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Kröger C, Lerminiaux NA, Ershova AS, MacKenzie KD, Kirzinger MW, Märtlbauer E, Perry BJ, Cameron ADS, Schauer K. Plasmid-encoded lactose metabolism and mobilized colistin resistance ( mcr-9) genes in Salmonella enterica serovars isolated from dairy facilities in the 1980s. Microb Genom 2023; 9. [PMID: 38031909 DOI: 10.1099/mgen.0.001149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Horizontal gene transfer by plasmids can confer metabolic capabilities that expand a host cell's niche. Yet, it is less understood whether the coalescence of specialized catabolic functions, antibiotic resistances and metal resistances on plasmids provides synergistic benefits. In this study, we report whole-genome assembly and phenotypic analysis of five Salmonella enterica strains isolated in the 1980s from milk powder in Munich, Germany. All strains exhibited the unusual phenotype of lactose-fermentation and encoded either of two variants of the lac operon. Surprisingly, all strains encoded the mobilized colistin resistance gene 9 (mcr-9), long before the first report of this gene in the literature. In two cases, the mcr-9 gene and the lac locus were linked within a large gene island that formed an IncHI2A-type plasmid in one strain but was chromosomally integrated in the other strain. In two other strains, the mcr-9 gene was found on a large IncHI1B/IncP-type plasmid, whereas the lac locus was encoded on a separate chromosomally integrated plasmidic island. The mcr-9 sequences were identical and genomic contexts could not explain the wide range of colistin resistances exhibited by the Salmonella strains. Nucleotide variants did explain phenotypic differences in motility and exopolysaccharide production. The observed linkage of mcr-9 to lactose metabolism, an array of heavy-metal detoxification systems, and other antibiotic resistance genes may reflect a coalescence of specialized phenotypes that improve the spread of colistin resistance in dairy facilities, much earlier than previously suspected.
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Affiliation(s)
- Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Nicole A Lerminiaux
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
| | - Anna S Ershova
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Keith D MacKenzie
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
| | - Morgan W Kirzinger
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Present address: National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, 85764, Germany
| | - Benjamin J Perry
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Present address: AgResearch, 176 Puddle Alley, Mosgiel 9092, New Zealand
| | - Andrew D S Cameron
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
| | - Kristina Schauer
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, 85764, Germany
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Mattiello SP, Barth VC, Scaria J, Ferreira CAS, Oliveira SD. Fluoroquinolone and beta-lactam antimicrobials induce different transcriptome profiles in Salmonella enterica persister cells. Sci Rep 2023; 13:18696. [PMID: 37907566 PMCID: PMC10618250 DOI: 10.1038/s41598-023-46142-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023] Open
Abstract
Here, we investigate the transcriptome profiles of two S. Enteritidis and one S. Schwarzengrund isolates that present different persister levels when exposed to ciprofloxacin or ceftazidime. It was possible to note a distinct transcript profile among isolates, time of exposure, and treatment. We could not find a commonly expressed transcript profile that plays a role in persister formation after S. enterica exposure to beta-lactam or fluoroquinolone, as only three DEGs presented the same behavior under the conditions and isolates tested. It appears that the formation of persisters in S. enterica after exposure to ciprofloxacin is linked to the overexpression of genes involved in the SOS response (recA), cell division inhibitor (sulA), iron-sulfur metabolism (hscA and iscS), and type I TA system (tisB). On the other hand, most genes differentially expressed in S. enterica after exposure to ceftazidime appeared to be downregulated and were part of the flagellar assembly apparatus, citrate cycle (TCA cycle), glycolysis/gluconeogenesis, carbon metabolism, bacterial secretion system, quorum sensing, pyruvate metabolism pathway, and biosynthesis of secondary metabolites. The different transcriptome profiles found in S. enterica persisters induced by ciprofloxacin and ceftazidime suggest that these cells modulate their response differently according to each stress.
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Affiliation(s)
- S P Mattiello
- Laboratório de Imunologia e Microbiologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga, 6681, Porto Alegre, 90619-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
- College of Mathematics and Science, The University of Tennessee Southern, UTS, Pulaski, TN, USA
- Department of Veterinary and Biomedical Sciences, South Dakota State University, SDSU, Brookings, SD, USA
| | - V C Barth
- Laboratório de Imunoterapia, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - J Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, SDSU, Brookings, SD, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, USA
| | - C A S Ferreira
- Laboratório de Imunologia e Microbiologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga, 6681, Porto Alegre, 90619-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - S D Oliveira
- Laboratório de Imunologia e Microbiologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga, 6681, Porto Alegre, 90619-900, Brazil.
- Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.
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Luo Q, Wu Y, Bao D, Xu L, Chen H, Yue M, Draz MS, Kong Y, Ruan Z. Genomic epidemiology of mcr carrying multidrug-resistant ST34 Salmonella enterica serovar Typhimurium in a one health context: The evolution of a global menace. Sci Total Environ 2023; 896:165203. [PMID: 37406695 DOI: 10.1016/j.scitotenv.2023.165203] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
The rapid global dissemination of Salmonella enterica sequence type 34 (ST34) has sparked significant concern due to its resistance to critical antimicrobials and its ability to spread across various sectors. In order to investigate the evolution and transmission dynamics of this epidemic clonal lineage, as well as the horizontal transfer of mcr-carrying plasmids within the One Health framework, we conducted a comprehensive genomic epidemiological study. This study focused on the 11 mcr-carrying S. enterica isolates obtained from clinical settings in China, while also considering 2337 publicly available genomes of mcr-carrying S. enterica collected from 20 countries and diverse sources spanning over a 22-year period. Among the mcr-positive Salmonella isolates, ST34 was found to be the predominant lineage, comprising 30.12 % (704/2337) of the total collection. These isolates were identified as either serovar Typhimurium or its monophasic variant, which were obtained from both clinical and non-clinical sources. Phylogeographic analyses traced the global spread of the mcr-carrying ST34 lineage, which was divided into three distinct clusters, with 83.10 % of them carrying mcr-1 or/and mcr-9 genes. Notably, the mcr-1 positive ST34 isolates were primarily found in China (190/298, 63.76 %), with only four from the United States. Conversely, mcr-9 positive ST34 isolates were predominantly identified in the United States (261/293, 89.08 %), while none were observed in China. The mcr-1 positive ST34 isolates was predicted to have originated from clinical sources in United Kingdom, whereas mcr-9 positive ST34 isolates was likely derived from environmental sources in Germany. The most recent common ancestor for mcr-1 and mcr-9 carrying ST34 S. enterica was estimated to have emerged around 1983 and 1951. These findings provided thorough and intuitive insights into the intercontinental spread of mcr-carrying S. enterica ST34 lineage in a One Health context. Ongoing surveillance is crucial for effectively monitoring the worldwide dissemination of this multidrug-resistant high-risk clone.
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Affiliation(s)
- Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Danni Bao
- Department of Clinical Laboratory, Sanmen People's Hospital, Taizhou, China
| | - Linna Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; School of Laboratory Medicine and Biotechnology, Hangzhou Medical College, Hangzhou, China
| | - Hangfei Chen
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Meina Yue
- Department of Clinical Laboratory, Hangzhou Children's Hospital, Hangzhou, China
| | - Mohamed S Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH, USA
| | - Yingying Kong
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China.
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Chung The H, Pham P, Ha Thanh T, Phuong LVK, Yen NP, Le SNH, Vu Thuy D, Chau TTH, Le Phuc H, Ngoc NM, Vi LL, Mather AE, Thwaites GE, Thomson NR, Baker S, Pham DT. Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 1,4,[5],12:i:- ST34 in Southeast Asia. Commun Biol 2023; 6:1007. [PMID: 37789208 PMCID: PMC10547704 DOI: 10.1038/s42003-023-05365-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
Salmonella enterica serotype 1,4,[5],12:i:- (Typhimurium monophasic variant) of sequence type (ST) 34 has emerged as the predominant pandemic genotype in recent decades. Despite increasing reports of resistance to antimicrobials in Southeast Asia, Salmonella ST34 population structure and evolution remained understudied in the region. Here we performed detailed genomic investigations on 454 ST34 genomes collected from Vietnam and diverse geographical sources to elucidate the pathogen's epidemiology, evolution and antimicrobial resistance. We showed that ST34 has been introduced into Vietnam in at least nine occasions since 2000, forming five co-circulating major clones responsible for paediatric diarrhoea and bloodstream infection. Most expansion events were associated with acquisitions of large multidrug resistance plasmids of IncHI2 or IncA/C2. Particularly, the self-conjugative IncA/C2 pST34VN2 (co-transferring blaCTX-M-55, mcr-3.1, and qnrS1) underlies local expansion and intercontinental spread in two separate ST34 clones. At the global scale, Southeast Asia was identified as a potential hub for the emergence and dissemination of multidrug resistant Salmonella ST34, and mutation analysis suggests of selection in antimicrobial responses and key virulence factors.
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Affiliation(s)
- Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
| | - Phuong Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Son-Nam H Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Duong Vu Thuy
- Children's Hospital No. 1, Ho Chi Minh City, Vietnam
| | | | - Hoang Le Phuc
- Children's Hospital No. 1, Ho Chi Minh City, Vietnam
| | | | - Lu Lan Vi
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen Baker
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases (CITIID), University of Cambridge, Cambridge, UK
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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55
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Liu S, Xue R, Qin W, Yang X, Ye Q, Wu Q. Performance and transcriptome analysis of Salmonella enterica serovar Enteritidis PT 30 under persistent desiccation stress: Cultured by lawn and broth methods. Food Microbiol 2023; 115:104323. [PMID: 37567618 DOI: 10.1016/j.fm.2023.104323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/04/2023] [Accepted: 06/13/2023] [Indexed: 08/13/2023]
Abstract
Lawn-harvest method uses a solid medium (e.g., tryptic soy agar, TSA) to produce bacterial lawns and is widely accepted for the culture of microorganisms in microbial studies of low-moisture foods (LMFs, foods with water activity less than 0.85). It produces desiccation-tolerant cells with higher D-values in LMFs; however, little is known about the molecular mechanisms underlying bacterial resistance. Salmonella enterica Enteritidis PT 30 (S. Enteritidis), the most pertinent pathogen in LMFs, was cultured in TSA and tryptic soy broth (TSB). Cells were harvested and inoculated on filter papers to assess their performance under a relative humidity of 32 ± 2%. Transcriptome analysis of cultured cells during long-term desiccation (24, 72, and 168 h) was conducted in TruSeq PE Cluster Kit (Illumina) by paired-end methods. Lawn-cultured S. Enteritidis cells have stronger survivability (only decreased by 0.78 ± 0.12 log after 130 d of storage) and heat tolerance (higher D/β value) than those from the broth method. More desiccation genes of lawn-cultured cells were significantly upregulated from growth to long-term desiccation. Differentially expressed genes were the most enriched in the ribosome and sulfur metabolism pathways in the lawn- and broth-cultured groups. This study tracked the transcriptomic differences between two cultured groups in response to long-term desiccation stress and revealed some molecular mechanisms underlying their different suitability in microbial studies of LMFs.
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Affiliation(s)
- Shuxiang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, 625014, China; Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Ruimin Xue
- College of Food Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Wen Qin
- College of Food Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xiaojuan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
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Rodríguez EC, Saavedra SY, Montaño LA, Sossa DP, Correa FP, Vaca JA, Duarte C. Characterization of extended spectrum β-lactamases in Colombian clinical isolates of non-typhoidal Salmonella enterica between 1997 and 2022. Biomedica 2023; 43:374-384. [PMID: 37871566 PMCID: PMC10637434 DOI: 10.7705/biomedica.6891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/11/2023] [Indexed: 10/25/2023]
Abstract
Introduction. Salmonella spp. is a zoonotic pathogen transmitted to humans through contaminated water or food. The presence of extended-spectrum β-lactamases is a growing public health problem because these enzymes are resistant to third and fourth generation cephalosporins. Objective. To characterize extended-spectrum β-lactamases in Salmonella spp. isolates received by the acute diarrheal disease/foodborne disease surveillance program of the Grupo de Microbiología of the Instituto Nacional de Salud. Materials and methods. A total of 444 Salmonella spp. isolates, resistant to at least one of the cephalosporins, were obtained between January 1997 and June 2022. The extendedspectrum β-lactamases phenotype was identified by the double disk test. DNA extraction was carried out by the boiling method, and the blaCTX-M, blaSHV, and blaTEM genes were amplified by PCR. Results. All the isolates were positive for the extended-spectrum β-lactamases test. The genes identified were: blaCTX-M + blaTEM (n=200), blaCTX-M (n=177), blaSHV (n=16), blaSHV + blaCTX-M (n=6), blaTEM (n=13) and blaSHV + blaCTX-M + blaTEM (n=3). Twenty-six isolates were negative for the evaluated genes. Positive extended-spectrum β-lactamases isolates were identified in Bogotá and 21 departments: Chocó, Magdalena, Meta, Bolívar, Casanare, Cesar, Córdoba, Quindío, Atlántico, Tolima, Cauca, Cundinamarca, Huila, Boyacá, Caldas, Norte de Santander, Risaralda, Antioquia, Nariño, Santander y Valle del Cauca. Conclusion. Resistance to third generation cephalosporins in Salmonella spp. isolates was mainly caused by blaCTX-M. Isolates were resistant to ampicillin, tetracycline, chloramphenicol, and trimethoprim-sulfamethoxazole (44 %; 197/444). The most frequent extended-spectrum β-lactamases-expressing serotypes were Salmonella Typhimurium and Salmonella Infantis.
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Affiliation(s)
| | | | | | | | | | | | - Carolina Duarte
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, D.C., Colombia.
