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Wang Z, Zhou H, Liu Y, Huang C, Chen J, Siddique A, Yin R, Jia C, Li Y, Zhao G, Yue M. Nationwide trends and features of human salmonellosis outbreaks in China. Emerg Microbes Infect 2024; 13:2372364. [PMID: 38923510 PMCID: PMC11259058 DOI: 10.1080/22221751.2024.2372364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
Salmonellosis is one of the most common causes of diarrhea, affecting 1/10 of the global population. Salmonellosis outbreaks (SO) pose a severe threat to the healthcare systems of developing regions. To elucidate the patterns of SO in China, we conducted a systematic review and meta-analysis encompassing 1,134 reports across 74 years, involving 89,050 patients and 270 deaths. A rising trend of SO reports has been observed since the 1970s, with most outbreaks occurring east of the Hu line, especially in coastal and populated regions. It is estimated to have an overall attack rate of 36.66% (95% CI, 33.88-39.45%), and antimicrobial resistance towards quinolone (49.51%) and beta-lactam (73.76%) remains high. Furthermore, we developed an online website, the Chinese Salmonellosis Outbreak Database (CSOD), for visual presentation and data-sharing purposes. This study indicated that healthcare-associated SO required further attention, and our study served as a foundational step in pursuing outbreak intervention and prediction.
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Affiliation(s)
- Zining Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, People’s Republic of China
- Hainan Institute of Zhejiang University, Sanya, People’s Republic of China
| | - Haiyang Zhou
- Hainan Institute of Zhejiang University, Sanya, People’s Republic of China
| | - Yuhao Liu
- Hainan Institute of Zhejiang University, Sanya, People’s Republic of China
| | - Chenghu Huang
- Hainan Institute of Zhejiang University, Sanya, People’s Republic of China
| | - Jiaqi Chen
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, People’s Republic of China
| | - Abubakar Siddique
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, People’s Republic of China
| | - Rui Yin
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, People’s Republic of China
| | - Chenghao Jia
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, People’s Republic of China
| | - Yan Li
- Hainan Institute of Zhejiang University, Sanya, People’s Republic of China
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, People’s Republic of China
| | - Guoping Zhao
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, People’s Republic of China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Min Yue
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, People’s Republic of China
- Hainan Institute of Zhejiang University, Sanya, People’s Republic of China
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, People’s Republic of China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
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Nambiar RB, Elbediwi M, Ed-Dra A, Wu B, Yue M. Epidemiology and antimicrobial resistance of Salmonella serovars Typhimurium and 4,[5],12:i- recovered from hospitalized patients in China. Microbiol Res 2024; 282:127631. [PMID: 38330818 DOI: 10.1016/j.micres.2024.127631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Global emergence of multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium is a continuing challenge for modern healthcare. However, the knowledge, regarding the epidemiology of salmonellosis caused by the monophasic variant S. 4,[5],12:i:- in hospitalized patients, is limited in China. To bridge this gap, we carried out a retrospective study to determine the antimicrobial resistance, trends, and risk factors of S. Typhimurium and S. 4,[5],12:i:- (n = 329) recovered from patients in Zhejiang province between 2011 and 2019. The results showed that 90.57% (298/329) of the isolates were MDR; among them, 48.94% (161/329) and 12.46% (41/329) were phenotypically resistant to cephalosporins and fluoroquinolones, respectively, which are the drugs of choice used to treat salmonellosis in clinics. Additionally, we observed a higher incidence of infections among the young population (<5 years old). Notably, the higher prevalence of ST34 (sequence type 34) isolates, especially after 2014, with MDR (57.05%, 170/298) phenotype, and incidence of ST34 isolates co-harbouring mcr-1 (mobile colistin resistance gene) and blaCTX-M-14 (β-lactamase gene) suggest an association between STs and drug resistance. Together, the increasing prevalence of MDR ST34 calls for enhanced monitoring strategies to mitigate the spread and dissemination of MDR clones of S. Typhimurium and S. 4,[5],12:i-. Our study provides improved knowledge about non-typhoid Salmonella (NTS) infections, which could help in the effective recommendation of antimicrobials in hospitalized patients.
