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Mather AE, Gilmour MW, Reid SWJ, French NP. Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world. Nat Rev Microbiol 2024; 22:543-555. [PMID: 38789668 DOI: 10.1038/s41579-024-01051-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2024] [Indexed: 05/26/2024]
Abstract
Foodborne illnesses pose a substantial health and economic burden, presenting challenges in prevention due to the diverse microbial hazards that can enter and spread within food systems. Various factors, including natural, political and commercial drivers, influence food production and distribution. The risks of foodborne illness will continue to evolve in step with these drivers and with changes to food systems. For example, climate impacts on water availability for agriculture, changes in food sustainability targets and evolving customer preferences can all have an impact on the ecology of foodborne pathogens and the agrifood niches that can carry microorganisms. Whole-genome and metagenome sequencing, combined with microbial surveillance schemes and insights from the food system, can provide authorities and businesses with transformative information to address risks and implement new food safety interventions across the food chain. In this Review, we describe how genome-based approaches have advanced our understanding of the evolution and spread of enduring bacterial foodborne hazards as well as their role in identifying emerging foodborne hazards. Furthermore, foodborne hazards exist in complex microbial communities across the entire food chain, and consideration of these co-existing organisms is essential to understanding the entire ecology supporting pathogen persistence and transmission in an evolving food system.
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Affiliation(s)
- Alison E Mather
- Quadram Institute Bioscience, Norwich, UK.
- University of East Anglia, Norwich, UK.
| | - Matthew W Gilmour
- Quadram Institute Bioscience, Norwich, UK
- University of East Anglia, Norwich, UK
| | | | - Nigel P French
- Tāuwharau Ora, School of Veterinary Science, Te Kunenga Ki Pūrehuroa, Massey University, Papaioea, Palmerston North, Aotearoa New Zealand
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2
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Liu C, Guo J, Fan S, Guo W, Qi H, Baker S, Du P, Cao B. An increased prevalence of carbapenem-resistant hypervirulent Klebsiella pneumoniae associated with the COVID-19 pandemic. Drug Resist Updat 2024; 77:101124. [PMID: 39128195 DOI: 10.1016/j.drup.2024.101124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/27/2024] [Accepted: 07/30/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND Klebsiella pneumoniae (Kp) is a common community-acquired and nosocomial pathogen. Carbapenem-resistant and hypervirulent (CR-hvKp) variants can emerge rapidly within healthcare facilities and impacted by other infectious agents such as COVID-19 virus. METHODS To understand the impact of COVID-19 virus on the prevalence of CR-hvKp, we accessed Kp genomes with corresponding metadata from GenBank. Sequence types (STs), antimicrobial resistance genes, and virulence genes, and those scores and CR-hvKp were identified. We analyzed population diversity and phylogenetic characteristics of five most common STs, measured the prevalence of CR-hvKp, identified CR-hvKp subtypes, and determined associations between carbapenem resistance gene subtypes with STs and plasmid types. These variables were compared pre- and during the COVID-19 pandemic. FINDINGS The proportion of CR-hvKp isolates increased within multiple STs in different continents during the COVID-19 pandemic and persistent CR-hvKp subtypes were found in common STs. blaKPC was dominant in CG258, blaKPC-2 was detected in 97 % of the ST11 CR-hvKp, blaNDM subtypes were prominent in ST147 (87.4 %) and ST307 (70.8 %); blaOXA-48 and its subtypes were prevalent in ST15 (80.5 %). The possession of carbapenemase genes was different among subclades from different origins in different periods of time within each ST. IncFIB/IncHI1B hybrid plasmids contained virulence genes and carbapenemase genes and were predominant in ST147 (67.37 %) and ST307 (56.25 %). INTERPRETATION The prevalence of CR-hvKp increased during the COVID-19 pandemic, which was evident by an increase in local endemic clones. This process was facilitated by the convergence of plasmids containing carbapenemase genes and virulence genes. These findings have implications for the appropriate use of antimicrobials and infection prevention and control during outbreaks of respiratory viruses and pandemic management.
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Affiliation(s)
- Chao Liu
- Department of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Jun Guo
- Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Shuaihua Fan
- Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Wei Guo
- Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Huaiqing Qi
- Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Department of Respiratory Medicine, Capital Medical University, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijiing, China.