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Abukhattab S, Hosch S, Abu-Rmeileh NME, Hasan S, Vonaesch P, Crump L, Hattendorf J, Daubenberger C, Zinsstag J, Schindler T. Whole-genome sequencing for One Health surveillance of antimicrobial resistance in conflict zones: a case study of Salmonella spp. and Campylobacter spp. in the West Bank, Palestine. Appl Environ Microbiol 2023; 89:e0065823. [PMID: 37655921 PMCID: PMC10540982 DOI: 10.1128/aem.00658-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/13/2023] [Indexed: 09/02/2023] Open
Abstract
Antimicrobial resistance (AMR) is a critical global concern driven by the overuse, misuse, and/or usage of inadequate antibiotics on humans, animals' agriculture, and as a result of contaminated environments. This study is the first One Health survey in the Middle East that incorporated whole-genome sequencing (WGS) to examine the spread of AMR in Campylobacter spp. and Salmonella spp. This cross-sectional study was conducted to examine the role of AMR at the human-animal-environmental interface and was performed in Ramallah/Al-Bireh and Jerusalem governorates of the central West Bank, Palestine. In 2021 and 2022, a total of 592 samples were collected and analyzed. From a total of 65 Campylobacter jejuni and 19 Salmonella spp. isolates, DNA was extracted for WGS using Oxford Nanopore Technologies MinION platform. We found that the dominant serotypes of C. jejuni and Salmonella enterica were present in chicken manure, chicken meat sold in markets, and feces of asymptomatic farm workers, with high genetic similarities between the isolates regardless of origin. Additionally, our results showed rapid strain turnover in C. jejuni from the same sites between 2021 and 2022. Most of the positive Salmonella spp. samples were multidrug-resistant (MDR) S. enterica serovar Muenchen carrying the plasmid of emerging S. infantis (pESI) megaplasmid, conferring resistance to multiple antibiotics. Our findings highlight the spread of MDR foodborne pathogens from animals to humans through the food chain, emphasizing the importance of a One Health approach that considers the interconnections between human, animal, and environmental health. IMPORTANCE Prior to this study, there existed hardly an integrated human-animal-environmental study of Salmonellosis and Campylobacteriosis and related AMR in Middle Eastern countries. The few existing studies lack robust epidemiological study designs, adequate for a One Health approach, and did not use WGS to determine the circulating serotypes and their AMR profiles. Civil unrest and war in Middle Eastern countries drive AMR because of the breakdown of public health and food security services. This study samples simultaneously humans, animals, and the environment to comprehensively investigate foodborne pathogens in the broiler chicken production chain in Palestine using WGS. We show that identical serotypes of C. jejuni and S. enterica can be found in samples from chicken farms, chicken meat sold in markets, and asymptomatic broiler chicken production workers. The most striking feature is the rapid dynamic of change in the genetic profile of the detected species in the same sampling locations. The majority of positive Salmonella spp. samples are MDR S. enterica serovar Muenchen isolates carrying the pESI megaplasmid. The results demonstrate a close relationship between the S. enterica serovar Muenchen isolates found in our sample collection and those responsible for 40% of all clinical Salmonella spp. isolates in Israel as previously reported, with a sequence identity of over 99.9%. These findings suggest the transboundary spread of MDR S. enterica serovar Muenchen strains from animals to humans through the food chain. The study underscores the importance of combining integrated One Health studies with WGS for detecting environmental-animal-human transmission of foodborne pathogens that could not be detected otherwise. This study showcases the benefits of integrated environmental-animal-human sampling and WGS for monitoring AMR. Environmental samples, which may be more accessible in conflict-torn places where monitoring systems are limited and regulations are weak, can provide an effective AMR surveillance solution. WGS of bacterial isolates provides causal inference of the distribution and spread of bacterial serotypes and AMR in complex social-ecological systems. Consequently, our results point toward the expected benefits of operationalizing a One Health approach through closer cooperation of public and animal health and food safety authorities.
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Affiliation(s)
- Said Abukhattab
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Salome Hosch
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Shadi Hasan
- Master program in Clinical Laboratory Sciences, Birzeit University, Birzeit, Palestine
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Lisa Crump
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Jan Hattendorf
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Claudia Daubenberger
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
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Konyali D, Guzel M, Soyer Y. Genomic Characterization of Salmonella enterica Resistant to Cephalosporin, Quinolones, And Macrolides. Curr Microbiol 2023; 80:344. [PMID: 37725171 DOI: 10.1007/s00284-023-03458-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 08/26/2023] [Indexed: 09/21/2023]
Abstract
Salmonella enterica subsp. enterica (Salmonella), one of the most common causes of bacterial foodborne infections, causes salmonellosis, which is usually self-limiting. However, immunocompromised individuals and children often require antimicrobial therapy. The first line of treatment includes fluoroquinolones, to which Salmonella has emerging resistance worldwide. In fact, the WHO classified fluoroquinolone-resistant Salmonella as a high-priority pathogen. Salmonella carrying genes such as blaCTX and blaCMY can show resistance to cephalosporins which are also regularly used for treatment. This study focused on determining the antimicrobial resistance of 373 Salmonella isolates, collected from various foods, humans, and animals, as well as the environmental sludge between 2005 and 2020 in Türkiye. Phenotypic analysis of the resistance was determined by disk diffusion method. Isolates resistant to any of the following: ciprofloxacin, pefloxacin, azithromycin, and ceftriaxone were tested for the presence of quinolone, beta-lactamase, and/or macrolide resistance genes by PCR and gel electrophoresis. Five multi-drug-resistant isolates were then further whole genome sequenced and analyzed. More than 32% (n = 120) of the isolates showed resistance to fluoroquinolones by disc diffusion. A significant number of quinolone-resistant isolates are presented with mutated parC and gyrA. Furthermore, 42% (n = 106) of the isolates were resistant to azithromycin and 10% of them harbored mphA gene. On the bright side, only eight isolates showed resistance to ceftriaxone. Overall, we observed an increase in the number of isolates showing resistance to fluoroquinolones and azithromycin over the years and low resistance to ceftriaxone.
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Affiliation(s)
- Diala Konyali
- Department of Biotechnology, Middle East Technical University, Ankara, Türkiye
| | - Mustafa Guzel
- Department of Biotechnology, Middle East Technical University, Ankara, Türkiye
- Department of Food Engineering, Hitit University, Corum, Türkiye
| | - Yeşim Soyer
- Department of Biotechnology, Middle East Technical University, Ankara, Türkiye.
- Faculty of Engineering, Department of Food Engineering, Middle East Technical University, Ankara, Türkiye.
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Moyne AL, Lawal OU, Gauthier J, Kukavica-Ibrulj I, Potvin M, Goodridge L, Levesque RC, Harris LJ. Genetic diversity of Salmonella enterica isolated over 13 years from raw California almonds and from an almond orchard. PLoS One 2023; 18:e0291109. [PMID: 37676871 PMCID: PMC10484465 DOI: 10.1371/journal.pone.0291109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023] Open
Abstract
A comparative genomic analysis was conducted for 171 Salmonella isolates recovered from raw inshell almonds and raw almond kernels between 2001 and 2013 and for 30 Salmonella Enteritidis phage type (PT) 30 isolates recovered between 2001 and 2006 from a 2001 salmonellosis outbreak-associated almond orchard. Whole genome sequencing was used to measure the genetic distance among isolates by single nucleotide polymorphism (SNP) analyses and to predict the presence of plasmid DNA and of antimicrobial resistance (AMR) and virulence genes. Isolates were classified by serovars with Parsnp, a fast core-genome multi aligner, before being analyzed with the CFSAN SNP Pipeline (U.S. Food and Drug Administration Center for Food Safety and Applied Nutrition). Genetically similar (≤18 SNPs) Salmonella isolates were identified among several serovars isolated years apart. Almond isolates of Salmonella Montevideo (2001 to 2013) and Salmonella Newport (2003 to 2010) differed by ≤9 SNPs. Salmonella Enteritidis PT 30 isolated between 2001 and 2013 from survey, orchard, outbreak, and clinical samples differed by ≤18 SNPs. One to seven plasmids were found in 106 (62%) of the Salmonella isolates. Of the 27 plasmid families that were identified, IncFII and IncFIB plasmids were the most predominant. AMR genes were identified in 16 (9%) of the survey isolates and were plasmid encoded in 11 of 16 cases; 12 isolates (7%) had putative resistance to at least one antibiotic in three or more drug classes. A total of 303 virulence genes were detected among the assembled genomes; a plasmid that harbored a combination of pef, rck, and spv virulence genes was identified in 23% of the isolates. These data provide evidence of long-term survival (years) of Salmonella in agricultural environments.
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Affiliation(s)
- Anne-laure Moyne
- Department of Food Science and Technology, University of California, Davis, California, United States of America
- Western Center for Food Safety, University of California, Davis, California, United States of America
| | - Opeyemi U. Lawal
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Jeff Gauthier
- Institut de biologie intégrative et des systèmes (IBIS), Faculté de médecine, Université Laval, Québec, Québec, Canada
| | - Irena Kukavica-Ibrulj
- Institut de biologie intégrative et des systèmes (IBIS), Faculté de médecine, Université Laval, Québec, Québec, Canada
| | - Marianne Potvin
- Institut de biologie intégrative et des systèmes (IBIS), Faculté de médecine, Université Laval, Québec, Québec, Canada
| | - Lawrence Goodridge
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Sainte Anne de Bellevue, Quebec, Canada
| | - Roger C. Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Faculté de médecine, Université Laval, Québec, Québec, Canada
| | - Linda J. Harris
- Department of Food Science and Technology, University of California, Davis, California, United States of America
- Western Center for Food Safety, University of California, Davis, California, United States of America
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Vitt JD, Hansen EG, Garg R, Bowden SD. Bacteria intrinsic to Medicago sativa (alfalfa) reduce Salmonella enterica growth in planta. J Appl Microbiol 2023; 134:lxad204. [PMID: 37669894 DOI: 10.1093/jambio/lxad204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/03/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023]
Abstract
AIMS The purpose of this study was to determine whether plant-associated bacteria (PAB) can reduce Salmonella enterica colonization and infection of alfalfa sprouts to reduce the risk of foodborne illness. METHODS We isolated PAB from alfalfa seeds and sprouts. Monoclonal isolates of the bacteria were obtained and tested for their ability to inhibit Salmonella Typhimurium growth in alfalfa sprouts over 6 days. Genome sequencing and annotation were used to construct draft genomes of the bacteria isolated in this study using Illumina sequencing platform. RESULTS We observed that a cocktail of five PAB could reduce Salmonella growth in alfalfa sprouts from ∼108 to ∼105 CFU g-1, demonstrating a protective role. Genome sequencing revealed that these bacteria were members of the Pseudomonas, Pantoea, and Priestia genus, and did not possess genes that were pathogenic to plants or animals. CONCLUSIONS This work demonstrates that PAB can be utilized to reduce pathogen levels in fresh produce, which may be synergistic with other technologies to improve the safety of sprouts and other fresh produce.
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Affiliation(s)
- Jacob D Vitt
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN 55108, United States
| | - Eleanore G Hansen
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN 55108, United States
| | - Raghav Garg
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN 55108, United States
| | - Steven D Bowden
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN 55108, United States
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Merkushova AV, Shikov AE, Nizhnikov AA, Antonets KS. For Someone, You Are the Whole World: Host-Specificity of Salmonella enterica. Int J Mol Sci 2023; 24:13670. [PMID: 37761974 PMCID: PMC10530738 DOI: 10.3390/ijms241813670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/27/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Salmonella enterica is a bacterial pathogen known to cause gastrointestinal infections in diverse hosts, including humans and animals. Despite extensive knowledge of virulence mechanisms, understanding the factors driving host specificity remains limited. In this study, we performed a comprehensive pangenome-wide analysis of S. enterica to identify potential loci determining preference towards certain hosts. We used a dataset of high-quality genome assemblies grouped into 300 reference clusters with a special focus on four host groups: humans, pigs, cattle, and birds. The reconstructed pangenome was shown to be open and enriched with the accessory component implying high genetic diversity. Notably, phylogenetic inferences did not correspond to the distribution of affected hosts, as large compact phylogenetic groups were absent. By performing a pangenome-wide association study, we identified potential host specificity determinants. These included multiple genes encoding proteins involved in distinct infection stages, e.g., secretion systems, surface structures, transporters, transcription regulators, etc. We also identified antibiotic resistance loci in host-adapted strains. Functional annotation corroborated the results obtained with significant enrichments related to stress response, antibiotic resistance, ion transport, and surface or extracellular localization. We suggested categorizing the revealed specificity factors into three main groups: pathogenesis, resistance to antibiotics, and propagation of mobile genetic elements (MGEs).
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Affiliation(s)
- Anastasiya V. Merkushova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.V.M.); (A.E.S.); (A.A.N.)
| | - Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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62
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Leekitcharoenphon P, Vigre H, Kaas RS, Aarestrup FM. Trends in Salmonella Dublin over time in Denmark from food and animal related isolates. Infect Genet Evol 2023; 113:105475. [PMID: 37394050 DOI: 10.1016/j.meegid.2023.105475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023]
Abstract
Salmonella enterica serovar Dublin is highly adapted to cattle and a relatively rare cause of human infections. In Denmark S. Dublin has been endemic in the cattle population for many years. A national surveillance program in the cattle population was established at herd-level to reduce the occurrence of S. Dublin. In this study, we analyzed 421 S. Dublin genomes from cattle and food in order to determine the trend of S. Dublin's population size over time in Denmark and the impact of intervention in the cattle industry on the bacterial population size. A phylogenetic tree based on SNPs exhibited two major clades and one small cluster. All isolates were ST10. The temporal phylogenetic tree for the S. Dublin isolates showed that the most recent common ancestor was estimated to be in ∼1980 for the two major clades. An effective population size over time based on a Bayesian skyline plot showed that the population size of S. Dublin decreased significantly between 2014 and 2019 in both major clades. This result was concordant with the decrease of infected human cases by S. Dublin in Denmark. The strengthening of a surveillance program in Denmark could be the cause for the reduction of S. Dublin's effective population size. This study showed that whole genome sequencing combined with computer intensive phylogenetic analysis estimating the effective size of the S. Dublin's population over time is a strongly relevant measure with respect to assessing the impact of control measures aiming to reduce the bacterial population in the reservoir and the risk for human infection.
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Affiliation(s)
- Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - Håkan Vigre
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Rolf Sommer Kaas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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63
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Richards AK, Kue S, Norris CG, Shariat NW. Genomic and phenotypic characterization of Salmonella enterica serovar Kentucky. Microb Genom 2023; 9:001089. [PMID: 37750759 PMCID: PMC10569734 DOI: 10.1099/mgen.0.001089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/27/2023] [Indexed: 09/27/2023] Open
Abstract
Non-typhoidal Salmonella are extremely diverse and different serovars can exhibit varied phenotypes, including host adaptation and the ability to cause clinical illness in animals and humans. In the USA, Salmonella enterica serovar Kentucky is infrequently found to cause human illness, despite being the top serovar isolated from broiler chickens. Conversely, in Europe, this serovar falls in the top 10 serovars linked to human salmonellosis. Serovar Kentucky is polyphyletic and has two lineages, Kentucky-I and Kentucky-II; isolates belonging to Kentucky-I are frequently isolated from poultry in the USA, while Kentucky-II isolates tend to be associated with human illness. In this study, we analysed whole-genome sequences and associated metadata deposited in public databases between 2017 and 2021 by federal agencies to determine serovar Kentucky incidence across different animal and human sources. Of 5151 genomes, 90.3 % were from isolates that came from broilers, while 5.9 % were from humans and 3.0 % were from cattle. Kentucky-I isolates were associated with broilers, while isolates belonging to Kentucky-II and a new lineage, Kentucky-III, were more commonly associated with cattle and humans. Very few serovar Kentucky isolates were associated with turkey and swine sources. Phylogenetic analyses showed that Kentucky-III genomes were more closely related to Kentucky-I, and this was confirmed by CRISPR-typing and multilocus sequence typing (MLST). In a macrophage assay, serovar Kentucky-II isolates were able to replicate over eight times better than Kentucky-I isolates. Analysis of virulence factors showed unique patterns across these three groups, and these differences may be linked to their association with different hosts.