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Affiliation(s)
- Reshma B Nambiar
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Mohammed Elbediwi
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Abdelaziz Ed-Dra
- Laboratory of Engineering and Applied Technologies, Higher School of Technology, M'ghila Campus, Sultan Moulay Slimane University, BP: 591, Beni Mellal, Morocco
| | - Beibei Wu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Min Yue
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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Thilliez G, Mashe T, Chaibva BV, Robertson V, Bawn M, Tarupiwa A, Takawira FT, Kock MM, Midzi S, Mwamakamba LW, Matheu J, Juru A, Kingsley RA, Ehlers MM. Population structure of Salmonella enterica Typhi in Harare, Zimbabwe (2012-19) before typhoid conjugate vaccine roll-out: a genomic epidemiology study. THE LANCET. MICROBE 2023; 4:e1005-e1014. [PMID: 37952554 PMCID: PMC10686908 DOI: 10.1016/s2666-5247(23)00214-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND The continued emergence of Salmonella enterica serovar Typhi, with ever increasing antimicrobial resistance, necessitates the use of vaccines in endemic countries. A typhoid fever outbreak in Harare, Zimbabwe, in 2018 from a multidrug resistant S Typhi with additional resistance to ciprofloxacin was the catalyst for the introduction of a typhoid conjugate vaccine programme. We aimed to investigate the emergence and evolution of antimicrobial resistance of endemic S Typhi in Zimbabwe and to determine the population structure, gene flux, and sequence polymorphisms of strains isolated before a typhoid conjugate vaccine programme to provide a baseline for future evaluation of the effect of the vaccination programme. METHODS In this genomic epidemiology study, we used short-read whole-genome sequencing of S Typhi isolated from clinical cases of typhoid fever in Harare, Zimbabwe, between Jan 1, 2012, and Feb 9, 2019, to determine the S Typhi population structure, gene flux, and sequence polymorphisms and reconstructed the evolution of antimicrobial resistance. Maximum likelihood time-scaled phylogenetic trees of Zimbabwe isolates in the context of global isolates obtained from the National Center for Biotechnology Information were constructed to infer spread and emergence of antimicrobial resistance. FINDINGS The population structure of S Typhi in Harare, Zimbabwe, from 2012 to 2019 was dominated by multidrug resistant genotype 4.3.1.1.EA1 (H58) that spread to Zimbabwe from neighbouring countries in around 2009 (95% credible interval 2008·5-2010·0). Acquisition of an IncN plasmid carrying antimicrobial resistance genes including a qnrS gene and a mutation in the quinolone resistance determining region of gyrA gene contributed to non-susceptibility and resistance to quinolone antibiotics. A minority population of antimicrobial susceptible S Typhi genotype 3.3.1 strains were present throughout. INTERPRETATION The currently dominant S Typhi population is genotype 4.3.1.1 that spread to Zimbabwe and acquired additional antimicrobial resistance though acquisition of a plasmid and mutation in the gyrA gene. This study provides a baseline population structure for future evaluation of the effect of the typhoid conjugate vaccine programme in Harare. FUNDING Bill & Melinda Gates Foundation and the Biotechnology and Biological Sciences Research Council Institute Strategic Programme.
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Affiliation(s)
- Gaetan Thilliez
- Microbes and Food Safety, Quadram Institute Bioscience, Norwich, UK
| | - Tapfumanei Mashe
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa; National Microbiology Reference Laboratory, Harare, Zimbabwe; World Health Organization, Harare, Zimbabwe.
| | | | - Valerie Robertson
- Department of Laboratory Diagnostic and Investigative Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Matt Bawn
- Microbes and Food Safety, Quadram Institute Bioscience, Norwich, UK; Earlham Institute, Norwich, UK; Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Andrew Tarupiwa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Faustinos T Takawira
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa; National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Marleen M Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa; Department of Medical Microbiology, National Health Laboratory Service, Pretoria, South Africa
| | | | - Lusubilo W Mwamakamba
- World Health Organization Regional Office for Africa, Brazzaville, Republic of the Congo
| | | | - Agnes Juru
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Robert A Kingsley
- Microbes and Food Safety, Quadram Institute Bioscience, Norwich, UK; School of Biological Sciences, University of East Anglia, Norwich, UK.
