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Went SC, Picton DM, Morgan RD, Nelson A, Brady A, Mariano G, Dryden DTF, Smith DL, Wenner N, Hinton JCD, Blower TR. Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence. Nat Commun 2024; 15:7236. [PMID: 39174540 PMCID: PMC11341690 DOI: 10.1038/s41467-024-51629-7] [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: 12/20/2023] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
Bacteria have evolved a broad range of systems that provide defence against their viral predators, bacteriophages. Bacteriophage Exclusion (BREX) systems recognise and methylate 6 bp non-palindromic motifs within the host genome, and prevent replication of non-methylated phage DNA that encodes these same motifs. How BREX recognises cognate motifs has not been fully understood. In this study we characterise BREX from pathogenic Salmonella and present X-ray crystallographic structures of the conserved BREX protein, PglX. The PglX N-terminal domain encodes the methyltransferase, whereas the C-terminal domain is for motif recognition. We also present the structure of PglX bound to the phage-derived DNA mimic, Ocr, an inhibitor of BREX activity. Our analyses propose modes for DNA-binding by PglX and indicate that both methyltransferase activity and defence require larger BREX complexes. Through rational engineering of PglX we broaden both the range of phages targeted, and the host motif sequences that are methylated by BREX. Our data demonstrate that PglX is used to recognise specific DNA sequences for BREX activity, contributing to motif recognition for both phage defence and host methylation.
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Affiliation(s)
- Sam C Went
- Department of Biosciences, Durham University, South Road, Durham, UK
| | - David M Picton
- Department of Biosciences, Durham University, South Road, Durham, UK
| | | | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Aisling Brady
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Giuseppina Mariano
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - David T F Dryden
- Department of Biosciences, Durham University, South Road, Durham, UK
| | - Darren L Smith
- Faculty of Health and Life Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Nicolas Wenner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jay C D Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, South Road, Durham, UK.
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2
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Martin LB, Tack B, Marchello CS, Sikorski MJ, Owusu-Dabo E, Nyirenda T, Mogasale V, Crump JA. Vaccine value profile for invasive non-typhoidal Salmonella disease. Vaccine 2024; 42:S101-S124. [PMID: 39003017 DOI: 10.1016/j.vaccine.2024.04.045] [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: 10/02/2022] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 07/15/2024]
Abstract
Invasive non-typhoidal Salmonella (iNTS) disease is an under-recognized high-burden disease causing major health and socioeconomic issues in sub-Saharan Africa (sSA), predominantly among immune-naïve infants and young children, including those with recognized comorbidities such as HIV infection. iNTS disease is primarily caused by Salmonella enterica serovar Typhimurium sequence type (ST) 313 and 'African-restricted clades' of Salmonella Enteritidis ST11 that have emerged across the African continent as a series of epidemics associated with acquisition of new antimicrobial resistance. Due to genotypes with a high prevalence of antimicrobial resistance and scarcity of therapeutic options, these NTS serovars are designated by the World Health Organization as a priority pathogen for research and development of interventions, including vaccines, to address and reduce NTS associated bacteremia and meningitis in sSA. Novel and traditional vaccine technologies are being applied to develop vaccines against iNTS disease, and the results of the first clinical trials in the infant target population should become available in the near future. The "Vaccine Value Profile" (VVP) addresses information related predominantly to invasive disease caused by Salmonella Enteritidis and Salmonella Typhimurium prevalent in sSA. Information is included on stand-alone iNTS disease candidate vaccines and candidate vaccines targeting iNTS disease combined with another invasive serotype, Salmonella Typhi, that is also common across sSA. Out of scope for the first version of this VVP is a wider discussion on either diarrheagenic NTS disease (dNTS) also associated with Salmonella Enteritidis and Salmonella Typhimurium or the development of a multivalent Salmonella vaccines targeting key serovars for use globally. This VVP for vaccines to prevent iNTS disease is intended to provide a high-level, holistic assessment of the information and data that are currently available to inform the potential public health, economic, and societal value of pipeline vaccines and vaccine-like products. Future versions of this VVP will be updated to reflect ongoing activities such as vaccine development strategies and a "Full Vaccine Value Assessment" that will inform the value proposition of an iNTS disease vaccine. This VVP was developed by a working group of subject matter experts from academia, non-profit organizations, public private partnerships, and multi-lateral organizations, and in collaboration with stakeholders from the World Health Organization African Region. All contributors have extensive expertise on various elements of the iNTS disease VVP and collectively aimed to identify current research and knowledge gaps. The VVP was developed using only existing and publicly available information.
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Affiliation(s)
| | - Bieke Tack
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Belgium and Department of Microbiology, Immunology and Transplantation, KU Leuven, Belgium.
| | | | - Michael J Sikorski
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
| | | | | | | | - John A Crump
- Centre for International Health, University of Otago, New Zealand.
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3
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Xiang Y, Zhu K, Min K, Zhang Y, Liu J, Liu K, Han Y, Li X, Du X, Wang X, Huang Y, Li X, Peng Y, Yang C, Liu H, Liu H, Li X, Wang H, Wang C, Wang Q, Jia H, Yang M, Wang L, Wu Y, Cui Y, Chen F, Yang H, Baker S, Xu X, Yang J, Song H, Qiu S. Characterization of a Salmonella enterica serovar Typhimurium lineage with rough colony morphology and multidrug resistance. Nat Commun 2024; 15:6123. [PMID: 39033143 PMCID: PMC11271444 DOI: 10.1038/s41467-024-50331-y] [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: 08/28/2023] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of salmonellosis, and the emergence of multidrug-resistant pathovariants has become a growing concern. Here, we investigate a distinct rough colony variant exhibiting a strong biofilm-forming ability isolated in China. Whole-genome sequencing on 2,212 Chinese isolates and 1,739 publicly available genomes reveals the population structure and evolutionary history of the rough colony variants. Characterized by macro, red, dry, and rough (mrdar) colonies, these variants demonstrate enhanced biofilm formation at 28 °C and 37 °C compared to typical rdar colonies. The mrdar variants exhibit extensive multidrug resistance, with significantly higher resistance to at least five classes of antimicrobial agents compared to non-mrdar variants. This resistance is primarily conferred by an IncHI2 plasmid harboring 19 antimicrobial resistance genes. Phylogenomic analysis divides the global collections into six lineages. The majority of mrdar variants belong to sublineage L6.5, which originated from Chinese smooth colony strains and possibly emerged circa 1977. Among the mrdar variants, upregulation of the csgDEFG operons is observed, probably due to a distinct point mutation (-44G > T) in the csgD gene promoter. Pangenome and genome-wide association analyses identify 87 specific accessory genes and 72 distinct single nucleotide polymorphisms associated with the mrdar morphotype.
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Affiliation(s)
- Ying Xiang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Kunpeng Zhu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
- Kaifeng Center for Disease Control and Prevention, Kaifeng, China
| | - Kaiyuan Min
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yaowen Zhang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
- Daxing Center for Disease Control and Prevention, Beijing, China
| | - Jiangfeng Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Kangkang Liu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Yiran Han
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xinge Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xinying Du
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xin Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Ying Huang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xinping Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Yuqian Peng
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Chaojie Yang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Hongbo Liu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Hongbo Liu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xiaoying Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Hui Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Chao Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Qi Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Huiqun Jia
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Mingjuan Yang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Ligui Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China.
| | - Juntao Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.
| | - Hongbin Song
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China.
| | - Shaofu Qiu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China.
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4
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Sun RY, Fang LX, Dai JJ, Chen KC, Ke BX, Sun J, Ke CW, Wai Chi Chan E, Liu YH, Chen S, Liao XP. Antimicrobial resistance and population genomics of emerging multidrug-resistant Salmonella 4,[5],12:i:- in Guangdong, China. mSystems 2024; 9:e0116423. [PMID: 38747582 PMCID: PMC11237462 DOI: 10.1128/msystems.01164-23] [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: 11/06/2023] [Accepted: 04/09/2024] [Indexed: 06/19/2024] Open
Abstract
Salmonella 4,[5],12:i:-, a monophasic variant of Salmonella Typhimurium, has emerged as a global cause of multidrug-resistant salmonellosis and has become endemic in many developing and developed countries, especially in China. Here, we have sequenced 352 clinical isolates in Guangdong, China, during 2009-2019 and performed a large-scale collection of Salmonella 4,[5],12:i:- with whole genome sequencing (WGS) data across the globe, to better understand the population structure, antimicrobial resistance (AMR) genomic characterization, and transmission routes of Salmonella 4,[5],12:i:- across Guangdong. Salmonella 4,[5],12:i:- strains showed broad genetic diversity; Guangdong isolates were found to be widely distributed among the global lineages. Of note, we identified the formation of a novel Guangdong clade (Bayesian analysis of population structure lineage 1 [BAPS1]) genetically diversified from the global isolates and likely emerged around 1990s. BAPS1 exhibits unique genomic features, including large pan-genome, decreased ciprofloxacin susceptibility due to mutation in gyrA and carriage of plasmid-mediated quinolone resistance (PMQR) genes, and the multidrug-resistant IncHI2 plasmid. Furthermore, high genetic similarity was found between strains collected from Guangdong, Europe, and North America, indicating the association with multiple introductions from overseas. These results suggested that global dissemination and local clonal expansion simultaneously occurred in Guangdong, China, and horizontally acquired resistance to first-line and last-line antimicrobials at local level, underlying emergences of extensive drug and pan-drug resistance. Our findings have increased the knowledge of global and local epidemics of Salmonella 4,[5],12:i:- in Guangdong, China, and provided a comprehensive baseline data set essential for future molecular surveillance.IMPORTANCESalmonella 4,[5],12:i:- has been regarded as the predominant pandemic serotype causing diarrheal diseases globally, while multidrug resistance (MDR) constitutes great public health concerns. This study provided a detailed and comprehensive genome-scale analysis of this important Salmonella serovar in the past decade in Guangdong, China. Our results revealed the complexity of two distinct transmission modes, namely global transmission and local expansion, circulating in Guangdong over a decade. Using phylogeography models, the origin of Salmonella 4,[5],12:i:- was predicted from two aspects, year and country, that is, Salmonella 4,[5],12:i:- emerged in 1983, and was introduced from the UK, and subsequently differentiated into the local endemic lineage circa 1991. Additionally, based on the pan-genome analysis, it was found that the gene accumulation rate in local endemic BAPS 1 lineage was higher than in other lineages, and the horizontal transmission of MDR IncHI2 plasmid associated with high resistance played a major role, which showed the potential threat to public health.
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Affiliation(s)
- Ruan-Yang Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Jing-Jing Dai
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
| | - Kai-Chao Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Bi-Xia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Chang-Wen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Edward Wai Chi Chan
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Sheng Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
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5
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Belman S, Pesonen H, Croucher NJ, Bentley SD, Corander J. Estimating between-country migration in pneumococcal populations. G3 (BETHESDA, MD.) 2024; 14:jkae058. [PMID: 38507601 PMCID: PMC11152062 DOI: 10.1093/g3journal/jkae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/29/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Streptococcus pneumoniae (the pneumococcus) is a globally distributed, human obligate opportunistic bacterial pathogen which, although often carried commensally, is also a significant cause of invasive disease. Apart from multi-drug resistant and virulent clones, the rate and direction of pneumococcal dissemination between different countries remains largely unknown. The ability for the pneumococcus to take a foothold in a country depends on existing population configuration, the extent of vaccine implementation, as well as human mobility since it is a human obligate bacterium. To shed light on its international movement, we used extensive genome data from the Global Pneumococcal Sequencing project and estimated migration parameters between multiple countries in Africa. Data on allele frequencies of polymorphisms at housekeeping-like loci for multiple different lineages circulating in the populations of South Africa, Malawi, Kenya, and The Gambia were used to calculate the fixation index (Fst) between countries. We then further used these summaries to fit migration coalescent models with the likelihood-free inference algorithms available in the ELFI software package. Synthetic datawere additionally used to validate the inference approach. Our results demonstrate country-pair specific migration patterns and heterogeneity in the extent of migration between different lineages. Our approach demonstrates that coalescent models can be effectively used for inferring migration rates for bacterial species and lineages provided sufficiently granular population genomics surveillance data. Further, it can demonstrate the connectivity of respiratory disease agents between countries to inform intervention policy in the longer term.
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Affiliation(s)
- Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Henri Pesonen
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, 0372, Norway
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, White City Campus, Imperial College London, London W12 0BZ, UK
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, 0372, Norway
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Espoo, Helsinki, 02150, Finland
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6
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Cuco A, Mkupasi E, Mzula A, Mdegela R. Non-typhoidal Salmonella contributes to gastrointestinal infections in Morogoro: Evidence from patients attending Morogoro regional referral hospital in Tanzania. PLoS Negl Trop Dis 2024; 18:e0012249. [PMID: 38848444 PMCID: PMC11189249 DOI: 10.1371/journal.pntd.0012249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/20/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024] Open
Abstract
INTRODUCTION Salmonella is one of the most common causes of food-borne outbreaks and infection worldwide. Non-typhoidal Salmonella (NTS) infections are common and remain a significant public health problem among important bacterial foodborne diseases. The current study aimed to establish the Non typhoidal Salmonella infection and antimicrobial resistance status among selected patients at Morogoro Regional Referral Hospital (MRRH), Morogoro Region, Tanzania, to inform clinical care management and public health interventions. METHODOLOGY A cross-sectional study was conducted using medical records and samples were collected from hospitalised and outpatients between October and December 2021. A total of 153 participants were enrolled in the study and 132 consented to being sampled. The collected samples were analysed using standard microbiological techniques. The isolates were subjected to molecular genotyping, where Polymerase Chain Reaction (PCR) was performed targeting the 16S rDNA gene. PCR products were then submitted for sequencing to establish phylogenetic relatedness. Antimicrobial susceptibility testing and resistance genes screening were also conducted. RESULTS The phylogenetic analysis identified two Salmonella serovars; Salmonella Enteritidis and Salmonella Typhimurium. The isolates were from four adults and seven children patients. The isolates were tested against six antimicrobial agents: tetracycline, trimethoprim, gentamycin, ciprofloxacin, ampicillin and cefotaxime. Further antimicrobial assays were performed by screening 10 antimicrobial resistance genes using PCR. Overall, the highest resistance was observed in ampicillin (100%), whereas the lowest resistance was recorded for ciprofloxacin and gentamicin (9.1%). In addition, four (36.4%) of the isolates were resistant to cefotaxime and three (27.3%) to tetracycline and trimethoprim. The isolates also exhibit the presence of resistance genes for sulfamethoxazole 1&2, tetracycline (tet) A&B, Beta-lactamase CTXM, Beta-lactamase TEM, Beta-lactamase SHV, Gentamycine, Acra and acc3-1 in different occurrences. The overall prevalence of Salmonella species in Morogoro region was 8.3% (11/132) with Salmonella Enteritidis and Salmonella Typhimurium being the only serovars detected from adults and children stool samples. CONCLUSION Our investigation showed that both children and adults had been exposed to Salmonella spp. However, the occurrence of NTS was higher in children (5.3% (7/132) compared to adults (3.0% (4/132). To stop zoonotic infections and the development of antimicrobial resistance in the community, this calls for Infection Prevention and Control (IPC) and stewardship programmes on rational use of antimicrobials in both health facilities and at the community level.