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Affiliation(s)
- Amber K. Richards
- Department of Population Health, University of Georgia, Athens, GA, USA
| | - Song Kue
- Department of Population Health, University of Georgia, Athens, GA, USA
| | - Connor G. Norris
- Department of Population Health, University of Georgia, Athens, GA, USA
| | - Nikki W. Shariat
- Department of Population Health, University of Georgia, Athens, GA, USA
- Center for Food Safety, University of Georgia, Griffin, GA, USA
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64
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Lin Y, Liu Y, Zhang Y, Yuan W, Wang D, Zhu W. Biological and genomic characterization of a polyvalent bacteriophage (S19cd) strongly inhibiting Salmonella enterica serovar Choleraesuis. Vet Microbiol 2023; 284:109822. [PMID: 37437367 DOI: 10.1016/j.vetmic.2023.109822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/14/2023]
Abstract
Bacteriophages are a promising alternative for the control of pathogenic bacteria. In this study, we isolated a virulent bacteriophage, S19cd, from pig gut that could infect both a non-pathogenic bacteria Escherichia coli 44 (EC44) and two pathogenic bacterial strains (ATCC 13312 (SC13312) and CICC 21493 (SC21493)) of Salmonella enterica serovar Choleraesuis (SC). S19cd exhibited strong lytic ability in both SC13312 and SC21493 with an optimal multiplicity of infection (MOI) of 10-6 and 10-5, respectively, and inhibited their growth at an MOI of 10-7 within 24 h. Mice pre-treated with S19cd exhibited protection against the SC13312 challenge. Moreover, S19cd has good heat resistance (80 ℃) and pH tolerance (pH 3-12). Genome analysis revealed that S19cd belongs to the Felixounavirus genus and does not contain any virulence or drug-resistance-related genes. Additionally, S19cd encodes an adenine-specific methyltransferase that has no similarity to methyltransferases from other Felixounavirus phages and shares limited similarity with other methyltransferases in the NCBI protein database. Metagenomic analysis of S19cd genomes from 500 pigs revealed that S19cd-like phages may be widespread in Chinese pig gut. In conclusion, S19cd can be a potential phage therapy targeting SC infections.
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Affiliation(s)
- Yan Lin
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yankun Liu
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuyu Zhang
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenyuan Yuan
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongyang Wang
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiyun Zhu
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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65
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Fei X, Schroll C, Huang K, Christensen JP, Christensen H, Lemire S, Kilstrup M, Thomsen LE, Jelsbak L, Olsen JE. The global transcriptomes of Salmonella enterica serovars Gallinarum, Dublin and Enteritidis in the avian host. Microb Pathog 2023; 182:106236. [PMID: 37419218 DOI: 10.1016/j.micpath.2023.106236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023]
Abstract
Salmonella enterica serovar Gallinarum causes Fowl Typhoid in poultry, and it is host specific to avian species. The reasons why S. Gallinarum is restricted to avians, and at the same time predominately cause systemic infections in these hosts, are unknown. In the current study, we developed a surgical approach to study gene expression inside the peritoneal cavity of hens to shed light on this. Strains of the host specific S. Gallinarum, the cattle-adapted S. Dublin and the broad host range serovar, S. Enteritidis, were enclosed in semi-permeable tubes and surgically placed for 4 h in the peritoneal cavity of hens and for control in a minimal medium at 41.2 °C. Global gene-expression under these conditions was compared between serovars using tiled-micro arrays with probes representing the genome of S. Typhimurium, S. Dublin and S. Gallinarum. Among other genes, genes of SPI-13, SPI-14 and the macrophage survival gene mig-14 were specifically up-regulated in the host specific serovar, S. Gallinarum, and further studies into the role of these genes in host specific infection are highly indicated. Analysis of pathways and GO-terms, which were enriched in the host specific S. Gallinarum without being enriched in the two other serovars indicated that host specificity was characterized by a metabolic fine-tuning as well as unique expression of virulence associated pathways. The cattle adapted serovar S. Dublin differed from the two other serovars by a lack of up-regulation of genes encoded in the virulence associated pathogenicity island 2, and this may explain the inability of this serovar to cause disease in poultry.
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Affiliation(s)
- Xiao Fei
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, China
| | - Casper Schroll
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Kaisong Huang
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark; Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Jens P Christensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Sebastien Lemire
- Department of Systems Biology, Technical University of Denmark, Denmark
| | - Mogens Kilstrup
- Department of Systems Biology, Technical University of Denmark, Denmark
| | - Line E Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lotte Jelsbak
- Department of Science and Environment, Roskilde University, Denmark
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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She Y, Jiang Y, Luo M, Duan X, Xie L, Yang C, Xu L, Fu Y, Lv Z, Cai R, Li Y, Qiu Y, Hu L, Shi X, Wang L, Wu S, Chen Q, Jiang M, Hu Q. Emergence of chromosomally located bla CTX-M-14b and qnrS1 in Salmonella enterica serotype Kentucky ST198 in China. Int J Antimicrob Agents 2023; 62:106896. [PMID: 37343807 DOI: 10.1016/j.ijantimicag.2023.106896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 06/23/2023]
Abstract
Highly fluoroquinolone-resistant Salmonella enterica serotype Kentucky has become widespread in recent years, largely associated with the spread of sequence type 198 (ST198), which often leads to multidrug resistance. Research on the genomic epidemiology of Salmonella Kentucky in China is currently uncommon. In this study, we analysed the genomic epidemiology and antimicrobial resistance characteristics of Salmonella Kentucky ST198 collected from foodborne disease surveillance in Shenzhen, China, during 2010-2021, using whole-genome sequencing and antibiotic susceptibility testing. In addition, 158 global Salmonella Kentucky ST198 genomes were included for comparison. Among 8559 Salmonella isolates, 43 Salmonella Kentucky ST198 isolates were detected during 2010-2021. The global Salmonella Kentucky ST198 evolutionary tree was divided into five clades, with Shenzhen isolates distributed in clades 198.1, 198.2-1 and 198.2-2, mainly clustered with Chinese strains. Strains in clade 198.2 dominated in Shenzhen and all of them showed multidrug resistance. Nine strains showed high resistance to ceftriaxone, which was associated with blaCTX-M-14b in clade 198.2-1, which was demonstrated to be located on the chromosome. Fifteen strains showed high resistance to ciprofloxacin, which was associated with carriage of qnrS1 in clade 198.2-2. qnrS1 was first located on an IncHI2 plasmid and then transferred into the chromosome. Here we report the genomic and antimicrobial resistance characterisation of Salmonella Kentucky ST198 in Shenzhen. Of particular concern, we identified for the first time a clade 198.2-1 isolate carrying blaCTX-M-14b as well as chromosomally located qnrS1 in clade 198.2-2 of Salmonella Kentucky ST198 in China, highlighting the necessity of surveillance of clade 198.2.
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Affiliation(s)
- Yiying She
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yixiang Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Miaomiao Luo
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Xiangke Duan
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Li Xie
- University of South China, Hengyang, China
| | - Chao Yang
- Institute Pasteur of Shanghai Chinese Academy of Sciences, Shanghai, China
| | - Liangcai Xu
- Shenzhen Futian District Center for Disease Control and Prevention, Shenzhen, China
| | - Yulin Fu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ziquan Lv
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Rui Cai
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yinghui Li
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yaqun Qiu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Lulu Hu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaolu Shi
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Lei Wang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Shuang Wu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Qiongcheng Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Min Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China.
| | - Qinghua Hu
- School of Public Health, Shanxi Medical University, Taiyuan, China; Shenzhen Center for Disease Control and Prevention, Shenzhen, China; Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen, China.
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67
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Fieldsend TW, Catenazzi A, Krysko KL, Shepack A, Collins TM. Salmonella enterica Infection of Synanthropic Non-native Geckos in Southern Florida. Ecohealth 2023; 20:227-230. [PMID: 38104295 DOI: 10.1007/s10393-023-01666-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 10/17/2023] [Indexed: 12/19/2023]
Abstract
Wild geckos are a significant source of human salmonellosis. We swabbed the cloacas of 37 non-native synanthropic geckos (Gekko gecko, n = 16; Phelsuma grandis, n = 21) from southern Florida, USA, and assayed swab DNA extracts using quantitative polymerase chain reaction of the invA gene. Salmonella enterica was detected in both species with a pooled prevalence of 13.5% (5/37; 95% CI 5.3-27.1%), indicating the potential for zoonotic transmission. Implications for human health in the region are discussed.
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Affiliation(s)
- Thomas W Fieldsend
- Department of Biological Sciences, Florida International University, Miami, FL, USA.
- School of Basic and Medical Biosciences, King's College London, New Hunt's House, Newcomen St, London, SE1 1UL, UK.
| | - Alessandro Catenazzi
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Kenneth L Krysko
- Division of Herpetology, Florida Museum of Natural History, Gainesville, FL, USA
| | - Alexander Shepack
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Timothy M Collins
- Department of Biological Sciences, Florida International University, Miami, FL, USA
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Liu X, Jiang Z, Liu Z, Li D, Liu Z, Dong X, Yan S, Zhu L, Cui D, Chen L, Wang J. Biofilm-forming ability of Salmonella enterica strains of different serotypes isolated from multiple sources in China. Microb Pathog 2023; 182:106275. [PMID: 37516211 DOI: 10.1016/j.micpath.2023.106275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Salmonella is an important zoonotic and foodborne pathogen that can infect humans and animals, causing severe concerns about food safety and a heavy financial burden worldwide. The pathogen can adhere to living and abiotic surfaces by forming biofilms, which increases the risk of transmission and infection. In this study, we investigated the biofilm-forming ability of 243 Salmonella strains of 36 serotypes from different sources in China using microplate crystal violet staining method. The results showed that 99.6% tested strains, with the exception of one strain of S. Thompson, were capable of forming biofilms. The strains with the biofilm-forming ability of strong, medium and weak accounted for 2.88%, 24.28% and 72.43%, respectively. The strains of S. Havana and S. Hvittingfoss had the strongest biofilm-forming ability, with the OD570 of 0.81 ± 0.02 and 0.81 ± 0.38, respectively, while the strains of S. Agona and S. Bovismorbificans had the weakest biofilm-forming ability, with the OD570 of 0.16 ± 0.02 and 0.15 ± 0.00, respectively. Furthermore, statistical analysis results demonstrated that isolation of source had no effect on the biofilm formation ability, while the detection rates of pefABCD and ddhC were positively correlated with the biofilm formation ability of Salmonella. In particular, the detection rate of ddhC gene was more than 60% in the biofilm forming strains. These findings have important guiding significance for the investigation of pathogenesis, as well as the prevention and control of salmonellosis.
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Affiliation(s)
- Xu Liu
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Zhaoxu Jiang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Zijun Liu
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Donghui Li
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Zhenhai Liu
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Xiaorui Dong
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Shigan Yan
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
| | - Liping Zhu
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
| | - Daoshi Cui
- Qilu Animal Health Products Co., Ltd, Jinan, 250100, China
| | - Leilei Chen
- Institute of Agro-Food Sciences and Technology, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Junwei Wang
- Laboratory of Pathogenic Microorganism Inspection, China Animal Health and Epidemiology Center, Qingdao, 266032, China
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Cobo-Simón M, Hart R, Ochman H. Gene flow and species boundaries of the genus Salmonella. mSystems 2023; 8:e0029223. [PMID: 37486130 PMCID: PMC10470047 DOI: 10.1128/msystems.00292-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/07/2023] [Indexed: 07/25/2023] Open
Abstract
The genus Salmonella comprises two species, Salmonella bongori and Salmonella enterica, which are infectious to a wide variety of animal hosts. The diversity within S. enterica has been further partitioned into 6-10 subspecies based on such features as host range, geography, and most recently, genetic relatedness and phylogenetic affiliation. Although Salmonella pathogenicity is attributable to large numbers of acquired virulence factors, the extent of homologous exchange in the species at large is apparently constrained such that the species and subspecies form distinct clusters of strains. To explore the extent of gene flow within and among subspecies, and to ultimately define true biological species, we evaluated patterns of recombination in over 1,000 genomes currently assigned to the genus. Those Salmonella subspecies containing sufficient numbers of sequenced genomes to allow meaningful analysis-i.e., subsp. enterica and diarizonae-were found to be reproductively isolated from one another and from all other subspecies. Based on the configuration of genomic sequence divergence among subspecies, it is expected that each of the other Salmonella subspecies will also represent a biological species. Our findings argue against the application of prescribed nucleotide-identity thresholds to delineate bacterial species and contend that the Biological Species Concept should not be disregarded for bacteria, even those, like Salmonella, that demonstrate complex patterns of species and subspecies divergence. IMPORTANCE The Biological Species Concept (BSC), which defines species boundaries based on the capacity for gene exchange, is widely used to classify sexually reproducing eukaryotes but is generally thought to be inapplicable to bacteria due to their completely asexual mode of reproduction. We show that the genus Salmonella, whose thousands of described serovars were formerly considered to be strictly clonal, undergoes sufficient levels of homologous recombination to be assigned to species according to the BSC. Aside from the two recognized species, Salmonella enterica and Salmonella bongori, several (and likely all) of the subspecies within S. enterica are reproductively isolated from one another and should each be considered a separate biological species. These findings demonstrate that species barriers in bacteria can form despite high levels of nucleotide identity and that commonly applied thresholds of genomic sequence identity are not reliable indicators of bacterial species status.
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Affiliation(s)
- Marta Cobo-Simón
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Rowan Hart
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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Vinayaka AC, Huynh VN, Quyen TL, Nguyen T, Golabi M, Madsen M, Bang DD, Wolff A. Validation of Point-of-Care Device for Rapid Detection of Salmonella enterica in Meat Products. Anal Chem 2023; 95:12656-12663. [PMID: 37585497 DOI: 10.1021/acs.analchem.3c00970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Accurate and rapid detection of pathogens in foods of animal origin has been a critical part of the One Health Action Plan of the European Union (EU). Biosensors have the potential in bringing required technologies to accomplish this on the field, wherein loop-mediated isothermal amplification (LAMP) and lab-on-a-chip have proven to be ideal. We have developed a LAMP-based point-of-care (POC) device, the VETPOD, as a solution to the contemporary challenges in the rapid detection of Salmonella spp. The core technology in the VETPOD is a ready-to-use cartridge that included an injection-molded polymer chip with pyramid-shaped optical structures embedded within the chip. These pyramid-shaped optical structures direct the incident light, due to total internal reflection (TIR), through the reaction chambers to the phototransistor. The VETPOD was validated against the ISO 6579-1 reference method. A total of 310 samples were tested that included 180 Salmonella spiked samples in 6 different meat categories and 130 strains to determine the specificity. The overall results were satisfactory, wherein the VETPOD had an acceptable sensitivity (96.51%) compared to the reference (98.81%) and near perfect agreement with ISO 6579-1 with an overall Cohen's kappa of 0.94. The relative level of detection (RLOD) for the VETPOD was 1.38 CFU/25 g that was found to be 1.17 times higher than the reference. The VETPOD showed 98% precision for inclusivity and 100% precision for the exclusivity samples. The VETPOD proved as a useful alternative to detect Salmonella spp. that can be adaptable to a broader spectrum of pathogens in future.