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3
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Hulme PE, Beggs JR, Binny RN, Bray JP, Cogger N, Dhami MK, Finlay-Smits SC, French NP, Grant A, Hewitt CL, Jones EE, Lester PJ, Lockhart PJ. Emerging advances in biosecurity to underpin human, animal, plant, and ecosystem health. iScience 2023; 26:107462. [PMID: 37636074 PMCID: PMC10450416 DOI: 10.1016/j.isci.2023.107462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
One Biosecurity is an interdisciplinary approach to policy and research that builds on the interconnections between human, animal, plant, and ecosystem health to effectively prevent and mitigate the impacts of invasive alien species. To support this approach requires that key cross-sectoral research innovations be identified and prioritized. Following an interdisciplinary horizon scan for emerging research that underpins One Biosecurity, four major interlinked advances were identified: implementation of new surveillance technologies adopting state-of-the-art sensors connected to the Internet of Things, deployable handheld molecular and genomic tracing tools, the incorporation of wellbeing and diverse human values into biosecurity decision-making, and sophisticated socio-environmental models and data capture. The relevance and applicability of these innovations to address threats from pathogens, pests, and weeds in both terrestrial and aquatic ecosystems emphasize the opportunity to build critical mass around interdisciplinary teams at a global scale that can rapidly advance science solutions targeting biosecurity threats.
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Affiliation(s)
- Philip E. Hulme
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Jacqueline R. Beggs
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Rachelle N. Binny
- Manaaki Whenua - Landcare Research, PO Box 69040, Lincoln, New Zealand
| | - Jonathan P. Bray
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Naomi Cogger
- Tāwharau Ora, School of Veterinary Science, Massey University, Palmerston North 4472, New Zealand
| | - Manpreet K. Dhami
- Manaaki Whenua - Landcare Research, PO Box 69040, Lincoln, New Zealand
| | | | - Nigel P. French
- Tāwharau Ora, School of Veterinary Science, Massey University, Palmerston North 4472, New Zealand
| | - Andrea Grant
- Scion, 10 Kyle Street, Riccarton, Christchurch 8011, New Zealand
| | - Chad L. Hewitt
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Eirian E. Jones
- The Centre for One Biosecurity Research, Analysis and Synthesis, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
- Department of Pest Management and Conservation, Lincoln University, PO Box 85084, Lincoln, Christchurch 7648, New Zealand
| | - Phil J. Lester
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Peter J. Lockhart
- School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand
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Milani G, Belloso Daza MV, Cortimiglia C, Bassi D, Cocconcelli PS. Genome engineering of Stx1-and Stx2-converting bacteriophages unveils the virulence of the dairy isolate Escherichia coli O174:H2 strain UC4224. Front Microbiol 2023; 14:1156375. [PMID: 37426006 PMCID: PMC10326431 DOI: 10.3389/fmicb.2023.1156375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
The past decade witnessed the emergence in Shiga toxin-producing Escherichia coli (STEC) infections linked to the consumption of unpasteurized milk and raw milk cheese. The virulence of STEC is primarily attributed to the presence of Shiga toxin genes (stx1 and stx2) carried by Stx-converting bacteriophages, along with the intimin gene eae. Most of the available information pertains to the "Top 7" serotypes associated with STEC infections. The objectives of this study were to characterize and investigate the pathogenicity potential of E. coli UC4224, a STEC O174:H2 strain isolated from semi-hard raw milk cheese and to develop surrogate strains with reduced virulence for use in food-related studies. Complete genome sequence analysis of E. coli UC4224 unveiled the presence of a Stx1a bacteriophage, a Stx2a bacteriophage, the Locus of Adhesion and Autoaggregation (LAA) pathogenicity island, plasmid-encoded virulence genes, and other colonization facilitators. In the Galleria mellonella animal model, E. coli UC4224 demonstrated high pathogenicity potential with an LD50 of 6 CFU/10 μL. Upon engineering E. coli UC4224 to generate single and double mutant derivatives by inactivating stx1a and/or stx2a genes, the LD50 increased by approximately 1 Log-dose in the single mutants and 2 Log-doses in the double mutants. However, infectivity was not completely abolished, suggesting the involvement of other virulence factors contributing to the pathogenicity of STEC O174:H2. Considering the possibility of raw milk cheese serving as a reservoir for STEC, cheesemaking model was developed to evaluate the survival of UC4224 and the adequacy of the respective mutants as reduced-virulence surrogates. All tested strains exhibited the ability to survive the curd cooking step at 48°C and multiplied (3.4 Log CFU) in cheese within the subsequent 24 h. These findings indicate that genomic engineering did not exert any unintended effect on the double stx1-stx2 mutant behaviour, making it as a suitable less-virulent surrogate for conducting studies during food processing.