| | - Marthie M Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa; Department of Medical Microbiology, National Health Laboratory Service, Pretoria, South Africa
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Chung The H, Pham P, Ha Thanh T, Phuong LVK, Yen NP, Le SNH, Vu Thuy D, Chau TTH, Le Phuc H, Ngoc NM, Vi LL, Mather AE, Thwaites GE, Thomson NR, Baker S, Pham DT. Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 1,4,[5],12:i:- ST34 in Southeast Asia. Commun Biol 2023; 6:1007. [PMID: 37789208 PMCID: PMC10547704 DOI: 10.1038/s42003-023-05365-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
Salmonella enterica serotype 1,4,[5],12:i:- (Typhimurium monophasic variant) of sequence type (ST) 34 has emerged as the predominant pandemic genotype in recent decades. Despite increasing reports of resistance to antimicrobials in Southeast Asia, Salmonella ST34 population structure and evolution remained understudied in the region. Here we performed detailed genomic investigations on 454 ST34 genomes collected from Vietnam and diverse geographical sources to elucidate the pathogen's epidemiology, evolution and antimicrobial resistance. We showed that ST34 has been introduced into Vietnam in at least nine occasions since 2000, forming five co-circulating major clones responsible for paediatric diarrhoea and bloodstream infection. Most expansion events were associated with acquisitions of large multidrug resistance plasmids of IncHI2 or IncA/C2. Particularly, the self-conjugative IncA/C2 pST34VN2 (co-transferring blaCTX-M-55, mcr-3.1, and qnrS1) underlies local expansion and intercontinental spread in two separate ST34 clones. At the global scale, Southeast Asia was identified as a potential hub for the emergence and dissemination of multidrug resistant Salmonella ST34, and mutation analysis suggests of selection in antimicrobial responses and key virulence factors.
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Affiliation(s)
- Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
| | - Phuong Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Son-Nam H Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Duong Vu Thuy
- Children's Hospital No. 1, Ho Chi Minh City, Vietnam
| | | | - Hoang Le Phuc
- Children's Hospital No. 1, Ho Chi Minh City, Vietnam
| | | | - Lu Lan Vi
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen Baker
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases (CITIID), University of Cambridge, Cambridge, UK
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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Fu Y, M’ikanatha NM, Dudley EG. Whole-Genome Subtyping Reveals Population Structure and Host Adaptation of Salmonella Typhimurium from Wild Birds. J Clin Microbiol 2023; 61:e0184722. [PMID: 37249426 PMCID: PMC10281135 DOI: 10.1128/jcm.01847-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
Within-host evolution of bacterial pathogens can lead to host-associated variants of the same species or serovar. Identification and characterization of closely related variants from diverse host species are crucial to public health and host-pathogen adaptation research. However, the work remained largely underexplored at a strain level until the advent of whole-genome sequencing (WGS). Here, we performed WGS-based subtyping and analyses of Salmonella enterica serovar Typhimurium (n = 787) from different wild birds across 18 countries over a 75-year period. We revealed seven avian host-associated S. Typhimurium variants/lineages. These lineages emerged globally over short timescales and presented genetic features distinct from S. Typhimurium lineages circulating among humans and domestic animals. We further showed that, in terms of virulence, host adaptation of these variants was driven by genome degradation. Our results provide a snapshot of the population structure and genetic diversity of S. Typhimurium within avian hosts. We also demonstrate the value of WGS-based subtyping and analyses in unravelling closely related variants at the strain level.