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Affiliation(s)
- Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Van Ngoc Huynh
- Biolabchip Group, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Than Linh Quyen
- Biolabchip Group, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Trieu Nguyen
- Biolabchip Group, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Mohsen Golabi
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Mogens Madsen
- Biolabchip Group, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Anders Wolff
- Biolabchip Group, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby 2800, Denmark
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71
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Sun X, Zhang L, Meng J, Peng K, Huang W, Lei G, Wang Z, Li R, Yang X. The characteristics of mcr-bearing plasmids in clinical Salmonella enterica in Sichuan, China, 2014 to 2017. Front Cell Infect Microbiol 2023; 13:1240580. [PMID: 37705933 PMCID: PMC10495832 DOI: 10.3389/fcimb.2023.1240580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023] Open
Abstract
Salmonella is one of the most important zoonotic pathogens and a major cause of foodborne illnesses, posing a serious global public health hazard. The emergence of plasmid-mediated mcr genes in Salmonella has greatly reduced the clinical choice of salmonellosis treatment. The aim of this study was to investigate the plasmid characteristics of mcr-positive Salmonella identified from patients in Sichuan, China during 2014 to 2017 by whole genomes sequencing. In this study, a total of 12 mcr-positive isolates (1.15%, ; mcr-1, n=10; mcr-3, n=2) were identified from 1046 Salmonella isolates using PCR. Further characterization of these isolates was performed through antimicrobial susceptibility testing, conjugation assays, whole genome sequencing, and bioinformatics analysis. The mcr-1 gene in these isolates were carried by three types of typical mcr-1-bearing plasmids widely distributed in Enterobacteriaceae (IncX4, IncI2 and IncHI2). Of note, two mcr-1-harboring IncHI2 plasmids were integrated into chromosomes by insertion sequences. Two mcr-3-bearing plasmids were IncC and IncFIB broad-host-range plasmids respectively. Genetic context analysis found that mcr-1 was mainly located in Tn6330 or truncated Tn6300, and mcr-3 shared a common genetic structure tnpA-mcr-3-dgkA-ISKpn40. Overall, we found that mcr gene in clinical Salmonella were commonly carried by broad-host plasmids and have potential to transfer into other bacteria by these plasmids. Continuous surveillance of MDR Salmonella in humans and investigation the underlying transmission mechanisms of ARGs are vital to curb the current severe AMR concern.
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Affiliation(s)
- Xinran Sun
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Lin Zhang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, Sichuan, China
| | - Jiantong Meng
- Center for Disease Control and Prevention of Chengdu City, Chengdu, China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Weifeng Huang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, Sichuan, China
| | - Gaopeng Lei
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, Sichuan, China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Xiaorong Yang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, Sichuan, China
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Indrajith S, Natarajan S, Thangasamy S, Natesan S. Drug Resistance, Characterization and Phylogenetic Discrepancy of Salmonella enterica Isolates from Distinct Sources. Curr Microbiol 2023; 80:314. [PMID: 37544954 DOI: 10.1007/s00284-023-03343-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/23/2023] [Indexed: 08/08/2023]
Abstract
Salmonella enterica is one of the foodborne pathogens that can infect humans, spreading from one person to another by contaminated food and water. To identify the pathogenic S. enterica from the contaminated food product, culture-based and molecular identifications, drug resistance profiling, virulence and genetic traits of the strains have been used. Herein, different animal products was subjected to screen for S. enterica prevalence, pathogenic characterization and compared with clinical Salmonella isolates (human). A total of 173 isolates from animal products and 51 isolates from clinical samples were collected. S. Typhi, S. Agona and S. Ohio were predominant serovars in blood, stool and different animal products. Both, clinical [37% (n = 19/51)] and animal product-associated isolates [21% (n = 37/173)] expressed their highest resistance to nalidixic acid. Thirty-one percentage of (n = 16/51) clinical isolates and 12% (n = 21/173) animal food-associated isolates were resistant to multiple classes of antibiotics. Class 1 integrons encoded by S. Typhi, S. Infantis and S. Emek were screened for sequence analysis, the result revealed that the cassettes encoded-aminoglycoside acetyltransferase and dihydrofolate reductase enzymes. Salmonella pathogenicity island-1 encoded-hilA gene was detected most frequently in all the isolates. PFGE profile revealed the genetic traits of the isolates which were closely linked with antibiotic-resistant properties and virulent characteristics. Only S. Enteritidis, collected from different samples had clonal similarities. In summary, drug-resistant pathogenic Salmonella prevalence was observed in the animal product that could be an important alarm to consumers with the risk of enteric fever and it causes the potential risk to public health.
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Affiliation(s)
- Sureka Indrajith
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Sisubalan Natarajan
- Department of Botany, Bishop Heber College (Autonomous), Affi. To Bharathidasan University, Trichy, Tamil Nadu, 620017, India
| | - Selvankumar Thangasamy
- PG and Research Department of Biotechnology, Mahendra Arts and Science College (Autonomous), Kalippatti, Namakkal, Tamil Nadu, 637501, India
| | - Sivakumar Natesan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India.
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Kristensen T, Sørensen LH, Pedersen SK, Jensen JD, Mordhorst H, Lacy-Roberts N, Lukjancenko O, Luo Y, Hoffmann M, Hendriksen RS. Results of the 2020 Genomic Proficiency Test for the network of European Union Reference Laboratory for Antimicrobial Resistance assessing whole-genome-sequencing capacities. Microb Genom 2023; 9:mgen001076. [PMID: 37526643 PMCID: PMC10483428 DOI: 10.1099/mgen.0.001076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023] Open
Abstract
The global surveillance and outbreak investigation of antimicrobial resistance (AMR) is amidst a paradigm shift from traditional biology to bioinformatics. This is due to developments in whole-genome-sequencing (WGS) technologies, bioinformatics tools, and reduced costs. The increased use of WGS is accompanied by challenges such as standardization, quality control (QC), and data sharing. Thus, there is global need for inter-laboratory WGS proficiency test (PT) schemes to evaluate laboratories' capacity to produce reliable genomic data. Here, we present the results of the first iteration of the Genomic PT (GPT) organized by the Global Capacity Building Group at the Technical University of Denmark in 2020. Participating laboratories sequenced two isolates and corresponding DNA of Salmonella enterica, Escherichia coli and Campylobacter coli, using WGS methodologies routinely employed at their laboratories. The participants' ability to obtain consistently good-quality WGS data was assessed based on several QC WGS metrics. A total of 21 laboratories from 21 European countries submitted WGS and meta-data. Most delivered high-quality sequence data with only two laboratories identified as overall underperforming. The QC metrics, N50 and number of contigs, were identified as good indicators for high-sequencing quality. We propose QC thresholds for N50 greater than 20 000 and 25 000 for Campylobacter coli and Escherichia coli, respectively, and number of contigs >200 bp greater than 225, 265 and 100 for Salmonella enterica, Escherichia coli and Campylobacter coli, respectively. The GPT2020 results confirm the importance of systematic QC procedures, ensuring the submission of reliable WGS data for surveillance and outbreak investigation to meet the requirements of the paradigm shift in methodology.
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Affiliation(s)
- Thea Kristensen
- National Food Institute, Research Group of Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Plant and Environmental Sciences, Section for Organismal Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Lauge Holm Sørensen
- National Food Institute, Research Group of Global Capacity Building, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Susanne Karlsmose Pedersen
- National Food Institute, Research Group of Global Capacity Building, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jacob Dyring Jensen
- National Food Institute, Research Group of Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Hanne Mordhorst
- National Food Institute, Research Group of Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Niamh Lacy-Roberts
- National Food Institute, Research Group of Global Capacity Building, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Yan Luo
- Center for Food and Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Maria Hoffmann
- Center for Food and Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Rene S. Hendriksen
- National Food Institute, Research Group of Global Capacity Building, Technical University of Denmark, Kgs. Lyngby, Denmark
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74
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Esteves NC, Bigham DN, Scharf BE. Phages on filaments: A genetic screen elucidates the complex interactions between Salmonella enterica flagellin and bacteriophage Chi. PLoS Pathog 2023; 19:e1011537. [PMID: 37535496 PMCID: PMC10399903 DOI: 10.1371/journal.ppat.1011537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023] Open
Abstract
The bacterial flagellum is a rotary motor organelle and important virulence factor that propels motile pathogenic bacteria, such as Salmonella enterica, through their surroundings. Bacteriophages, or phages, are viruses that solely infect bacteria. As such, phages have myriad applications in the healthcare field, including phage therapy against antibiotic-resistant bacterial pathogens. Bacteriophage χ (Chi) is a flagellum-dependent (flagellotropic) bacteriophage, which begins its infection cycle by attaching its long tail fiber to the S. enterica flagellar filament as its primary receptor. The interactions between phage and flagellum are poorly understood, as are the reasons that χ only kills certain Salmonella serotypes while others entirely evade phage infection. In this study, we used molecular cloning, targeted mutagenesis, heterologous flagellin expression, and phage-host interaction assays to determine which domains within the flagellar filament protein flagellin mediate this complex interaction. We identified the antigenic N- and C-terminal D2 domains as essential for phage χ binding, with the hypervariable central D3 domain playing a less crucial role. Here, we report that the primary structure of the Salmonella flagellin D2 domains is the major determinant of χ adhesion. The phage susceptibility of a strain is directly tied to these domains. We additionally uncovered important information about flagellar function. The central and most variable domain, D3, is not required for motility in S. Typhimurium 14028s, as it can be deleted or its sequence composition can be significantly altered with minimal impacts on motility. Further knowledge about the complex interactions between flagellotropic phage χ and its primary bacterial receptor may allow genetic engineering of its host range for use as targeted antimicrobial therapy against motile pathogens of the χ-host genera Salmonella, Escherichia, or Serratia.
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Affiliation(s)
- Nathaniel C. Esteves
- Dept. of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Danielle N. Bigham
- Dept. of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Birgit E. Scharf
- Dept. of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
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Priya T T, Jacob JJ, M Y, Karthik R, Iyadurai R, G K, Devi B Y, Walia K, Veeraraghavan B. Is it time to move on to gene-based Salmonella typing: Evidence and implications. Indian J Med Microbiol 2023; 44:100359. [PMID: 37356840 DOI: 10.1016/j.ijmmb.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 06/27/2023]
Abstract
Non-typhoidal Salmonella (NTS) is the major cause of foodborne infections globally, with considerable morbidity and mortality. The accurate identification of Salmonella serovars is important in disease management and public health surveillance. However, traditional serotyping methods are laborious, time-consuming and may produce ambiguous results. In this study, we evaluated traditional serotyping and seven gene-based multilocus sequence typing (MLST) methods to determine the serogroups of Salmonella strains. This study analysis suggests that MLST based serotyping is accurate in serogroup identification and discrimination of Salmonella serovars compared to the traditional serotyping method and can be implemented in routine clinical practice.
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Affiliation(s)
- Tharani Priya T
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Yesudoss M
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Rajiv Karthik
- Department of Infectious Disease & Hospital Infection Control Committee, Christian Medical College, Vellore, India
| | - Ramya Iyadurai
- Department of Medicine, Unit V, Christian Medical College, Vellore, India
| | - Karthik G
- Department of Medicine, Unit V, Christian Medical College, Vellore, India
| | - Yamuna Devi B
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Kamini Walia
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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76
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Chen Y, Hu Y, Lu X. Polyethersulfone-Based Microfluidic Device Integrated with DNA Extraction on Paper and Recombinase Polymerase Amplification for the Detection of Salmonella enterica. ACS Sens 2023; 8:2331-2339. [PMID: 37228176 DOI: 10.1021/acssensors.3c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Rising consumption, large-scale production, and widespread distribution have been accompanied by an increase in the number of Salmonella infections reported to implicate contaminated food products. We developed a portable origami microfluidic device that enabled rapid detection of S. enterica from sample preparation to end-point detection, including nucleic acid extraction on paper dipstick without pipetting, nucleic acid amplification using isothermal recombinase polymerase amplification (RPA), and lateral flow assay for results readout. We also explored the feasibility of the polyethersulfone (PES) membrane as a new reaction matrix against the widely used chromatography paper to optimize nucleic acid amplification. Nucleic acid amplification was achieved within 20 min and demonstrated 100% specificity to S. enterica. The limit of detection of this PES-based microfluidic device was 260 CFU/mL and equivalent to RPA reaction in tube. A chromatography paper-based microfluidic device was found 1-log less in sensitivity for Salmonella detection compared to the use of PES. This PES-based microfluidic device could detect S. enterica in lettuce, chicken breast, and milk at concentrations of 6 CFU/g, 9 CFU/g, and 58 CFU/mL, respectively, after 6 h enrichment. PES has shown high compatibility to isothermal nucleic acid amplification and great potential to be implemented as an integrated sample-to-answer microfluidic device for the detection of pathogens in various food commodities.
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Affiliation(s)
- Yunxuan Chen
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yaxi Hu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Food Science Program, Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Food Science and Agricultural Chemistry, McGill University, 21111 Lakeshore Road,Sainte-Anne-de-Bellevue H9X 3V9 Quebec, Canada
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Fei X, Li Q, Jiao X, Olsen JE. Identification of Salmonella Pullorum Factors Affecting Immune Reaction in Macrophages from the Avian Host. Microbiol Spectr 2023; 11:e0078623. [PMID: 37191575 PMCID: PMC10269470 DOI: 10.1128/spectrum.00786-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023] Open
Abstract
The host-specific Salmonella serovar S. Pullorum (SP) modulates the chicken immune response to a Th2-biased response associated with persistent infection. This is different from the Th1-biased immune response induced by the genetically close serovar, S. Enteritidis (SE). Based on core genome differences between SP and SE, we used three complementary bioinformatics approaches to identify SP genes, which may be important for stimulation of the immune response. Defined mutants were constructed in selected genes, and the infection potential and ability of mutants to stimulate cytokine production in avian derived HD11 macrophages were determined. Deletion of large genomic regions unique to SP did not change infection potential nor immune stimulation significantly. Mutants in genes with conserved single nucleotide polymorphisms (SNPs) between the two serovars in the region 100 bp upstream of the start codon (conserved upstream SNPs [CuSNPs]) such as sseE, osmB, tolQ, a putative immune antigen, and a putative persistent infection factor, exhibited differences in induction of inflammatory cytokines compared to wild-type SP, suggesting a possible role of these CuSNPs in immune regulation. Single nucleotide SP mutants correcting for the CuSNP difference were constructed in the upstream region of sifA and pipA. The SNP corrected pipA mutant expressed pipA at a higher level than the wild-type SP strain, and the mutant differentially caused upregulation of proinflammatory cytokines. It suggests that this CuSNP is important for the suppression of proinflammatory responses. In conclusion, this study has identified putative immune stimulating factors of relevance to the difference in infection dynamics between SP and SE in avian macrophages. IMPORTANCE Salmonella Pullorum is host specific to avian species, where it causes life-threatening infection in young birds. It is unknown why it is host restricted and causes systemic disease, rather than gastroenteritis normally seen with Salmonella. In the present study, we identified genes and single nucleotide polymorphisms (SNPs; relative to the broad-host-range type Salmonella Enteritidis), which affected survival and immune induction in macrophages from hens suggesting a role in development of the host specific infection. Further studies of such genes may enable understanding of which genetic factors determine the development of host specific infection by S. Pullorum. In this study, we developed an in silico approach to predict candidate genes and SNPs for development of the host-specific infection and the specific induction of immunity associated with this infection. This study flow can be used in similar studies in other clades of bacteria.