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Pakbin B, Brück WM, Brück TB, Allahyari S, Ashrafi Tamai I. A quantitative prevalence of Escherichia coliO157 in different food samples using real-time qPCR method. Food Sci Nutr 2022; 11:228-235. [PMID: 36655112 PMCID: PMC9834875 DOI: 10.1002/fsn3.3055] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/09/2022] [Accepted: 08/25/2022] [Indexed: 01/21/2023] Open
Abstract
Escherichia coli serogroup O157 is the main causative agent of several intestinal and extra-intestinal foodborne diseases in humans through consumption of low-dose contaminated foods such as milk, beef, and vegetables. To date, studies regarding the quantitative prevalence of E. coli O157 in foods are so limited. Therefore, this study aimed to evaluate the quantitative prevalence rate of E. coli serogroup O157 in raw milk (n = 144), vegetable salad (n = 174), and minced beef samples (n = 108) using the real-time qPCR SYBR green melting curve method targeting the rfbA gene. First, we evaluated the method and found a sensitive and specific qPCR assay with 1 log of CFU/ml detection limit to detect E. coli O157 (Tm = 80.3 ± 0.1°C). About 2.77%, 10.18%, and 9.19% of raw milk, minced beef, and vegetable salad samples, respectively, were contaminated with E. coli O157. Minced beef and vegetable salad samples were significantly more contaminated than raw milk samples. Population average of E. coli O157 in raw milk, minced beef, and vegetable salad samples were 2.22 ± 0.57, 3.30 ± 0.40, and 1.65 ± 0.44 log CFU/ml or gr, respectively. Significantly higher levels of population of E. coli O157 were observed in minced beef samples. Minced beef can be regarded as the main food in the transmission of this foodborne pathogen. Routine quantitative rapid monitoring is strongly suggested to be carried out to prevent foodborne diseases caused by E. coli O157.
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Affiliation(s)
- Babak Pakbin
- Institute for Life TechnologiesUniversity of Applied Sciences Western Switzerland Valais‐WallisSion 2Switzerland,Department of Chemistry, Werner Siemens Chair of Synthetic BiotechnologyTechnical University of Munich (TUM)MünchenGermany,Medical Microbiology Research CenterQazvin University of Medical SciencesQazvinIran
| | - Wolfram Manuel Brück
- Institute for Life TechnologiesUniversity of Applied Sciences Western Switzerland Valais‐WallisSion 2Switzerland
| | - Thomas B. Brück
- Department of Chemistry, Werner Siemens Chair of Synthetic BiotechnologyTechnical University of Munich (TUM)MünchenGermany
| | - Samaneh Allahyari
- Medical Microbiology Research CenterQazvin University of Medical SciencesQazvinIran
| | - Iradj Ashrafi Tamai
- Department of Microbiology and Immunology, Faculty of Veterinary MedicineUniversity of TehranTehranIran
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Identification of domestic reservoirs and common exposures in an emerging lineage of Shiga toxin-producing Escherichia coli O157:H7 in England: a genomic epidemiological analysis. THE LANCET MICROBE 2022; 3:e606-e615. [DOI: 10.1016/s2666-5247(22)00089-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 01/01/2023] Open
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Wang T, Guo Y, Roellig DM, Li N, Santín M, Lombard J, Kváč M, Naguib D, Zhang Z, Feng Y, Xiao L. Sympatric Recombination in Zoonotic Cryptosporidium Leads to Emergence of Populations with Modified Host Preference. Mol Biol Evol 2022; 39:6625830. [PMID: 35776423 PMCID: PMC9317183 DOI: 10.1093/molbev/msac150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genetic recombination plays a critical role in the emergence of pathogens with phenotypes such as drug resistance, virulence, and host adaptation. Here, we tested the hypothesis that recombination between sympatric ancestral populations leads to the emergence of divergent variants of the zoonotic parasite Cryptosporidium parvum with modified host ranges. Comparative genomic analyses of 101 isolates have identified seven subpopulations isolated by distance. They appear to be descendants of two ancestral populations, IIa in northwestern Europe and IId from southwestern Asia. Sympatric recombination in areas with both ancestral subtypes and subsequent selective sweeps have led to the emergence of new subpopulations with mosaic genomes and modified host preference. Subtelomeric genes could be involved in the adaptive selection of subpopulations, while copy number variations of genes encoding invasion-associated proteins are potentially associated with modified host ranges. These observations reveal ancestral origins of zoonotic C. parvum and suggest that pathogen import through modern animal farming might promote the emergence of divergent subpopulations of C. parvum with modified host preference.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yaqiong Guo
- Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Dawn M Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, USA
| | - Na Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Mónica Santín
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, Beltsville, MD 20705, USA
| | - Jason Lombard
- Center for Epidemiology and Animal Health, Veterinary Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO 80526, USA
| | - Martin Kváč
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Doaa Naguib
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yaoyu Feng
- Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Lihua Xiao
- Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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8
