Integration in Pathogen Phylodynamics. Syst Biol 2017; 66:e47-e65. [PMID: 28173504 PMCID: PMC5837209 DOI: 10.1093/sysbio/syw054] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 06/02/2016] [Indexed: 12/24/2022] Open
Abstract
Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.
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Affiliation(s)
- Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3FL, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Edinburgh EH9 3FL, UK
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
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150
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Edlind T, Brewster JD, Paoli GC. Enrichment, Amplification, and Sequence-Based Typing of Salmonella enterica and Other Foodborne Pathogens. J Food Prot 2017; 80:15-24. [PMID: 28221883 DOI: 10.4315/0362-028x.jfp-16-014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Detection of Salmonella enterica in foods typically involves microbiological enrichment, molecular-based assay, and subsequent isolation and identification of a pure culture. This is ideally followed by strain typing, which provides information critical to the investigation of outbreaks and the attribution of their sources. Pulsed-field gel electrophoresis is the "gold standard" for S. enterica strain typing, but its limitations have encouraged the search for alternative methods, including whole genome sequencing. Both methods typically require a pure culture, which adds to the cost and turnaround time. A more rapid and cost-effective method with sufficient discriminatory power would benefit food industries, regulatory agencies, and public health laboratories. To address this need, a novel enrichment, amplification, and sequence-based typing (EAST) approach was developed involving (i) overnight enrichment and total DNA preparation, (ii) amplification of polymorphic tandem repeat-containing loci with electrophoretic detection, and (iii) DNA sequencing and bioinformatic analysis to identify related strains. EAST requires 3 days or less and provides a strain resolution that exceeds serotyping and is comparable to pulsed-field gel electrophoresis. Evaluation with spiked ground turkey demonstrated its sensitivity (with a starting inoculum of ≤1 CFU/g) and specificity (with unique or nearly unique alleles relative to databases of >1,000 strains). In tests with unspiked retail chicken parts, 3 of 11 samples yielded S. enterica -specific PCR products. Sequence analysis of three distinct typing targets (SeMT1, SeCRISPR1, and SeCRISPR2) revealed consistent similarities to specific serotype Schwarzengrund, Montevideo, and Typhimurium strains. EAST provides a time-saving and cost-effective approach for detecting and typing foodborne S. enterica , and postenrichment steps can be commercially outsourced to facilitate its implementation. Initial studies with Listeria monocytogenes and Shiga toxigenic Escherichia coli suggest that EAST can be extended to these foodborne pathogens.
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Affiliation(s)
- Tom Edlind
- MicrobiType LLC, 5110 Campus Drive, Plymouth Meeting, Pennsylvania 19462
| | - Jeffrey D Brewster
- U.S. Department of Agriculture, Agricultural Research Service, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19038, USA
| | - George C Paoli
- U.S. Department of Agriculture, Agricultural Research Service, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19038, USA
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