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Affiliation(s)
- Xiao Fei
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, People’s Republic of China
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Qiuchun Li
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, People’s Republic of China
| | - Xinan Jiao
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, People’s Republic of China
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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Yamasaki S, Zwama M, Yoneda T, Hayashi-Nishino M, Nishino K. Drug resistance and physiological roles of RND multidrug efflux pumps in Salmonella enterica, Escherichia coli and Pseudomonas aeruginosa. Microbiology (Reading) 2023; 169:001322. [PMID: 37319001 PMCID: PMC10333786 DOI: 10.1099/mic.0.001322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/18/2023] [Indexed: 06/17/2023]
Abstract
Drug efflux pumps transport antimicrobial agents out of bacteria, thereby reducing the intracellular antimicrobial concentration, which is associated with intrinsic and acquired bacterial resistance to these antimicrobials. As genome analysis has advanced, many drug efflux pump genes have been detected in the genomes of bacterial species. In addition to drug resistance, these pumps are involved in various essential physiological functions, such as bacterial adaptation to hostile environments, toxin and metabolite efflux, biofilm formation and quorum sensing. In Gram-negative bacteria, efflux pumps in the resistance–nodulation–division (RND) superfamily play a clinically important role. In this review, we focus on Gram-negative bacteria, including Salmonella enterica , Escherichia coli and Pseudomonas aeruginosa , and discuss the role of RND efflux pumps in drug resistance and physiological functions.
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Affiliation(s)
- Seiji Yamasaki
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute for Advanced Co-Creation Studies, Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Martijn Zwama
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Tomohiro Yoneda
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mitsuko Hayashi-Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kunihiko Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research, 2-8 Yamadaoka, Osaka University, Suita, Osaka 565-0871, Japan
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Pye HV, Thilliez G, Acton L, Kolenda R, Al-Khanaq H, Grove S, Kingsley RA. Strain and serovar variants of Salmonella enterica exhibit diverse tolerance to food chain-related stress. Food Microbiol 2023; 112:104237. [PMID: 36906307 DOI: 10.1016/j.fm.2023.104237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/12/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023]
Abstract
Non-Typhoidal Salmonella (NTS) continues to be a leading cause of foodborne illness worldwide. Food manufacturers implement hurdle technology by combining more than one approach to control food safety and quality, including preservatives such as organic acids, refrigeration, and heating. We assessed the variation in survival in stresses of genotypically diverse isolates of Salmonella enterica to identify genotypes with potential elevated risk to sub-optimal processing or cooking. Sub-lethal heat treatment, survival in desiccated conditions and growth in the presence of NaCl or organic acids were investigated. S. Gallinarum strain 287/91 was most sensitive to all stress conditions. While none of the strains replicated in a food matrix at 4 °C, S. Infantis strain S1326/28 retained the greatest viability, and six strains exhibited a significantly reduced viability. A S. Kedougou strain exhibited the greatest resistance to incubation at 60 °C in a food matrix that was significantly greater than S. Typhimurium U288, S Heidelberg, S. Kentucky, S. Schwarzengrund and S. Gallinarum strains. Two isolates of monophasic S. Typhimurium, S04698-09 and B54Col9 exhibited the greatest tolerance to desiccation that was significantly more than for the S. Kentucky and S. Typhimurium U288 strains. In general, the presence of 12 mM acetic acid or 14 mM citric acid resulted in a similar pattern of decreased growth in broth, but this was not observed for S. Enteritidis, and S. Typhimurium strains ST4/74 and U288 S01960-05. Acetic acid had a moderately greater effect on growth despite the lower concentration tested. A similar pattern of decreased growth was observed in the presence of 6% NaCl, with the notable exception that S. Typhimurium strain U288 S01960-05 exhibited enhanced growth in elevated NaCl concentrations.
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Affiliation(s)
- Hannah V Pye
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK; University of East Anglia, Norwich Research Park, Norwich, UK
| | - Gaёtan Thilliez
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK
| | - Luke Acton
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK; University of East Anglia, Norwich Research Park, Norwich, UK
| | - Rafał Kolenda
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK
| | - Haider Al-Khanaq
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK
| | - Stephen Grove
- Nestlé Development Centre, Cannon Road, Solon, OH, USA; McCain Foods, 1 Tower Lane, Oakbrook Terrace, Illinois, USA
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich, UK; University of East Anglia, Norwich Research Park, Norwich, UK.
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80
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Roy PK, Ha AJW, Nahar S, Hossain MI, Ashrafudoulla M, Toushik SH, Mizan MFR, Kang I, Ha SD. Inhibitory effects of vorinostat (SAHA) against food-borne pathogen Salmonella enterica serotype Kentucky mixed culture biofilm with virulence and quorum-sensing relative expression. Biofouling 2023; 39:617-628. [PMID: 37580896 DOI: 10.1080/08927014.2023.2242263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 08/16/2023]
Abstract
Salmonella is a food-borne microorganism that is also a zoonotic bacterial hazard in the food sector. This study determined how well a mixed culture of Salmonella Kentucky formed biofilms on plastic (PLA), silicon rubber (SR), rubber gloves (RG), chicken skin and eggshell surfaces. In vitro interactions between the histone deacetylase inhibitor-vorinostat (SAHA)-and S. enterica serotype Kentucky were examined utilizing biofilms. The minimum inhibitory concentration (MIC) of SAHA was 120 µg mL-1. The addition of sub-MIC (60 µg mL-1) of SAHA decreased biofilm formation for 24 h on PLA, SR, RG, Chicken skin, and eggshell by 3.98, 3.84, 4.11, 2.86 and 3.01 log (p < 0.05), respectively. In addition, the initial rate of bacterial biofilm formation was higher on chicken skin than on other surfaces, but the inhibitory effect was reduced. Consistent with this conclusion, virulence genes expression (avrA, rpoS and hilA) and quorum-sensing (QS) gene (luxS) was considerably downregulated at sub-MIC of SAHA. SAHA has potential as an anti-biofilm agent against S. enterica serotype Kentucky biofilm, mostly by inhibiting virulence and quorum-sensing gene expression, proving the histone deacetylase inhibitor could be used to control food-borne biofilms in the food industry.
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Affiliation(s)
- Pantu Kumar Roy
- Advanced Food Safety Research Group, Department of Food Science and Technology, Chung-Ang University, Gyeonggi-do, Republic of Korea
- Department of Seafood Science and Technology, Institute of Marine Industry, Gyeongsang National University, Tongyeong, Republic of Korea
| | - Angela Ji-Won Ha
- Advanced Food Safety Research Group, Department of Food Science and Technology, Chung-Ang University, Gyeonggi-do, Republic of Korea
| | - Shamsun Nahar
- Advanced Food Safety Research Group, Department of Food Science and Technology, Chung-Ang University, Gyeonggi-do, Republic of Korea
| | - Md Iqbal Hossain
- Advanced Food Safety Research Group, Department of Food Science and Technology, Chung-Ang University, Gyeonggi-do, Republic of Korea
| | - Md Ashrafudoulla
- Advanced Food Safety Research Group, Department of Food Science and Technology, Chung-Ang University, Gyeonggi-do, Republic of Korea
| | - Sazzad Hossen Toushik
- Advanced Food Safety Research Group, Department of Food Science and Technology, Chung-Ang University, Gyeonggi-do, Republic of Korea
| | - Md Furkanur Rahaman Mizan
- Advanced Food Safety Research Group, Department of Food Science and Technology, Chung-Ang University, Gyeonggi-do, Republic of Korea
| | - Iksoon Kang
- Department of Animal Science, College of Agriculture, Food and Environmental Science, CA Polytechnic State University, San Luis Obispo, California, USA
| | - Sang-Do Ha
- Advanced Food Safety Research Group, Department of Food Science and Technology, Chung-Ang University, Gyeonggi-do, Republic of Korea
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81
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Han M, Schierstaedt J, Duan Y, Trotereau J, Virlogeux-Payant I, Schikora A. Novel method to recover Salmonella enterica cells for Tn-Seq approaches from lettuce leaves and agricultural environments using combination of sonication, filtration, and dialysis membrane. J Microbiol Methods 2023; 208:106724. [PMID: 37054820 DOI: 10.1016/j.mimet.2023.106724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 04/05/2023] [Accepted: 04/08/2023] [Indexed: 04/15/2023]
Abstract
Salmonella enterica in agricultural environments has become an important concern, due to its potential transmission to humans and the associated public health risks. To identify genes contributing to Salmonella adaptation to such environments, transposon sequencing has been used in recent years. However, isolating Salmonella from atypical hosts, such as plant leaves, can pose technical challenges due to low bacterial content and the difficulty to separate an adequate number of bacteria from host tissues. In this study, we describe a modified methodology using a combination of sonication and filtration to recover S. enterica cells from lettuce leaves. We successfully recovered over a total of 3.5 × 106Salmonella cells in each biological replicate from two six-week old lettuce leaves, 7 days after infiltration with a Salmonella suspension of 5 × 107 colony forming units (CFU)/mL. Moreover, we have developed a dialysis membrane system as an alternative method for recovering bacteria from culture medium, mimicking a natural environment. Inoculating 107 CFU/mL of Salmonella into the media based on plant (lettuce and tomato) leaf and diluvial sand soil, a final concentration of 109.5 and 108.5 CFU/mL was obtained, respectively. One millilitre of the bacterial suspension after 24 h incubation at 28 °C using 60 rpm agitation was pelleted, corresponding to 109.5 and 108.5 cells from leaf- or soil-based media. The recovered bacterial population, from both lettuce leaves and environment-mimicking media, can adequately cover a presumptive library density of 106 mutants. In conclusion, this protocol provides an effective method to recover a Salmonella transposon sequencing library from in planta and in vitro systems. We expect this novel technique to foster the study of Salmonella in atypical hosts and environments, as well as other comparable scenarios.
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Affiliation(s)
- Min Han
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany
| | - Jasper Schierstaedt
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany; Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Department Plant-Microbe Systems, Theodor-Echtermeyer Weg 1, Großbeeren 14979, Germany
| | - Yongming Duan
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany
| | - Jérôme Trotereau
- INRAE Val de Loire, Université de Tours, UMR ISP, Nouzilly 37380, France
| | | | - Adam Schikora
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany.
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Wang H, Cheng H, Huang B, Hu X, Chen Y, Zheng L, Yang L, Deng J, Wang Q. Characterization of resistance genes and plasmids from sick children caused by Salmonella enterica resistance to azithromycin in Shenzhen, China. Front Cell Infect Microbiol 2023; 13:1116172. [PMID: 37065212 PMCID: PMC10090516 DOI: 10.3389/fcimb.2023.1116172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/15/2023] [Indexed: 03/31/2023] Open
Abstract
IntroductionSamonella is 1 of 4 key global causes of diarrhoeal diseases, sometimes it can be serious, especially for yong children. Due to the extensive resistance of salmonella serotypes to conventional first-line drugs, macrolides (such as azithromycin) have been designated as the most important antibiotics for the treatment of salmonella. Antimicrobial resistance is a major public health problem in the world, and the mechanism of azithromycin resistance is rarely studied.MethodsThis study determined the azithromycin resistance and plasmids of Salmonella enterica isolates from children attending the Shenzhen Children’s Hospital. The susceptibility of ampicillin (AMP), ciprofloxacin (CIP), ceftriaxone (CRO), sulfamethoxazole (SMZ), chloramphenicol (CL), and azithromycin (AZM) were detected and the genes and plasmids from azithromycin-resistant Salmonella were detected by Illumina hi-seq and Nanopore MinIone whole genome sequencing (WGS) using a map-based method, and the genomic background of these factors was evaluated using various bioinformatics tools.ResultsIn total, 15 strains of nontyphoid Salmonella strains that were isolated (including S. typhimurium, S.London, S. Goldcoast, and S.Stanley) demonstrated resistance to azithromycin (minimum inhibitory concentration,MIC from 32 to >256 µg/mL), and the resistance rate was 3.08% (15/487). The sensitivity test to other antibiotics demonstrated 100% resistance to AMP, and the resistance to SMZ and CL was 86.7% and 80.0%, respectively. Through WGS analysis, all isolates were positive for a plasmid-encoded mphA gene. Plasmid incompatibility typing identified five IncFIB(K), five IncHI2/HI2A/Q1, two IncC, one IncHI2/HI2A/N, one IncR, one IncFII and one IncHI2/HI2A plasmids. Sequence analyses of plasmids revealed extensive homology to various plasmids or transposons in regions involved in plasmid replication/maintenance functions and/or in antibiotic resistance gene clusters.ConclusionmphA is the main gene involved in azithromycin, a macrolide, and resistance to Salmonella. It is usually located on plasmids and easily spreads, hence posing a great threat to the current treatment of Salmonella infection. The plasmid sequence similarities suggest that the plasmids acquired resistance genes from a variety of enterica bacteria and underscore the importance of a further understanding of horizontal gene transfer among enterica bacteria.