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Affiliation(s)
- Anacleta Cuco
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Ernatus Mkupasi
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Alexanda Mzula
- Department of Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Robinson Mdegela
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
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7
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Flórez NY, Silva C, Villarreal JM, Wiesner M. Presence of integrons and their correlation with multidrug resistance in Salmonella enterica serovar Typhimurium: Exploratory systematic review. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2024; 44:258-276. [PMID: 39088536 DOI: 10.7705/biomedica.6816] [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: 12/05/2022] [Accepted: 03/18/2024] [Indexed: 08/03/2024]
Abstract
In Salmonella enterica serovar Typhimurium (Typhimurium), multidrug resistance is associated with integrons carrying resistance genes dispersed by mobile genetic elements. This exploratory systematic review sought to identify integron types and their resistance genes in multidrug resistance Typhimurium isolates. We used Medline, PubMed, SciELO, ScienceDirect, Redalyc, and Google Scholar as motor searchers for articles in Spanish or English published between 2012 and 2020, including the keywords “integrons”, “antibiotic resistance”, and “Salmonella Typhimurium”. We included 38 articles reporting multidrug resistance up to five antibiotic families. Class 1 integrons with aadA2 and blaPSE-1 gene cassettes were predominant, some probably related to the Salmonella genomic island 1. We did not find studies detailing class 1 and 2 integrons in the same isolate, nor class 3 integrons reported. The presence of integrons largely explains the resistance profiles found in isolates from different sources in 15 countries.
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Affiliation(s)
- Nancy Yaneth Flórez
- Grupo de Microbiología, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D. C., Colombia; Doctorado en Ciencias de la Salud, Facultad de Medicina, Universidad Antonio Nariño, Bogotá, D. C., Colombia
| | - Claudia Silva
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - José Miguel Villarreal
- Grupo de Bioquímica y Biología Molecular de las Micobacterias, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, D. C., Colombia; Grupo de Investigación en Enfermedades Infecciosas, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, D. C., Colombia
| | - Magdalena Wiesner
- Grupo de Microbiología, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D. C., Colombia
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8
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Ferrer-Bustins N, Yvon C, Martín B, Leclerc V, Leblanc JC, Corominas L, Sabaté S, Tolosa-Muñoz E, Chacón-Villanueva C, Bover-Cid S, Cadel-Six S, Jofré A. Genomic insights of Salmonella isolated from dry fermented sausage production chains in Spain and France. Sci Rep 2024; 14:11660. [PMID: 38777847 PMCID: PMC11111747 DOI: 10.1038/s41598-024-62141-9] [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: 03/18/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
The presence of Salmonella in dry fermented sausages is source of recalls and outbreaks. The genomic diversity of 173 Salmonella isolates from the dry fermented sausage production chains (pig carcasses, pork, and sausages) from France and Spain were investigated through their core phylogenomic relationships and accessory genome profiles. Ten different serovars and thirteen sequence type profiles were identified. The most frequent serovar from sausages was the monophasic variant of S. Typhimurium (1,4,[5],12:i:-, 72%) while S. Derby was in pig carcasses (51%). Phylogenomic clusters found in S. 1,4,[5],12:i:-, S. Derby, S. Rissen and S. Typhimurium serovars identified closely related isolates, with less than 10 alleles and 20 SNPs of difference, displaying Salmonella persistence along the pork production chain. Most of the S. 1,4,[5],12:i:- contained the Salmonella genomic island-4 (SGI-4), Tn21 and IncFIB plasmid. More than half of S. Derby strains contained the SGI-1 and Tn7. S. 1,4,[5],12:i:- genomes carried the most multidrug resistance genes (91% of the strains), whereas extended-spectrum β-lactamase genes were found in Typhimurium and Derby serovars. Salmonella monitoring and characterization in the pork production chains, specially S. 1,4,[5],12:i:- serovar, is of special importance due to its multidrug resistance capacity and persistence in dry fermented sausages.
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Affiliation(s)
- Núria Ferrer-Bustins
- IRTA, Food Safety and Functionality Programme, Finca Camps I Armet s/n, 17121, Monells, Spain
| | - Claire Yvon
- Salmonella and Listeria Unit (SEL), Laboratory for Food Safety, ANSES, Pierre and Marie Curie Street 14, 94700, Maisons-Alfort, France
| | - Belén Martín
- IRTA, Food Safety and Functionality Programme, Finca Camps I Armet s/n, 17121, Monells, Spain
| | - Vincent Leclerc
- Salmonella and Listeria Unit (SEL), Laboratory for Food Safety, ANSES, Pierre and Marie Curie Street 14, 94700, Maisons-Alfort, France
| | - Jean-Charles Leblanc
- Salmonella and Listeria Unit (SEL), Laboratory for Food Safety, ANSES, Pierre and Marie Curie Street 14, 94700, Maisons-Alfort, France
| | - Laura Corominas
- LASPCAT_Girona, Public Health Agency, Department of Health, Government of Catalonia, Sol Street 15, 17004, Gerona, Spain
| | - Sara Sabaté
- Public Health Agency of Barcelona (ASPB), Lesseps Square 1, 08023, Barcelona, Spain
- Sant Pau Institute of Biomedical Research (IIB SANT PAU), Sant Quintí 77-79, 08041, Barcelona, Spain
| | - Eva Tolosa-Muñoz
- Surveillance Service, Food Control and Alerts Management, General Subdirectorate of Food Safety and Health Protection, Department of Health, Government of Catalonia, Roc Boronat Street 81-95, 08005, Barcelona, Spain
| | - Carme Chacón-Villanueva
- Public Health Office, Department of Health, Government of Catalonia, Roc Boronat Street 81-95, 08005, Barcelona, Spain
| | - Sara Bover-Cid
- IRTA, Food Safety and Functionality Programme, Finca Camps I Armet s/n, 17121, Monells, Spain
| | - Sabrina Cadel-Six
- Salmonella and Listeria Unit (SEL), Laboratory for Food Safety, ANSES, Pierre and Marie Curie Street 14, 94700, Maisons-Alfort, France.
| | - Anna Jofré
- IRTA, Food Safety and Functionality Programme, Finca Camps I Armet s/n, 17121, Monells, Spain.
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9
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Kumwenda B, Canals R, Predeus AV, Zhu X, Kröger C, Pulford C, Wenner N, Lora LL, Li Y, Owen SV, Everett D, Hokamp K, Heyderman RS, Ashton PM, Gordon MA, Msefula CL, Hinton JCD. Salmonella enterica serovar Typhimurium ST313 sublineage 2.2 has emerged in Malawi with a characteristic gene expression signature and a fitness advantage. MICROLIFE 2024; 5:uqae005. [PMID: 38623411 PMCID: PMC11018118 DOI: 10.1093/femsml/uqae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024]
Abstract
Invasive non-typhoidal Salmonella (iNTS) disease is a serious bloodstream infection that targets immune-compromised individuals, and causes significant mortality in sub-Saharan Africa. Salmonella enterica serovar Typhimurium ST313 causes the majority of iNTS in Malawi. We performed an intensive comparative genomic analysis of 608 S. Typhimurium ST313 isolates dating between 1996 and 2018 from Blantyre, Malawi. We discovered that following the arrival of the well-characterized S. Typhimurium ST313 lineage 2 in 1999, two multidrug-resistant variants emerged in Malawi in 2006 and 2008, designated sublineages 2.2 and 2.3, respectively. The majority of S. Typhimurium isolates from human bloodstream infections in Malawi now belong to sublineages 2.2 or 2.3. To understand the emergence of the prevalent ST313 sublineage 2.2, we studied two representative strains, D23580 (lineage 2) and D37712 (sublineage 2.2). The chromosome of ST313 lineage 2 and sublineage 2.2 only differed by 29 SNPs/small indels and a 3 kb deletion of a Gifsy-2 prophage region including the sseI pseudogene. Lineage 2 and sublineage 2.2 had distinctive plasmid profiles. The transcriptome was investigated in 15 infection-relevant in vitro conditions and within macrophages. During growth in physiological conditions that do not usually trigger S. Typhimurium SPI2 gene expression, the SPI2 genes of D37712 were transcriptionally active. We identified down-regulation of flagellar genes in D37712 compared with D23580. Following phenotypic confirmation of transcriptomic differences, we discovered that sublineage 2.2 had increased fitness compared with lineage 2 during mixed growth in minimal media. We speculate that this competitive advantage is contributing to the emergence of sublineage 2.2 in Malawi.
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Affiliation(s)
- Benjamin Kumwenda
- School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences Blantyre, Blantyre, 265, Malawi
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
| | - Rocío Canals
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Alexander V Predeus
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Xiaojun Zhu
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Carsten Kröger
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Caisey Pulford
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Nicolas Wenner
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Lizeth Lacharme Lora
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Yan Li
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Siân V Owen
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Dean Everett
- Department of Public Health and Epidemiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, P.O. Box 127788, United Arab Emirates
| | - Karsten Hokamp
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Robert S Heyderman
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
- Research Department of Infection, Division of Infection & Immunity, University College London, London, WC1E 6BT, United Kingdom
| | | | - Melita A Gordon
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
| | - Chisomo L Msefula
- School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences Blantyre, Blantyre, 265, Malawi
- Malawi–Liverpool–Wellcome Programme, Blantyre, 3, Malawi
| | - Jay C D Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
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10
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Acton L, Pye HV, Thilliez G, Kolenda R, Matthews M, Turner AK, Yasir M, Holden E, Al-Khanaq H, Webber M, Adriaenssens EM, Kingsley RA. Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica. J Virol 2024; 98:e0147623. [PMID: 38376991 PMCID: PMC10949491 DOI: 10.1128/jvi.01476-23] [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: 09/20/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing, and agriculture. In this study, we isolated 12 bacteriophages termed SPLA phage which infect the foodborne pathogen Salmonella enterica. To determine phage host range, a diverse collection of Enterobacteriaceae and Salmonella enterica was used and genes involved in infection by six SPLA phages were identified using Salmonella Typhimurium strain ST4/74. Candidate host receptors included lipopolysaccharide (LPS), cellulose, and BtuB. Lipopolysaccharide was identified as a susceptibility factor for phage SPLA1a and mutations in LPS biosynthesis genes spontaneously emerged during culture with S. Typhimurium. Conversely, LPS was a resistance factor for phage SPLA5b which suggested that emergence of LPS mutations in culture with SPLA1a represented collateral sensitivity to SPLA5b. We show that bacteria-phage co-culture with SPLA1a and SPLA5b was more successful in limiting the emergence of phage resistance compared to single phage co-culture. Identification of host susceptibility and resistance genes and understanding infection dynamics are critical steps in the rationale design of phage cocktails against specific bacterial pathogens.IMPORTANCEAs antibiotic resistance continues to emerge in bacterial pathogens, bacterial viruses (phage) represent a potential alternative or adjunct to antibiotics. One challenge for their implementation is the predisposition of bacteria to rapidly acquire resistance to phages. We describe a functional genomics approach to identify mechanisms of susceptibility and resistance for newly isolated phages that infect and lyse Salmonella enterica and use this information to identify phage combinations that exploit collateral sensitivity, thus increasing efficacy. Collateral sensitivity is a phenomenon where resistance to one class of antibiotics increases sensitivity to a second class of antibiotics. We report a functional genomics approach to rationally design a phage combination with a collateral sensitivity dynamic which resulted in increased efficacy. Considering such evolutionary trade-offs has the potential to manipulate the outcome of phage therapy in favor of resolving infection without selecting for escape mutants and is applicable to other virus-host interactions.
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Affiliation(s)
- Luke Acton
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | - Hannah V. Pye
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | - Gaëtan Thilliez
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Rafał Kolenda
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Michaela Matthews
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - A. Keith Turner
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Muhammad Yasir
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Emma Holden
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Haider Al-Khanaq
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Mark Webber
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | | | - Robert A. Kingsley
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
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11
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Gordon MA. Tackling non-typhoidal Salmonella with humility. Nat Microbiol 2024; 9:582-583. [PMID: 38413835 DOI: 10.1038/s41564-024-01623-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Affiliation(s)
- Melita A Gordon
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi.