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Weinroth MD, Clawson ML, Arthur TM, Wells JE, Brichta-Harhay DM, Strachan N, Bono JL. Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche. BMC Genomics 2022; 23:275. [PMID: 35392797 PMCID: PMC8991562 DOI: 10.1186/s12864-022-08497-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/23/2022] [Indexed: 11/25/2022] Open
Abstract
Background Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a pathogen known to reside in cattle feedlots. This retrospective study examined 181 STEC O157:H7 strains collected over 23 years from a closed-system feedlot. All strains were subjected to short-read sequencing, with a subset of 36 also subjected to long-read sequencing. Results Over 96% of the strains fell into four phylogenetically distinct clades. Clade membership was associated with multiple factors including stx composition and the alleles of a well-characterized polymorphism (tir 255 T > A). Small plasmids (2.7 to 40 kb) were found to be primarily clade specific. Within each clade, chromosomal rearrangements were observed along with a core phageome and clade specific phages. Across both core and mobile elements of the genome, multiple SNP alleles were in complete linkage disequilibrium across all strains within specific clades. Clade evolutionary rates varied between 0.9 and 2.8 SNP/genome/year with two tir A allele clades having the lowest evolutionary rates. Investigation into possible causes of the differing rates was not conclusive but revealed a synonymous based mutation in the DNA polymerase III of the fastest evolving clade. Phylogenetic trees generated through our bioinformatic pipeline versus the NCBI’s pathogen detection project were similar, with the two tir A allele clades matching individual NCBI SNP clusters, and the two tir T allele clades assigned to multiple closely-related SNP clusters. Conclusions In one ecological niche, a diverse STEC O157:H7 population exhibited different rates of evolution that associated with SNP alleles in linkage disequilibrium in the core genome and mobile elements, including tir 255 T > A. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08497-6.
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Affiliation(s)
- Margaret D Weinroth
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.,Present address: U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA, 30605, USA
| | - Michael L Clawson
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Terrance M Arthur
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - James E Wells
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Dayna M Brichta-Harhay
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Norval Strachan
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, Scotland, AB24 3UU, UK
| | - James L Bono
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.
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Guo Y, Ryan U, Feng Y, Xiao L. Association of Common Zoonotic Pathogens With Concentrated Animal Feeding Operations. Front Microbiol 2022; 12:810142. [PMID: 35082774 PMCID: PMC8784678 DOI: 10.3389/fmicb.2021.810142] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/17/2021] [Indexed: 12/24/2022] Open
Abstract
Animal farming has intensified significantly in recent decades, with the emergence of concentrated animal feeding operations (CAFOs) in industrialized nations. The congregation of susceptible animals in CAFOs can lead to heavy environmental contamination with pathogens, promoting the emergence of hyper-transmissible, and virulent pathogens. As a result, CAFOs have been associated with emergence of highly pathogenic avian influenza viruses, hepatitis E virus, Escherichia coli O157:H7, Streptococcus suis, livestock-associated methicillin-resistant Staphylococcus aureus, and Cryptosporidium parvum in farm animals. This has led to increased transmission of zoonotic pathogens in humans and changes in disease patterns in general communities. They are exemplified by the common occurrence of outbreaks of illnesses through direct and indirect contact with farm animals, and wide occurrence of similar serotypes or subtypes in both humans and farm animals in industrialized nations. Therefore, control measures should be developed to slow down the dispersal of zoonotic pathogens associated with CAFOs and prevent the emergence of new pathogens of epidemic and pandemic potential.
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Affiliation(s)
- Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Una Ryan
- Vector- and Water-Borne Pathogen Research Group, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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10
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Guo Y, Ryan U, Feng Y, Xiao L. Emergence of zoonotic Cryptosporidium parvum in China. Trends Parasitol 2021; 38:335-343. [PMID: 34972653 DOI: 10.1016/j.pt.2021.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/29/2022]
Abstract
Zoonotic cryptosporidiosis is a major public health problem in industrialized nations; in those countries it is caused mainly by Cryptosporidium parvum IIa subtypes that are prevalent in dairy calves. Because of the short history of intensive animal farming in China, strains of C. parvum are found only on some dairy farms in this country and are the IId subtypes. However, the prevalence of C. parvum is increasing rapidly, with IIa subtypes recently detected in a few grazing animals, and both IIa and IId subtypes are emerging in humans. As animal farming intensifies, China may follow in the footsteps of industrialized nations where zoonotic cryptosporidiosis is rampant. One Health and biosecurity measures are urgently needed to slow down the dispersal of autochthonous IId subtypes and imported IIa subtypes.