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Affiliation(s)
- Hongmei Wang
- Laboratory Medicine Centre, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hang Cheng
- School of Medicine, Southern University of Science and Technology, ShenZhen, Guangdong, China
| | - Baoxing Huang
- Department of Infectious Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Xiumei Hu
- Laboratory Medicine Centre, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yunsheng Chen
- Department of Infectious Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Lei Zheng
- Laboratory Medicine Centre, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Qian Wang, ; Jikui Deng, ; Liang Yang, ; Lei Zheng,
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, ShenZhen, Guangdong, China
- *Correspondence: Qian Wang, ; Jikui Deng, ; Liang Yang, ; Lei Zheng,
| | - Jikui Deng
- Department of Infectious Diseases, Shenzhen Children’s Hospital, Shenzhen, China
- *Correspondence: Qian Wang, ; Jikui Deng, ; Liang Yang, ; Lei Zheng,
| | - Qian Wang
- Laboratory Medicine Centre, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Qian Wang, ; Jikui Deng, ; Liang Yang, ; Lei Zheng,
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83
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Karanth S, Pradhan AK. Development of a novel machine learning-based weighted modeling approach to incorporate Salmonella enterica heterogeneity on a genetic scale in a dose-response modeling framework. Risk Anal 2023; 43:440-450. [PMID: 35413139 DOI: 10.1111/risa.13924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Estimating microbial dose-response is an important aspect of a food safety risk assessment. In recent years, there has been considerable interest to advance these models with potential incorporation of gene expression data. The aim of this study was to develop a novel machine learning model that considers the weights of expression of Salmonella genes that could be associated with illness, given exposure, in hosts. Here, an elastic net-based weighted Poisson regression method was proposed to identify Salmonella enterica genes that could be significantly associated with the illness response, irrespective of serovar. The best-fit elastic net model was obtained by 10-fold cross-validation. The best-fit elastic net model identified 33 gene expression-dose interaction terms that added to the predictability of the model. Of these, nine genes associated with Salmonella metabolism and virulence were found to be significant by the best-fit Poisson regression model (p < 0.05). This method could improve or redefine dose-response relationships for illness from relative proportions of significant genes from a microbial genetic dataset, which would help in refining endpoint and risk estimations.
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Affiliation(s)
- Shraddha Karanth
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
| | - Abani K Pradhan
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
- Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
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84
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Grossi JL, Yamatogi RS, Call DR, Nero LA. High prevalence of intermediate resistance to ciprofloxacin in Salmonella enterica isolated from a Brazilian poultry production chain, located in Minas Gerais state. Int J Food Microbiol 2023; 394:110180. [PMID: 36989931 DOI: 10.1016/j.ijfoodmicro.2023.110180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
We characterized the distribution and diversity of antimicrobial-resistance Salmonella enterica isolated from a poultry production chain in Minas Gerais, Brazil, with special attention to ciprofloxacin and multidrug resistance (MDR). S. enterica (n = 96) of different serotypes and from different processing steps were subjected to broth dilution assay to estimate the minimum inhibitory concentration (MIC) for 12 antibiotics (8 classes) and screened using PCR for the presence of 17 antimicrobial-resistance genes. Isolates presented mainly resistance to ampicillin (11/96), and most presented intermediate resistance to ciprofloxacin (92/96). Roughly one-third (33/96) were resistant to streptomycin based on our interpretive criteria. Most strains resistant to streptomycin and ciprofloxacin were PCR-positive for aphA (51/96) and qnrB (94/96), respectively. Ciprofloxacin resistance was further investigated through high-resolution melting qPCR (HRM-qPCR) and sequencing of quinolone resistance-determining region (QRDR: gyrA, gyrB, parC, and parE). Minor differences were identified in melting temperatures (Tm), and a Thr57Sr mutation was observed in parC. MDR isolates harboring acrA and capable of expressing the AcrAB-TolC multidrug efflux pump were resistant to ethidium bromide at 0.4 mg/mL. The intermediate resistance to ciprofloxacin may be associated with qnrB, and the potential role of Thr57Ser mutation warrants further investigation. The high prevalence of antibiotic related genes and its association with the observed intermediary resistance to ciprofloxacin indicates the widespread of this hazard in the studied poultry production chain.
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Affiliation(s)
- Juliana Líbero Grossi
- InsPOA - Laboratory of Food Inspection, Federal University of Viçosa, Department of Veterinary Medicine, Av. PH Rolfs, s/n, Campus Universitário, 36570-900 Viçosa, MG, Brazil
| | - Ricardo Seiti Yamatogi
- InsPOA - Laboratory of Food Inspection, Federal University of Viçosa, Department of Veterinary Medicine, Av. PH Rolfs, s/n, Campus Universitário, 36570-900 Viçosa, MG, Brazil
| | - Douglas Ruben Call
- Paul G. Allen School for Global Health, Washington State University, 240 SE Ott Road, PO Box 647090, 99164-7090 Pullman, WA, USA
| | - Luís Augusto Nero
- InsPOA - Laboratory of Food Inspection, Federal University of Viçosa, Department of Veterinary Medicine, Av. PH Rolfs, s/n, Campus Universitário, 36570-900 Viçosa, MG, Brazil.
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85
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Chiou CS, Hong YP, Wang YW, Chen BH, Teng RH, Song HY, Liao YS. Antimicrobial Resistance and Mechanisms of Azithromycin Resistance in Nontyphoidal Salmonella Isolates in Taiwan, 2017 to 2018. Microbiol Spectr 2023; 11:e0336422. [PMID: 36688703 PMCID: PMC9927516 DOI: 10.1128/spectrum.03364-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/04/2023] [Indexed: 01/24/2023] Open
Abstract
Antimicrobial resistance was investigated in 2,341 nontyphoidal Salmonella (NTS) isolates recovered from humans in Taiwan from 2017 to 2018 using antimicrobial susceptibility testing. Azithromycin resistance determinants were detected in 175 selected isolates using PCR and confirmed in 81 selected isolates using whole-genome sequencing. Multidrug resistance was found in 47.3% of total isolates and 96.2% of Salmonella enterica serovar Anatum and 81.7% of S. enterica serovar Typhimurium isolates. Resistance to the conventional first-line drugs (ampicillin, chloramphenicol, and cotrimoxazole), cefotaxime and ceftazidime, and ciprofloxacin was found in 32.5 to 49.0%, 20.3 to 20.4%, and 3.2% of isolates, respectively. A total of 76 (3.1%) isolates were resistant to azithromycin, which was associated with mph(A), erm(42), erm(B), and possibly the enhanced expression of efflux pump(s) due to ramAp or defective ramR. mph(A) was found in 53% of the 76 azithromycin-resistant isolates from 11 serovars and located in an IS26-mph(A)-mrx(A)-mphR(A)-IS6100 unit in various incompatibility plasmids and the chromosomes. erm(42) in S. enterica serovar Albany was carried by an integrative and conjugative element, ICE_erm42, and in S. enterica serovar Enteritidis and S. Typhimurium was located in IS26 composite transposons in the chromosomes. erm(B) was carried by IncI1-I(α) plasmids in S. Enteritidis and S. Typhimurium. ramAp was a plasmid-borne ramA, a regulatory activator of efflux pump(s), found in only S. enterica serovar Goldcoast. Since the azithromycin resistance determinants are primarily carried on mobile genetic elements, they could easily be disseminated among human bacterial pathogens. The ramAp-carrying S. Goldcoast isolates displayed azithromycin MICs of 16 to 32 mg/L. Thus, the epidemiological cutoff value of ≤16 mg/L of azithromycin proposed for wild-type NTS should be reconsidered. IMPORTANCE Antimicrobial resistance in NTS isolates is a major public health concern in Taiwan, and the mechanisms of azithromycin resistance are rarely investigated. Azithromycin and carbapenems are the last resort for the treatment of invasive salmonellosis caused by multidrug-resistant (MDR) and extensively drug-resistant Salmonella strains. Our study reports the epidemiological trend of resistance in NTS in Taiwan and the genetic determinants involved in azithromycin resistance. We point out that nearly half of NTS isolates from 2017 to 2018 are MDR, and 20% are resistant to third-generation cephalosporins. The azithromycin resistance rate (3.1%) for the NTS isolates from Taiwan is much higher than those for the NTS isolates from the United States and Europe. Our study also indicates that azithromycin resistance is primarily mediated by mph(A), erm(42), erm(B), and ramAp, which are frequently carried on mobile genetic elements. Thus, the azithromycin resistance determinants could be expected to be disseminated among diverse bacterial pathogens.
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Affiliation(s)
- Chien-Shun Chiou
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Yu-Ping Hong
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - You-Wun Wang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Bo-Han Chen
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Ru-Hsiou Teng
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Hui-Yung Song
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Ying-Shu Liao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
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86
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Gebremichael Y, Crandall J, Mukhopadhyay R, Xu F. Salmonella Subpopulations Identified from Human Specimens Express Heterogenous Phenotypes That Are Relevant to Clinical Diagnosis. Microbiol Spectr 2023; 11:e0167922. [PMID: 36507668 PMCID: PMC9927314 DOI: 10.1128/spectrum.01679-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
Clonal bacterial cells can give rise to functionally heterogeneous subpopulations. This diversification is considered an adaptation strategy that has been demonstrated for several bacterial species, including Salmonella enterica serovar Typhimurium. In previous studies on mouse models infected orally with pure Salmonella cultures, derived bacterial cells collected from animal tissues were found to express heterogenous phenotypes. Here, we show mixed Salmonella populations, apparently derived from the same progenitor, present in human specimens collected at a single disease time point, and in a long-term-infected patient, these Salmonella were no longer expressing surface-exposed antigen epitopes by isolates collected at earlier days of the disease. The subpopulations express different phenotypes related to cell surface antigen expression, motility, biofilm formation, biochemical metabolism, and antibiotic resistance, which can all contribute to pathogenicity. Some of the phenotypes correlate with single nucleotide polymorphisms or other sequence changes in bacterial genomes. These genetic variations can alter synthesis of cell membrane-associated molecules such as lipopolysaccharides and lipoproteins, leading to changes in bacterial surface structure and function. This study demonstrates the limitation of Salmonella diagnostic methods that are based on a single-cell population which may not represent the heterogenous bacterial community in infected humans. IMPORTANCE In animal model systems, heterogenous Salmonella phenotypes were found previously to regulate bacterial infections. We describe in this communication that different Salmonella phenotypes also exist in infected humans at a single disease time point and that their phenotypic and molecular traits are associated with different aspects of pathogenicity. Notably, variation in genes encoding antibiotic resistance and two-component systems were observed from the subpopulations of a patient suffering from persistent salmonellosis. Therefore, clinical and public health interventions of the disease that are based on diagnosis of a single-cell population may miss other subpopulations that can cause residual human infections.
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Affiliation(s)
- Yismashoa Gebremichael
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - John Crandall
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - Rituparna Mukhopadhyay
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - Fengfeng Xu
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
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Qiu Y, Ozturk S, Cui X, Qin W, Wu Q, Liu S. Increased heat tolerance and transcriptome analysis of Salmonella enterica Enteritidis PT 30 heat-shocked at 42 ℃. Food Res Int 2023; 167:112636. [PMID: 37087231 DOI: 10.1016/j.foodres.2023.112636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
In this study, we compared the heat tolerance parameter (D65℃) values of Salmonella enterica serovar Enteritidis PT 30 (S. Enteritidis ) heat adapted at different degrees (at 42 ℃ for 20-180 min) and cultivated using two methods. The treated group with the highest D65℃ value (LP-42 ℃-60 min) and the untreated groups (Control-TSB and Control-TSA) were subjected to transcriptome analysis. Heat-adaptation increased the D65℃ values of S. Enteritidis by 24.5-60.8%. The D65℃ values of the LP-42 ℃-60 min group (1.85 ± 0.13 min, 7.7% higher) was comparable to that of the Control-TSA. A total of 483 up- and 443 downregulated genes of S. enteritidis were identified in the LP-42 ℃-60 min group (log2fold change > 1, adjusted p-value < 0.05). Among these genes, 5 co-expressed and 15 differentially expressed genes in the LP-42 ℃-60 min and Control-TSA grops possibly contributed to the high D65℃ values of S. Enteritidis . The Rpo regulon was involved in the heat adaptation of S. Enteritidis , as evidenced by the significant upregulation of rpoS, rpoN, and rpoE. KEGG enrichment pathways, such as biosynthesis of secondary metabolites, tricarboxylic acid, and ribosomes were identified and mapped to reveal the molecular mechanisms of S. enteritidis during heat adaptation. This study quantified the enhanced heat tolerance of S. Enteritidis heat adapted at different degrees of heat-adaptation. The results of this study may serve as a basis for elucidating the molecular mechanisms underlying the enhanced heat tolerance at the transcriptome level.
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Affiliation(s)
- Yan Qiu
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | - Samet Ozturk
- Department of Food Engineering, Gümüşhane University, Gümüşhane, Turkey
| | - Xinyao Cui
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | - Wen Qin
- College of Food Science, Sichuan Agricultural University, Ya'an, China; Food Processing and Safety Institute, Sichuan Agricultural University, Ya'an, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Shuxiang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, China; Food Processing and Safety Institute, Sichuan Agricultural University, Ya'an, China; State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China.
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88
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Enam SU, Cherry JL, Leonard SR, Zheludev IN, Lipman DJ, Fire AZ. Restriction Endonuclease-Based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing. Appl Environ Microbiol 2023; 89:e0167022. [PMID: 36519847 PMCID: PMC9888230 DOI: 10.1128/aem.01670-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Metagenomic sequencing is a swift and powerful tool to ascertain the presence of an organism of interest in a sample. However, sequencing coverage of the organism of interest can be insufficient due to an inundation of reads from irrelevant organisms in the sample. Here, we report a nuclease-based approach to rapidly enrich for DNA from certain organisms, including enterobacteria, based on their differential endogenous modification patterns. We exploit the ability of taxon-specific methylated motifs to resist the action of cognate methylation-sensitive restriction endonucleases that thereby digest unwanted, unmethylated DNA. Subsequently, we use a distributive exonuclease or electrophoretic separation to deplete or exclude the digested fragments, thus enriching for undigested DNA from the organism of interest. As a proof of concept, we apply this method to enrich for the enterobacteria Escherichia coli and Salmonella enterica by 11- to 142-fold from mock metagenomic samples and validate this approach as a versatile means to enrich for genomes of interest in metagenomic samples. IMPORTANCE Pathogens that contaminate the food supply or spread through other means can cause outbreaks that bring devastating repercussions to the health of a populace. Investigations to trace the source of these outbreaks are initiated rapidly but can be drawn out due to the labored methods of pathogen isolation. Metagenomic sequencing can alleviate this hurdle but is often insufficiently sensitive. The approach and implementations detailed here provide a rapid means to enrich for many pathogens involved in foodborne outbreaks, thereby improving the utility of metagenomic sequencing as a tool in outbreak investigations. Additionally, this approach provides a means to broadly enrich for otherwise minute levels of modified DNA, which may escape unnoticed in metagenomic samples.