- Department of Clinical Infection, Microbiology and Infection, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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12
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Gasperini G, Massai L, De Simone D, Raso MM, Palmieri E, Alfini R, Rossi O, Ravenscroft N, Kuttel MM, Micoli F. O-Antigen decorations in Salmonella enterica play a key role in eliciting functional immune responses against heterologous serovars in animal models. Front Cell Infect Microbiol 2024; 14:1347813. [PMID: 38487353 PMCID: PMC10937413 DOI: 10.3389/fcimb.2024.1347813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024] Open
Abstract
Introduction Different serovars of Salmonella enterica cause systemic diseases in humans including enteric fever, caused by S. Typhi and S. Paratyphi A, and invasive nontyphoidal salmonellosis (iNTS), caused mainly by S. Typhimurium and S. Enteritidis. No vaccines are yet available against paratyphoid fever and iNTS but different strategies, based on the immunodominant O-Antigen component of the lipopolysaccharide, are currently being tested. The O-Antigens of S. enterica serovars share structural features including the backbone comprising mannose, rhamnose and galactose as well as further modifications such as O-acetylation and glucosylation. The importance of these O-Antigen decorations for the induced immunogenicity and cross-reactivity has been poorly characterized. Methods These immunological aspects were investigated in this study using Generalized Modules for Membrane Antigens (GMMA) as delivery systems for the different O-Antigen variants. This platform allowed the rapid generation and in vivo testing of defined and controlled polysaccharide structures through genetic manipulation of the O-Antigen biosynthetic genes. Results Results from mice and rabbit immunization experiments highlighted the important role played by secondary O-Antigen decorations in the induced immunogenicity. Moreover, molecular modeling of O-Antigen conformations corroborated the likelihood of cross-protection between S. enterica serovars. Discussion Such results, if confirmed in humans, could have a great impact on the design of a simplified vaccine composition able to maximize functional immune responses against clinically relevant Salmonella enterica serovars.
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Affiliation(s)
| | - Luisa Massai
- GSK Vaccines Institute for Global Health (GVGH), Siena, Italy
| | | | | | - Elena Palmieri
- GSK Vaccines Institute for Global Health (GVGH), Siena, Italy
| | - Renzo Alfini
- GSK Vaccines Institute for Global Health (GVGH), Siena, Italy
| | - Omar Rossi
- GSK Vaccines Institute for Global Health (GVGH), Siena, Italy
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch, South Africa
| | - Michelle M. Kuttel
- Department of Computer Science, University of Cape Town, Rondebosch, South Africa
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13
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Nhu NTK, Rahman MA, Goh KGK, Kim SJ, Phan MD, Peters KM, Alvarez-Fraga L, Hancock SJ, Ravi C, Kidd TJ, Sullivan MJ, Irvine KM, Beatson SA, Sweet MJ, Irwin AD, Vukovic J, Ulett GC, Hasnain SZ, Schembri MA. A convergent evolutionary pathway attenuating cellulose production drives enhanced virulence of some bacteria. Nat Commun 2024; 15:1441. [PMID: 38383596 PMCID: PMC10881479 DOI: 10.1038/s41467-024-45176-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/16/2024] [Indexed: 02/23/2024] Open
Abstract
Bacteria adapt to selective pressure in their immediate environment in multiple ways. One mechanism involves the acquisition of independent mutations that disable or modify a key pathway, providing a signature of adaptation via convergent evolution. Extra-intestinal pathogenic Escherichia coli (ExPEC) belonging to sequence type 95 (ST95) represent a global clone frequently associated with severe human infections including acute pyelonephritis, sepsis, and neonatal meningitis. Here, we analysed a publicly available dataset of 613 ST95 genomes and identified a series of loss-of-function mutations that disrupt cellulose production or its modification in 55.3% of strains. We show the inability to produce cellulose significantly enhances ST95 invasive infection in a rat model of neonatal meningitis, leading to the disruption of intestinal barrier integrity in newborn pups and enhanced dissemination to the liver, spleen and brain. Consistent with these observations, disruption of cellulose production in ST95 augmented innate immune signalling and tissue neutrophil infiltration in a mouse model of urinary tract infection. Mutations that disrupt cellulose production were also identified in other virulent ExPEC STs, Shigella and Salmonella, suggesting a correlative association with many Enterobacteriaceae that cause severe human infection. Together, our findings provide an explanation for the emergence of hypervirulent Enterobacteriaceae clones.
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Affiliation(s)
- Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - M Arifur Rahman
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Immunopathology Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
- QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Kelvin G K Goh
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, Australia
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Seung Jae Kim
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Kate M Peters
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Laura Alvarez-Fraga
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- INRAE, Univ Montpellier, LBE, 102 Avenue des Etangs, Narbonne, 11100, France
| | - Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Chitra Ravi
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Matthew J Sullivan
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, Australia
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Katharine M Irvine
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Immunopathology Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Adam D Irwin
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- University of Queensland Centre for Clinical Research, Brisbane, Australia
- Queensland Children's Hospital, Brisbane, Australia
| | - Jana Vukovic
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
| | - Glen C Ulett
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, Australia.
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia.
| | - Sumaira Z Hasnain
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia.
- Immunopathology Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia.
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia.
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14
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Jolaosho TL, Elegbede IO, Ndimele PE, Falebita TE, Abolaji OY, Oladipupo IO, Ademuyiwa FE, Mustapha AA, Oresanya ZO, Isaac OO. Occurrence, distribution, source apportionment, ecological and health risk assessment of heavy metals in water, sediment, fish and prawn from Ojo River in Lagos, Nigeria. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:109. [PMID: 38172417 DOI: 10.1007/s10661-023-12148-y] [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: 12/07/2022] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
Abstract
The study investigates the occurrence and bioaccumulation of heavy metals in water, sediment, fish, and prawn from the Ojo River with a view to identify the source of origin and the associated ecological and human health risks. The result shows that heavy metal concentrations in water [As = 0.010, Cd = 0.001, Cr = 0.041, Cu = 0.019, Co = 0.050, Fe = 0.099, Pb = 0.006, Ni = 0.003, and Zn = 0.452(mg/L)] were within the acceptable limits. The heavy metals in the sediment [As = 0.050, Cd = 0.287, Cr = 0.509, Cu = 0.207, Co = 0.086, Fe = 33.093, Pb = 0.548, Ni = 0.153 and Zn = 4.249 (mg/kg)] were within their respective background levels or earth's crust and the TEL and PEL standard limits. The bioaccumulation of heavy metals in fish and prawn tissues are in this hierarchical form: Fe > Zn > Cu > Cr > Ni > Co > Pb > Ar > Cd and Fe > Zn > Cu > Cr > Pb > Ar > Ni > Co > Cd, respectively. The bioaccumulation factors of heavy metals in fish ranged from 0.893 - 16.611 and 1.056 - 49.204 in prawn, which were higher than the biota-sedimentation factors (BSAF) values, inferring that the fish and prawns of this study ingested heavy metals highly from water column. The aggregated BSAF scores (fish = 5.584 and prawn = 9.137) showed that these organisms are good concentrators of heavy metals in sediments. The water quality index and other pollution indices (Single pollution index, Heavy metal assessment index, and Heavy metal pollution index) demonstrates slightly clean water, with a moderate level of contamination. The HI values of heavy metals in water, fish, and prawn were lower than 1, implying non-carcinogenic risk in children or adults. The ADD and EDI values of the metals were within their respective oral reference doses (RfD). The TCR values showed that exposure to water, either by ingestion or dermal absorption and the consumption of P. obscura and M. vollenhovenii from the Ojo River would not induce cancer risks in people, though As, Cr, Cd, and Pb showed carcinogenic potentials. The sediment contamination indices such as CF, mCd, EF, and Igeo showed a moderate level of pollution. The ecological risk values (NMPI, mCd = 0.068, PLI = 0.016, and R.I = 86.651) of heavy metals implies "no-moderate risk" except for Cd, which showed high risk. The ecotoxicological parameters, m-PEL-Q (0.024) and m-ERM-Q (0.016) denotes low contamination and no probability of acute toxicity. The CV analysis showed high dispersions and variabilities in the distributions of the heavy metals in water. Other source analyses (Pearson's correlation matrix, PCA, and HCA) showed that both natural processes and anthropogenic activities are responsible for the occurrence of heavy metals in water and sediment from the Ojo River.
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Affiliation(s)
- Toheeb Lekan Jolaosho
- Department of Fisheries, Lagos State University, Ojo, Lagos State, Nigeria.
- Department of Fisheries Technology, Lagos State Polytechnic, Ikorodu, Nigeria.
| | - Isa Olalekan Elegbede
- Department of Fisheries, Lagos State University, Ojo, Lagos State, Nigeria
- Department of Environmental Planning, University of Technology, Cottbus-Senftenberg, Brandenburg, Germany
| | | | - Taiwo Elijah Falebita
- Department of Zoology and Environmental Biology, Lagos State University, Ojo, Lagos State, Nigeria
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15
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Hajra D, Nair AV, Chakravortty D. Decoding the invasive nature of a tropical pathogen of concern: The invasive non-Typhoidal Salmonella strains causing host-restricted extraintestinal infections worldwide. Microbiol Res 2023; 277:127488. [PMID: 37716125 DOI: 10.1016/j.micres.2023.127488] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/18/2023]
Abstract
Invasive-Non-Typhoidal Salmonella (iNTS) are the major cause of health concern in the low-income, under-developed nations in Africa and Asia that lack proper sanitation facilities. Around 5% of the NTS cases give rise to invasive, extraintestinal diseases leading to focal infections like osteomyelitis, meningitis, osteoarthritis, endocarditis and neonatal sepsis. iNTS serovars like S. Typhimurium, S. Enteritidis, S. Dublin, S. Choleraesuis show a greater propensity to become invasive than others which hints at the genetic basis of their emergence. The major risk factors attributing to the invasive diseases include immune-compromised individuals having co-infection with malaria or HIV, or suffering from malnutrition. The rampant use of antibiotics leading to the emergence of multi-drug resistant strains poses a great challenge in disease management. An extensive understanding of the iNTS pathogenesis and its epidemiology will open up avenues for the development of new vaccination and therapeutic strategies to restrict the spread of this neglected disease.
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Affiliation(s)
- Dipasree Hajra
- Department of Microbiology & Cell Biology, Indian Institute of Science, India
| | - Abhilash Vijay Nair
- Department of Microbiology & Cell Biology, Indian Institute of Science, India
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16
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Gómez-Baltazar A, Godínez-Oviedo A, Vázquez-Marrufo G, Vázquez-Garcidueñas MS, Hernández-Iturriaga M. Genomic analysis of the MLST population structure and antimicrobial resistance genes associated with Salmonella enterica in Mexico. Genome 2023; 66:319-332. [PMID: 37478495 DOI: 10.1139/gen-2023-0007] [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] [Indexed: 07/23/2023]
Abstract
Salmonella enterica is one of the most commonly reported foodborne pathogens by public health agencies worldwide. In this study, the multilocus sequence typing (MLST) population structure and frequency of antimicrobial resistance (AMR) genes were evaluated in S. enterica strains from Mexico (n = 2561). The most common sources of isolation were food (44.28%), environment (27.41%), animal-related (24.83%), and human (3.48%). The most prevalent serovars were Newport (8.51%), Oranienburg (7.03%), Anatum (5.78%), Typhimurium (5.12%), and Infantis (4.57%). As determined by the 7-gene MLST scheme, the most frequent sequence types were ST23, ST64, and ST32. The core genome MLST scheme identified 132 HC2000 and 195 HC900 hierarchical clusters, with the HC2000_2 cluster being the most prevalent in Mexico (n = 256). A total of 78 different AMR genes belonging to 13 antimicrobial classes were detected in 638 genomic assemblies of S. enterica. The most frequent class was aminoglycosides (31.76%), followed by tetracyclines (12.53%) and sulfonamides (11.91%). These results can help public health agencies in Mexico prioritize their efforts and resources to increase the genomic sequencing of circulating Salmonella strains. Additionally, they provide valuable information for local and global public health efforts to reduce the impact of foodborne diseases and AMR.
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Affiliation(s)
- Adrián Gómez-Baltazar
- Departamento de Investigación y Posgrado en Alimentos, Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro C.P. 76010, Querétaro, Mexico
| | - Angélica Godínez-Oviedo
- Departamento de Investigación y Posgrado en Alimentos, Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro C.P. 76010, Querétaro, Mexico
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro C.P. 58893, Michoacán, Mexico
| | - Ma Soledad Vázquez-Garcidueñas
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez," Universidad Michoacana de San Nicolás de Hidalgo, Morelia C.P. 58020, Michoacán, Mexico
| | - Montserrat Hernández-Iturriaga
- Departamento de Investigación y Posgrado en Alimentos, Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro C.P. 76010, Querétaro, Mexico
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Baker KS, Jauneikaite E, Hopkins KL, Lo SW, Sánchez-Busó L, Getino M, Howden BP, Holt KE, Musila LA, Hendriksen RS, Amoako DG, Aanensen DM, Okeke IN, Egyir B, Nunn JG, Midega JT, Feasey NA, Peacock SJ. Genomics for public health and international surveillance of antimicrobial resistance. THE LANCET. MICROBE 2023; 4:e1047-e1055. [PMID: 37977162 DOI: 10.1016/s2666-5247(23)00283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
Historically, epidemiological investigation and surveillance for bacterial antimicrobial resistance (AMR) has relied on low-resolution isolate-based phenotypic analyses undertaken at local and national reference laboratories. Genomic sequencing has the potential to provide a far more high-resolution picture of AMR evolution and transmission, and is already beginning to revolutionise how public health surveillance networks monitor and tackle bacterial AMR. However, the routine integration of genomics in surveillance pipelines still has considerable barriers to overcome. In 2022, a workshop series and online consultation brought together international experts in AMR and pathogen genomics to assess the status of genomic applications for AMR surveillance in a range of settings. Here we focus on discussions around the use of genomics for public health and international AMR surveillance, noting the potential advantages of, and barriers to, implementation, and proposing recommendations from the working group to help to drive the adoption of genomics in public health AMR surveillance. These recommendations include the need to build capacity for genome sequencing and analysis, harmonising and standardising surveillance systems, developing equitable data sharing and governance frameworks, and strengthening interactions and relationships among stakeholders at multiple levels.