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Affiliation(s)
- Yezhi Fu
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Edward G. Dudley
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- E. coli Reference Center, The Pennsylvania State University, University Park, Pennsylvania, USA
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Pye HV, Thilliez G, Acton L, Kolenda R, Al-Khanaq H, Grove S, Kingsley RA. Strain and serovar variants of Salmonella enterica exhibit diverse tolerance to food chain-related stress. Food Microbiol 2023; 112:104237. [PMID: 36906307 DOI: 10.1016/j.fm.2023.104237] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/12/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023]
Abstract
Non-Typhoidal Salmonella (NTS) continues to be a leading cause of foodborne illness worldwide. Food manufacturers implement hurdle technology by combining more than one approach to control food safety and quality, including preservatives such as organic acids, refrigeration, and heating. We assessed the variation in survival in stresses of genotypically diverse isolates of Salmonella enterica to identify genotypes with potential elevated risk to sub-optimal processing or cooking. Sub-lethal heat treatment, survival in desiccated conditions and growth in the presence of NaCl or organic acids were investigated. S. Gallinarum strain 287/91 was most sensitive to all stress conditions. While none of the strains replicated in a food matrix at 4 °C, S. Infantis strain S1326/28 retained the greatest viability, and six strains exhibited a significantly reduced viability. A S. Kedougou strain exhibited the greatest resistance to incubation at 60 °C in a food matrix that was significantly greater than S. Typhimurium U288, S Heidelberg, S. Kentucky, S. Schwarzengrund and S. Gallinarum strains. Two isolates of monophasic S. Typhimurium, S04698-09 and B54Col9 exhibited the greatest tolerance to desiccation that was significantly more than for the S. Kentucky and S. Typhimurium U288 strains. In general, the presence of 12 mM acetic acid or 14 mM citric acid resulted in a similar pattern of decreased growth in broth, but this was not observed for S. Enteritidis, and S. Typhimurium strains ST4/74 and U288 S01960-05. Acetic acid had a moderately greater effect on growth despite the lower concentration tested. A similar pattern of decreased growth was observed in the presence of 6% NaCl, with the notable exception that S. Typhimurium strain U288 S01960-05 exhibited enhanced growth in elevated NaCl concentrations.
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Affiliation(s)
- Hannah V Pye
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK; University of East Anglia, Norwich Research Park, Norwich, UK
| | - Gaёtan Thilliez
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK
| | - Luke Acton
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK; University of East Anglia, Norwich Research Park, Norwich, UK
| | - Rafał Kolenda
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK
| | - Haider Al-Khanaq
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK
| | - Stephen Grove
- Nestlé Development Centre, Cannon Road, Solon, OH, USA; McCain Foods, 1 Tower Lane, Oakbrook Terrace, Illinois, USA
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK; University of East Anglia, Norwich Research Park, Norwich, UK.
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Almuzaini AM. Phytochemicals: potential alternative strategy to fight Salmonella enterica serovar Typhimurium. Front Vet Sci 2023; 10:1188752. [PMID: 37261108 PMCID: PMC10228746 DOI: 10.3389/fvets.2023.1188752] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/20/2023] [Indexed: 06/02/2023] Open
Abstract
The rise of multidrug resistant (MDR) microorganisms is a great hazard worldwide and has made it difficult to treat many infectious diseases adequately. One of the most prevalent causes of outbreaks of foodborne illness worldwide is Salmonella. The ability of this and other harmful bacteria to withstand antibiotics has recently proven crucial to their effective control. Since the beginning of time, herbal medicines and phytochemicals have been employed for their potent antibacterial action and there is a growing trend toward the production of plant based natural products for the prevention and treatment of pathogenic infections. Numerous phytochemicals have been proven effective against the molecular determinants responsible for attaining drug resistance in pathogens like efflux pumps, membrane proteins, bacterial cell communications and biofilms. The medicinal plants having antibacterial activity and antibiotics combination with phytochemicals have shown synergetic activity against Salmonella enterica serovar Typhimurium. The inhibitory effects of tannins on rumen proteolytic bacteria can be exploited in ruminant nutrition. Improved control of the rumen ecology and practical use of this feed additive technology in livestock production will be made possible by a better knowledge of the modulatory effects of phytochemicals on the rumen microbial populations in combination with fermentation. This review focuses on the development of antibacterial resistance in Salmonella, the mechanism of action of phytochemicals and the use of phytochemicals against S. enterica serovar Typhimurium. The advances and potential future applications of phytochemicals in the fight against resistant are also discussed.