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Affiliation(s)
- Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Una Ryan
- Harry Butler Institute, Vector- and Water-Borne Pathogen Research Group, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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11
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Moura A, Lefrancq N, Wirth T, Leclercq A, Borges V, Gilpin B, Dallman TJ, Frey J, Franz E, Nielsen EM, Thomas J, Pightling A, Howden BP, Tarr CL, Gerner-Smidt P, Cauchemez S, Salje H, Brisse S, Lecuit M. Emergence and global spread of Listeria monocytogenes main clinical clonal complex. SCIENCE ADVANCES 2021; 7:eabj9805. [PMID: 34851675 PMCID: PMC8635441 DOI: 10.1126/sciadv.abj9805] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
The bacterial foodborne pathogen Listeria monocytogenes clonal complex 1 (Lm-CC1) is the most prevalent clonal group associated with human listeriosis and is strongly associated with cattle and dairy products. Here, we analyze 2021 isolates collected from 40 countries, covering Lm-CC1 first isolation to present days, to define its evolutionary history and population dynamics. We show that Lm-CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19th century and the rapid growth of cattle farming and food industrialization in the 20th century. In sharp contrast to its global spread over the past century, transmission chains are now mostly local, with limited inter- and intra-country spread. This study provides an unprecedented insight into L. monocytogenes phylogeography and population dynamics and highlights the importance of genome analyses for a better control of pathogen transmission.
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Affiliation(s)
- Alexandra Moura
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Noémie Lefrancq
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Thierry Wirth
- Institut Systématique Evolution Biodiversité (ISYEB),Museum National d’Histoire Naturelle, CNRS, Sorbonne Université, Université des Antilles, EPHE, Paris, France
- PSL University, EPHE, Paris, France
| | - Alexandre Leclercq
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
| | - Vítor Borges
- Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Brent Gilpin
- Christchurch Science Centre, Institute of Environmental Science and Research Limited, Christchurch, New Zealand
| | | | - Joachim Frey
- Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | | | - Juno Thomas
- Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Arthur Pightling
- Biostatistics and Bioinformatics, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria, Australia
| | - Cheryl L. Tarr
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Simon Cauchemez
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Henrik Salje
- Institut Pasteur, Université de Paris, Mathematical Modelling of Infectious Diseases Unit, CNRS UMR 2000, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Marc Lecuit
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, Paris, France
- Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, 75015 Paris, France
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, Paris, France
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12
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Zhi S, Parsons BD, Szelewicki J, Yuen YTK, Fach P, Delannoy S, Li V, Ferrato C, Freedman SB, Lee BE, Pang XL, Chui L. Identification of Shiga-Toxin-Producing Shigella Infections in Travel and Non-Travel Related Cases in Alberta, Canada. Toxins (Basel) 2021; 13:toxins13110755. [PMID: 34822539 PMCID: PMC8618429 DOI: 10.3390/toxins13110755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 01/21/2023] Open
Abstract
It has long been accepted that Shiga toxin (Stx) only exists in Shigella dysenteriae serotype 1. However, in recent decades, the presence of Shiga toxin genes (stx) in other Shigella spp. have been reported. We screened 366 Shigella flexneri strains from Alberta, Canada (2003 to 2016) for stx and 26 positive strains were identified. These isolates are highly related with the majority originating from the Dominican Republic and three isolates with Haiti origin. Both phylogenetic and spanning tree analysis of the 26 Alberta and 29 stx positive S. flexneri originating from the U.S., France, Canada (Quebec) and Haiti suggests that there are geographic specific distribution patterns (Haiti and Dominican Republic clades). This study provides the first comprehensive whole genome based phylogenetic analysis of stx positive S. flexneri strains as well as their global transmission, which signify the public health risks of global spreading of these strains.
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Affiliation(s)
- Shuai Zhi
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315000, China;
- School of Medicine, Ningbo University, Ningbo 315000, China
| | - Brendon D. Parsons
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
| | - Jonas Szelewicki
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
| | - Yue T. K. Yuen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
| | - Patrick Fach
- Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, COLiPATH Research Unit & IDPA Genomics Platform, FR-94700 Maisons-Alfort, France; (P.F.); (S.D.)
| | - Sabine Delannoy
- Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, COLiPATH Research Unit & IDPA Genomics Platform, FR-94700 Maisons-Alfort, France; (P.F.); (S.D.)