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Affiliation(s)
- Syed Usman Enam
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Joshua L. Cherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Susan R. Leonard
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Ivan N. Zheludev
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - David J. Lipman
- Office of the Center Director, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Andrew Z. Fire
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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89
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Kurasz JE, Crawford MC, Porwollik S, Gregory O, Tadlock KR, Balding EC, Weinert EE, McClelland M, Karls AC. Strain-Specific Gifsy-1 Prophage Genes Are Determinants for Expression of the RNA Repair Operon during the SOS Response in Salmonella enterica Serovar Typhimurium. J Bacteriol 2023; 205:e0026222. [PMID: 36622230 PMCID: PMC9879122 DOI: 10.1128/jb.00262-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023] Open
Abstract
The adaptation of Salmonella enterica serovar Typhimurium to stress conditions involves expression of genes within the regulon of the alternative sigma factor RpoN (σ54). RpoN-dependent transcription requires an activated bacterial enhancer binding protein (bEBP) that hydrolyzes ATP to remodel the RpoN-holoenzyme-promoter complex for transcription initiation. The bEBP RtcR in S. Typhimurium strain 14028s is activated by genotoxic stress to direct RpoN-dependent expression of the RNA repair operon rsr-yrlBA-rtcBA. The molecular signal for RtcR activation is an oligoribonucleotide with a 3'-terminal 2',3'-cyclic phosphate. We show in S. Typhimurium 14028s that the molecular signal is not a direct product of nucleic acid damage, but signal generation is dependent on a RecA-controlled SOS-response pathway, specifically, induction of prophage Gifsy-1. A genome-wide mutant screen and utilization of Gifsy prophage-cured strains indicated that the nucleoid-associated protein Fis and the Gifsy-1 prophage significantly impact RtcR activation. Directed-deletion analysis and genetic mapping by transduction demonstrated that a three-gene region (STM14_3218-3220) in Gifsy-1, which is variable between S. Typhimurium strains, is required for RtcR activation in strain 14028s and that the absence of STM14_3218-3220 in the Gifsy-1 prophages of S. Typhimurium strains LT2 and 4/74, which renders these strains unable to activate RtcR during genotoxic stress, can be rescued by complementation in cis by the region encompassing STM14_3218-3220. Thus, even though RtcR and the RNA repair operon are highly conserved in Salmonella enterica serovars, RtcR-dependent expression of the RNA repair operon in S. Typhimurium is controlled by a variable region of a prophage present in only some strains. IMPORTANCE The transcriptional activator RtcR and the RNA repair proteins whose expression it regulates, RtcA and RtcB, are widely conserved in Proteobacteria. In Salmonella Typhimurium 14028s, genotoxic stress activates RtcR to direct RpoN-dependent expression of the rsr-yrlBA-rtcBA operon. This work identifies key elements of a RecA-dependent pathway that generates the signal for RtcR activation in strain 14028s. This signaling pathway requires the presence of a specific region within the prophage Gifsy-1, yet this region is absent in most other wild-type Salmonella strains. Thus, we show that the activity of a widely conserved regulatory protein can be controlled by prophages with narrow phylogenetic distributions. This work highlights an underappreciated phenomenon where bacterial physiological functions are altered due to genetic rearrangement of prophages.
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Affiliation(s)
| | | | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California–Irvine School of Medicine, Irvine, California, USA
| | - Oliver Gregory
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | | | - Eve C. Balding
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Emily E. Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California–Irvine School of Medicine, Irvine, California, USA
| | - Anna C. Karls
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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Nakayama T, Shiori Yamamoto, Natsuki Ohata, Takahiro Yamaguchi, Michio Jinnai, Doan Tran Nguyen Minh, Oanh Nguyen Hoang, Hien LE Thi, Phong Ngo Thanh, Phuong Hoang Hoai, Phuc Nguyen DO, Chinh Dang VAN, Yuko Kumeda, Atsushi Hase. Common presence of plasmid encoding bla CTX-M-55 in extended-spectrum β-lactamase-producing Salmonella enterica and Escherichia coli isolates from the same edible river fish. J Microorg Control 2023; 28:49-56. [PMID: 37394527 DOI: 10.4265/jmc.28.2_49] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The transmission of potentially life-threatening plasmid-mediated antibiotic-resistant bacteria poses a major threat to public health. This study aimed to determine the presence of commonly observed plasmids encoding plasmid-mediated antibiotic-resistance genes in Salmonella and Escherichia coli isolates from fishery products. Eighty river fishes were purchased from retail stores and supermarkets in Vietnam. Only Salmonella-positive fishes were used for antibiotic-resistant E. coli isolation. Salmonella serotyping was performed using Salmonella antisera. Isolated bacterial DNA was extracted, and antibiotic susceptibility, resistance genes, and replicon typing were determined. Our results showed that Salmonella was isolated from 12.5% (10/80) of the river fishes. Cefotaxime-resistant Salmonella was isolated from 3.8% (3/80) of the fishes and colistin-resistant Salmonella from 1.3% (1/80) . Salmonella serotyping revealed Potsdam, Schwarzengrund, Bardo/Newport, Give, Infantis, Kentucky, and Typhimurium. Multiplex polymerase chain reaction revealed the presence of extended-spectrum β-lactamase-related genes blaCTX-M-55 and blaCTX-M-65 and the colistin resistance gene mcr-1. To date, no study has reported an antibiotic-resistance plasmid present in multiple bacteria collected from the same food. Thus, horizontal transmission of antibiotic-resistance plasmids may occur at the food level.
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Affiliation(s)
- Tatsuya Nakayama
- Graduate School of Integrated Sciences for Life
- Division of Biomedical Food Research, National Institute of Health Sciences
| | - Shiori Yamamoto
- Division of Biomedical Food Research, National Institute of Health Sciences
| | | | | | - Michio Jinnai
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health
| | | | | | | | | | | | | | | | - Yuko Kumeda
- Research Center of Microorganism Control, Osaka Metropolitan University
| | - Atsushi Hase
- Faculty of Contemporary Human Life Science, Tezukayama University
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91
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Papić B, Kušar D, Mićunović J, Pirš M, Ocepek M, Avberšek J. Clonal Spread of pESI-Positive Multidrug-Resistant ST32 Salmonella enterica Serovar Infantis Isolates among Broilers and Humans in Slovenia. Microbiol Spectr 2022; 10:e0248122. [PMID: 36250854 PMCID: PMC9769575 DOI: 10.1128/spectrum.02481-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar Infantis is the most prevalent serovar found in broilers and broiler meat and is among the top five serovars responsible for human infections in Europe. In 2008, a multidrug-resistant S. Infantis isolate emerged in Israel with a mosaic megaplasmid named pESI, associated with increased virulence, biofilm formation, and multidrug resistance. Since then, S. Infantis clones with pESI-like plasmids have been reported worldwide, replacing pESI-free clones. Here, we typed 161 S. Infantis isolates of poultry (n = 133) and human clinical (n = 28) origin using whole-genome sequencing. The isolates were collected between 2007 and 2021. In addition, we performed PacBio/Illumina sequencing for two representative pESI-like plasmids and compared them with publicly available sequences. All isolates belonged to sequence type 32 (ST32), except for one isolate that represented a novel single-locus variant of ST32. Core genome MLST (cgMLST) analysis revealed 14 clusters of genetically closely related isolates, of which four suggested broiler-to-human transmission of S. Infantis. pESI-like plasmids were present in 148/161 (91.9%) isolates; all were highly similar to the publicly available pESI-like sequences but lacked extended-spectrum beta-lactamase (ESBL) genes. PacBio/Illumina hybrid assembly allowed the reconstruction of two novel complete pESI variants. The present study revealed that the multidrug-resistant, pESI-positive S. Infantis clone became the predominant S. Infantis clone in Slovenian broilers and humans during the last decade. Continued surveillance of resistant S. Infantis clones along the food chain is needed to guide public health efforts. IMPORTANCE Salmonella Infantis clones with pESI-like plasmids harboring several virulence and resistance genes have been reported worldwide. In the present study, we compared the population structure of 161 Salmonella Infantis isolates obtained from humans and broilers in Slovenia from 2007 to 2021. Whole-genome sequencing showed that most human isolates clustered apart from broiler isolates, suggesting an alternative source of infection. Most isolates were multidrug resistant due to the presence of pESI-like plasmids, of which two variants (pS89 and pS19) were fully reconstructed using long-read sequencing. Both exhibited high similarity with the original Israeli pESI plasmid and German p2747 plasmid. The prototype plasmid pS89 harbored the typical pESI-associated resistance genes aadA1, qacEΔ1, sul1, and tet(A), which were absent in the truncated plasmid pS19.
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Affiliation(s)
- Bojan Papić
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Darja Kušar
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jasna Mićunović
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Mateja Pirš
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Matjaž Ocepek
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Avberšek
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
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92
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Boulanger EF, Sabag-Daigle A, Baniasad M, Kokkinias K, Schwieters A, Wrighton KC, Wysocki VH, Ahmer BMM. Sugar-Phosphate Toxicities Attenuate Salmonella Fitness in the Gut. J Bacteriol 2022; 204:e0034422. [PMID: 36383008 PMCID: PMC9765134 DOI: 10.1128/jb.00344-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
Pathogens are becoming resistant to antimicrobials at an increasing rate, and novel therapeutic strategies are needed. Using Salmonella as a model, we have investigated the induction of sugar-phosphate toxicity as a potential therapeutic modality. The approach entails providing a nutrient while blocking the catabolism of that nutrient, resulting in the accumulation of a toxic intermediate. We hypothesize that this build-up will decrease the fitness of the organism during infection given nutrient availability. We tested this hypothesis using mutants lacking one of seven genes whose mutation is expected to cause the accumulation of a toxic metabolic intermediate. The araD, galE, rhaD, glpD, mtlD, manA, and galT mutants were then provided the appropriate sugars, either in vitro or during gastrointestinal infection of mice. All but the glpD mutant had nutrient-dependent growth defects in vitro, suggestive of sugar-phosphate toxicity. During gastrointestinal infection of mice, five mutants had decreased fitness. Providing the appropriate nutrient in the animal's drinking water was required to cause fitness defects with the rhaD and manA mutants and to enhance the fitness defect of the araD mutant. The galE and mtlD mutants were severely attenuated regardless of the nutrient being provided in the drinking water. Homologs of galE are widespread among bacteria and in humans, rendering the specific targeting of bacterial pathogens difficult. However, the araD, mtlD, and rhaD genes are not present in humans, appear to be rare in most phyla of bacteria, and are common in several genera of Enterobacteriaceae, making the encoded enzymes potential narrow-spectrum therapeutic targets. IMPORTANCE Bacterial pathogens are becoming increasingly resistant to antibiotics. There is an urgent need to identify novel drug targets and therapeutic strategies. In this work we have assembled and characterized a collection of mutations in our model pathogen, Salmonella enterica, that block a variety of sugar utilization pathways in such a way as to cause the accumulation of a toxic sugar-phosphate. Mutations in three genes, rhaD, araD, and mtlD, dramatically decrease the fitness of Salmonella in a mouse model of gastroenteritis, suggesting that RhaD, AraD, and MtlD may be good narrow-spectrum drug targets. The induction of sugar-phosphate toxicities may be a therapeutic strategy that is broadly relevant to other bacterial and fungal pathogens.
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Affiliation(s)
- Erin F. Boulanger
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Maryam Baniasad
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Katherine Kokkinias
- Department of Soil and Crop Science, Colorado State University, Ft. Collins, Colorado, USA
| | - Andrew Schwieters
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Kelly C. Wrighton
- Department of Soil and Crop Science, Colorado State University, Ft. Collins, Colorado, USA
| | - Vicki H. Wysocki
- 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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Vilela FP, Rodrigues DDP, Ferreira JC, Darini ALDC, Allard MW, Falcão JP. Genomic characterization of Salmonella enterica serovar Choleraesuis from Brazil reveals a swine gallbladder isolate harboring colistin resistance gene mcr-1.1. Braz J Microbiol 2022; 53:1799-1806. [PMID: 35984599 PMCID: PMC9679059 DOI: 10.1007/s42770-022-00812-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/29/2022] [Indexed: 01/13/2023] Open
Abstract
Salmonella enterica serovar Choleraesuis (S. Choleraesuis) is a swine-adapted serovar associated to invasive infections in humans. In Brazil, data of strains of this serovar are scarce. In the present study, six S. Choleraesuis strains of animal (n = 5) and human (n = 1) origin from Brazil were screened for phenotypic antimicrobial resistance using disk-diffusion assay and using whole-genome sequencing data to search for antimicrobial resistance genes, plasmids, prophages, and Salmonella pathogenicity islands (SPIs). Its genetic relatedness was evaluated by MLST and SNP analysis. A single isolate from swine gallbladder harbored the colistin resistance gene mcr-1.1 into a IncX4 plasmid. In the six strains analyzed, resistance was found to tetracycline, nalidixic acid, ciprofloxacin, ampicillin, piperacillin, streptomycin, cefazoline, gentamycin, sulfamethoxazole-trimethoprim, and choloramphenicol, along with resistance genes aac(6')-Iaa, aac(3)-IV, aph(3'')-Ib, aph(6)-Id, aph(4)-Ia, aadA1, aph(3')-IIa, blaTEM-1A, floR, sul1, sul2, tet(B), drfA1, erm(B), mph(B), lnu(G), qacE, and gyrA point mutation Serine83 → Tyrosine and parC Threonine57 → Serine. Furthermore, IncF and IncH plasmids, ten SPIs, and seven prophage types were detected. All strains were assigned to ST145 and five belonged to a common SNP cluster of S. Choleraesuis strains from Brazil. The presence of S. Choleraesuis isolated from animals harboring relevant antimicrobial resistance profiles and virulence determinants reinforced the urge for enhanced surveillance to avoid its transmission to humans through food items.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. do Café, s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | | | - Joseane Cristina Ferreira
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. do Café, s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Ana Lúcia da Costa Darini
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. do Café, s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Marc William Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA.
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. do Café, s/n, Ribeirão Preto, SP, 14040-903, Brazil.