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García P, Moscoso M, Fuentes-Valverde V, Rodicio MR, Herrera-León S, Bou G. A highly-safe live auxotrophic vaccine protecting against disease caused by non-typhoidal Salmonella Typhimurium in mice. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023; 56:324-336. [PMID: 37610206 DOI: 10.1016/j.jmii.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/26/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Salmonella enterica serovar Typhimurium (S. Typhimurium) has become an important intestinal pathogen worldwide and is responsible for lethal invasive infections in populations at risk. There is at present an unmet need for preventive vaccines. METHODS IRTA GN-3728 genome was sequenced by Illumina and d-glutamate and d-glutamate/d-alanine knockout-auxotrophs were constructed. They were characterized using electron microscopy, growth/viability curves, reversion analysis, and motility/agglutination assays. Their potential as vaccine candidates were explored using two BALB/c mouse models for Salmonella infections: a systemic and an intestinal inflammation. Clinical signs/body weight and survival were monitored, mucosal lactoferrin and specific/cross-reactive IgA/IgG were quantified by enzyme-linked-immunosorbent assays and bacterial shedding/burden in fecal/tissues were evaluated. RESULTS The d-glutamate auxotroph, IRTA ΔmurI, is highly attenuated, immunogenic and fully protective against systemic infection. The IRTA ΔmurI Δalr ΔdadX double auxotroph, constructed to reinforce vaccine safety, showed a higher level of attenuation and was 100% effective against systemic disease. In the intestinal model, it proved to be safe, yielding a low-degree of mucosal inflammation, short-term shedding and undetectable invasiveness in the long-term, while eliciting cross-reactive fecal IgA/serum IgG against clinically relevant multidrug-resistant (MDR) S. Typhimurium strains. It also conferred protection against homologous oral challenge, and protected mice from local and extra-intestinal dissemination caused by one MDR strain responsible for an international outbreak of highly severe human infections. Additionally, oral vaccination promoted extended survival after lethal heterologous infection. CONCLUSION This study yielded a very safe S. Typhimurium vaccine candidate that could be further refined for mucosal application against disease in humans.
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Affiliation(s)
- Patricia García
- Department of Microbiology, University Hospital A Coruña (CHUAC) - Biomedical Research Institute A Coruña (INIBIC), 15006 - A Coruña, Spain.
| | - Miriam Moscoso
- Department of Microbiology, University Hospital A Coruña (CHUAC) - Biomedical Research Institute A Coruña (INIBIC), 15006 - A Coruña, Spain.
| | - Víctor Fuentes-Valverde
- Department of Microbiology, University Hospital A Coruña (CHUAC) - Biomedical Research Institute A Coruña (INIBIC), 15006 - A Coruña, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 - Madrid, Spain.
| | - M Rosario Rodicio
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006 - Oviedo, Spain; Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 - Oviedo, Spain.
| | - Silvia Herrera-León
- Laboratorio de Referencia e Investigación en Enfermedades Bacterianas Transmitidas por Alimentos, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Madrid, Spain.
| | - Germán Bou
- Department of Microbiology, University Hospital A Coruña (CHUAC) - Biomedical Research Institute A Coruña (INIBIC), 15006 - A Coruña, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 - Madrid, Spain.
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Charity OJ, Acton L, Bawn M, Tassinari E, Thilliez G, Chattaway MA, Dallman TJ, Petrovska L, Kingsley RA. Increased phage resistance through lysogenic conversion accompanying emergence of monophasic Salmonella Typhimurium ST34 pandemic strain. Microb Genom 2022; 8:mgen000897. [PMID: 36382789 PMCID: PMC9836087 DOI: 10.1099/mgen.0.000897] [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: 11/17/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) comprises a group of closely related human and animal pathogens that account for a large proportion of all Salmonella infections globally. The epidemiological record of S. Typhimurium in Europe is characterized by successive waves of dominant clones, each prevailing for approximately 10-15 years before replacement. Succession of epidemic clones may represent a moving target for interventions aimed at controlling the spread and impact of this pathogen on human and animal health. Here, we investigate the relationship of phage sensitivity and population structure of S. Typhimurium using data from the Anderson phage typing scheme. We observed greater resistance to phage predation of epidemic clones circulating in livestock over the past decades compared to variants with a restricted host range implicating increased resistance to phage in the emergence of epidemic clones of particular importance to human health. Emergence of monophasic S. Typhimurium ST34, the most recent dominant multidrug-resistant clone, was accompanied by increased resistance to phage predation during clonal expansion, in part by the acquisition of the mTmII prophage that may have contributed to the fitness of the strains that replaced ancestors lacking this prophage.
