1
|
Nakayama M, Arai N, Ogawa Y, Kusumoto M, Eguchi M. Quantitative method for measuring the proportion of bacterial cells expressing phase 1 or 2 of flagellin of Salmonella enterica serovar Typhimurium. J Microbiol Methods 2024; 225:107013. [PMID: 39128548 DOI: 10.1016/j.mimet.2024.107013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/13/2024]
Abstract
Salmonella enterica subsp. enterica is a major pathogen that causes zoonotic foodborne diseases worldwide. Some Salmonella serovars possess two antigenic phases for flagellin: phase 1 and 2. In Salmonella enterica serovar Typhimurium (S. Typhimurium), the flagellin is antigenically divided into "Hi" as phase 1 and "H1 or H2" as phase 2. Flagellin phase variation is regulated by inversion of hin gene. We focused on the inversion of hin and developed a real-time PCR system to quantitatively measure the proportion of bacterial cells expressing each phase of flagellin. In this study, we demonstrated that our newly developed real-time PCR system shows high quantitative accuracy and aligns with flagellin expression status. Furthermore, the newly developed real-time PCR system was applicable to various S. Typhimurium laboratory and field strains. This newly developed real-time PCR system has the potential to become a powerful tool for analyzing flagellin phase variation.
Collapse
Affiliation(s)
- Momoko Nakayama
- National Institute of Animal Health, NARO, Tsukuba, Ibaraki 305-0856, Japan
| | - Nobuo Arai
- National Institute of Animal Health, NARO, Tsukuba, Ibaraki 305-0856, Japan
| | - Yohsuke Ogawa
- National Institute of Animal Health, NARO, Tsukuba, Ibaraki 305-0856, Japan
| | - Masahiro Kusumoto
- National Institute of Animal Health, NARO, Tsukuba, Ibaraki 305-0856, Japan
| | - Masahiro Eguchi
- National Institute of Animal Health, NARO, Tsukuba, Ibaraki 305-0856, Japan.
| |
Collapse
|
2
|
Yang L, Wu X, Wu G, Wu Y, Li H, Shao B. Association analysis of antibiotic and disinfectant resistome in human and foodborne E. coli in Beijing, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173888. [PMID: 38866143 DOI: 10.1016/j.scitotenv.2024.173888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/21/2024] [Accepted: 06/08/2024] [Indexed: 06/14/2024]
Abstract
The widespread use of chemical disinfectants and antibiotics poses a major threat to food safety and human health. However, the mechanisms of co-transmission of antimicrobial resistance genes (ARGs) and biocides and metal resistance genes (BMRGs) of foodborne pathogens in the food chain is still unclear. This study isolated 343 E. coli strains from animal-derived foods in Beijing and incorporated online data of human-derived E. coli strains from NCBI. Our results demonstrated a relatively uniform distribution of strains from various regions in Beijing, indicating a lack of region-specific clustering. Additionally, predominant sequence types varied between food- and human-derived strains, suggesting a preference for different hosts and environments. Phenotypic association analysis showed that the chlorine disinfectants peroxides had a significant positive correlation with tetracyclines. Many more ARGs and BMRGs were enriched in human-associated E. coli compared with those in chicken- and pork-origin. The quaternary ammonium compounds (QACs) resistance gene qacEΔ1 had a strong correlation with aminoglycoside resistance gene aadA5, folate pathway antagonist resistance gene dfrA17, sul1 and macrolide resistance gene mph(A). The correlation results indicated a significant association between the copper resistance gene cluster pco and the silver resistance gene cluster sil. Coexistence of many resistance genes was observed within the qacEΔ1 gene structure, with qacEΔ1-sul1 being the most common combination. Our findings demonstrated that the epidemiological spread of resistance is affected by a combination of heavy metals, disinfectants and antibiotic use, suggesting that the prevention and control strategies of antimicrobial resistance need to be multifaceted and comprehensive.
Collapse
Affiliation(s)
- Lu Yang
- Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai 200438, China; Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing 100013, China
| | - Xuan Wu
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing 100013, China; School of Public Health, Capital Medical University, Beijing 100069, China
| | - Guoquan Wu
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing 100013, China; National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yige Wu
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing 100013, China; National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hui Li
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing 100013, China; School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Bing Shao
- Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai 200438, China; Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing 100013, China; National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
3
|
Hikal AF, Hasan S, Gudeta D, Zhao S, Foley S, Khan AA. The acquired pco gene cluster in Salmonella enterica mediates resistance to copper. Front Microbiol 2024; 15:1454763. [PMID: 39290517 PMCID: PMC11406079 DOI: 10.3389/fmicb.2024.1454763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
The pervasive environmental metal contamination has led to selection of heavy-metal resistance genes in bacteria. The pco and sil clusters are located on a mobile genetic element and linked to heavy-metal resistance. These clusters have been found in Salmonella enterica serovars isolated from human clinical cases and foods of animal origin. This may be due to the use of heavy metals, such as copper, in animal feed for their antimicrobial and growth promotion properties. The sil cluster can be found alone or in combination with pco cluster, either in the chromosome or on a plasmid. Previous reports have indicated that sil, but not pco, cluster contributes to copper resistance in S. enterica Typhimurium. However, the role of the pco cluster on the physiology of non-typhoidal S. enterica remains poorly understood. To understand the function of the pco gene cluster, a deletion mutant of pcoABCD genes was constructed using allelic exchange mutagenesis. Deletion of pcoABCD genes inhibited growth of S. enterica in high-copper medium, but only under anaerobic environment. Complementation of the mutant reversed the growth phenotype. The survival of S. enterica in RAW264.7 macrophages was not affected by the loss of pcoABCD genes. This study indicates that the acquired pco cluster is crucial for copper detoxification in S. enterica, but it is not essential for intracellular replication within macrophages.
Collapse
Affiliation(s)
- Ahmed F Hikal
- Division of Microbiology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR, United States
| | - Sameer Hasan
- Division of Microbiology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR, United States
| | - Dereje Gudeta
- Division of Microbiology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR, United States
| | - Shaohua Zhao
- Office of Applied Science, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, United States
| | - Steven Foley
- Division of Microbiology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR, United States
| | - Ashraf A Khan
- Division of Microbiology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR, United States
| |
Collapse
|
4
|
Arrieta-Gisasola A, Martínez-Ballesteros I, Martinez-Malaxetxebarria I, Bikandi J, Laorden L. Detection of mobile genetic elements conferring resistance to heavy metals in Salmonella 4,[5],12:i:- and Salmonella Typhimurium serovars and their association with antibiotic resistance. Int J Food Microbiol 2024; 426:110890. [PMID: 39241546 DOI: 10.1016/j.ijfoodmicro.2024.110890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/22/2024] [Accepted: 08/25/2024] [Indexed: 09/09/2024]
Abstract
Salmonella enterica subsp. enterica serovar Typhimurium variant 4,[5],12:i:- (referred to as S. 4,[5],12:i:-) has emerged rapidly as the predominant Salmonella serovar in pigs, often associated with the acquisition of antibiotic resistance (ABR) and heavy metal resistance (HMR) genes. Our study analysed 78 strains of S. 4,[5],12:i:- (n = 57) and S. Typhimurium (n = 21), collected from 1999 to 2021, to investigate the evolution of mobile genetic elements (MGEs) containing HMR and ABR genes. Five MGEs harbouring HMR genes were identified: pUO-STVR2, pSTM45, pUO-STmRV1, SGI-4 and MREL. Among the strains, 91.23 % (52/57) of S. 4,[5],12:i:- carried at least one of these elements, compared to only 14.29 % (3/21) of S. Typhimurium. Since 2008, S. 4,[5],12:i:- have shifted from predominantly carrying pUO-STmRV1 to the emergence of SGI-4 and MREL, reducing ABR genes, reflecting the European Union ban on the use of antibiotics as feed additives. Increased resistance to copper and silver in S. 4,[5],12:i:-, conferred by SGI-4 and MREL, reflected that their acquisition was linked to the ongoing use of heavy metals in food-animal production. However, strains carrying SGI-4 and MREL still exhibit multidrug resistance, emphasising the need for targeted interventions to mitigate multidrug-resistant Salmonella spread in veterinary and public health settings.