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Affiliation(s)
- Kate S Baker
- Department for Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Katie L Hopkins
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Leonor Sánchez-Busó
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain; CIBERESP, ISCIII, Madrid, Spain
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Benjamin P Howden
- The Centre for Pathogen Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Lillian A Musila
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate - Africa, Nairobi, Kenya; Kenya Medical Research Institute, Nairobi, Kenya
| | - Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Daniel G Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa; School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Oxford, UK
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana, West Africa
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Malawi
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Stenhouse GE, Keddy KH, Bengtsson RJ, Hall N, Smith AM, Thomas J, Iturriza-Gómara M, Baker KS. The genomic epidemiology of shigellosis in South Africa. Nat Commun 2023; 14:7715. [PMID: 38001075 PMCID: PMC10673971 DOI: 10.1038/s41467-023-43345-5] [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: 05/23/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.
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Affiliation(s)
- George E Stenhouse
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
| | | | - Rebecca J Bengtsson
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Miren Iturriza-Gómara
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Kate S Baker
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
- Department of Genetics, University of Cambridge, CB23EH, Cambridge, UK.
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19
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Hanumunthadu B, Kanji N, Owino N, Ferreira Da Silva C, Robinson H, White R, Ferruzzi P, Nakakana U, Canals R, Pollard AJ, Ramasamy M. Salmonella Vaccine Study in Oxford (SALVO) trial: protocol for an observer-participant blind randomised placebo-controlled trial of the iNTS-GMMA vaccine within a European cohort. BMJ Open 2023; 13:e072938. [PMID: 37963701 PMCID: PMC10649500 DOI: 10.1136/bmjopen-2023-072938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/03/2023] [Indexed: 11/16/2023] Open
Abstract
INTRODUCTION Invasive non-typhoidal Salmonellosis (iNTS) is mainly caused by Salmonella enterica serovars Typhimurium and Enteritidis and is estimated to result in 77 500 deaths per year, disproportionately affecting children under 5 years of age in sub-Saharan Africa. Invasive non-typhoidal Salmonellae serovars are increasingly acquiring resistance to first-line antibiotics, thus an effective vaccine would be a valuable tool in reducing morbidity and mortality from infection. While NTS livestock vaccines are in wide use, no licensed vaccines exist for use in humans. Here, a first-in-human study of a novel vaccine (iNTS-GMMA) containing S. Typhimurium and S. Enteritidis Generalised Modules for Membrane Antigens (GMMA) outer membrane vesicles is presented. METHOD AND ANALYSIS The Salmonella Vaccine Study in Oxford is a randomised placebo-controlled participant-observer blind phase I study of the iNTS-GMMA vaccine. Healthy adult volunteers will be randomised to receive three intramuscular injections of the iNTS-GMMA vaccine, containing equal quantities of S. Typhimurium and S. Enteritidis GMMA particles adsorbed on Alhydrogel, or an Alhydrogel placebo at 0, 2 and 6 months. Participants will be sequentially enrolled into three groups: group 1, 1:1 randomisation to low dose iNTS-GMMA vaccine or placebo; group 2, 1:1 randomisation to full dose iNTS-GMMA vaccine or placebo; group 3, 2:1 randomisation to full dose or lower dose (dependant on DSMC reviews of groups 1 and 2) iNTS-GMMA vaccine or placebo.The primary objective is safety and tolerability of the vaccine. The secondary objective is immunogenicity as measured by O-antigen based ELISA. Further exploratory objectives will characterise the expanded human immune profile. ETHICS AND DISSEMINATION Ethical approval for this study has been obtained from the South Central-Oxford A Research Ethics Committee (Ethics REF:22/SC/0059). Appropriate documentation and regulatory approvals have been acquired. Results will be disseminated via peer-reviewed articles and conferences. TRIAL REGISTRATION NUMBER EudraCT Number: 2020-000510-14.
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Affiliation(s)
- Brama Hanumunthadu
- Department of Paediatrics, University of Oxford, Oxford Vaccine Group, Oxford, Oxfordshire, UK
| | - Nasir Kanji
- Department of Paediatrics, University of Oxford, Oxford Vaccine Group, Oxford, Oxfordshire, UK
| | - Nelly Owino
- Department of Paediatrics, University of Oxford, Oxford Vaccine Group, Oxford, Oxfordshire, UK
| | - Carla Ferreira Da Silva
- Department of Paediatrics, University of Oxford, Oxford Vaccine Group, Oxford, Oxfordshire, UK
| | - Hannah Robinson
- Department of Paediatrics, University of Oxford, Oxford Vaccine Group, Oxford, Oxfordshire, UK
- NIHR Oxford Biomedical Research Centre, Oxford, Oxfordshire, UK
| | - Rachel White
- Department of Paediatrics, University of Oxford, Oxford Vaccine Group, Oxford, Oxfordshire, UK
| | | | | | - Rocio Canals
- GSK Vaccines Institute for Global Health, Siena, Italy
| | - Andrew J Pollard
- Department of Paediatrics, University of Oxford, Oxford Vaccine Group, Oxford, Oxfordshire, UK
| | - Maheshi Ramasamy
- Department of Paediatrics, University of Oxford, Oxford Vaccine Group, Oxford, Oxfordshire, UK
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20
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Van Puyvelde S, de Block T, Sridhar S, Bawn M, Kingsley RA, Ingelbeen B, Beale MA, Barbé B, Jeon HJ, Mbuyi-Kalonji L, Phoba MF, Falay D, Martiny D, Vandenberg O, Affolabi D, Rutanga JP, Ceyssens PJ, Mattheus W, Cuypers WL, van der Sande MAB, Park SE, Kariuki S, Otieno K, Lusingu JPA, Mbwana JR, Adjei S, Sarfo A, Agyei SO, Asante KP, Otieno W, Otieno L, Tahita MC, Lompo P, Hoffman IF, Mvalo T, Msefula C, Hassan-Hanga F, Obaro S, Mackenzie G, Deborggraeve S, Feasey N, Marks F, MacLennan CA, Thomson NR, Jacobs J, Dougan G, Kariuki S, Lunguya O. A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa. Nat Commun 2023; 14:6392. [PMID: 37872141 PMCID: PMC10593746 DOI: 10.1038/s41467-023-41152-6] [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: 06/10/2022] [Accepted: 08/23/2023] [Indexed: 10/25/2023] Open
Abstract
Invasive non-typhoidal Salmonella (iNTS) disease manifesting as bloodstream infection with high mortality is responsible for a huge public health burden in sub-Saharan Africa. Salmonella enterica serovar Typhimurium (S. Typhimurium) is the main cause of iNTS disease in Africa. By analysing whole genome sequence data from 1303 S. Typhimurium isolates originating from 19 African countries and isolated between 1979 and 2017, here we show a thorough scaled appraisal of the population structure of iNTS disease caused by S. Typhimurium across many of Africa's most impacted countries. At least six invasive S. Typhimurium clades have already emerged, with ST313 lineage 2 or ST313-L2 driving the current pandemic. ST313-L2 likely emerged in the Democratic Republic of Congo around 1980 and further spread in the mid 1990s. We observed plasmid-borne as well as chromosomally encoded fluoroquinolone resistance underlying emergences of extensive-drug and pan-drug resistance. Our work provides an overview of the evolution of invasive S. Typhimurium disease, and can be exploited to target control measures.
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Affiliation(s)
- Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | | | - Sushmita Sridhar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Division of Infectious Disease, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich, UK
- Earlham Institute, Norwich, UK
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich, UK
- School of Biological Science, University of East Anglia, Norwich, UK
| | - Brecht Ingelbeen
- Institute of Tropical Medicine, Antwerp, Belgium
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Mathew A Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Hyon Jin Jeon
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
- International Vaccine Institute, 1 Gwanak-ro, Seoul, 08826, Republic of Korea
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Lisette Mbuyi-Kalonji
- Department of Medical Biology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
- National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
| | - Marie-France Phoba
- Department of Medical Biology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
- National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
| | - Dadi Falay
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles-Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), 1000, Brussels, Belgium
- Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium
| | - Olivier Vandenberg
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles-Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), 1000, Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, UK
| | - Dissou Affolabi
- Centre National Hospitalier Universitaire Hubert Koutoukou Maga, Cotonou, Benin
| | - Jean Pierre Rutanga
- Institute of Tropical Medicine, Antwerp, Belgium
- College of Science and Technology, University of Rwanda, Kigali, Rwanda
| | - Pieter-Jan Ceyssens
- National Reference Center for Salmonella, Unit of Human Bacterial Diseases, Sciensano, J. Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Wesley Mattheus
- National Reference Center for Salmonella, Unit of Human Bacterial Diseases, Sciensano, J. Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Wim L Cuypers
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Marianne A B van der Sande
- Institute of Tropical Medicine, Antwerp, Belgium
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Se Eun Park
- International Vaccine Institute, 1 Gwanak-ro, Seoul, 08826, Republic of Korea
- Yonsei University Graduate School of Public Health, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Simon Kariuki
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu, Kenya
| | - Kephas Otieno
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu, Kenya
| | - John P A Lusingu
- National Institute for Medical Research, Tanga, Tanzania
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, København, Denmark
| | - Joyce R Mbwana
- National Institute for Medical Research, Tanga, Tanzania
| | - Samuel Adjei
- University of Health & Allied Sciences, Ho, Volta Region, Ghana
| | - Anima Sarfo
- University of Health & Allied Sciences, Ho, Volta Region, Ghana
| | - Seth O Agyei
- University of Health & Allied Sciences, Ho, Volta Region, Ghana
| | - Kwaku P Asante
- Kintampo Health Research Centre, Research and Development Division, Ghana Health Service, Kintampo North Municipality, Ho, Volta Region, Ghana
| | | | | | - Marc C Tahita
- Institut de Recherche en Science de la Santé, Direction Régionale du Centre-Ouest/ClinicalResearch Unit of Nanoro, Nanoro, Burkina Faso
| | - Palpouguini Lompo
- Institut de Recherche en Science de la Santé, Direction Régionale du Centre-Ouest/ClinicalResearch Unit of Nanoro, Nanoro, Burkina Faso
| | | | - Tisungane Mvalo
- University of North Carolina Project, Lilongwe, Malawi
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chisomo Msefula
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Fatimah Hassan-Hanga
- Department of Paediatrics, Bayero University, Kano, Nigeria
- Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Stephen Obaro
- University of Nebraska Medical Center, Omaha, NE, USA
- International Foundation Against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
| | - Grant Mackenzie
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
- London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London, WC1E 7HT, UK
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | | | - Nicholas Feasey
- University of North Carolina Project, Lilongwe, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Florian Marks
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
- International Vaccine Institute, 1 Gwanak-ro, Seoul, 08826, Republic of Korea
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
| | - Calman A MacLennan
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London, WC1E 7HT, UK
| | - Jan Jacobs
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Octavie Lunguya
- Department of Medical Biology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
- National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
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Petrin S, Orsini M, Massaro A, Olsen JE, Barco L, Losasso C. Phenotypic and genotypic antimicrobial resistance correlation and plasmid characterization in Salmonella spp. isolates from Italy reveal high heterogeneity among serovars. Front Public Health 2023; 11:1221351. [PMID: 37744490 PMCID: PMC10513437 DOI: 10.3389/fpubh.2023.1221351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction The spread of antimicrobial resistance among zoonotic pathogens such as Salmonella is a serious health threat, and mobile genetic elements (MGEs) carrying antimicrobial resistance genes favor this phenomenon. In this work, phenotypic antimicrobial resistance to commonly used antimicrobials was studied, and the antimicrobial resistance genes (ARGs) and plasmid replicons associated with the resistances were determined. Methods Eighty-eight Italian Salmonella enterica strains (n = 88), from human, animal and food sources, isolated between 2009 and 2019, were selected to represent serovars with different frequency of isolation in human cases of salmonellosis. The presence of plasmid replicons was also investigated. Results and discussion Resistances to sulphonamides (23.9%), ciprofloxacin (27.3%), ampicillin (29.5%), and tetracycline (32.9%) were the most found phenotypes. ARGs identified in the genomes correlated with the phenotypical results, with blaTEM-1B, sul1, sul2, tetA and tetB genes being frequently identified. Point mutations in gyrA and parC genes were also detected, in addition to many different aminoglycoside-modifying genes, which, however, did not cause phenotypic resistance to aminoglycosides. Many genomes presented plasmid replicons, however, only a limited number of ARGs were predicted to be located on the contigs carrying these replicons. As an expectation of this, multiple ARGs were identified on contigs with IncQ1 plasmid replicon in strains belonging to the monophasic variant of Salmonella Typhimurium. In general, high variability in ARGs and plasmid replicons content was observed among isolates, highlighting a high level of heterogeneity in Salmonella enterica. Irrespective of the serovar., many of the ARGs, especially those associated with critically and highly important antimicrobials for human medicine were located together with plasmid replicons, thus favoring their successful dissemination.
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Affiliation(s)
- Sara Petrin
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Massimiliano Orsini
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
| | - Andrea Massaro
- Applied Chemistry Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicenza, Italy
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lisa Barco
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
| | - Carmen Losasso
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
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22
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Bloomfield SJ, Janecko N, Palau R, Alikhan NF, Mather AE. Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK. Microb Genom 2023; 9:mgen001075. [PMID: 37523225 PMCID: PMC10438825 DOI: 10.1099/mgen.0.001075] [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: 03/15/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
Non-typhoidal Salmonella (NTS) is a major cause of bacterial gastroenteritis. Although many countries have implemented whole genome sequencing (WGS) of NTS, there is limited knowledge on NTS diversity on food and its contribution to human disease. In this study, the aim was to characterise the NTS genomes from retail foods in a particular region of the UK and assess the contribution to human NTS infections. Raw food samples were collected at retail in a repeated cross-sectional design in Norfolk, UK, including chicken (n=311), leafy green (n=311), pork (n=311), prawn (n=279) and salmon (n=157) samples. Up to eight presumptive NTS isolates per positive sample underwent WGS and were compared to publicly available NTS genomes from UK human cases. NTS was isolated from chicken (9.6 %), prawn (2.9 %) and pork (1.3 %) samples and included 14 serovars, of which Salmonella Infantis and Salmonella Enteritidis were the most common. The S. Enteritidis isolates were only isolated from imported chicken. No antimicrobial resistance determinants were found in prawn isolates, whilst 5.1 % of chicken and 0.64 % of pork samples contained multi-drug resistant NTS. The maximum number of pairwise core non-recombinant single nucleotide polymorphisms (SNPs) amongst isolates from the same sample was used to measure diversity and most samples had a median of two SNPs (range: 0-251). NTS isolates that were within five SNPs to clinical UK isolates belonged to specific serovars: S. Enteritidis and S. Infantis (chicken), and S. I 4,[5],12:i- (pork and chicken). Most NTS isolates that were closely related to human-derived isolates were obtained from imported chicken, but further epidemiological data are required to assess definitively the probable source of the human cases. Continued WGS surveillance of Salmonella on retail food involving multiple isolates from each sample is necessary to capture the diversity of Salmonella and determine the relative importance of different sources of human disease.