| | - Vincent Li
- Alberta Precision Laboratories-ProvLab, Edmonton, AB T6G 2J2, Canada;
| | - Christina Ferrato
- Alberta Precision Laboratories-ProvLab, Calgary, AB T2N 4W4, Canada;
| | - Stephen B. Freedman
- Alberta Children’s Hospital, Division of Pediatric Emergency Medicine and Gastroenterology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Alberta Children’s Hospital Research Institute, Department of Emergency Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine & Dentistry, Women and Children’s Health Research Institute, Stollery Children’s Hospital, University of Alberta, Edmonton, AB T6G 1C9, Canada;
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
- Alberta Precision Laboratories-ProvLab, Edmonton, AB T6G 2J2, Canada;
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
- Alberta Precision Laboratories-ProvLab, Edmonton, AB T6G 2J2, Canada;
- Correspondence:
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13
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Torti JF, Cuervo P, Nardello A, Pizarro M. Epidemiology and Characterization of Shiga Toxin-Producing Escherichia Coli of Hemolytic Uremic Syndrome in Argentina. Cureus 2021; 13:e17213. [PMID: 34540440 PMCID: PMC8443070 DOI: 10.7759/cureus.17213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
Argentina has one of the highest prevalence in Shiga toxin-producing Escherichia coli (STEC) and the high rate of hemolytic uremic syndrome (HUS) in the world. Though preventive steps such as food safety have been implemented as a way to reduce STEC infections, these have proven to be insufficient. STEC's pathogenesis, virulence factors, relationship with the environment, and emerging strains have been studied in the past few years in the country. Many factors that contribute to the morbidity and mortality of STEC infections include the expression of pathologic genes, alternative characteristics (inhibition of phagocytosis, invasion, cytotoxicity, and bacterial attachment), and host factors (age, immune status, treatments, medical history). However, research studies in combination with epidemiological data suggest trends of the prognosis, with the relationship between and genetic combinations of adherence, Shiga toxin (Stx) genes, and virulence genes, which significantly influence disease outcomes. This review explains the characteristics and epidemiology of STEC in Argentina. All these facts show that the application of molecular subtyping techniques in real-time is essential for detecting and controlling outbreaks. Applying molecular subtyping techniques in hemorrhagic diarrhea can avoid severe consequences caused by progression to HUS, and help the epidemiological analysis of the outbreak.
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Affiliation(s)
| | - Paula Cuervo
- Biochemistry, National University of Cuyo, Mendoza, ARG
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14
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Clermont O, Condamine B, Dion S, Gordon DM, Denamur E. The E phylogroup of Escherichia coli is highly diverse and mimics the whole E. coli species population structure. Environ Microbiol 2021; 23:7139-7151. [PMID: 34431197 DOI: 10.1111/1462-2920.15742] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/16/2021] [Accepted: 08/22/2021] [Indexed: 12/11/2022]
Abstract
To get a global picture of the population structure of the Escherichia coli phylogroup E, encompassing the O157:H7 EHEC lineage, we analysed the whole genome of 144 strains isolated from various continents, hosts and lifestyles and representative of the phylogroup diversity. The strains possess 4331 to 5440 genes with a core genome of 2771 genes and a pangenome of 33 722 genes. The distribution of these genes among the strains shows an asymmetric U-shaped distribution. E phylogenetic strains have the largest genomes of the species, partly explained by the presence of mobile genetic elements. Sixty-eight lineages were delineated, some of them exhibiting extra-intestinal virulence genes and being virulent in the mouse sepsis model. Except for the EHEC lineages and the reference EPEC, EIEC and ETEC strains, very few strains possess intestinal virulence genes. Most of the strains were devoid of acquired resistance genes, but eight strains possessed extended-spectrum beta-lactamase genes. Human strains belong to specific lineages, some of them being virulent and antibiotic-resistant [sequence type complexes (STcs) 350 and 2064]. The E phylogroup mimics all the features of the species as a whole, a phenomenon already observed at the STc level, arguing for a fractal population structure of E. coli.
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Affiliation(s)
- Olivier Clermont
- Université de Paris, IAME, UMR 1137, INSERM, Paris, F-75018, France
| | | | - Sara Dion
- Université de Paris, IAME, UMR 1137, INSERM, Paris, F-75018, France
| | - David M Gordon
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, Paris, F-75018, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat-Claude Bernard, Paris, F-75018, France
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15
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Han Z, Ma J, Yang CH, Ibekwe AM. Soil salinity, pH, and indigenous bacterial community interactively influence the survival of E. coli O157:H7 revealed by multivariate statistics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:5575-5586. [PMID: 32974826 DOI: 10.1007/s11356-020-10942-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
Complexities of biotic-abiotic interactions in soils result in the lack of integrated understanding of environmental variables that restrict the survival of shiga toxin-producing E. coli O157:H7. Herein, we reanalyzed previously published data and highlighted the influence of soil abiotic factors on E. coli O157:H7 survivability and elucidated how these factors took effect indirectly through affecting indigenous bacterial community. Interaction network analysis indicated salinity and pH decreased the relative abundances of some bacterial taxa (e.g., Acidobacteria_Gp4, Acidobacteria_Gp6, and Deltaproteobacteria) which were positively correlated with the survival of E. coli O157:H7 in soils, and vice versa (e.g., Gammaproteobacteria and Flavobacteria) (P < 0.05). An array of multivariate statistical approaches including partial Mantel test, variation partition analysis (VPA), and structural equation model (SEM) further confirmed that biotic and abiotic factors interactively shaped the survival profile of E. coli O157:H7. This study revealed that some bacterial taxa were correlated with survival of E. coli O157:H7 directly, and salinity and pH could affect E. coli O157:H7 survival through changing these bacterial taxa. These findings suggest that salinity in soil might benefit the control of fecal pathogenic E. coli invasion, while soil acidification caused by anthropogenic influences could potentially increase the persistence of E. coli O157:H7 in agro-ecosystem.