Collapse
Affiliation(s)
- A Arrieta-Gisasola
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Diseases, Antimicrobial Agents and Gene Therapy, 01006 Vitoria-Gasteiz, Spain
| | - I Martínez-Ballesteros
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Diseases, Antimicrobial Agents and Gene Therapy, 01006 Vitoria-Gasteiz, Spain
| | - I Martinez-Malaxetxebarria
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Diseases, Antimicrobial Agents and Gene Therapy, 01006 Vitoria-Gasteiz, Spain
| | - J Bikandi
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Diseases, Antimicrobial Agents and Gene Therapy, 01006 Vitoria-Gasteiz, Spain
| | - L Laorden
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Diseases, Antimicrobial Agents and Gene Therapy, 01006 Vitoria-Gasteiz, Spain.
| |
Collapse
|
5
|
Peng J, Feng J, Ji H, Kong X, Hong J, Zhu L, Qian H. Emergence of Rarely Reported Extensively Drug-Resistant Salmonella Enterica Serovar Paratyphi B among Patients in East China. Antibiotics (Basel) 2024; 13:519. [PMID: 38927185 PMCID: PMC11201502 DOI: 10.3390/antibiotics13060519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND In recent years, global concern over increasing multidrug resistance (MDR) among various Salmonella serotypes has grown significantly. However, reports on MDR Salmonella Paratyphi B remain scarce, let alone the extensively drug-resistant (XDR) strains. METHODS In this retrospective study, we investigated the isolates of Salmonella Paratyphi B in Jiangsu Province over the past decade and carried out antimicrobial susceptibility tests, then the strains were sequenced and bioinformatics analyses were performed. RESULTS 27 Salmonella Paratyphi B strains were identified, of which the predominant STs were ST42 (11), ST86 (10), and ST2814 (5). Among these strains, we uncovered four concerning XDR Salmonella Paratyphi B ST2814 strains (4/5) which were previously unreported. These alarmingly resistant isolates showed resistance to all three major antibiotic classes for Salmonella treatment and even the last resort treatment tigecycline. Bioinformatics analysis revealed high similarity between the plasmids harbored by these XDR strains and diverse Salmonella serotypes and Escherichia coli from China and neighboring regions. Notably, these four plasmids carried the ramAp gene responsible for multiple antibiotic resistance by regulating the AcrAB-TolC pump, predominantly originating from China. Additionally, a distinct MDR ST42(1/11) strain with an ICE on chromosome was also identified. Furthermore, phylogenetic analysis of global ST42/ST2814 isolates highlighted the regional specificity of these strains, with Jiangsu isolates clustering together with domestic isolates and XDR ST2814 forming a distinct branch, suggesting adaptation to local antibiotic pressures. CONCLUSIONS This research underscores the pressing need for closely monitoring the MDR/XDR Salmonella Paratyphi B, particularly the emerging ST2814 strains in Jiangsu Province, to effectively curb its spread and protect public health. Moreover, surveillance should be strengthened across different ecological niches and genera to track resistance genes and horizontal gene transfer elements under the concept of "ONE HEALTH".
Collapse
Affiliation(s)
- Jiefu Peng
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
| | - Jingchao Feng
- School of Public Health, Xiamen University, Xiamen 361102, China
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Hong Ji
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
| | - Xiaoxiao Kong
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
| | - Jie Hong
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
| | - Liguo Zhu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
| | - Huimin Qian
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; (J.P.)
| |
Collapse
|
6
|
Elsen S, Simon V, Attrée I. Cross-regulation and cross-talk of conserved and accessory two-component regulatory systems orchestrate Pseudomonas copper resistance. PLoS Genet 2024; 20:e1011325. [PMID: 38861577 PMCID: PMC11195947 DOI: 10.1371/journal.pgen.1011325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/24/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024] Open
Abstract
Bacteria use diverse strategies and molecular machinery to maintain copper homeostasis and to cope with its toxic effects. Some genetic elements providing copper resistance are acquired by horizontal gene transfer; however, little is known about how they are controlled and integrated into the central regulatory network. Here, we studied two copper-responsive systems in a clinical isolate of Pseudomonas paraeruginosa and deciphered the regulatory and cross-regulation mechanisms. To do so, we combined mutagenesis, transcriptional fusion analyses and copper sensitivity phenotypes. Our results showed that the accessory CusRS two-component system (TCS) responds to copper and activates both its own expression and that of the adjacent nine-gene operon (the pcoA2 operon) to provide resistance to elevated levels of extracellular copper. The same locus was also found to be regulated by two core-genome-encoded TCSs-the copper-responsive CopRS and the zinc-responsive CzcRS. Although the target palindromic sequence-ATTCATnnATGTAAT-is the same for the three response regulators, transcriptional outcomes differ. Thus, depending on the operon/regulator pair, binding can result in different activation levels (from none to high), with the systems demonstrating considerable plasticity. Unexpectedly, although the classical CusRS and the noncanonical CopRS TCSs rely on distinct signaling mechanisms (kinase-based vs. phosphatase-based), we discovered cross-talk in the absence of the cognate sensory kinases. This cross-talk occurred between the proteins of these two otherwise independent systems. The cusRS-pcoA2 locus is part of an Integrative and Conjugative Element and was found in other Pseudomonas strains where its expression could provide copper resistance under appropriate conditions. The results presented here illustrate how acquired genetic elements can become part of endogenous regulatory networks, providing a physiological advantage. They also highlight the potential for broader effects of accessory regulatory proteins through interference with core regulatory proteins.
Collapse
Affiliation(s)
- Sylvie Elsen
- University Grenoble Alpes, Institute of Structural Biology, UMR5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
| | - Victor Simon
- University Grenoble Alpes, Institute of Structural Biology, UMR5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
| | - Ina Attrée
- University Grenoble Alpes, Institute of Structural Biology, UMR5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
| |
Collapse
|
7
|
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] [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.
Collapse
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
| |
Collapse
|
8
|
Gomes-Neto JC, Pavlovikj N, Korth N, Naberhaus SA, Arruda B, Benson AK, Kreuder AJ. Salmonella enterica induces biogeography-specific changes in the gut microbiome of pigs. Front Vet Sci 2023; 10:1186554. [PMID: 37781286 PMCID: PMC10537282 DOI: 10.3389/fvets.2023.1186554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023] Open
Abstract
Swine are a major reservoir of an array of zoonotic Salmonella enterica subsp. enterica lineage I serovars including Derby, Typhimurium, and 4,[5],12:i:- (a.k.a. Monophasic Typhimurium). In this study, we assessed the gastrointestinal (GI) microbiome composition of pigs in different intestinal compartments and the feces following infection with specific zoonotic serovars of S. enterica (S. Derby, S. Monophasic, and S. Typhimurium). 16S rRNA based microbiome analysis was performed to assess for GI microbiome changes in terms of diversity (alpha and beta), community structure and volatility, and specific taxa alterations across GI biogeography (small and large intestine, feces) and days post-infection (DPI) 2, 4, and 28; these results were compared to disease phenotypes measured as histopathological changes. As previously reported, only S. Monophasic and S. Typhimurium induced morphological alterations that marked an inflammatory milieu restricted to the large intestine in this experimental model. S. Typhimurium alone induced significant changes at the alpha- (Simpson's and Shannon's indexes) and beta-diversity levels, specifically at the peak of inflammation in the large intestine and feces. Increased community dispersion and volatility in colonic apex and fecal microbiomes were also noted for S. Typhimurium. All three Salmonella serovars altered community structure as measured by co-occurrence networks; this was most prominent at DPI 2 and 4 in colonic apex samples. At the genus taxonomic level, a diverse array of putative short-chain fatty acid (SCFA) producing bacteria were altered and often decreased during the peak of inflammation at DPI 2 and 4 within colonic apex and fecal samples. Among all putative SCFA producing bacteria, Prevotella showed a broad pattern of negative correlation with disease scores at the peak of inflammation. In addition, Prevotella 9 was found to be significantly reduced in all Salmonella infected groups compared to the control at DPI 4 in the colonic apex. In conclusion, this work further elucidates that distinct swine-related zoonotic serovars of S. enterica can induce both shared (high resilience) and unique (altered resistance) alterations in gut microbiome biogeography, which helps inform future investigations of dietary modifications aimed at increasing colonization resistance against Salmonella through GI microbiome alterations.