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Affiliation(s)
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Raphaёlle Palau
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Alison E. Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
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23
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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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24
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Song Z, Zheng J, Zhao Y, Yin J, Zheng D, Hu H, Liu H, Sun M, Ruan L, Liu F. Population genomics and pathotypic evaluation of the bacterial leaf blight pathogen of rice reveals rapid evolutionary dynamics of a plant pathogen. Front Cell Infect Microbiol 2023; 13:1183416. [PMID: 37305415 PMCID: PMC10250591 DOI: 10.3389/fcimb.2023.1183416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/05/2023] [Indexed: 06/13/2023] Open
Abstract
The Xanthomonas oryzae pv. oryzae (Xoo) is a bacterial pathogen causing bacterial blight disease in rice, resulting in significant yield reductions of up to 50% in rice production. Despite its serious threat to food production globally, knowledge of its population structure and virulence evolution is relatively limited. In this study, we employed whole-genome sequencing to explore the diversity and evolution of Xoo in the main rice-growing areas of China over the past 30 years. Using phylogenomic analysis, we revealed six lineages. CX-1 and CX-2 primarily contained Xoo isolates from South China, while CX-3 represented Xoo isolates from North China. Xoo isolates belonging to CX-5 and CX-6 were the most prevalent across all studied areas, persisting as dominant lineages for several decades. Recent sporadic disease outbreaks were primarily caused by Xoo isolates derived from the two major lineages, CX-5 and CX-6, although Xoo isolates from other lineages also contributed to these outbreaks. The lineage and sub-lineage distributions of Xoo isolates were strongly correlated with their geographical origin, which was found to be mainly determined by the planting of the two major rice subspecies, indica and japonica. Moreover, large-scale virulence testing was conducted to evaluate the diversity of pathogenicity for Xoo. We found rapid virulence evolution against rice, and its determinant factors included the genetic background of Xoo, rice resistance genes, and planting environment of rice. This study provides an excellent model for understanding the evolution and dynamics of plant pathogens in the context of their interactions with their hosts, which are shaped by a combination of geographical conditions and farming practices. The findings of this study may have important implications for the development of effective strategies for disease management and crop protection in rice production systems.
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Affiliation(s)
- Zhiwei Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Yancun Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jiakang Yin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Dehong Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Huifeng Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Hongxia Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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25
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Uzairue LI, Shittu OB, Ojo OE, Obuotor TM, Olanipekun G, Ajose T, Arogbonlo R, Medugu N, Ebruke B, Obaro SK. Antimicrobial resistance and virulence genes of invasive Salmonella enterica from children with bacteremia in north-central Nigeria. SAGE Open Med 2023; 11:20503121231175322. [PMID: 37223673 PMCID: PMC10201152 DOI: 10.1177/20503121231175322] [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] [Received: 12/27/2022] [Accepted: 04/25/2023] [Indexed: 05/25/2023] Open
Abstract
Objectives Bacteremia due to invasive Salmonella enterica has been reported earlier in children in Nigeria. This study aimed to detect the virulence and antibiotic resistance genes of invasive Salmonella enterica from children with bacteremia in north-central Nigeria. Method From June 2015 to June 2018, 4163 blood cultures yielded 83 Salmonella isolates. This is a secondary cross-sectional analysis of the Salmonella isolates. The Salmonella enterica were isolated and identified using standard bacteriology protocol. Biochemical identifications of the Salmonella enterica were made by Phoenix MD 50 identification system. Further identification and confirmation were done with polyvalent antisera O and invA gene. Antimicrobial susceptibility testing was done following clinical and laboratory standard institute guidelines. Resistant genes and virulence genes were determined using a real-time polymerase chain reaction. Result Salmonella typhi 51 (61.4%) was the most prevalent serovar, followed by Salmonella species 13 (15.7%), choleraesuis 8 (9.6%), enteritidis 6 (7.2%), and typhimurium 5 (6.1%). Fifty-one (61.4%) of 83 Salmonella enterica were typhoidal, while 32 (38.6%) were not. Sixty-five (78.3%) of the 83 Salmonella enterica isolates were resistant to ampicillin and trimethoprim-sulfamethoxazole, followed by chloramphenicol 39 (46.7%), tetracycline 41 (41.4%), piperacillin 33 (33.9%), amoxicillin-clavulanate, and streptomycin 21 (25.3%), while cephalothin was 19 (22.9%). Thirty-nine (46.9%) of the 83 Salmonella enterica isolates were multi-drug resistant, and none were extensive drug resistant or pan-drug resistant. A blaTEM 42 (50.6%), floR 32 (38.6%), qnrA 24 (28.9%), tetB 20 (20.1%), tetA 10 (10.0%), and tetG 5 (6.0%) were the antibiotic resistance genes detected. There were perfect agreement between phenotypic and genotypic detection of antimicrobial resistance in tetracycline, ciprofloxacin, and chloramphenicol, while beta-lactam showed κ = 0.60 agreement. All of the Salmonella enterica isolates had the virulence genes invA, sopB, mgtC, and sip4D, while 33 (39.8%), 45 (51.8%), and 2 (2.4%) had ssaQ, spvC, and ljsGI-1, respectively. Conclusion Our findings showed multi-drug resistant Salmonella enterica in children with bacteremia in northern Nigeria. In addition, significant virulence and antimicrobial resistance genes were found in invasive Salmonella enterica in northern Nigeria. Thus, our study emphasizes the need to monitor antimicrobial resistance in Salmonella enterica from invasive sources in Nigeria and supports antibiotic prudence.
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Affiliation(s)
- Leonard I Uzairue
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Department of Medical Laboratory
Sciences, Federal University Oye Ekiti, Ekiti State, Nigeria
| | - Olufunke B Shittu
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Olufemi E Ojo
- Department of Veterinary Microbiology
and Parasitology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Tolulope M Obuotor
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Grace Olanipekun
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Theresa Ajose
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Ronke Arogbonlo
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Nubwa Medugu
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Department of Microbiology and
Parasitology, National Hospital, Abuja, FCT, Nigeria
| | - Bernard Ebruke
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Stephen K Obaro
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Pediatric Infectious Division, the
University of Nebraska Medical Center, Omaha, NE, USA
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26
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Casaux ML, D'Alessandro B, Vignoli R, Fraga M. Phenotypic and genotypic survey of antibiotic resistance in Salmonella enterica isolates from dairy farms in Uruguay. Front Vet Sci 2023; 10:1055432. [PMID: 36968467 PMCID: PMC10033963 DOI: 10.3389/fvets.2023.1055432] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/15/2023] [Indexed: 03/11/2023] Open
Abstract
Salmonella enterica is an important zoonotic pathogen that is frequently identified in dairy farming systems. An increase in antibiotic resistance has led to inadequate results of treatments, with impacts on animal and human health. Here, the phenotypic and genotypic susceptibility patterns of Salmonella isolates from dairy cattle and dairy farm environments were evaluated and compared. A collection of 75 S. enterica isolates were evaluated, and their phenotypic susceptibility was determined. For genotypic characterization, the whole genomes of the isolates were sequenced, and geno-serotypes, sequence types (STs) and core-genome-sequence types were determined using the EnteroBase pipeline. To characterize antibiotic resistance genes and gene mutations, tools from the Center for Genomic Epidemiology were used. Salmonella Dublin (SDu), S. Typhimurium (STy), S. Anatum (SAn), S. Newport (SNe), S. Agona (Sag), S. Montevideo (SMo) and IIIb 61:i:z53 were included in the collection. A single sequence type was detected per serovar. Phenotypic non-susceptibility to streptomycin and tetracycline was very frequent in the collection, and high non-susceptibility to ciprofloxacin was also observed. Multidrug resistance (MDR) was observed in 42 isolates (56.0%), with SAn and STy presenting higher MDR than the other serovars, showing non-susceptibility to up to 6 groups of antibiotics. Genomic analysis revealed the presence of 21 genes associated with antimicrobial resistance (AMR) in Salmonella isolates. More than 60% of the isolates carried some gene associated with resistance to aminoglycosides and tetracyclines. Only one gene associated with beta-lactam resistance was found, in seven isolates. Two different mutations were identified, parC_T57S and acrB_R717Q, which confer resistance to quinolones and azithromycin, respectively. The accuracy of predicting antimicrobial resistance phenotypes based on AMR genotypes was 83.7%. The genomic approach does not replace the phenotypic assay but offers valuable information for the survey of circulating antimicrobial resistance. This work represents one of the first studies evaluating phenotypic and genotypic AMR in Salmonella from dairy cattle in South America.
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Affiliation(s)
- María Laura Casaux
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA La Estanzuela, Colonia, Uruguay
- *Correspondence: María Laura Casaux
| | - Bruno D'Alessandro
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Vignoli
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Martín Fraga
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA La Estanzuela, Colonia, Uruguay
- Martín Fraga
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27
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Khambhati K, Bhattacharjee G, Gohil N, Dhanoa GK, Sagona AP, Mani I, Bui NL, Chu DT, Karapurkar JK, Jang SH, Chung HY, Maurya R, Alzahrani KJ, Ramakrishna S, Singh V. Phage engineering and phage-assisted CRISPR-Cas delivery to combat multidrug-resistant pathogens. Bioeng Transl Med 2023; 8:e10381. [PMID: 36925687 PMCID: PMC10013820 DOI: 10.1002/btm2.10381] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/30/2022] [Accepted: 07/16/2022] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance ranks among the top threats to humanity. Due to the frequent use of antibiotics, society is facing a high prevalence of multidrug resistant pathogens, which have managed to evolve mechanisms that help them evade the last line of therapeutics. An alternative to antibiotics could involve the use of bacteriophages (phages), which are the natural predators of bacterial cells. In earlier times, phages were implemented as therapeutic agents for a century but were mainly replaced with antibiotics, and considering the menace of antimicrobial resistance, it might again become of interest due to the increasing threat of antibiotic resistance among pathogens. The current understanding of phage biology and clustered regularly interspaced short palindromic repeats (CRISPR) assisted phage genome engineering techniques have facilitated to generate phage variants with unique therapeutic values. In this review, we briefly explain strategies to engineer bacteriophages. Next, we highlight the literature supporting CRISPR-Cas9-assisted phage engineering for effective and more specific targeting of bacterial pathogens. Lastly, we discuss techniques that either help to increase the fitness, specificity, or lytic ability of bacteriophages to control an infection.
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Affiliation(s)
- Khushal Khambhati
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Gargi Bhattacharjee
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Nisarg Gohil
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Gurneet K Dhanoa
- School of Life Sciences University of Warwick, Gibbet Hill Campus Coventry United Kindgom
| | - Antonia P Sagona
- School of Life Sciences University of Warwick, Gibbet Hill Campus Coventry United Kindgom
| | - Indra Mani
- Department of Microbiology Gargi College, University of Delhi New Delhi India
| | - Nhat Le Bui
- Center for Biomedicine and Community Health International School, Vietnam National University Hanoi Vietnam
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health International School, Vietnam National University Hanoi Vietnam.,Faculty of Applied Sciences International School, Vietnam National University Hanoi Vietnam
| | | | - Su Hwa Jang
- Graduate School of Biomedical Science and Engineering Hanyang University Seoul South Korea.,Hanyang Biomedical Research Institute Hanyang University Seoul South Korea
| | - Hee Yong Chung
- Graduate School of Biomedical Science and Engineering Hanyang University Seoul South Korea.,Hanyang Biomedical Research Institute Hanyang University Seoul South Korea.,College of Medicine Hanyang University Seoul South Korea
| | - Rupesh Maurya
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences College of Applied Medical Sciences, Taif University Taif Saudi Arabia
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering Hanyang University Seoul South Korea.,College of Medicine Hanyang University Seoul South Korea
| | - Vijai Singh
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
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28
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Sabag-Daigle A, Boulanger EF, Thirugnanasambantham P, Law JD, Bogard AJ, Behrman EJ, Gopalan V, Ahmer BMM. Identification of Small-Molecule Inhibitors of the Salmonella FraB Deglycase Using a Live-Cell Assay. Microbiol Spectr 2023; 11:e0460622. [PMID: 36809033 PMCID: PMC10100877 DOI: 10.1128/spectrum.04606-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/18/2023] [Indexed: 02/23/2023] Open
Abstract
Nontyphoidal salmonellosis is one of the most significant foodborne diseases in the United States and globally. There are no vaccines available for human use to prevent this disease, and only broad-spectrum antibiotics are available to treat complicated cases of the disease. However, antibiotic resistance is on the rise and new therapeutics are needed. We previously identified the Salmonella fraB gene, that mutation of causes attenuation of fitness in the murine gastrointestinal tract. The FraB gene product is encoded in an operon responsible for the uptake and utilization of fructose-asparagine (F-Asn), an Amadori product found in several human foods. Mutations in fraB cause an accumulation of the FraB substrate, 6-phosphofructose-aspartate (6-P-F-Asp), which is toxic to Salmonella. The F-Asn catabolic pathway is found only in the nontyphoidal Salmonella serovars, a few Citrobacter and Klebsiella isolates, and a few species of Clostridium; it is not found in humans. Thus, targeting FraB with novel antimicrobials is expected to be Salmonella specific, leaving the normal microbiota largely intact and having no effect on the host. We performed high-throughput screening (HTS) to identify small-molecule inhibitors of FraB using growth-based assays comparing a wild-type Salmonella and a Δfra island mutant control. We screened 224,009 compounds in duplicate. After hit triage and validation, we found three compounds that inhibit Salmonella in an fra-dependent manner, with 50% inhibitory concentration (IC50) values ranging from 89 to 150 μM. Testing these compounds with recombinant FraB and synthetic 6-P-F-Asp confirmed that they are uncompetitive inhibitors of FraB with Ki' (inhibitor constant) values ranging from 26 to 116 μM. IMPORTANCE Nontyphoidal salmonellosis is a serious threat in the United States and globally. We have recently identified an enzyme, FraB, that when mutated renders Salmonella growth defective in vitro and unfit in mouse models of gastroenteritis. FraB is quite rare in bacteria and is not found in humans or other animals. Here, we have identified small-molecule inhibitors of FraB that inhibit the growth of Salmonella. These could provide the foundation for a therapeutic to reduce the duration and severity of Salmonella infections.