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Affiliation(s)
- Ziming Han
- Key Laboratory of Ground Water Resource and Environment, Ministry of Education, Jilin University, Changchun, 130021, China
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun, 130021, China
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jincai Ma
- Key Laboratory of Ground Water Resource and Environment, Ministry of Education, Jilin University, Changchun, 130021, China.
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun, 130021, China.
- College of New Energy and Environment, Jilin University, Changchun, 130021, China.
| | - Ching-Hong Yang
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, USA
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16
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Mulder AC, van de Kassteele J, Heederik D, Pijnacker R, Mughini‐Gras L, Franz E. Spatial Effects of Livestock Farming on Human Infections With Shiga Toxin-Producing Escherichia coli O157 in Small but Densely Populated Regions: The Case of the Netherlands. GEOHEALTH 2020; 4:e2020GH000276. [PMID: 33283126 PMCID: PMC7682566 DOI: 10.1029/2020gh000276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/26/2020] [Accepted: 09/28/2020] [Indexed: 06/12/2023]
Abstract
The role of environmental transmission of typically foodborne pathogens like Shiga toxin-producing Escherichia coli (STEC) O157 is increasingly recognized. To gain more insights into spatially restricted risk factors that play a role in this transmission, we assessed the spatial association between sporadic STEC O157 human infections and the exposure to livestock (i.e. small ruminants, cattle, poultry, and pigs) in a densely populated country: the Netherlands. This was done for the years 2007-2016, using a state-of-the-art spatial analysis method in which hexagonal areas with different sizes (90, 50, 25 and 10 km2) were used in combination with a novel probability of exposure metric: the population-weighted number of animals per hexagon. To identify risk factors for STEC O157 infections and their population attributable fraction (PAF), a spatial regression model was fitted using integrated nested Laplace approximation (INLA). Living in hexagonal areas of 25, 50 and 90 km2 with twice as much population-weighted small ruminants was associated with an increase of the incidence rate of human STEC O157 infections in summer (RR of 1.09 [95%CI;1.01-1.17], RR of 1.17 [95%CI;1.07-1.28] and RR of 1.13 [95%CI;1.01-1.26]), with a PAF of 49% (95%CI;8-72%). Results suggest exposure to small ruminants to be a risk factor, although no evidence on the mode of transmission is provided. Therefore, the underlying mechanisms warrant further investigation and could offer new targets for control. The newly proposed exposure metric has potential to improve existing spatial modeling studies on infectious diseases related to livestock exposure, especially in densely populated countries like the Netherlands.
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Affiliation(s)
- A. C. Mulder
- Centre for Infectious Disease ControlNational Institute for Public Health and the Environment (RIVM)Bilthoventhe Netherlands
| | - J. van de Kassteele
- Centre for Infectious Disease ControlNational Institute for Public Health and the Environment (RIVM)Bilthoventhe Netherlands
| | - D. Heederik
- Institute for Risk Assessment Sciences (IRAS), Division of Environmental EpidemiologyUtrecht UniversityUtrechtthe Netherlands
| | - R. Pijnacker
- Centre for Infectious Disease ControlNational Institute for Public Health and the Environment (RIVM)Bilthoventhe Netherlands
| | - L. Mughini‐Gras
- Centre for Infectious Disease ControlNational Institute for Public Health and the Environment (RIVM)Bilthoventhe Netherlands
- Institute for Risk Assessment Sciences (IRAS), Division of Environmental EpidemiologyUtrecht UniversityUtrechtthe Netherlands
| | - E. Franz
- Centre for Infectious Disease ControlNational Institute for Public Health and the Environment (RIVM)Bilthoventhe Netherlands
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17
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Baba H, Kanamori H. Are Reservoirs and Transmission Routes the Same or Different Between O157 and Non-O157 Shiga Toxin-Producing Escherichia coli? Clin Infect Dis 2020; 71:1352-1353. [PMID: 31711218 DOI: 10.1093/cid/ciz1111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hiroaki Baba
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hajime Kanamori
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
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18
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Franz E, Rotariu O, Lopes BS, Bono JL, Laing C, Gannon V, Van Hoek AHAM, Friesema I, French NP, George T, Biggs PJ, Jaros P, Rivas M, Chinen I, Campos J, Mellor GE, Chandry PS, Perez-Reche F, Forbes KJ, Strachan NJ. Reply to Baba and Kanamori. Clin Infect Dis 2020; 71:1353-1355. [PMID: 31711208 DOI: 10.1093/cid/ciz1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Eelco Franz
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Ovidiu Rotariu
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Bruno S Lopes
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, Scotland, United Kingdom
| | - James L Bono
- United States (US) Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska, USA
| | - Chad Laing
- National Centre for Animal Diseases, Canadian Food Inspection Agency, Lethbridge, Alberta, Canada
| | - Victor Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | - Angela H A M Van Hoek
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Ingrid Friesema
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Nigel P French
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Tessy George
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patricia Jaros
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Marta Rivas
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Isabel Chinen
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Glen E Mellor
- The Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Werribee, Australia
| | - P Scott Chandry
- The Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Werribee, Australia
| | - Francisco Perez-Reche
- Institute of Complex Systems and Mathematical Biology, Scottish Universities Physics Alliance, School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Ken J Forbes
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, Scotland, United Kingdom
| | - Norval Jc Strachan
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
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19
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Abstract
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.