Collapse
Affiliation(s)
- Joao Carlos Gomes-Neto
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Natasha Pavlovikj
- Holland Computing Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Nate Korth
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Samantha A. Naberhaus
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Bailey Arruda
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Andrew K. Benson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Amanda J. Kreuder
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| |
Collapse
|
9
|
Algarni S, Han J, Gudeta DD, Khajanchi BK, Ricke SC, Kwon YM, Rhoads DD, Foley SL. In silico analyses of diversity and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens. Front Microbiol 2023; 13:1095128. [PMID: 36777021 PMCID: PMC9908598 DOI: 10.3389/fmicb.2022.1095128] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/22/2022] [Indexed: 01/27/2023] Open
Abstract
Introduction The antimicrobial resistance (AMR) mobilome plays a key role in the dissemination of resistance genes encoded by mobile genetics elements (MGEs) including plasmids, transposons (Tns), and insertion sequences (ISs). These MGEs contribute to the dissemination of multidrug resistance (MDR) in enteric bacterial pathogens which have been considered as a global public health risk. Methods To further understand the diversity and distribution of AMR genes and MGEs across different plasmid types, we utilized multiple sequence-based computational approaches to evaluate AMR-associated plasmid genetics. A collection of 1,309 complete plasmid sequences from Gammaproteobacterial species, including 100 plasmids from each of the following 14 incompatibility (Inc) types: A/C, BO, FIA, FIB, FIC, FIIA, HI1, HI2, I1, K, M, N, P except W, where only 9 sequences were available, was extracted from the National Center for Biotechnology Information (NCBI) GenBank database using BLAST tools. The extracted FASTA files were analyzed using the AMRFinderPlus web-based tools to detect antimicrobial, disinfectant, biocide, and heavy metal resistance genes and ISFinder to identify IS/Tn MGEs within the plasmid sequences. Results and Discussion In silico prediction based on plasmid replicon types showed that the resistance genes were diverse among plasmids, yet multiple genes were widely distributed across the plasmids from enteric bacterial species. These findings provide insights into the diversity of resistance genes and that MGEs mediate potential transmission of these genes across multiple plasmid replicon types. This notion was supported by the observation that many IS/Tn MGEs and resistance genes known to be associated with them were common across multiple different plasmid types. Our results provide critical insights about how the diverse population of resistance genes that are carried by the different plasmid types can allow for the dissemination of AMR across enteric bacteria. The results also highlight the value of computational-based approaches and in silico analyses for the assessment of AMR and MGEs, which are important elements of molecular epidemiology and public health outcomes.
Collapse
Affiliation(s)
- Suad Algarni
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Jing Han
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Dereje D. Gudeta
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Bijay K. Khajanchi
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Steven C. Ricke
- Meat Science & Animal Biologics Discovery Program and Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Young Min Kwon
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Douglas D. Rhoads
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven L. Foley
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| |
Collapse
|
10
|
Bloomfield S, Duong VT, Tuyen HT, Campbell JI, Thomson NR, Parkhill J, Le Phuc H, Chau TTH, Maskell DJ, Perron GG, Ngoc NM, Vi LL, Adriaenssens EM, Baker S, Mather AE. Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam. Microb Genom 2022; 8. [PMID: 35511231 PMCID: PMC9465066 DOI: 10.1099/mgen.0.000798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Non-typhoidal Salmonella (NTS) is a major cause of bacterial enterocolitis globally but also causes invasive bloodstream infections. Antimicrobial resistance (AMR) hampers the treatment of these infections and understanding how AMR spreads between NTS may help in developing effective strategies. We investigated NTS isolates associated with invasive disease, diarrhoeal disease and asymptomatic carriage in animals and humans from Vietnam. Isolates included multiple serovars and both common and rare phenotypic AMR profiles; long- and short-read sequencing was used to investigate the genetic mechanisms and genomic backgrounds associated with phenotypic AMR profiles. We demonstrate concordance between most AMR genotypes and phenotypes but identified large genotypic diversity in clinically relevant phenotypes and the high mobility potential of AMR genes (ARGs) in this setting. We found that 84 % of ARGs identified were located on plasmids, most commonly those containing IncHI1A_1 and IncHI1B(R27)_1_R27 replicons (33%), and those containing IncHI2_1 and IncHI2A_1 replicons (31%). The vast majority (95%) of ARGS were found within 10 kbp of IS6/IS26 elements, which provide plasmids with a mechanism to exchange ARGs between plasmids and other parts of the genome. Whole genome sequencing with targeted long-read sequencing applied in a One Health context identified a comparatively limited number of insertion sequences and plasmid replicons associated with AMR. Therefore, in the context of NTS from Vietnam and likely for other settings as well, the mechanisms by which ARGs move contribute to a more successful AMR profile than the specific ARGs, facilitating the adaptation of bacteria to different environments or selection pressures.
Collapse
Affiliation(s)
| | | | - Ha Thanh Tuyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - James I Campbell
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Tran Thi Hong Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Gabriel G Perron
- Department of Biology, Bard College, Annandale-on-Hudson, New York, USA
| | | | - Lu Lan Vi
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.,University of East Anglia, Norwich, UK
| |
Collapse
|
11
|
Trachsel JM, Bearson BL, Brunelle BW, Bearson SMD. Relationship and distribution of Salmonella enterica serovar I 4,[5],12:i:- strain sequences in the NCBI Pathogen Detection database. BMC Genomics 2022; 23:268. [PMID: 35387579 PMCID: PMC8985322 DOI: 10.1186/s12864-022-08458-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/10/2022] [Indexed: 11/14/2022] Open
Abstract
Background Of the > 2600 Salmonella serovars, Salmonella enterica serovar I 4,[5],12:i:- (serovar I 4,[5],12:i:-) has emerged as one of the most common causes of human salmonellosis and the most frequent multidrug-resistant (MDR; resistance to ≥3 antimicrobial classes) nontyphoidal Salmonella serovar in the U.S. Serovar I 4,[5],12:i:- isolates have been described globally with resistance to ampicillin, streptomycin, sulfisoxazole, and tetracycline (R-type ASSuT) and an integrative and conjugative element with multi-metal tolerance named Salmonella Genomic Island 4 (SGI-4). Results We analyzed 13,612 serovar I 4,[5],12:i:- strain sequences available in the NCBI Pathogen Detection database to determine global distribution, animal sources, presence of SGI-4, occurrence of R-type ASSuT, frequency of antimicrobial resistance (AMR), and potential transmission clusters. Genome sequences for serovar I 4,[5],12:i:- strains represented 30 countries from 5 continents (North America, Europe, Asia, Oceania, and South America), but sequences from the United States (59%) and the United Kingdom (28%) were dominant. The metal tolerance island SGI-4 and the R-type ASSuT were present in 71 and 55% of serovar I 4,[5],12:i:- strain sequences, respectively. Sixty-five percent of strain sequences were MDR which correlates to serovar I 4,[5],12:i:- being the most frequent MDR serovar. The distribution of serovar I 4,[5],12:i:- strain sequences in the NCBI Pathogen Detection database suggests that swine-associated strain sequences were the most frequent food-animal source and were significantly more likely to contain the metal tolerance island SGI-4 and genes for MDR compared to all other animal-associated isolate sequences. Conclusions Our study illustrates how analysis of genomic sequences from the NCBI Pathogen Detection database can be utilized to identify the prevalence of genetic features such as antimicrobial resistance, metal tolerance, and virulence genes that may be responsible for the successful emergence of bacterial foodborne pathogens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08458-z.