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Affiliation(s)
- Oliver J. Charity
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,University of East Anglia, Norwich NR4 7TJ, UK
| | - Luke Acton
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,University of East Anglia, Norwich NR4 7TJ, UK
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,Earlham Institute, Norwich, NR4 7UZ, UK
| | - Eleonora Tassinari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,University of East Anglia, Norwich NR4 7TJ, UK
| | - Gaёtan Thilliez
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Marie A. Chattaway
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency (UKHSA), London, NW9 5EQ, UK
| | - Timothy J. Dallman
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency (UKHSA), London, NW9 5EQ, UK
| | - Liljana Petrovska
- Animal & Plant Health Agency (APHA), Weybridge, London, KT15 3NB, UK
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,University of East Anglia, Norwich NR4 7TJ, UK,*Correspondence: Robert A. Kingsley,
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10
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Genomic Characterization of Salmonella Typhimurium Isolated from Guinea Pigs with Salmonellosis in Lima, Peru. Microorganisms 2022; 10:microorganisms10091726. [PMID: 36144328 PMCID: PMC9503038 DOI: 10.3390/microorganisms10091726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/07/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is one of the most important foodborne pathogens that infect humans globally. The gastrointestinal tracts of animals like pigs, poultry or cattle are the main reservoirs of Salmonella serotypes. Guinea pig meat is an important protein source for Andean countries, but this animal is commonly infected by S. Typhimurium, producing high mortality rates and generating economic losses. Despite its impact on human health, food security, and economy, there is no genomic information about the S. Typhimurium responsible for the guinea pig infections in Peru. Here, we sequence and characterize 11 S. Typhimurium genomes isolated from guinea pigs from four farms in Lima-Peru. We were able to identify two genetic clusters (HC100_9460 and HC100_9757) distinguishable at the H100 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing (HierCC-cgMLST) scheme with an average of 608 SNPs of distance. All sequences belonged to sequence type 19 (ST19) and HC100_9460 isolates were typed in silico as monophasic variants (1,4,[5],12:i:-) lacking the fljA and fljB genes. Phylogenomic analysis showed that human isolates from Peru were located within the same genetic clusters as guinea pig isolates, suggesting that these lineages can infect both hosts. We identified a genetic antimicrobial resistance cassette carrying the ant(3)-Ia, dfrA15, qacE, and sul1 genes associated with transposons TnAs3 and IS21 within an IncI1 plasmid in one guinea pig isolate, while antimicrobial resistance genes (ARGs) for β-lactam (blaCTX-M-65) and colistin (mcr-1) resistance were detected in Peruvian human-derived isolates. The presence of a virulence plasmid highly similar to the pSLT plasmid (LT2 reference strain) containing the spvRABCD operon was found in all guinea pig isolates. Finally, seven phage sequences (STGP_Φ1 to STGP_Φ7) were identified in guinea pig isolates, distributed according to the genetic lineage (H50 clusters level) and forming part of the specific gene content of each cluster. This study presents, for the first time, the genomic characteristics of S. Typhimurium isolated from guinea pigs in South America, showing particular diversity and genetic elements (plasmids and prophages) that require special attention and also broader studies in different periods of time and locations to determine their impact on human health.