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94
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Ganji L, Shirazi MH, Ebrahimi-Daryani N, Eslami P, Rahbar M, Zali MR, Alebouyeh M. Carriage of CdtB Encoding Campylobacter spp., Salmonella enterica, and Yersinia entercolitica in Patients with Gastroenteritis and Irritable Bowel Syndrome. Dig Dis Sci 2022; 67:5522-5528. [PMID: 35357609 DOI: 10.1007/s10620-022-07468-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 03/01/2022] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Cytolethal distending toxin (Cdt) is one of the bacterial toxins that present in a variety of gram-negative human pathogens, such as E. coli, Salmonella spp., and Campylobacter spp. CDT is composed of three subunits encoded by three adjacent genes, including cdtA, cdtB, and cdtC. cdtB has been shown to have toxic activity and cause DNA damage in host cells. Despite its presence in different bacterial species, the role of CdtB in acute and chronic infections, such as gastroenteritis and irritable bowel syndrome (IBS), is unclear. To analyze this correlation, we studied the prevalence of cdtB among different enteropathogenic bacteria in patients with gastroenteritis and IBS compared with healthy people. MATERIALS AND METHODS In this cross-sectional descriptive study, 230 stool samples were collected from patients with gastroenteritis, IBS, and healthy people. The presence of CdtB encoding bacteria, including Escherichia coli, Campylobacter spp., Yersinia entercolitica, Providencia alkalifacience, and Salmonella enterica, was examined by polymerase chain reaction using genus-specific primers. RESULTS Out of 230 stool samples, CdtB encoding Campylobacter spp. were found in 34.6% (52/150), 6.25% (5/80), and 4% (2/50) of the patients with gastroenteritis, IBS, and the control group, respectively. Carriage of CdtB encoding Salmonella enterica was characterized among 5.3% (8/150) of the patients with gastroenteritis and 17.5% (14/80) of the IBS patients. Although none of the patients carried CdtB encoding E. coli and Providencia spp., cdtB of Y. enterocolitica was detected in one of the patients with gastroenteritis (0.6%). Statistical analysis showed significant correlation between infection with CdtB encoding Campylobacter spp. and IBS-D subtype. No significant correlation was found between infection with CdtB encoding bacteria and other clinical and demographic data. CONCLUSION Our results confirmed a relatively higher frequency of CdtB encoding bacteria in the intestine of patients with gastroenteritis and those with IBS compared with healthy individuals. Regarding the frequency of CdtB encoding Salmonella and Campylobacter bacteria, it was proposed that infection with these enteropathogens could be considered a risk factor for the development or progression of IBS among Iranian patients. Further studies are needed to establish this involvement.
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Affiliation(s)
- Leila Ganji
- Health Reference Laboratory Research Center, Reference Health Laboratory, Ministry of Health and Medical Education, Tehran, Iran
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hassan Shirazi
- Department of Pathobiology, School of Public Health, University of Medical Sciences, Tehran, Iran
| | - Nasser Ebrahimi-Daryani
- Department of Gastroenterology and Hepatology, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Eslami
- Department of Microbiology, Central Laboratory, Milad Hospital, Tehran, Iran
| | - Mohammad Rahbar
- Health Reference Laboratory Research Center, Reference Health Laboratory, Ministry of Health and Medical Education, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Alebouyeh
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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95
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Tang B, Elbediwi M, Nambiar RB, Yang H, Lin J, Yue M. Genomic Characterization of Antimicrobial-Resistant Salmonella enterica in Duck, Chicken, and Pig Farms and Retail Markets in Eastern China. Microbiol Spectr 2022; 10:e0125722. [PMID: 36047803 PMCID: PMC9603869 DOI: 10.1128/spectrum.01257-22] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/17/2022] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial-resistant Salmonella enterica poses a significant public health concern worldwide. However, the dissemination of Salmonella enterica among food animals in eastern China has not been fully addressed. Here, we demonstrated the antimicrobial resistance (AMR) patterns and the whole-genome characterization of 105 S. enterica isolates from 1,480 fecal samples and anal swabs collected from 22 different farms (chickens, ducks, and pigs) and two live animal markets located in Zhejiang and Fujian Provinces in eastern China in 2019. The prevalence of isolates in duck farms (19.17%, 23/120) was statistically significantly higher (P < 0.001) than that in chicken farms (6.61%, 37/523) and pig farms (3.50%, 7/200). Among these isolates, 75.26% (79/105) were multidrug resistant, with the highest rates of resistance to tetracycline (76.20%) and ampicillin (67.62%) and the lowest resistance rate to meropenem (0.00%). The serotypes were consistent with sequence types and were closely related to the sampling animal species and sites. S. enterica serotype Kentucky (20.95%, 22/105) was the most frequent serotype and harbored more AMR patterns and genes than others. Furthermore, IncFII(S) and IncHI2 were the most prevalent replicons. A total of 44 acquired AMR genes were found. Among those genes, aac(6')-Iaa, blaTEM-1B, floR, dfrA14, fosA7, mph(A), qnrS1, sul1, tet(A), and ARR-3 were the dominant AMR genes mediating the AMR toward aminoglycosides, β-lactams, phenicol, trimethoprim, fosfomycin, macrolide, quinolone, sulfonamides, tetracycline, and rifampin, respectively. The consistency of acquired AMR genes with AMR phenotypes for ampicillin, ceftiofur, ceftazidime, meropenem, sulfamethoxazole-trimethoprim, and tetracycline was >90%. Together, our study highlights the application of whole-genome sequencing to assess veterinary public health threats. IMPORTANCE Public health is a significant concern in China, and the foodborne pathogen Salmonella, which is spread via the animal-borne food chain, plays an important role in the overall disease burden in China annually. The development of advanced sequencing technologies has introduced a new way of understanding emerging pathogens. However, the routine surveillance application of this method in China remains in its infancy. Here, we applied a pool of all isolates from the prevalence data in Zhejiang and Fujian for whole-genome sequencing and combined these data with the cutting-edge bioinformatic analysis pipeline for one-step determination of the complete genetic makeup for all 105 genomes. The illustrated method could provide a cost-effective approach, without labor-intensive laboratory characterization, for predicting serotypes, genotypes, plasmid types, antimicrobial resistance genes, and virulence genes, and thus would provide essential knowledge for emerging pathogens. Our findings and perspectives are essential for delivering updated knowledge on foodborne pathogens in an understudied region in China.
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Affiliation(s)
- Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Mohammed Elbediwi
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Reshma B. Nambiar
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiahui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Min Yue
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- Hainan Institute of Zhejiang University, Sanya, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
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96
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Figueroa-Bossi N, Balbontín R, Bossi L. Working with Bacteria, Phage, and Plasmids. Cold Spring Harb Protoc 2022; 2022:Pdb.top107848. [PMID: 35960618 DOI: 10.1101/pdb.top107848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Methods for the in vivo manipulation of bacterial genomes have improved greatly in recent years because of the discovery of new mechanisms and the gigantic leap forward in DNA-sequencing technology. Many cutting-edge approaches still rely on a variety of technical routines, the correct implementation of which is critical for the success of an experiment. Here, we introduce some of these procedures as used for Escherichia coli and Salmonella enterica We begin by reviewing the aspects of the biology of these two species that are most relevant for their manipulation in the laboratory.
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Affiliation(s)
- Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), 91190 Gif-sur-Yvette, France
| | - Roberto Balbontín
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41080 Sevilla, Spain
| | - Lionello Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), 91190 Gif-sur-Yvette, France
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97
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Yin HB, Chen CH, Katchman B, Newland C, May M, Patel J. Rapid detection of Salmonella enterica in leafy greens by a novel DNA microarray-based PathogenDx system. Food Microbiol 2022; 107:104086. [PMID: 35953180 DOI: 10.1016/j.fm.2022.104086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/17/2022] [Accepted: 06/26/2022] [Indexed: 11/04/2022]
Abstract
The diverse matrices pose great challenges for rapid detection of low Salmonella level (<10 CFU) in fresh produce. The applicability of microarray-based PathogenDx system for detecting low contamination of Salmonella Newport from leafy greens was evaluated. A pre-PCR preparation protocol including enrichment in universal pre-enrichment broth for 3 h followed by sample concentration using an InnovaPrep bio-concentrator or 6 h enrichment without a concentration step was used for detecting S. Newport from leafy greens with initial inoculum level at ∼6 CFU/25 g. Among 205 samples tested, 98%, 93%, 76%, and 60% of Romaine lettuce, Iceberg lettuce, kale, and spinach samples were tested positive after 3 h of enrichment with sample concentration. After 6 h of enrichment, 100%, 98%, 90%, and 82% of Romaine lettuce, Iceberg lettuce, kale, and spinach samples were positive. The samples were parallelly tested by the FDA bacterial analytical manual (BAM) method and 100% of spiked produce samples were tested positive. The overall analysis time of this methodology was between 8 and 11 h, including all pre-enrichment and concentration steps, in contrast to 4-5 days required for BAM method. The system correctly differentiated all 108 Salmonella strains and 35 non-Salmonella strains used in the study. This novel microarray approach provides a rapid method for detecting Salmonella in leafy greens.
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Affiliation(s)
- Hsin-Bai Yin
- U.S.Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Chi-Hung Chen
- U.S.Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA; Oak Ridge Institute for Science and Education (ORISE), Research Participation Program, USA
| | | | | | | | - Jitendra Patel
- U.S.Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA.
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98
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Yang W, Fomenkov A, Heiter D, Xu SY, Ettwiller L. High-throughput sequencing of EcoWI restriction fragments maps the genome-wide landscape of phosphorothioate modification at base resolution. PLoS Genet 2022; 18:e1010389. [PMID: 36121836 PMCID: PMC9521924 DOI: 10.1371/journal.pgen.1010389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/29/2022] [Accepted: 08/18/2022] [Indexed: 11/26/2022] Open
Abstract
Phosphorothioation (PT), in which a non-bridging oxygen is replaced by a sulfur, is one of the rare modifications discovered in bacteria and archaea that occurs on the sugar-phosphate backbone as opposed to the nucleobase moiety of DNA. While PT modification is widespread in the prokaryotic kingdom, how PT modifications are distributed in the genomes and their exact roles in the cell remain to be defined. In this study, we developed a simple and convenient technique called EcoWI-seq based on a modification-dependent restriction endonuclease to identify genomic positions of PT modifications. EcoWI-seq shows similar performance than other PT modification detection techniques and additionally, is easily scalable while requiring little starting material. As a proof of principle, we applied EcoWI-seq to map the PT modifications at base resolution in the genomes of both the Salmonella enterica cerro 87 and E. coli expressing the dnd+ gene cluster. Specifically, we address whether the partial establishment of modified PT positions is a stochastic or deterministic process. EcoWI-seq reveals a systematic usage of the same subset of target sites in clones for which the PT modification has been independently established. Large number of bacteria have modified their DNA mainly as part of a strategy to resist virus infection. Most of the modifications are chemical variations on the canonical bases A, T, C or G with phosphorothioate (PT) being a rare exception of a modification that happens on the backbone of the DNA. Interestingly, this PT modification was first chemically synthesized for specific biotechnological processes before scientists discovered that bacteria and archaea naturally perform this modification using their enzymes. The exact roles of phosphorothioation in bacteria and archaea is still under investigation. To enable further investigation of PT modifications, we designed EcoWI-seq, a method to identify the exact positions of these modifications in bacterial genomes. Notably, we applied the EcoWI-seq to several strains of E. coli for which PT modification has been induced by cloning into these strains, the necessary genes for making such modification. We found that these strains, despite being independently made, followed a precise pattern of PT modification with always the same sites being modified. This result indicates a deterministic process for the establishment of PT modification.
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Affiliation(s)
- Weiwei Yang
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Alexey Fomenkov
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Dan Heiter
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Shuang-yong Xu
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
- * E-mail: (SYX); (LE)
| | - Laurence Ettwiller
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
- * E-mail: (SYX); (LE)
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99
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Pettengill JB, Rand H, Wang SS, Kautter D, Pightling A, Wang Y. Transient and resident pathogens: Intra-facility genetic diversity of Listeria monocytogenes and Salmonella from food production environments. PLoS One 2022; 17:e0268470. [PMID: 36048885 PMCID: PMC9436056 DOI: 10.1371/journal.pone.0268470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/01/2022] [Indexed: 11/18/2022] Open
Abstract
Food production facilities are often routinely tested over time for the presence of foodborne pathogens (e.g., Listeria monocytogenes or Salmonella enterica subsp. enterica). Strains detected in a single sampling event can be classified as transient; positive findings of the same strain across multiple sampling events can be classified as resident pathogens. We analyzed whole-genome sequence (WGS) data from 4,758 isolates (L. monocytogenes = 3,685; Salmonella = 1,073) from environmental samples taken by FDA from 536 U.S. facilities. Our primary objective was to determine the frequency of transient or resident pathogens within food production facilities. Strains were defined as isolates from the same facility that are less than 50 SNP (single-nucleotide polymorphisms) different from one another. Resident pathogens were defined as strains that had more than one isolate collected >59 days apart and from the same facility. We found 1,076 strains (median = 1 and maximum = 21 strains per facility); 180 were resident pathogens, 659 were transient, and 237 came from facilities that had only been sampled once. As a result, 21% of strains (180/ 839) from facilities with positive findings and that were sampled multiple times were found to be resident pathogens; nearly 1 in 4 (23%) of L. monocytogenes strains were found to be resident pathogens compared to 1 in 6 (16%) of Salmonella strains. Our results emphasize the critical importance of preventing the colonization of food production environments by foodborne pathogens, since when colonization does occur, there is an appreciable chance it will become a resident pathogen that presents an ongoing potential to contaminate product.
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Affiliation(s)
- James B. Pettengill
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, United States of America
- * E-mail:
| | - Hugh Rand
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, United States of America
| | - Shizhen S. Wang
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, United States of America
| | - Donald Kautter
- Division Of Plant Products & Beverages, Office of Food Safety, Center for Food Safety and Applied Nutrition; US Food and Drug Administration, College Park, MD, United States of America
| | - Arthur Pightling
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, United States of America
| | - Yu Wang
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, United States of America
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100
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Costa FG, Escalante-Semerena JC. Localization and interaction studies of the Salmonella enterica ethanolamine ammonia-lyase (EutBC), its reactivase (EutA), and the EutT corrinoid adenosyltransferase. Mol Microbiol 2022; 118:191-207. [PMID: 35785499 PMCID: PMC9481676 DOI: 10.1111/mmi.14962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022]
Abstract
Some prokaryotes compartmentalize select metabolic capabilities. Salmonella enterica subspecies enterica serovar Typhimurium LT2 (hereafter S. Typhimurium) catabolizes ethanolamine (EA) within a proteinaceous compartment that we refer to as the ethanolamine utilization (Eut) metabolosome. EA catabolism is initiated by the adenosylcobalamin (AdoCbl)-dependent ethanolamine ammonia-lyase (EAL), which deaminates EA via an adenosyl radical mechanism to yield acetaldehyde plus ammonia. This adenosyl radical can be quenched, requiring the replacement of AdoCbl by the ATP-dependent EutA reactivase. During growth on ethanolamine, S. Typhimurium synthesizes AdoCbl from cobalamin (Cbl) using the ATP:Co(I)rrinoid adenosyltransferase (ACAT) EutT. It is known that EAL localizes to the metabolosome, however, prior to this work, it was unclear where EutA and EutT localized, and whether they interacted with EAL. Here, we provide evidence that EAL, EutA, and EutT localize to the Eut metabolosome, and that EutA interacts directly with EAL. We did not observe interactions between EutT and EAL nor between EutT and the EutA/EAL complex. However, growth phenotypes of a ΔeutT mutant strain show that EutT is critical for efficient ethanolamine catabolism. This work provides a preliminary understanding of the dynamics of AdoCbl synthesis and its uses within the Eut metabolosome.
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Affiliation(s)
- Flavia G. Costa
- Department of Microbiology, University of Georgia, Athens, GA, USA 30602
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