Collapse
Affiliation(s)
- Julian M Trachsel
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA. .,Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, USA.
| | - Bradley L Bearson
- Agroecosystems Management Research Unit, National Laboratory for Agriculture and the Environment, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA.
| | - Brian W Brunelle
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA.,Present address: Arbor Biosciences, Ann Arbor, MI, USA
| | - Shawn M D Bearson
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA
| |
Collapse
|
12
|
Méndez AAE, Mendoza JI, Echarren ML, Terán I, Checa SK, Soncini FC. Evolution of Copper Homeostasis and Virulence in Salmonella. Front Microbiol 2022; 13:823176. [PMID: 35369444 PMCID: PMC8966772 DOI: 10.3389/fmicb.2022.823176] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/14/2022] [Indexed: 11/24/2022] Open
Abstract
Salmonella enterica sv. Typhimurium modulates the expression of factors essential for virulence, contributing to its survival against the surge of copper (Cu) in the Salmonella-containing vacuole. This bactericidal host innate immune component primarily targets the bacterial envelope, where most cuproproteins are localized. While in most enteric species periplasmic Cu homeostasis is maintained by the CusR/CusS-controlled CusCFBA efflux system encoded in the cus locus, we noticed that these genes were lost from the Salmonella-core genome. At the same time, Salmonella acquired cueP, coding for a periplasmic Cu chaperone. As cus, cueP was shown to be essential for bacterial survival in a copper-rich environment under anaerobiosis, suggesting that it can functionally substitute the CusCFBA system. In the present study, the whole Escherichia coli cus locus was reintroduced to the chromosome of the Salmonella wild-type or the ΔcueP strain. While the integrated cus locus did not affect Cu resistance under aerobic conditions, it increases Cu tolerance under anaerobiosis, irrespective of the presence or absence of cueP. In contrast to the Cus system, CueP expression is higher at high copper concentrations and persisted over time, suggesting separate functions. Finally, we observed that, regardless of the presence or absence of cus, a mutant deleted of cueP shows a deficiency in replication inside macrophages compared to the wild-type strain. Our results demonstrate that CueP and CusCFBA exert redundant functions for metal resistance, but not for intracellular survival, and therefore for the virulence of this pathogen.
Collapse
Affiliation(s)
- Andrea A E Méndez
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Julián I Mendoza
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - María Laura Echarren
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Ignacio Terán
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Susana K Checa
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Fernando C Soncini
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| |
Collapse
|
13
|
Whole genome sequence of Salmonella Rissen SCSW714, a porcine strain harbouring a novel multidrug-resistant Tn7-like pco- and sil-containing transposon. J Glob Antimicrob Resist 2022; 29:307-309. [DOI: 10.1016/j.jgar.2022.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022] Open
|
14
|
Algarni S, Ricke SC, Foley SL, Han J. The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria. Front Microbiol 2022; 13:859854. [PMID: 35432284 PMCID: PMC9008345 DOI: 10.3389/fmicb.2022.859854] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
The foodborne pathogen Salmonella enterica is considered a global public health risk. Salmonella enterica isolates can develop resistance to several antimicrobial drugs due to the rapid spread of antimicrobial resistance (AMR) genes, thus increasing the impact on hospitalization and treatment costs, as well as the healthcare system. Mobile genetic elements (MGEs) play key roles in the dissemination of AMR genes in S. enterica isolates. Multiple phenotypic and molecular techniques have been utilized to better understand the biology and epidemiology of plasmids including DNA sequence analyses, whole genome sequencing (WGS), incompatibility typing, and conjugation studies of plasmids from S. enterica and related species. Focusing on the dynamics of AMR genes is critical for identification and verification of emerging multidrug resistance. The aim of this review is to highlight the updated knowledge of AMR genes in the mobilome of Salmonella and related enteric bacteria. The mobilome is a term defined as all MGEs, including plasmids, transposons, insertion sequences (ISs), gene cassettes, integrons, and resistance islands, that contribute to the potential spread of genes in an organism, including S. enterica isolates and related species, which are the focus of this review.
Collapse
Affiliation(s)
- Suad Algarni
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Steven L. Foley
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Jing Han
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- *Correspondence: Jing Han,
| |
Collapse
|
15
|
A large transposable element mediates metal resistance in the fungus Paecilomyces variotii. Curr Biol 2022; 32:937-950.e5. [PMID: 35063120 DOI: 10.1016/j.cub.2021.12.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/11/2021] [Accepted: 12/17/2021] [Indexed: 12/19/2022]
Abstract
The horizontal transfer of large gene clusters by mobile elements is a key driver of prokaryotic adaptation in response to environmental stresses. Eukaryotic microbes face similar stresses; however, a parallel role for mobile elements has not been established. A stress faced by many microorganisms is toxic metal ions in their environment. In fungi, identified mechanisms for protection against metals generally rely on genes that are dispersed within an organism's genome. Here, we discover a large (∼85 kb) region that confers tolerance to five metal/metalloid ions (arsenate, cadmium, copper, lead, and zinc) in the genomes of some, but not all, strains of a fungus, Paecilomyces variotii. We name this region HEPHAESTUS (Hφ) and present evidence that it is mobile within the P. variotii genome with features characteristic of a transposable element. HEPHAESTUS contains the greatest complement of host-beneficial genes carried by a transposable element in eukaryotes, suggesting that eukaryotic transposable elements might play a role analogous to bacteria in the horizontal transfer of large regions of host-beneficial DNA. Genes within HEPHAESTUS responsible for individual metal tolerances include those encoding a P-type ATPase transporter-PcaA-required for cadmium and lead tolerance, a transporter-ZrcA-providing tolerance to zinc, and a multicopper oxidase-McoA-conferring tolerance to copper. In addition, a subregion of Hφ confers tolerance to arsenate. The genome sequences of other fungi in the Eurotiales contain further examples of HEPHAESTUS, suggesting that it is responsible for independently assembling tolerance to a diverse array of ions, including chromium, mercury, and sodium.
Collapse
|
16
|
Hyre A, Casanova-Hampton K, Subashchandrabose S. Copper Homeostatic Mechanisms and Their Role in the Virulence of Escherichia coli and Salmonella enterica. EcoSal Plus 2021; 9:eESP00142020. [PMID: 34125582 PMCID: PMC8669021 DOI: 10.1128/ecosalplus.esp-0014-2020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Copper is an essential micronutrient that also exerts toxic effects at high concentrations. This review summarizes the current state of knowledge on copper handling and homeostasis systems in Escherichia coli and Salmonella enterica. We describe the mechanisms by which transcriptional regulators, efflux pumps, detoxification enzymes, metallochaperones, and ancillary copper response systems orchestrate cellular response to copper stress. E. coli and S. enterica are important pathogens of humans and animals. We discuss the critical role of copper during killing of these pathogens by macrophages and in nutritional immunity at the bacterial-pathogen-host interface. In closing, we identify opportunities to advance our understanding of the biological roles of copper in these model enteric bacterial pathogens.