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Affiliation(s)
- Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Erin F. Boulanger
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | | | - Jamison D. Law
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Alex J. Bogard
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Edward J. Behrman
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Brian M. M. Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
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29
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Gómez-Baltazar A, Vázquez-Marrufo G, Astiazaran-Garcia H, Ochoa-Zarzosa A, Canett-Romero R, García-Galaz A, Torres-Vega C, Vázquez-Garcidueñas MS. Comparative virulence of the worldwide ST19 and emergent ST213 genotypes of Salmonella enterica serotype Typhimurium strains isolated from food. Microbes Infect 2023; 25:105019. [PMID: 35781097 DOI: 10.1016/j.micinf.2022.105019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 06/22/2022] [Accepted: 06/25/2022] [Indexed: 02/04/2023]
Abstract
Salmonella enterica Typhimurium represents one of the most frequent causal agents of food contamination associated to gastroenteritis. The sequence type ST19 is the founder and worldwide prevalent genotype within this serotype, but its replacement by emerging genotypes has been recently reported. Particularly, the ST213 genotype has replaced it as the most prevalent in clinical and contaminated food samples in Mexico and has been recently reported in several countries. In this study, the in vitro and in vivo virulence of ST213 and ST19 strains isolated from food samples in Mexico was evaluated. Three out of the five analyzed ST213 strains, showed a greater internalization capacity and increased secretion of interleukins IL-8 and IL-6 of Caco-2 cells than the ST19 strains. Microbiological counts in feces and tissues showed the ability of all strains tested to establish infection in the rat model. The ST213 strains also caused histopathological damage, characteristic of gastroenteritis in Wistar rats. In contrast to the in vitro result, one of the ST19 strains showed marked damage in the test animals. The ST213 genotype strains showed in vitro and in vivo virulence variability, but significantly higher than the observed in the ST19 genotype strains, thus such emergent genotype represents a public health concern.
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Affiliation(s)
- Adrián Gómez-Baltazar
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58020, Mexico; Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58893, Mexico
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58893, Mexico
| | - Humberto Astiazaran-Garcia
- Departamento de Nutrición y Metabolismo, Centro de Investigación en Alimentación y Desarrollo, Carretera al Ejido "La Victoria" Km 0.6, 83304, Mexico
| | - Alejandra Ochoa-Zarzosa
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58893, Mexico
| | - Rafael Canett-Romero
- Departamento de Investigación y Posgrado en Alimentos, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Alfonso García-Galaz
- Ciencias de los Alimentos, Centro de Investigación en Alimentación y Desarrollo AC, Carretera al Ejido La Victoria Km 0.6 CP 83304, Mexico
| | - Carlos Torres-Vega
- Laboratorio de Histología, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58020, Mexico
| | - Ma Soledad Vázquez-Garcidueñas
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58020, Mexico.
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30
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Multiplex PCR Assay for Clade Typing of Salmonella enterica Serovar Enteritidis. Microbiol Spectr 2022; 10:e0318222. [PMID: 36409092 PMCID: PMC9769638 DOI: 10.1128/spectrum.03182-22] [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: 11/23/2022] Open
Abstract
Salmonella enterica serovar Enteritidis is one of the most commonly reported serovars of nontyphoidal Salmonella causing human disease and is responsible for both gastroenteritis and invasive nontyphoidal Salmonella (iNTS) disease worldwide. Whole-genome sequence (WGS) comparison of Salmonella Enteritidis isolates from across the world has identified three distinct clades, global epidemic, Central/East African, and West African, all of which have been implicated in epidemics: the global epidemic clade was linked to poultry-associated gastroenteritis, while the two African clades were related to iNTS disease. However, the distribution and epidemiology of these clades across Africa are poorly understood because identification of these clades currently requires whole-genome sequencing capacity. Here, we report a sensitive, time- and cost-effective real-time PCR assay capable of differentiating between the Salmonella Enteritidis clades to facilitate surveillance and to inform public health responses. The assay described here is limited to previously confirmed S. Enteritidis isolates. IMPORTANCE Challenges in the diagnosis and treatment of invasive Salmonella Enteritidis bloodstream infections in sub-Saharan Africa are responsible for a case fatality rate of approximately 15%. It is important to identify distinct clades of S. Enteritidis in diagnostic laboratories in the African setting to determine the different health outcomes associated with particular outbreaks. Here, we describe the development of a high-quality molecular classification assay for clade typing of S. Enteritidis that is ideal for use in public health laboratories in resource-limited settings.
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Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures. mSystems 2022; 7:e0046722. [PMID: 36317888 PMCID: PMC9764980 DOI: 10.1128/msystems.00467-22] [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: 11/07/2022] Open
Abstract
Establishing transcriptional regulatory networks (TRNs) in bacteria has been limited to well-characterized model strains. Using machine learning methods, we established the transcriptional regulatory networks of six Salmonella enterica serovar Typhimurium strains from their transcriptomes. By decomposing a compendia of RNA sequencing (RNA-seq) data with independent component analysis, we obtained 400 independently modulated sets of genes, called iModulons. We (i) performed pan-genome analysis of the phylogroup structure of S. Typhimurium and analyzed the iModulons against this background, (ii) revealed different genetic signatures in pathogenicity islands that explained phenotypes, (iii) discovered three transport iModulons linked to antibiotic resistance, (iv) described concerted responses to cationic antimicrobial peptides, and (v) uncovered new regulons. Thus, by combining pan-genome and transcriptomic analytics, we revealed variations in TRNs across six strains of serovar Typhimurium. IMPORTANCE Salmonella enterica serovar Typhimurium is a pathogen involved in human nontyphoidal infections. Treating S. Typhimurium infections is difficult due to the species's dynamic adaptation to its environment, which is dictated by a complex transcriptional regulatory network (TRN) that is different across strains. In this study, we describe the use of independent component analysis to characterize the differential TRNs across the S. Typhimurium pan-genome using a compendium of high-quality RNA-seq data. This approach provided unprecedented insights into the differences between regulation of key cellular functions and pathogenicity in the different strains. The study provides an impetus to initiate a large-scale effort to reveal the TRN differences between the major phylogroups of the pathogenic bacteria, which could fundamentally impact personalizing treatments of bacterial pathogens.
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Phenotypic and genotypic characterization of multi-drug resistant, biofilm forming, human invasive strain of Salmonella Typhimurium SMC25 isolated from poultry meat in India. Microb Pathog 2022; 173:105830. [DOI: 10.1016/j.micpath.2022.105830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
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33
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Koolman L, Prakash R, Diness Y, Msefula C, Nyirenda TS, Olgemoeller F, Wigley P, Perez-Sepulveda B, Hinton JCD, Owen SV, Feasey NA, Ashton PM, Gordon MA. Case-control investigation of invasive Salmonella disease in Malawi reveals no evidence of environmental or animal transmission of invasive strains, and supports human to human transmission. PLoS Negl Trop Dis 2022; 16:e0010982. [PMID: 36508466 PMCID: PMC9779717 DOI: 10.1371/journal.pntd.0010982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 12/22/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Invasive Salmonella infections cause significant morbidity and mortality in Sub-Saharan Africa. However, the routes of transmission are uncertain. We conducted a case-control study of index-case and geographically-matched control households in Blantyre, Malawi, sampling Salmonella isolates from index cases, healthy people, animals, and the household environment. METHODOLOGY Sixty index cases of human invasive Salmonella infection were recruited (March 2015-Oct 2016). Twenty-eight invasive Non-Typhoidal Salmonella (iNTS) disease and 32 typhoid patients consented to household sampling. Each index-case household was geographically matched to a control household. Extensive microbiological sampling included stool sampling from healthy household members, stool or rectal swabs from household-associated animals and boot-sock sampling of the household environment. FINDINGS 1203 samples from 120 households, yielded 43 non-Typhoidal Salmonella (NTS) isolates from 25 households (overall sample positivity 3.6%). In the 28 iNTS patients, disease was caused by 3 STs of Salmonella Typhimurium, mainly ST313. In contrast, the isolates from households spanned 15 sequence types (STs). Two S. Typhimurium isolates from index cases closely matched isolates from their respective asymptomatic household members (2 and 3 SNP differences respectively). Despite the recovery of a diverse range of NTS, there was no overlap between the STs causing iNTS disease with any environmental or animal isolates. CONCLUSIONS The finding of NTS strains from index cases that matched household members, coupled with lack of related animal or environmental isolates, supports a hypothesis of human to human transmission of iNTS infections in the household. The breadth of NTS strains found in animals and the household environment demonstrated the robustness of NTS sampling and culture methodology, and suggests a diverse ecology of Salmonella in this setting. Healthy typhoid (S. Typhi) carrier state was not detected. The lack of S. Typhi isolates from the household environment suggests that further methodological development is needed to culture S. Typhi from the environment.
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Affiliation(s)
- Leonard Koolman
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Reenesh Prakash
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Yohane Diness
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
| | | | | | - Franziska Olgemoeller
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Paul Wigley
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Blanca Perez-Sepulveda
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Siân V. Owen
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nicholas A. Feasey
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Philip M. Ashton
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Melita A. Gordon
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Kamuzu University of Health Sciences, Blantyre, Malawi
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Wiradiputra MRD, Khuntayaporn P, Thirapanmethee K, Chomnawang MT. Toxin-Antitoxin Systems: A Key Role on Persister Formation in Salmonella enterica Serovar Typhimurium. Infect Drug Resist 2022; 15:5813-5829. [PMID: 36213766 PMCID: PMC9541301 DOI: 10.2147/idr.s378157] [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] [Received: 06/11/2022] [Accepted: 09/16/2022] [Indexed: 11/05/2022] Open
Abstract
The toxin and antitoxin modules in bacteria consist of a toxin molecule that has activity to inhibit various cellular processes and its cognate antitoxin that neutralizes the toxin. This system is considered taking part in the formation of persister cells, which are a subpopulation of recalcitrant cells able to survive antimicrobial treatment without any resistance mechanisms. Importantly, persisters have been associated with long-term infections and treatment failures in healthcare settings. It is a public health concern since persisters can be involved in the evolution and dissemination of antimicrobial resistance amidst the aggravating spread of multidrug-resistant bacteria and insufficient novel antimicrobial therapy to tackle this issue. Salmonella enterica serovar Typhimurium is one of the most prevalent Salmonella serotypes in the world and is a leading cause of food-borne salmonellosis. S. Typhimurium has been known to cause persistent infection and a wealth of investigations on Salmonella persisters indicates that toxin and antitoxin modules play a role in mediating the phenotypic switch of persisters, rendering its survival ability in the presence of antimicrobial agents. In this review, we discuss findings regarding mechanisms that underly persistence in S. Typhimurium, especially the involvement of toxin and antitoxin modules.
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Affiliation(s)
- Made Rai Dwitya Wiradiputra
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,Biopharmaceutical Sciences Program, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Piyatip Khuntayaporn
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Krit Thirapanmethee
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Mullika Traidej Chomnawang
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,Correspondence: Mullika Traidej Chomnawang, Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, 10400, Thailand, Tel +66 2 644 8692, Email
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Biggel M, Horlbog J, Nüesch-Inderbinen M, Chattaway MA, Stephan R. Epidemiological links and antimicrobial resistance of clinical Salmonella enterica ST198 isolates: a nationwide microbial population genomic study in Switzerland. Microb Genom 2022; 8:mgen000877. [PMID: 36301086 PMCID: PMC9676052 DOI: 10.1099/mgen.0.000877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/15/2022] [Indexed: 07/20/2023] Open
Abstract
Salmonella is a leading cause of foodborne outbreaks and systemic infections worldwide. Emerging multi-drug resistant Salmonella lineages such as a ciprofloxacin-resistant subclade (CIPR) within Salmonella enterica serovar Kentucky ST198 threaten the effective prevention and treatment of infections. To understand the genomic diversity and antimicrobial resistance gene content associated with S. Kentucky in Switzerland, we whole-genome sequenced 70 human clinical isolates obtained between 2010 and 2020. Most isolates belonged to ST198-CIPR. High- and low-level ciprofloxacin resistance among CIPR isolates was associated with variable mutations in ramR and acrB in combination with stable mutations in quinolone-resistance determining regions (QRDRs). Analysis of isolates from patients with prolonged ST198 colonization indicated subclonal adaptions with the ramR locus as a mutational hotspot. SNP analyses identified multiple clusters of near-identical isolates, which were often associated with travel but included spatiotemporally linked isolates from Switzerland. The largest SNP cluster was associated with travellers returning from Indonesia, and investigation of global data linked >60 additional ST198 salmonellosis isolates to this cluster. Our results emphasize the urgent need for implementing whole-genome sequencing as a routine tool for Salmonella surveillance and outbreak detection.