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20
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Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ. Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada. Microb Genom 2020; 6. [PMID: 32496181 PMCID: PMC7371104 DOI: 10.1099/mgen.0.000376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher’s exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E. coli; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.
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Affiliation(s)
- Lu Ya Ruth Wang
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | | | - Chad R Laing
- National Centre for Animal Disease, Canadian Food Inspection Agency, Lethbridge, Alberta, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Victor P J Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
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21
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Harrison S, Baker MG, Benschop J, Death RG, French NP, Harmsworth G, Lake RJ, Lamont IL, Priest PC, Ussher JE, Murdoch DR. One Health Aotearoa: a transdisciplinary initiative to improve human, animal and environmental health in New Zealand. ONE HEALTH OUTLOOK 2020; 2:4. [PMID: 32835167 PMCID: PMC7223671 DOI: 10.1186/s42522-020-0011-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/14/2020] [Indexed: 06/11/2023]
Abstract
There is increased recognition that complex health challenges at the human-animal-environmental interface require a transdisciplinary, "whole-of-society" approach. This philosophy is particularly pertinent in Aotearoa-New Zealand because of the country's relatively isolated island ecosystem, economic reliance on agriculture and its intensification, and existing indigenous worldview that emphasises holism and interconnectivity between humans, animals and the environment. In New Zealand, the One Health Aotearoa (OHA) alliance was established in order to better connect researchers and to address a growing number of infectious diseases challenges. The emphasis of OHA is to bring together and facilitate interactions between people from diverse disciplines, link to stakeholders and communities, and engage with policy-makers, government operational agencies, and funders, thus providing a holistic and integrative systems-thinking approach to address priority questions and achieve desired outcomes in One Health. The initial focus of OHA has been on infectious diseases, but there is increasing recognition of the potential benefits of the alliance to address broader complex issues. Greater involvement and overlap of the environmental sciences, human and animal health sciences, social science, and indigenous kaupapa Māori research is particularly critical for ensuring its success within the New Zealand context. Given the economic and cultural importance of New Zealand's "clean, green" image, a One Health approach that draws strongly on the environmental sciences makes particular sense. Furthermore, as the global environment becomes increasingly stressed by anthropogenic pressures our research may hold potential solutions for similar challenges elsewhere.
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Affiliation(s)
- Sarah Harrison
- Department of Preventive and Social Medicine, University of Otago, Dunedin, New Zealand
| | - Michael G. Baker
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Jackie Benschop
- Molecular Epidemiology and Public Health Laboratory, Massey University, Palmerston North, New Zealand
| | - Russell G. Death
- School of Agriculture and the Environment, Massey University, Palmerston North, New Zealand
| | - Nigel P. French
- Molecular Epidemiology and Public Health Laboratory, Massey University, Palmerston North, New Zealand
| | | | - Robin J. Lake
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Iain L. Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Patricia C. Priest
- Department of Preventive and Social Medicine, University of Otago, Dunedin, New Zealand
| | - James E. Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - David R. Murdoch
- Department of Pathology and Biomedical Science, University of Otago, P.O. Box 4345, Christchurch, 8140 New Zealand
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22
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jenkins C, Monteiro Pires S, Morabito S, Niskanen T, Scheutz F, da Silva Felício MT, Messens W, Bolton D. Pathogenicity assessment of Shiga toxin‐producing Escherichia coli (STEC) and the public health risk posed by contamination of food with STEC. EFSA J 2020. [DOI: 10.2903/j.efsa.2020.5967] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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