Collapse
Affiliation(s)
- Amanda Hyre
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC
| | - Kaitlin Casanova-Hampton
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| |
Collapse
|
17
|
Li C, Tyson GH, Hsu CH, Harrison L, Strain E, Tran TT, Tillman GE, Dessai U, McDermott PF, Zhao S. Long-Read Sequencing Reveals Evolution and Acquisition of Antimicrobial Resistance and Virulence Genes in Salmonella enterica. Front Microbiol 2021; 12:777817. [PMID: 34867920 PMCID: PMC8640207 DOI: 10.3389/fmicb.2021.777817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica is a significant and phylogenetically diverse zoonotic pathogen. To understand its genomic heterogeneity and antimicrobial resistance, we performed long-read sequencing on Salmonella isolated from retail meats and food animals. A collection of 134 multidrug-resistant isolates belonging to 33 serotypes were subjected to PacBio sequencing. One major locus of diversity among these isolates was the presence and orientation of Salmonella pathogenic islands (SPI), which varied across different serotypes but were largely conserved within individual serotypes. We also identified insertion of an IncQ resistance plasmid into the chromosome of fourteen strains of serotype I 4,[5],12:i:- and the Salmonella genomic island 1 (SGI-1) in five serotypes. The presence of various SPIs, SGI-1 and integrated plasmids contributed significantly to the genomic variability and resulted in chromosomal resistance in 55.2% (74/134) of the study isolates. A total of 93.3% (125/134) of isolates carried at least one plasmid, with isolates carrying up to seven plasmids. We closed 233 plasmid sequences of thirteen replicon types, along with twelve hybrid plasmids. Some associations between Salmonella isolate source, serotype, and plasmid type were seen. For instance, IncX plasmids were more common in serotype Kentucky from retail chicken. Plasmids IncC and IncHI had on average more than five antimicrobial resistance genes, whereas in IncX, it was less than one per plasmid. Overall, 60% of multidrug resistance (MDR) strains that carried >3 AMR genes also carried >3 heavy metal resistance genes, raising the possibility of co-selection of antimicrobial resistance in the presence of heavy metals. We also found nine isolates representing four serotypes that carried virulence plasmids with the spv operon. Together, these data demonstrate the power of long-read sequencing to reveal genomic arrangements and integrated plasmids with a high level of resolution for tracking and comparing resistant strains from different sources. Additionally, the findings from this study will help expand the reference set of closed Salmonella genomes that can be used to improve genome assembly from short-read data commonly used in One Health antimicrobial resistance surveillance.
Collapse
Affiliation(s)
- Cong Li
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Gregory H Tyson
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Chih-Hao Hsu
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Lucas Harrison
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Errol Strain
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Thu-Thuy Tran
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Glenn E Tillman
- Food Safety and Inspection Service, United States Department of Agriculture, Athens, GA, United States
| | - Uday Dessai
- Food Safety and Inspection Service, United States Department of Agriculture, Washington, DC, United States
| | - Patrick F McDermott
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Shaohua Zhao
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| |
Collapse
|
18
|
Humphrey S, Fillol-Salom A, Quiles-Puchalt N, Ibarra-Chávez R, Haag AF, Chen J, Penadés JR. Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements. Nat Commun 2021; 12:6509. [PMID: 34750368 PMCID: PMC8575950 DOI: 10.1038/s41467-021-26004-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/03/2021] [Indexed: 12/02/2022] Open
Abstract
It is commonly assumed that the horizontal transfer of most bacterial chromosomal genes is limited, in contrast to the frequent transfer observed for typical mobile genetic elements. However, this view has been recently challenged by the discovery of lateral transduction in Staphylococcus aureus, where temperate phages can drive the transfer of large chromosomal regions at extremely high frequencies. Here, we analyse previously published as well as new datasets to compare horizontal gene transfer rates mediated by different mechanisms in S. aureus and Salmonella enterica. We find that the horizontal transfer of core chromosomal genes via lateral transduction can be more efficient than the transfer of classical mobile genetic elements via conjugation or generalized transduction. These results raise questions about our definition of mobile genetic elements, and the potential roles played by lateral transduction in bacterial evolution.
Collapse
Affiliation(s)
- Suzanne Humphrey
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Alfred Fillol-Salom
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Ibarra-Chávez
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, Bldg. 1, DK2100, Copenhagen, Denmark
| | - Andreas F Haag
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, Singapore
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK.
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, Valencia, 46113, Spain.
| |
Collapse
|
19
|
Haendiges J, Davidson GR, Pettengill JB, Reed E, Ramachandran P, Blessington T, Miller JD, Anderson N, Myoda S, Brown EW, Zheng J, Tikekar R, Hoffmann M. Genomic evidence of environmental and resident Salmonella Senftenberg and Montevideo contamination in the pistachio supply-chain. PLoS One 2021; 16:e0259471. [PMID: 34735518 PMCID: PMC8568146 DOI: 10.1371/journal.pone.0259471] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/19/2021] [Indexed: 12/04/2022] Open
Abstract
Pistachios have been implicated in two salmonellosis outbreaks and multiple recalls in the U.S. This study performed an in-depth retrospective data analysis of Salmonella associated with pistachios as well as a storage study to evaluate the survivability of Salmonella on inoculated inshell pistachios to further understand the genetics and microbiological dynamics of this commodity-pathogen pair. The retrospective data analysis on isolates associated with pistachios was performed utilizing short-read and long-read sequencing technologies. The sequence data were analyzed using two methods: the FDA's Center for Food Safety and Applied Nutrition Single Nucleotide Polymorphism (SNP) analysis and Whole Genome Multilocus Sequence Typing (wgMLST). The year-long storage study evaluated the survival of five strains of Salmonella on pistachios stored at 25 °C at 35% and 54% relative humidity (RH). Our results demonstrate: i) evidence of persistent Salmonella Senftenberg and Salmonella Montevideo strains in pistachio environments, some of which may be due to clonal resident strains and some of which may be due to preharvest contamination; ii) presence of the Copper Homeostasis and Silver Resistance Island (CHASRI) in Salmonella Senftenberg and Montevideo strains in the pistachio supply chain; and iii) the use of metagenomic analysis is a novel tool for determining the composition of serovar survival in a cocktail inoculated storage study.
Collapse
Affiliation(s)
- Julie Haendiges
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States of America
| | - Gordon R Davidson
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - James B Pettengill
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Elizabeth Reed
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Tyann Blessington
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Jesse D Miller
- Neogen Corporation, Lansing, Michigan, United States of America
| | - Nathan Anderson
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, Illinois, United States of America
| | - Sam Myoda
- IEH Incorporated, Seattle, Washington, United States of America
| | - Eric W Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Rohan Tikekar
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States of America
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| |
Collapse
|
20
|
Bearson SMD. Salmonella in Swine: Prevalence, Multidrug Resistance, and Vaccination Strategies. Annu Rev Anim Biosci 2021; 10:373-393. [PMID: 34699256 DOI: 10.1146/annurev-animal-013120-043304] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An estimated 1.3 million Salmonella infections and 420 deaths occur annually in the United States, with an estimated economic burden of $3.7 billion. More than 50% of US swine operations test positive for Salmonella according to the National Animal Health Monitoring System, and 20% of Salmonella from swine are multidrug resistant (resistant to ≥3 antimicrobial classes) as reported by the National Antimicrobial Resistance Monitoring System. This review on Salmonella in swine addresses the current status of these topics by discussing antimicrobial resistance and metal tolerance in Salmonella and the contribution of horizontal gene transfer. A major challenge in controlling Salmonella is that Salmonella is a foodborne pathogen in humans but is often a commensal in food animals and thereby establishes an asymptomatic reservoir state in such animals, including swine. As food animal production systems continue to expand and antimicrobial usage becomes more limited, the need for Salmonella interventions has intensified. A promising mitigation strategy is vaccination against Salmonella in swine to limit animal, environmental, and food contamination. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Shawn M D Bearson
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Center, US Department of Agriculture, Ames, Iowa, USA;
| |
Collapse
|
21
|
Gomes-Neto JC, Pavlovikj N, Cano C, Abdalhamid B, Al-Ghalith GA, Loy JD, Knights D, Iwen PC, Chaves BD, Benson AK. Heuristic and Hierarchical-Based Population Mining of Salmonella enterica Lineage I Pan-Genomes as a Platform to Enhance Food Safety. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.725791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The recent incorporation of bacterial whole-genome sequencing (WGS) into Public Health laboratories has enhanced foodborne outbreak detection and source attribution. As a result, large volumes of publicly available datasets can be used to study the biology of foodborne pathogen populations at an unprecedented scale. To demonstrate the application of a heuristic and agnostic hierarchical population structure guided pan-genome enrichment analysis (PANGEA), we used populations of S. enterica lineage I to achieve two main objectives: (i) show how hierarchical population inquiry at different scales of resolution can enhance ecological and epidemiological inquiries; and (ii) identify population-specific inferable traits that could provide selective advantages in food production environments. Publicly available WGS data were obtained from NCBI database for three serovars of Salmonella enterica subsp. enterica lineage I (S. Typhimurium, S. Newport, and S. Infantis). Using the hierarchical genotypic classifications (Serovar, BAPS1, ST, cgMLST), datasets from each of the three serovars showed varying degrees of clonal structuring. When the accessory genome (PANGEA) was mapped onto these hierarchical structures, accessory loci could be linked with specific genotypes. A large heavy-metal resistance mobile element was found in the Monophasic ST34 lineage of S. Typhimurium, and laboratory testing showed that Monophasic isolates have on average a higher degree of copper resistance than the Biphasic ones. In S. Newport, an extra sugE gene copy was found among most isolates of the ST45 lineage, and laboratory testing of multiple isolates confirmed that isolates of S. Newport ST45 were on average less sensitive to the disinfectant cetylpyridimium chloride than non-ST45 isolates. Lastly, data-mining of the accessory genomic content of S. Infantis revealed two cryptic Ecotypes with distinct accessory genomic content and distinct ecological patterns. Poultry appears to be the major reservoir for Ecotype 1, and temporal analysis further suggested a recent ecological succession, with Ecotype 2 apparently being displaced by Ecotype 1. Altogether, the use of a heuristic hierarchical-based population structure analysis that includes bacterial pan-genomes (core and accessory genomes) can (1) improve genomic resolution for mapping populations and accessing epidemiological patterns; and (2) define lineage-specific informative loci that may be associated with survival in the food chain.