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Affiliation(s)
- Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zürich, Zürich, Switzerland
| | - Jule Horlbog
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zürich, Zürich, Switzerland
- National Reference Center for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | | | | | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zürich, Zürich, Switzerland
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Choy RKM, Bourgeois AL, Ockenhouse CF, Walker RI, Sheets RL, Flores J. Controlled Human Infection Models To Accelerate Vaccine Development. Clin Microbiol Rev 2022; 35:e0000821. [PMID: 35862754 PMCID: PMC9491212 DOI: 10.1128/cmr.00008-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The timelines for developing vaccines against infectious diseases are lengthy, and often vaccines that reach the stage of large phase 3 field trials fail to provide the desired level of protective efficacy. The application of controlled human challenge models of infection and disease at the appropriate stages of development could accelerate development of candidate vaccines and, in fact, has done so successfully in some limited cases. Human challenge models could potentially be used to gather critical information on pathogenesis, inform strain selection for vaccines, explore cross-protective immunity, identify immune correlates of protection and mechanisms of protection induced by infection or evoked by candidate vaccines, guide decisions on appropriate trial endpoints, and evaluate vaccine efficacy. We prepared this report to motivate fellow scientists to exploit the potential capacity of controlled human challenge experiments to advance vaccine development. In this review, we considered available challenge models for 17 infectious diseases in the context of the public health importance of each disease, the diversity and pathogenesis of the causative organisms, the vaccine candidates under development, and each model's capacity to evaluate them and identify correlates of protective immunity. Our broad assessment indicated that human challenge models have not yet reached their full potential to support the development of vaccines against infectious diseases. On the basis of our review, however, we believe that describing an ideal challenge model is possible, as is further developing existing and future challenge models.
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Affiliation(s)
- Robert K. M. Choy
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
| | - A. Louis Bourgeois
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
| | | | - Richard I. Walker
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
| | | | - Jorge Flores
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
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Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level. mSystems 2022; 7:e0149321. [PMID: 35913188 PMCID: PMC9426430 DOI: 10.1128/msystems.01493-21] [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: 12/24/2022] Open
Abstract
Serovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens could identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range, and risk to human health. This promises to aid the design of interventions and serve as a knowledge base in the Salmonella research community. Here, we present SalmoNet2, a major update to SalmoNet1, the first multilayered interaction resource for Salmonella strains, containing protein-protein, transcriptional regulatory, and enzyme-enzyme interactions. The new version extends the number of Salmonella networks from 11 to 20. We now include a strain from the second species in the Salmonella genus, a strain from the Salmonella enterica subspecies arizonae and additional strains of importance from the subspecies enterica, including S. Typhimurium strain D23580, an epidemic multidrug-resistant strain associated with invasive nontyphoidal salmonellosis (iNTS). The database now uses strain specific metabolic models instead of a generalized model to highlight differences between strains. The update has increased the coverage of high-quality protein-protein interactions, and enhanced interoperability with other computational resources by adopting standardized formats. The resource website has been updated with tutorials to help researchers analyze their Salmonella data using molecular interaction networks from SalmoNet2. SalmoNet2 is accessible at http://salmonet.org/. IMPORTANCE Multilayered network databases collate interaction information from multiple sources, and are powerful both as a knowledge base and subject of analysis. Here, we present SalmoNet2, an integrated network resource containing protein-protein, transcriptional regulatory, and metabolic interactions for 20 Salmonella strains. Key improvements to the update include expanding the number of strains, strain-specific metabolic networks, an increase in high-quality protein-protein interactions, community standard computational formats to help interoperability, and online tutorials to help users analyze their data using SalmoNet2.
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Mellor KC, Blackwell GA, Cawthraw SA, Mensah NE, Reid SWJ, Thomson NR, Petrovska L, Mather AE. Contrasting long-term dynamics of antimicrobial resistance and virulence plasmids in Salmonella Typhimurium from animals. Microb Genom 2022; 8. [PMID: 35997596 PMCID: PMC9484752 DOI: 10.1099/mgen.0.000826] [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: 11/18/2022] Open
Abstract
Plasmids are mobile elements that can carry genes encoding traits of clinical concern, including antimicrobial resistance (AMR) and virulence. Population-level studies of Enterobacterales, including Escherichia coli, Shigella and Klebsiella, indicate that plasmids are important drivers of lineage expansions and dissemination of AMR genes. Salmonella Typhimurium is the second most common cause of salmonellosis in humans and livestock in the UK and Europe. The long-term dynamics of plasmids between S. Typhimurium were investigated using isolates collected through national surveillance of animals in England and Wales over a 25-year period. The population structure of S. Typhimurium and its virulence plasmid (where present) were inferred through phylogenetic analyses using whole-genome sequence data for 496 isolates. Antimicrobial resistance genes and plasmid markers were detected in silico. Phenotypic plasmid characterization, using the Kado and Liu method, was used to confirm the number and size of plasmids. The differences in AMR and plasmids between clades were striking, with livestock clades more likely to carry one or more AMR plasmid and be multi-drug-resistant compared to clades associated with wildlife and companion animals. Multiple small non-AMR plasmids were distributed across clades. However, all hybrid AMR–virulence plasmids and most AMR plasmids were highly clade-associated and persisted over decades, with minimal evidence of horizontal transfer between clades. This contrasts with the role of plasmids in the short-term dissemination of AMR between diverse strains in other Enterobacterales in high-antimicrobial-use settings, with implications for predicting plasmid dissemination amongst S. Typhimurium.
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Affiliation(s)
- Kate C Mellor
- Royal Veterinary College, Hatfield, UK.,London School of Hygiene and Tropical Medicine, London, UK
| | - Grace A Blackwell
- European Bioinformatics Institute, Hinxton, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | | | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Alison E Mather
- Quadram Institute Bioscience, Norwich, UK.,University of East Anglia, Norwich, UK
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Sun RY, Guo WY, Zhang JX, Wang MG, Wang LL, Lian XL, Ke BX, Sun J, Ke CW, Liu YH, Liao XP, Fang LX. Phylogenomic analysis of Salmonella Indiana ST17, an emerging MDR clonal group in China. J Antimicrob Chemother 2022; 77:2937-2945. [PMID: 35880764 DOI: 10.1093/jac/dkac243] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/24/2022] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To reconstruct the genomic epidemiology and evolution of MDR Salmonella Indiana in China. METHODS A total of 108 Salmonella Indiana strains were collected from humans and livestock in China. All isolates were subjected to WGS and antimicrobial susceptibility testing. Phylogenetic relationships and evolutionary analyses were conducted using WGS data from this study and the NCBI database. RESULTS Almost all 108 Salmonella Indiana strains displayed the MDR phenotype. Importantly, 84 isolates possessed concurrent resistance to ciprofloxacin and cefotaxime. WGS analysis revealed that class 1 integrons on the chromosome and IncHI2 plasmids were the key vectors responsible for multiple antibiotic resistance gene (ARG) [including ESBL and plasmid-mediated quinolone resistance (PMQR) genes] transmission among Salmonella Indiana. The 108 Salmonella Indiana dataset displayed a relatively large core genome and ST17 was the predominant ST. Moreover, the global ST17 Salmonella Indiana strains could be divided into five distinct lineages, each of which was significantly associated with a geographical distribution. Genomic analysis revealed multiple antimicrobial resistance determinants and QRDR mutations in Chinese lineages, which almost did not occur in other global lineages. Using molecular clock analysis, we hypothesized that ST17 isolates have existed since 1956 and underwent a major population expansion from the 1980s to the 2000s and the genetic diversity started to decrease around 2011, probably due to geographical barriers, antimicrobial selective pressure and MDR, favouring the establishment of this prevalent multiple antibiotic-resistant lineage and local epidemics. CONCLUSIONS This study revealed that adaptation to antimicrobial pressure was possibly pivotal in the recent evolutionary trajectory for the clonal spread of ST17 Salmonella Indiana in China.
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Affiliation(s)
- Ruan Yang Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Wen Ying Guo
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Ji Xing Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Min Ge Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Lin Lin Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Xin Lei Lian
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Bi Xia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, P. R. China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Chang Wen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, P. R. China
| | - Ya Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, P. R. China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Xiao Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Liang Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, P. R. China
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Genetic and Structural Variation in the O-Antigen of Salmonella enterica Serovar Typhimurium Isolates Causing Bloodstream Infections in the Democratic Republic of the Congo. mBio 2022; 13:e0037422. [PMID: 35862803 PMCID: PMC9426603 DOI: 10.1128/mbio.00374-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Salmonella enterica serovar Typhimurium causes a devastating burden of invasive disease in sub-Saharan Africa with high levels of antimicrobial resistance. No licensed vaccine is available, but O-antigen-based candidates are in development, as the O-antigen moiety of lipopolysaccharides is the principal target of protective immunity. The vaccines under development are designed based on isolates with O-antigen O-acetylated at position C-2 of abequose, giving the O:5 antigen. Serotyping data on recent Salmonella Typhimurium clinical isolates from the Democratic Republic of the Congo (DRC), however, indicate increasing levels of isolates without O:5. The importance and distribution of this loss of O:5 antigen in the population as well as the genetic mechanism responsible for the loss and chemical characteristics of the O-antigen are poorly understood. In this study, we Illumina whole-genome sequenced 354 Salmonella Typhimurium isolates from the DRC, which were isolated between 2002 and 2017. We used genomics and phylogenetics combined with chemical approaches (1H nuclear magnetic resonance [NMR], high-performance anion-exchange chromatography with pulsed amperometric detection [HPAEC-PAD], high-performance liquid chromatography–PAD [HPLC-PAD], and HPLC-size exclusion chromatography [HPLC-SEC]) to characterize the O-antigen features within the bacterial population. We observed convergent evolution toward the loss of the O:5 epitope predominantly caused by recombination events in a single gene, the O-acetyltransferase gene oafA. In addition, we observe further O-antigen variations, including O-acetylation of the rhamnose residue, different levels of glucosylation, and the absence of O-antigen repeating units. Large recombination events underlying O-antigen variation were resolved using long-read MinION sequencing. Our study suggests evolutionary pressure toward O-antigen variants in a region where invasive disease by Salmonella Typhimurium is highly endemic. This needs to be taken into account when developing O-antigen-based vaccines, as it might impact the breadth of coverage in such regions.
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Hernández-Díaz EA, Vázquez-Garcidueñas MS, Negrete-Paz AM, Vázquez-Marrufo G. Comparative Genomic Analysis Discloses Differential Distribution of Antibiotic Resistance Determinants between Worldwide Strains of the Emergent ST213 Genotype of Salmonella Typhimurium. Antibiotics (Basel) 2022; 11:925. [PMID: 35884180 PMCID: PMC9312005 DOI: 10.3390/antibiotics11070925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/17/2022] Open
Abstract
Salmonella enterica constitutes a global public health concern as one of the main etiological agents of human gastroenteritis. The Typhimurium serotype is frequently isolated from human, animal, food, and environmental samples, with its sequence type 19 (ST19) being the most widely distributed around the world as well as the founder genotype. The replacement of the ST19 genotype with the ST213 genotype that has multiple antibiotic resistance (MAR) in human and food samples was first observed in Mexico. The number of available genomes of ST213 strains in public databases indicates its fast worldwide dispersion, but its public health relevance is unknown. A comparative genomic analysis conducted as part of this research identified the presence of 44 genes, 34 plasmids, and five point mutations associated with antibiotic resistance, distributed across 220 genomes of ST213 strains, indicating the MAR phenotype. In general, the grouping pattern in correspondence to the presence/absence of genes/plasmids that confer antibiotic resistance cluster the genomes according to the geographical origin where the strain was isolated. Genetic determinants of antibiotic resistance group the genomes of North America (Canada, Mexico, USA) strains, and suggest a dispersion route to reach the United Kingdom and, from there, the rest of Europe, then Asia and Oceania. The results obtained here highlight the worldwide public health relevance of the ST213 genotype, which contains a great diversity of genetic elements associated with MAR.
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Affiliation(s)
- Elda Araceli Hernández-Díaz
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Col. La Palma Tarímbaro, Morelia 58893, Michoacán, Mexico; (E.A.H.-D.); (A.M.N.-P.)
| | - Ma. Soledad Vázquez-Garcidueñas
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas “Dr. Ignacio Chávez”, Universidad Michoacana de San Nicolás de Hidalgo, Ave. Rafael Carrillo esq. Dr. Salvador González Herrejón, Col. Cuauhtémoc, Morelia 58020, Michoacán, Mexico;
| | - Andrea Monserrat Negrete-Paz
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Col. La Palma Tarímbaro, Morelia 58893, Michoacán, Mexico; (E.A.H.-D.); (A.M.N.-P.)
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Km 9.5 Carretera Morelia-Zinapécuaro, Col. La Palma Tarímbaro, Morelia 58893, Michoacán, Mexico; (E.A.H.-D.); (A.M.N.-P.)
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Evaluating the Potential Health Risks of Selected Heavy Metals across Four Wastewater Treatment Water Works in Durban, South Africa. TOXICS 2022; 10:toxics10060340. [PMID: 35736948 PMCID: PMC9228299 DOI: 10.3390/toxics10060340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 12/10/2022]
Abstract
Poor and inadequate sanitation systems have been considered not only a human health issue, but also an environmental threat that instigates climate change. Nine heavy metals-arsenic (As), cadmium (Cd), cobalt (Co), chromium (Cr), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn)-were evaluated in influent and effluent water samples from four wastewater treatment plants in the Durban metropolis, KwaZulu-Natal, South Africa. The results indicate that the mean concentrations of all the heavy metals in the influent samples ranged from 0.122 to 1.808 mg/L, while the effluent samples had a concentration ranging from 0.118 to 0.854 mg/L. Iron was found to be in the highest concentration and the concentration of Co was the lowest across the wastewater treatment plants. The levels for most of the heavy metals in this study were found to be above the recommended maximum concentrations in surface and effluent waters as stipulated by the World Health Organization, United States Environmental Protection Agency, Food and Agriculture Organization, and the Department of Water Affairs and Forestry of South Africa. According to the toxicity effect due to non-carcinogenic risks, As, Pb, Cr, and Cd are considered to be of medium risk in this study, indicating that a probable adverse health risk is very likely to occur. Additionally, the cancer risk (RI) values were lower than 10-3, which shows that cancer development is very likely in individuals who are exposed. Cancer development associated with dermal absorption is quite negligible; thereby, it does not raise any concerns.