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Comparative Genomic Analysis of Salmonella enterica Serovar Typhimurium Isolates from Passerines Reveals Two Lineages Circulating in Europe, New Zealand, and the United States. Appl Environ Microbiol 2022; 88:e0020522. [PMID: 35435718 DOI: 10.1128/aem.00205-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Salmonella enterica serovar Typhimurium strains from passerines have caused wild bird deaths and human salmonellosis outbreaks in Europe, Oceania, and North America. Here, we performed comparative genomic analysis to explore the emergence, genetic relationship, and evolution of geographically dispersed passerine isolates. We found that passerine isolates from Europe and the United States clustered to form two lineages (EU and US passerine lineages), which were distinct from major S. Typhimurium lineages circulating in other diverse hosts (e.g., humans, cattle, pigs, chickens, and other avian hosts, such as pigeons and ducks). Further, passerine isolates from New Zealand clustered to form a sublineage (NZ passerine lineage) of the US passerine lineage. We inferred that the passerine isolates mutated at a rate of 3.2 × 10-7 substitutions/site/year, and the US, EU, and NZ passerine lineages emerged in approximately 1952, 1970, and 1996, respectively. Isolates from the three lineages presented genetic similarity, such as lack of antimicrobial resistance genes and accumulation of the same virulence pseudogenes. In addition, genetic diversity due to microevolution existed in the three passerine lineages. Specifically, pseudogenization in the type 1 fimbrial gene fimC (deletion of G at position 87) was detected only in the US and NZ passerine isolates, while single-base deletions in type 3 secretion system effector genes (i.e., gogB, sseJ, and sseK2) cooccurred solely in the EU passerine isolates. These findings provide insights into the evolution, host adaptation, and epidemiology of S. Typhimurium in passerines. IMPORTANCE Passerine-associated S. Typhimurium strains have been linked to human salmonellosis outbreaks in recent years. Here, we investigated the phylogenetic relationship of globally distributed passerine isolates and profiled their genomic similarity and diversity. Our study reveals two passerine-associated S. Typhimurium lineages circulating in Europe, Oceania, and North America. Isolates from the two lineages presented phylogenetic and genetic signatures that were distinct from those of isolates from other hosts. The findings shed light on the host adaptation of S. Typhimurium in passerines and are important for source attribution of S. Typhimurium strains to avian hosts. Further, we found that S. Typhimurium definitive phage type 160 (DT160) from passerines, which caused decades-long human salmonellosis outbreaks in New Zealand and Australia, formed a sublineage of the US passerine lineage, suggesting that DT160 might have originated from passerines outside Oceania. Our study demonstrates the importance of whole-genome sequencing and genomic analysis of historical microbial collections to modern epidemiologic surveillance.
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Fu Y, Smith JC, Shariat NW, M'ikanatha NM, Dudley EG. Evidence for common ancestry and microevolution of passerine-adapted Salmonella enterica serovar Typhimurium in the UK and USA. Microb Genom 2022; 8. [PMID: 35195512 PMCID: PMC8942035 DOI: 10.1099/mgen.0.000775] [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] [Indexed: 01/22/2023] Open
Abstract
The evolution of Salmonella enterica serovar Typhimurium (S. Typhimurium) within passerines has resulted in pathoadaptation of this serovar to the avian host in Europe. Recently, we identified an S. Typhimurium lineage from passerines in North America. The emergence of passerine-adapted S. Typhimurium in Europe and North America raises questions regarding its evolutionary origin. Here, we demonstrated that the UK and US passerine-adapted S. Typhimurium shared a common ancestor from ca. 1838, and larids played a key role in the clonal expansion by disseminating the common ancestor between North America and Europe. Further, we identified virulence gene signatures common in the passerine- and larid-adapted S. Typhimurium, including conserved pseudogenes in fimbrial gene lpfD and Type 3 Secretion System (T3SS) effector gene steC. However, the UK and US passerine-adapted S. Typhimurium also possessed unique virulence gene signatures (i.e. pseudogenes in fimbrial gene fimC and T3SS effector genes sspH2, gogB, sseJ and sseK2), and the majority of them (38/47) lost a virulence plasmid pSLT that was present in the larid-adapted S. Typhimurium. These results provide evidence that passerine-adapted S. Typhimurium share a common ancestor with those from larids, and the divergence of passerine- and larid-adapted S. Typhimurium might be due to pseudogenization or loss of specific virulence genes.