Collapse
|
22
|
Pajarillo EAB, Lee E, Kang DK. Trace metals and animal health: Interplay of the gut microbiota with iron, manganese, zinc, and copper. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2021; 7:750-761. [PMID: 34466679 PMCID: PMC8379138 DOI: 10.1016/j.aninu.2021.03.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/27/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022]
Abstract
Metals such as iron, manganese, copper, and zinc are recognized as essential trace elements. These trace metals play critical roles in development, growth, and metabolism, participating in various metabolic processes by acting as cofactors of enzymes or providing structural support to proteins. Deficiency or toxicity of these metals can impact human and animal health, giving rise to a number of metabolic and neurological disorders. Proper breakdown, absorption, and elimination of these trace metals is a tightly regulated process that requires crosstalk between the host and these micronutrients. The gut is a complex system that serves as the interface between these components, but other factors that contribute to this delicate interaction are not well understood. The gut is home to trillions of microorganisms and microbial genes (the gut microbiome) that can regulate the metabolism and transport of micronutrients and contribute to the bioavailability of trace metals through their assimilation from food sources or by competing with the host. Furthermore, deficiency or toxicity of these metals can modulate the gut microenvironment, including microbiota, nutrient availability, stress, and immunity. Thus, understanding the role of the gut microbiota in the metabolism of manganese, iron, copper, and zinc, as well as in heavy metal deficiencies and toxicities, and vice versa, may provide insight into developing improved or alternative therapeutic strategies to address emerging health concerns. This review describes the current understanding of how the gut microbiome and trace metals interact and affect host health, particularly in pigs.
Collapse
Affiliation(s)
- Edward Alain B. Pajarillo
- Department of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee 32307, FL, USA
| | - Eunsook Lee
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Republic of Korea
| | - Dae-Kyung Kang
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Republic of Korea
| |
Collapse
|
23
|
Ingle DJ, Ambrose RL, Baines SL, Duchene S, Gonçalves da Silva A, Lee DYJ, Jones M, Valcanis M, Taiaroa G, Ballard SA, Kirk MD, Howden BP, Pearson JS, Williamson DA. Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia. Nat Commun 2021; 12:4786. [PMID: 34373455 PMCID: PMC8352879 DOI: 10.1038/s41467-021-25073-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergence and evolution of Salmonella 4,[5],12:i:- in Australia. We show that the interruption of the genetic region surrounding the phase II flagellin, FljB, causing a monophasic phenotype, represents a stepwise evolutionary event through the accumulation of mobile resistance elements with minimal impairment to bacterial fitness. We identify three lineages with different population dynamics and discrete antimicrobial resistance profiles emerged, likely reflecting differential antimicrobial selection pressures. Two lineages are associated with travel to South-East Asia and the third lineage is endemic to Australia. Moreover antimicrobial-resistant Salmonella 4,[5],12:i- lineages efficiently infected and survived in host phagocytes and epithelial cells without eliciting significant cellular cytotoxicity, suggesting a suppression of host immune response that may facilitate the persistence of Salmonella 4,[5],12:i:-.
Collapse
Affiliation(s)
- Danielle J Ingle
- Research School of Population Health, Australian National University, Canberra, ACT, Australia.
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Rebecca L Ambrose
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Darren Y J Lee
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Miriam Jones
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Martyn D Kirk
- Research School of Population Health, Australian National University, Canberra, ACT, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jaclyn S Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia.
| |
Collapse
|
24
|
Analysis of 56,348 Genomes Identifies the Relationship between Antibiotic and Metal Resistance and the Spread of Multidrug-Resistant Non-Typhoidal Salmonella. Microorganisms 2021; 9:microorganisms9071468. [PMID: 34361911 PMCID: PMC8306355 DOI: 10.3390/microorganisms9071468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 01/14/2023] Open
Abstract
Salmonella enterica is common foodborne pathogen that generates both enteric and systemic infections in hosts. Antibiotic resistance is common is certain serovars of the pathogen and of great concern to public health. Recent reports have documented the co-occurrence of metal resistance with antibiotic resistance in one serovar of S. enterica. Therefore, we sought to identify possible co-occurrence in a large genomic dataset. Genome assemblies of 56,348 strains of S. enterica comprising 20 major serovars were downloaded from NCBI. The downloaded assemblies were quality controlled and in silico serotyped to ensure consistency and avoid improper annotation from public databases. Metal and antibiotic resistance genes were identified in the genomes as well as plasmid replicons. Co-occurrent genes were identified by constructing a co-occurrence matrix and grouping said matrix using k-means clustering. Three groups of co-occurrent genes were identified using k-means clustering. Group 1 was comprised of the pco and sil operons that confer resistance to copper and silver, respectively. Group 1 was distributed across four serovars. Group 2 contained the majority of the genes and little to no co-occurrence was observed. Metal and antibiotic co-occurrence was identified in group 3 that contained genes conferring resistance to: arsenic, mercury, beta-lactams, sulfonamides, and tetracyclines. Group 3 genes were also associated with an IncQ1 class plasmid replicon. Metal and antibiotic co-occurrence from group 3 genes is mostly isolated to one clade of S. enterica I 4,[5],12:i:-.
Collapse
|
25
|
Arai N, Sekizuka T, Tamamura-Andoh Y, Barco L, Hinenoya A, Yamasaki S, Iwata T, Watanabe-Yanai A, Kuroda M, Akiba M, Kusumoto M. Identification of a Recently Dominant Sublineage in Salmonella 4,[5],12:i:- Sequence Type 34 Isolated From Food Animals in Japan. Front Microbiol 2021; 12:690947. [PMID: 34276624 PMCID: PMC8281233 DOI: 10.3389/fmicb.2021.690947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/09/2021] [Indexed: 12/03/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Typhimurium sequence type 34 (ST34) and its monophasic variant (Salmonella 4,[5],12:i:-) are among the most frequently isolated clones from both humans and animals worldwide. Our previous study demonstrated that Salmonella Typhimurium/4,[5],12:i:- strains isolated in Japan could be classified into nine clades and that clade 9 consisted of ST34 strains. In Japan, ST34/clade 9 was first found in the 1990s and has become predominant among food animals in recent years. In the present study, we analyzed the whole genome-based phylogenetic relationships and temporal information of 214 Salmonella Typhimurium/4,[5],12:i:- ST34/clade 9 strains isolated from 1998 to 2017 in Japan. The 214 strains were classified into two sublineages: the newly identified clade 9–2 diverged from clade 9 in the early 2000s and has predominated in recent years. Clonally expanding subclades in clades 9–1 or 9–2 lacked Gifsy-1 or HP1 prophages, respectively, and some strains in these subclades acquired plasmids encoding antimicrobial resistance genes. Additional genome reduction around the fljB gene encoding the phase 2-H antigen was generated by an IS26-mediated deletion adjacent to the transposon in clade 9–2. Although most of the clade 9 strains were isolated from cattle in Japan, the clonally expanding subclades in clade 9–2 (i.e., all and 24% strains of subclades 9–2a and 9–2b, respectively) were isolated from swine. The spread of clade 9 in recent years among food animals in Japan was responsible for the emergence of multiple host-adapted sublineages involving the clonally expanding subclades generated by mobile genetic element-mediated microevolution.