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Antimicrobial susceptibility and genomic profiling of Salmonella enterica from bloodstream infections at a tertiary referral hospital in Lusaka, Zambia, 2018–2019. IJID REGIONS 2022; 3:248-255. [PMID: 35755477 PMCID: PMC9216281 DOI: 10.1016/j.ijregi.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 12/02/2022]
Abstract
Salmonella enterica Typhi found to be most prevalent, with genetic diversity Low prevalence of invasive non-typhoidal Salmonella infections Salmonella enterica Typhimurium isolated, belonging to serotype 313 High prevalence of multidrug-resistant strains Emergence of fluoroquinolone and cephalosporin resistance
Objectives This study investigated antimicrobial susceptibility and genomic profiling of S. enterica isolated from bloodstream infections at a tertiary referral hospital in Lusaka, Zambia, 2018–2019. Method This was a prospective hospital-based study involving routine blood culture samples submitted to the microbiology laboratory at the University Teaching Hospital. Identification of S. enterica and determination of antimicrobial susceptibility profiles was achieved through conventional and automated methods. Whole-genome sequencing (WGS) was conducted, and the sequence data outputs were processed for species identification, serotype determination, multilocus sequence typing (MLST) profile determination, identification of antimicrobial resistance determinants, and phylogeny. Results Seventy-six Salmonella enterica were isolated and 64 isolates underwent WGS. Salmonella Typhi (72%) was the most prevalent serotype. Notable was the occurrence of invasive non-typhoidal Salmonella Typhimurium ST313 (3%), resistance to cephalosporins (4%) and ciprofloxacin (5%), multidrug resistance (46%), and reduced susceptibility to ciprofloxacin (30%) and imipenem (3%). Phylogenetic cluster analysis showed multiple Salmonella serovars with a wide range of genetic diversity. Conclusion The genetic diversity of Salmonella Typhi, high prevalence of multidrug resistance, and the emergence of ciprofloxacin and cephalosporin resistance warrants improved hygiene and water and sanitation provision, continued surveillance to apprise antibiograms and inform policy, and the introduction of the typhoid conjugate vaccine.
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Darboe S, Bradbury RS, Phelan J, Kanteh A, Muhammad AK, Worwui A, Yang S, Nwakanma D, Perez-Sepulveda B, Kariuki S, Kwambana-Adams B, Antonio M. Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia. Microb Genom 2022; 8:000785. [PMID: 35302932 PMCID: PMC9176284 DOI: 10.1099/mgen.0.000785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/24/2022] [Indexed: 11/18/2022] Open
Abstract
Non-typhoidal Salmonella associated with multidrug resistance cause invasive disease in sub-Saharan Africa. Specific lineages of serovars Typhimurium and Enteritidis have been implicated. Here we characterized the genomic diversity of 100 clinical non-typhoidal Salmonella collected from 93 patients in 2001 from the eastern, and in 2006-2018 from the western regions of The Gambia respectively. A total of 93 isolates (64 invasive, 23 gastroenteritis and six other sites) representing a single infection episode were phenotypically tested for antimicrobial susceptibility using the Kirby-Bauer disc diffusion technique. Whole genome sequencing of 100 isolates was performed using Illumina, and the reads were assembled and analysed using SPAdes. The Salmonella in Silico Typing Resource (SISTR) was used for serotyping. SNP differences among the 93 isolates were determined using Roary, and phylogenetic analysis was performed in the context of 495 African strains from the European Nucleotide Archive. Salmonella serovars Typhimurium (26/64; 30.6 %) and Enteritidis (13/64; 20.3 %) were associated with invasive disease, whilst other serovars were mainly responsible for gastroenteritis (17/23; 73.9 %). The presence of three major serovar Enteritidis clades was confirmed, including the invasive West African clade, which made up more than half (11/16; 68.8 %) of the genomes. Multidrug resistance was confined among the serovar Enteritidis West African clade. The presence of this epidemic virulent clade has potential for spread of resistance and thus important implications for systematic patient management. Surveillance and epidemiological investigations to inform control are warranted.
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Affiliation(s)
- Saffiatou Darboe
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | | | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, UK
| | - Abdoulie Kanteh
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | - Abdul-Khalie Muhammad
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | - Archibald Worwui
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | - Shangxin Yang
- University of California, Los Angeles, California, USA
| | - Davis Nwakanma
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | | | | | - Brenda Kwambana-Adams
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
- University College London, London, UK
| | - Martin Antonio
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
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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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MacLennan CA. The Background, Role and Approach for Development of a Controlled Human Infection Model for Nontyphoidal Salmonella. Curr Top Microbiol Immunol 2021. [PMID: 34958419 DOI: 10.1007/82_2021_246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Nontyphoidal Salmonella (NTS) is responsible for a major global burden of disease and economic loss, particularly in low- and middle-income countries. It is designated a priority pathogen by the WHO for vaccine development and, with new impetus from vaccine developers, the establishment of an NTS controlled human infection model (CHIM) is timely and valuable. The broadly dichotomous clinical presentations of diarrhoea and invasive disease, commonly bacteraemia, present significant challenges to the development of an NTS CHIM. Nevertheless, if successful, such a CHIM will be invaluable for understanding the pathogenesis of NTS disease, identifying correlates of protection and advancing candidate vaccines towards licensure. This article describes the background case for a CHIM for NTS, the role of such a CHIM and outlines a potential approach to its development.
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Affiliation(s)
- Calman A MacLennan
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
- Bill & Melinda Gates Foundation, 62 Buckingham Gate, London, SW16AJ, UK.
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Siggins MK, MacLennan CA. An adsorption method to prepare specific antibody-depleted normal human serum as a source of complement for human serum bactericidal assays for Salmonella. Vaccine 2021; 39:7503-7509. [PMID: 34794820 DOI: 10.1016/j.vaccine.2021.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 10/19/2022]
Abstract
Serum bactericidal assays (SBA) are valuable for assessing the functional activity of natural and vaccine-induced antibodies against many Gram-negative bacteria, such as meningococcus and Salmonella. However, SBA often require an exogenous source of complement and the presence of pre-existing naturally acquired antibodies limits the use of human complement for this purpose. To remove pre-existing Salmonella-specific antibodies, in the context of SBA for Salmonella vaccine research, we incubated human sera with preparations of Salmonella. By incubating at 4 °C, pre-existing antibodies were adsorbed onto the Salmonella bacteria with only minimal complement deposition. We assessed the effects of adsorption on specific antibody levels, complement activity and the bactericidal activity of sera using flow cytometry, SBA and haemolytic assays. Adsorption removed Salmonella-specific antibodies and bactericidal activity against Salmonella from whole serum but was not detrimental to serum complement activity, even after five adsorption cycles. Bactericidal activity could be reconstituted in the adsorbed serum by the addition of exogenous specific antibodies. Sera preadsorbed with Salmonella are suitable as a source of human complement to measure the bactericidal activity of Salmonella antibodies. The adsorption method can be used to deplete, simply and rapidly, specific antibodies from serum to prepare a source of human complement for use in SBA for vaccine research and assessment.
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Affiliation(s)
- Matthew K Siggins
- The Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, United Kingdom; National Heart and Lung Institute, St Mary's Hospital, Faculty of Medicine, Imperial College London, W2 1PG, United Kingdom.
| | - Calman A MacLennan
- The Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT, United Kingdom; The Jenner Institute, Nuffield Department of Medicine, University of Oxford, OX3 7DQ, United Kingdom; Bill & Melinda Gates Foundation, 62 Buckingham Gate, London SW1E 6AJ, United Kingdom.
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Brown EW, Bell R, Zhang G, Timme R, Zheng J, Hammack TS, Allard MW. Salmonella Genomics in Public Health and Food Safety. EcoSal Plus 2021; 9:eESP00082020. [PMID: 34125583 PMCID: PMC11163839 DOI: 10.1128/ecosalplus.esp-0008-2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/16/2021] [Indexed: 12/26/2022]
Abstract
The species Salmonella enterica comprises over 2,600 serovars, many of which are known to be intracellular pathogens of mammals, birds, and reptiles. It is now apparent that Salmonella is a highly adapted environmental microbe and can readily persist in a number of environmental niches, including water, soil, and various plant (including produce) species. Much of what is known about the evolution and diversity of nontyphoidal Salmonella serovars (NTS) in the environment is the result of the rise of the genomics era in enteric microbiology. There are over 340,000 Salmonella genomes available in public databases. This extraordinary breadth of genomic diversity now available for the species, coupled with widespread availability and affordability of whole-genome sequencing (WGS) instrumentation, has transformed the way in which we detect, differentiate, and characterize Salmonella enterica strains in a timely way. Not only have WGS data afforded a detailed and global examination of the molecular epidemiological movement of Salmonella from diverse environmental reservoirs into human and animal hosts, but they have also allowed considerable consolidation of the diagnostic effort required to test for various phenotypes important to the characterization of Salmonella. For example, drug resistance, serovar, virulence determinants, and other genome-based attributes can all be discerned using a genome sequence. Finally, genomic analysis, in conjunction with functional and phenotypic approaches, is beginning to provide new insights into the precise adaptive changes that permit persistence of NTS in so many diverse and challenging environmental niches.
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Affiliation(s)
- Eric W. Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Rebecca Bell
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Guodong Zhang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Ruth Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Thomas S. Hammack
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
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Phylogeographic Clustering Suggests that Distinct Clades of Salmonella enterica Serovar Mississippi Are Endemic in Australia, the United Kingdom, and the United States. mSphere 2021; 6:e0048521. [PMID: 34550008 PMCID: PMC8550085 DOI: 10.1128/msphere.00485-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Salmonella enterica serovar Mississippi is the 2nd and 14th leading cause of human clinical salmonellosis in the Australian island state of Tasmania and the United States, respectively. Despite its public health relevance, relatively little is known about this serovar. Comparison of whole-genome sequence (WGS) data of S. Mississippi isolates with WGS data for 317 additional S. enterica serovars placed one clade of S. Mississippi within S. enterica clade B (“clade B Mississippi”) and the other within section Typhi in S. enterica clade A (“clade A Mississippi”), suggesting that these clades evolved from different ancestors. Phylogenetic analysis of 364 S. Mississippi isolates from Australia, the United Kingdom, and the United States suggested that the isolates cluster geographically, with U.S. and Australian isolates representing different subclades (Ai and Aii, respectively) within clade A Mississippi and clade B isolates representing the predominant S. Mississippi isolates in the United Kingdom. Intraclade comparisons suggested that different mobile elements, some of which encode virulence factors, are responsible for the observed differences in gene content among isolates within these clades. Specifically, genetic differences among clade A isolates reflect differences in prophage contents, while differences among clade B isolates are due to the acquisition of a 47.1-kb integrative conjugative element (ICE). Phylogenies inferred from antigenic components (fliC, fljB, and O-antigen-processing genes) support that clade A and B Mississippi isolates acquired these loci from different ancestral serovars. Overall, these data support that different S. Mississippi phylogenetic clades are endemic in Australia, the United Kingdom, and the United States. IMPORTANCE The number of known so-called “polyphyletic” serovars (i.e., phylogenetically distinct clades with the same O and H antigenic formulas) continues to increase as additional Salmonella isolates are sequenced. While serotyping remains a valuable tool for reporting and monitoring Salmonella, more discriminatory analyses for classifying polyphyletic serovars may improve surveillance efforts for these serovars, as we found that for S. Mississippi, distinct genotypes predominate at different geographic locations. Our results suggest that the acquisition of genes encoding O and H antigens from different ancestors led to the emergence of two Mississippi clades. Furthermore, our results suggest that different mobile elements contribute to the microevolution and diversification of isolates within these two clades, which has implications for the acquisition of novel adaptations, such as virulence factors.
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Huang Z, Jin S, Lv Z. Dietary genistein supplementation alters mRNA expression profile and alternative splicing signature in the thymus of chicks with lipopolysaccharide challenge. Poult Sci 2021; 101:101561. [PMID: 34896964 PMCID: PMC8666715 DOI: 10.1016/j.psj.2021.101561] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 12/25/2022] Open
Abstract
Genistein is abundant in the soybean products, which exerts prominent effects on immune function. Little information is available about the effect of dietary genistein on thymic transcriptome, especially when suffering from lipopolysaccharide challenge. In this study, 180 one-day-old male broilers were randomly allocated to 3 groups: nonchallenged chicks given a basal diet (CON), and lipopolysaccharide-challenged chicks fed a basal diet (LPS), or lipopolysaccharide-challenged chicks fed a basal diet supplemented with 40 mg/kg genistein (GEN). Lipopolysaccharide injection induced thymocyte apoptosis and inflammatory reactions in the chicks. The results showed dietary genistein significantly reduced the percentage of CD3+ T lymphocytes by 10.04% and CD4+/CD8+ T lymphocyte ratio by 21.88% in the peripheral blood induced by lipopolysaccharide injection (P < 0.05). In addition, genistein significantly reduced the thymus index by 50% and apoptotic index by 12.34% induced by LPS challenge (P < 0.05). Transcriptomic analysis identified 1,926 DEGs (1,014 upregulated and 912 downregulated, P < 0.05) between GEN and LPS groups, which altered the mRNA expression profile and signaling pathways (Toll-like receptor, and NOD-like receptor signaling pathway) in the thymus. Furthermore, 5 splicing (AS) isoforms of the Drosophila Disabled-2 (DAB2) gene were detected, which were significantly upregulated in the GEN group compared with that in the LPS group. In summary, dietary genistein supplementation altered the RNA expression profile and AS signatures in the thymus, and alleviated immune response against lipopolysaccharide challenge.
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Affiliation(s)
- Zhenwu Huang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Song Jin
- Animal Disease Control Center of Changzhou, Jiangsu 213003, China
| | - Zengpeng Lv
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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