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Affiliation(s)
- Yezhi Fu
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jared C Smith
- Department of Population Health, Poultry Diagnostic and Research Center, University of Georgia, Athens, GA 30602, USA
| | - Nikki W Shariat
- Department of Population Health, Poultry Diagnostic and Research Center, University of Georgia, Athens, GA 30602, USA
| | | | - Edward G Dudley
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA.,E. coli Reference Center, The Pennsylvania State University, University Park, PA 16802, USA
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Zhang K, Ge H, He J, Hu M, Xu Z, Jiao X, Chen X. Salmonella Typhimurium ST34 Isolate Was More Resistant than the ST19 Isolate in China, 2007 - 2019. Foodborne Pathog Dis 2021; 19:62-69. [PMID: 34520252 DOI: 10.1089/fpd.2021.0047] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
To disclose the antimicrobial susceptibility and wide adaptability of commonly occurring genotypes of Salmonella enterica serovar Typhimurium, the antimicrobial resistance and multilocus sequence typing (MLST) profiles of 196 Salmonella Typhimurium isolates (136 from food-producing animals, 19 from environments, 15 from markets, and 26 from humans) in China between 2007 and 2019 were analyzed. Tests of susceptibility to 19 antimicrobial agents using the broth microdilution method showed that 84.7% of the isolates were resistant to at least one antimicrobial. Antimicrobial susceptibility analysis demonstrated that 66.8% of the isolates were multidrug-resistant (MDR) strains, with resistance to three or more antimicrobials. The highest antidrug resistance was to ampicillin, amoxicillin/clavulanic acid, and tetracycline. Three MLST types were detected, and sequence type (ST) 19 was the most common ST. However, ST34 was associated with a higher MDR rate and more complex MDR patterns, than ST19 and ST99, although the exact mechanism has not been reported. Our study highlights the variation of drug resistance and STs from different sources and the association between STs and drug resistance, providing useful information for epidemiological research and developing a public health strategy.
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Affiliation(s)
- Kai Zhang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Haojie Ge
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Jingjing He
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Maozhi Hu
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zhengzhong Xu
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xin'an Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xiang Chen
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
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Stevens MP, Kingsley RA. Salmonella pathogenesis and host-adaptation in farmed animals. Curr Opin Microbiol 2021; 63:52-58. [PMID: 34175673 DOI: 10.1016/j.mib.2021.05.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
Salmonella is an animal and zoonotic pathogen of global importance. Depending on pathogen and host factors, infections can be asymptomatic or involve acute gastroenteritis or invasive disease. Genomic signatures associated with host-range, tissue tropism or differential virulence of Salmonella enterica serovars, and their variants, have emerged. In turn, it is becoming feasible to predict invasive potential, host-adaptation and zoonotic risk of Salmonella from sequence data to improve outbreak investigation, risk assessment and control strategies. Functional annotation of Salmonella genomes has accelerated with the screening of high-density mutant libraries, revealing host-specific, niche-specific and serovar-specific virulence factors. As natural hosts and reservoirs, farmed animals provide powerful insights into host-adaptation and pathogenesis of Salmonella not always evident from surrogate rodent or cell-based models.
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Affiliation(s)
- Mark P Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom.
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, United Kingdom; School of Biological Science, University of East Anglia, Norwich, NR4 7EA, United Kingdom.
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Ecological niche adaptation of Salmonella Typhimurium U288 is associated with altered pathogenicity and reduced zoonotic potential. Commun Biol 2021; 4:498. [PMID: 33893390 PMCID: PMC8065163 DOI: 10.1038/s42003-021-02013-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 03/19/2021] [Indexed: 02/02/2023] Open
Abstract
The emergence of new bacterial pathogens is a continuing challenge for agriculture and food safety. Salmonella Typhimurium is a major cause of foodborne illness worldwide, with pigs a major zoonotic reservoir. Two phylogenetically distinct variants, U288 and ST34, emerged in UK pigs around the same time but present different risk to food safety. Here we show using genomic epidemiology that ST34 accounts for over half of all S. Typhimurium infections in people while U288 less than 2%. That the U288 clade evolved in the recent past by acquiring AMR genes, indels in the virulence plasmid pU288-1, and accumulation of loss-of-function polymorphisms in coding sequences. U288 replicates more slowly and is more sensitive to desiccation than ST34 isolates and exhibited distinct pathogenicity in the murine model of colitis and in pigs. U288 infection was more disseminated in the lymph nodes while ST34 were recovered in greater numbers in the intestinal contents. These data are consistent with the evolution of S. Typhimurium U288 adaptation to pigs that may determine their reduced zoonotic potential.
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