Collapse
Affiliation(s)
- Nobuo Arai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukino Tamamura-Andoh
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Lisa Barco
- Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| | - Atsushi Hinenoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Shinji Yamasaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Taketoshi Iwata
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Ayako Watanabe-Yanai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Akiba
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Masahiro Kusumoto
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| |
Collapse
|
26
|
Johansson MHK, Bortolaia V, Tansirichaiya S, Aarestrup FM, Roberts AP, Petersen TN. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother 2021; 76:101-109. [PMID: 33009809 PMCID: PMC7729385 DOI: 10.1093/jac/dkaa390] [Citation(s) in RCA: 279] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/19/2020] [Indexed: 11/17/2022] Open
Abstract
Objectives Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. Methods The tool MobileElementFinder was developed to enable rapid detection of MGEs and their genetic context in assembled sequence data. MGEs are detected based on sequence similarity to a database of 4452 known elements augmented with annotation of resistance genes, virulence factors and detection of plasmids. Results MobileElementFinder was applied to analyse the mobilome of 1725 sequenced Salmonella enterica isolates of animal origin from Denmark, Germany and the USA. We found that the MGEs were seemingly conserved according to multilocus ST and not restricted to either the host or the country of origin. Moreover, we identified putative translocatable units for specific aminoglycoside, sulphonamide and tetracycline genes. Several putative composite transposons were predicted that could mobilize, among others, AMR, metal resistance and phosphodiesterase genes associated with macrophage survivability. This is, to our knowledge, the first time the phosphodiesterase-like pdeL has been found to be potentially mobilized into S. enterica. Conclusions MobileElementFinder is a powerful tool to study the epidemiology of MGEs in a large number of genome sequences and to determine the potential for genomic plasticity of bacteria. This web service provides a convenient method of detecting MGEs in assembled sequence data. MobileElementFinder can be accessed at https://cge.cbs.dtu.dk/services/MobileElementFinder/.
Collapse
Affiliation(s)
- Markus H K Johansson
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Supathep Tansirichaiya
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Thomas N Petersen
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
27
|
Sklyar T, Kurahina N, Lavrentieva K, Burlaka V, Lykholat T, Lykholat O. Autonomic (Mobile) Genetic Elements of Bacteria and Their Hierarchy. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721030099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
28
|
Pavlovikj N, Gomes-Neto JC, Deogun JS, Benson AK. ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses. PeerJ 2021; 9:e11376. [PMID: 34055480 PMCID: PMC8142932 DOI: 10.7717/peerj.11376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/08/2021] [Indexed: 12/28/2022] Open
Abstract
Whole Genome Sequence (WGS) data from bacterial species is used for a variety of applications ranging from basic microbiological research, diagnostics, and epidemiological surveillance. The availability of WGS data from hundreds of thousands of individual isolates of individual microbial species poses a tremendous opportunity for discovery and hypothesis-generating research into ecology and evolution of these microorganisms. Flexibility, scalability, and user-friendliness of existing pipelines for population-scale inquiry, however, limit applications of systematic, population-scale approaches. Here, we present ProkEvo, an automated, scalable, reproducible, and open-source framework for bacterial population genomics analyses using WGS data. ProkEvo was specifically developed to achieve the following goals: (1) Automation and scaling of complex combinations of computational analyses for many thousands of bacterial genomes from inputs of raw Illumina paired-end sequence reads; (2) Use of workflow management systems (WMS) such as Pegasus WMS to ensure reproducibility, scalability, modularity, fault-tolerance, and robust file management throughout the process; (3) Use of high-performance and high-throughput computational platforms; (4) Generation of hierarchical-based population structure analysis based on combinations of multi-locus and Bayesian statistical approaches for classification for ecological and epidemiological inquiries; (5) Association of antimicrobial resistance (AMR) genes, putative virulence factors, and plasmids from curated databases with the hierarchically-related genotypic classifications; and (6) Production of pan-genome annotations and data compilation that can be utilized for downstream analysis such as identification of population-specific genomic signatures. The scalability of ProkEvo was measured with two datasets comprising significantly different numbers of input genomes (one with ~2,400 genomes, and the second with ~23,000 genomes). Depending on the dataset and the computational platform used, the running time of ProkEvo varied from ~3-26 days. ProkEvo can be used with virtually any bacterial species, and the Pegasus WMS uniquely facilitates addition or removal of programs from the workflow or modification of options within them. To demonstrate versatility of the ProkEvo platform, we performed a hierarchical-based population structure analyses from available genomes of three distinct pathogenic bacterial species as individual case studies. The specific case studies illustrate how hierarchical analyses of population structures, genotype frequencies, and distribution of specific gene functions can be integrated into an analysis. Collectively, our study shows that ProkEvo presents a practical viable option for scalable, automated analyses of bacterial populations with direct applications for basic microbiology research, clinical microbiological diagnostics, and epidemiological surveillance.
Collapse
Affiliation(s)
- Natasha Pavlovikj
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Joao Carlos Gomes-Neto
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America.,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jitender S Deogun
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Andrew K Benson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America.,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| |
Collapse
|
29
|
Cunrath O, Palmer JD. An overview of Salmonella enterica metal homeostasis pathways during infection. ACTA ACUST UNITED AC 2021; 2:uqab001. [PMID: 34250489 PMCID: PMC8264917 DOI: 10.1093/femsml/uqab001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/19/2021] [Indexed: 12/14/2022]
Abstract
Nutritional immunity is a powerful strategy at the core of the battlefield between host survival and pathogen proliferation. A host can prevent pathogens from accessing biological metals such as Mg, Fe, Zn, Mn, Cu, Co or Ni, or actively intoxicate them with metal overload. While the importance of metal homeostasis for the enteric pathogen Salmonella enterica Typhimurium was demonstrated many decades ago, inconsistent results across various mouse models, diverse Salmonella genotypes, and differing infection routes challenge aspects of our understanding of this phenomenon. With expanding access to CRISPR-Cas9 for host genome manipulation, it is now pertinent to re-visit past results in the context of specific mouse models, identify gaps and incongruities in current knowledge landscape of Salmonella homeostasis, and recommend a straight path forward towards a more universal understanding of this historic host-microbe relationship.
Collapse
Affiliation(s)
- Olivier Cunrath
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Rd, Oxford, UK OX1 3SZ
| | - Jacob D Palmer
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Rd, Oxford, UK OX1 3SZ
| |
Collapse
|
30
|
Mthembu TP, Zishiri OT, El Zowalaty ME. Genomic Characterization of Antimicrobial Resistance in Food Chain and Livestock-Associated Salmonella Species. Animals (Basel) 2021; 11:872. [PMID: 33803844 PMCID: PMC8003163 DOI: 10.3390/ani11030872] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/08/2021] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
The rising trend of antimicrobial resistance (AMR) by foodborne bacteria is a public health concern as these pathogens are easily transmitted to humans through the food chain. Non-typhoid Salmonella spp. is one of the leading foodborne pathogens which infect humans worldwide and is associated with food and livestock. Due to the lack of discovery of new antibiotics and the pressure exerted by antimicrobial resistance in the pharmaceutical industry, this review aimed to address the issue of antibiotic use in livestock which leads to AMR in Salmonella. Much attention was given to resistance to carbapenems and colistin which are the last-line antibiotics used in cases of multi drug resistant bacterial infections. In the present review, we highlighted data published on antimicrobial resistant Salmonella species and serovars associated with livestock and food chain animals. The importance of genomic characterization of carbapenem and colistin resistant Salmonella in determining the relationship between human clinical isolates and food animal isolates was also discussed in this review. Plasmids, transposons, and insertion sequence elements mediate dissemination of not only AMR genes but also genes for resistance to heavy metals and disinfectants, thus limiting the therapeutic options for treatment and control of Salmonella. Genes for resistance to colistin (mcr-1 to mcr-9) and carbapenem (blaVIM-1, blaDNM-1, and blaNDM-5) have been detected from poultry, pig, and human Salmonella isolates, indicating food animal-associated AMR which is a threat to human public health. Genotyping, plasmid characterization, and phylogenetic analysis is important in understanding the epidemiology of livestock-related Salmonella so that measures of preventing foodborne threats to humans can be improved.
Collapse
Affiliation(s)
- Thobeka P. Mthembu
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa; (T.P.M.); (O.T.Z.)
| | - Oliver T. Zishiri
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa; (T.P.M.); (O.T.Z.)
| | - Mohamed E. El Zowalaty
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala SE 751 23, Sweden
| |
Collapse
|
31
|
de Curraize C, Siebor E, Neuwirth C. Genomic islands related to Salmonella genomic island 1; integrative mobilisable elements in trmE mobilised in trans by A/C plasmids. Plasmid 2021; 114:102565. [PMID: 33582118 DOI: 10.1016/j.plasmid.2021.102565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/01/2022]
Abstract
Salmonella genomic island 1 (SGI1), an integrative mobilisable element (IME), was first reported 20 years ago, in the multidrug resistant Salmonella Typhimurium DT104 clone. Since this first report, many variants and relatives have been found in Salmonella enterica and Proteus mirabilis. Thanks to whole genome sequencing, more and more complete sequences of SGI1-related elements (SGI1-REs) have been reported in these last few years among Gammaproteobacteria. Here, the genetic organisation and main features common to SGI1-REs are summarised to help to classify them. Their integrases belong to the tyrosine-recombinase family and target the 3'-end of the trmE gene. They share the same genetic organisation (integrase and excisionase genes, replicase module, SgaCD-like transcriptional activator genes, traN, traG, mpsB/mpsA genes) and they harbour AcaCD binding sites promoting their excision, replication and mobilisation in presence of A/C plasmid. SGI1-REs are mosaic structures suggesting that recombination events occurred between them. Most of them harbour a multiple antibiotic resistance (MAR) region and the plasticity of their MAR region show that SGI1-REs play a key role in antibiotic resistance and might help multiple antibiotic resistant bacteria to adapt to their environment. This might explain the emergence of clones with SGI1-REs.
Collapse
Affiliation(s)
- Claire de Curraize
- Bacteriology Department, University Hospital Dijon, PBHU, BP 37013, 21070 Dijon Cedex, France; UMR 6249, Chrono-Environnement, PBHU, BP 37013, 21070 Dijon Cedex, France.
| | - Eliane Siebor
- Bacteriology Department, University Hospital Dijon, PBHU, BP 37013, 21070 Dijon Cedex, France; UMR 6249, Chrono-Environnement, PBHU, BP 37013, 21070 Dijon Cedex, France.
| | - Catherine Neuwirth
- Bacteriology Department, University Hospital Dijon, PBHU, BP 37013, 21070 Dijon Cedex, France; UMR 6249, Chrono-Environnement, PBHU, BP 37013, 21070 Dijon Cedex, France.
| |
Collapse
|
32
|
Copper Handling in the Salmonella Cell Envelope and Its Impact on Virulence. Trends Microbiol 2021; 29:384-387. [PMID: 33516594 DOI: 10.1016/j.tim.2021.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 12/22/2022]
Abstract
Copper (Cu) plays a key role at the host-pathogen interface as both an essential element and a toxic element. Intracellular strains of pathogenic Salmonella have acquired the periplasmic Cu chaperone, CueP, and the thiol oxidoreductases complex Scs, while losing the ancestral Cu-detoxification Cus system. Coregulation of these species-specific factors link Cu with redox stress and allows Salmonella to counteract Cu toxicity during infection.
Collapse
|
33
|
Bearson BL, Trachsel JM, Shippy DC, Sivasankaran SK, Kerr BJ, Loving CL, Brunelle BW, Curry SM, Gabler NK, Bearson SMD. The Role of Salmonella Genomic Island 4 in Metal Tolerance of Salmonella enterica Serovar I 4,[5],12:i:- Pork Outbreak Isolate USDA15WA-1. Genes (Basel) 2020; 11:genes11111291. [PMID: 33142960 PMCID: PMC7716197 DOI: 10.3390/genes11111291] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 12/16/2022] Open
Abstract
Multidrug-resistant (MDR; resistance to >3 antimicrobial classes) Salmonella enterica serovar I 4,[5],12:i:- strains were linked to a 2015 foodborne outbreak from pork. Strain USDA15WA-1, associated with the outbreak, harbors an MDR module and the metal tolerance element Salmonella Genomic Island 4 (SGI-4). Characterization of SGI-4 revealed that conjugational transfer of SGI-4 resulted in the mobile genetic element (MGE) replicating as a plasmid or integrating into the chromosome. Tolerance to copper, arsenic, and antimony compounds was increased in Salmonella strains containing SGI-4 compared to strains lacking the MGE. Following Salmonella exposure to copper, RNA-seq transcriptional analysis demonstrated significant differential expression of diverse genes and pathways, including induction of at least 38 metal tolerance genes (copper, arsenic, silver, and mercury). Evaluation of swine administered elevated concentrations of zinc oxide (2000 mg/kg) and copper sulfate (200 mg/kg) as an antimicrobial feed additive (Zn+Cu) in their diet for four weeks prior to and three weeks post-inoculation with serovar I 4,[5],12:i:- indicated that Salmonella shedding levels declined at a slower rate in pigs receiving in-feed Zn+Cu compared to control pigs (no Zn+Cu). The presence of metal tolerance genes in MDR Salmonella serovar I 4,[5],12:i:- may provide benefits for environmental survival or swine colonization in metal-containing settings.
Collapse
Affiliation(s)
- Bradley L. Bearson
- USDA, ARS, National Laboratory for Agriculture and the Environment, Agroecosystems Management Research Unit, Ames, IA 50011, USA; (B.J.K.); (S.M.C.)
- Correspondence: ; Tel.: +1-515-294-0209
| | - Julian M. Trachsel
- USDA, ARS, National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA 50010, USA; (J.M.T.); (D.C.S.); (S.K.S.); (C.L.L.); (B.W.B.); (S.M.D.B.)
| | - Daniel C. Shippy
- USDA, ARS, National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA 50010, USA; (J.M.T.); (D.C.S.); (S.K.S.); (C.L.L.); (B.W.B.); (S.M.D.B.)
| | - Sathesh K. Sivasankaran
- USDA, ARS, National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA 50010, USA; (J.M.T.); (D.C.S.); (S.K.S.); (C.L.L.); (B.W.B.); (S.M.D.B.)
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA
| | - Brian J. Kerr
- USDA, ARS, National Laboratory for Agriculture and the Environment, Agroecosystems Management Research Unit, Ames, IA 50011, USA; (B.J.K.); (S.M.C.)
| | - Crystal L. Loving
- USDA, ARS, National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA 50010, USA; (J.M.T.); (D.C.S.); (S.K.S.); (C.L.L.); (B.W.B.); (S.M.D.B.)
| | - Brian W. Brunelle
- USDA, ARS, National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA 50010, USA; (J.M.T.); (D.C.S.); (S.K.S.); (C.L.L.); (B.W.B.); (S.M.D.B.)
| | - Shelby M. Curry
- USDA, ARS, National Laboratory for Agriculture and the Environment, Agroecosystems Management Research Unit, Ames, IA 50011, USA; (B.J.K.); (S.M.C.)
| | | | - Shawn M. D. Bearson
- USDA, ARS, National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA 50010, USA; (J.M.T.); (D.C.S.); (S.K.S.); (C.L.L.); (B.W.B.); (S.M.D.B.)
| |
Collapse
|
34
|
Clark CG, Landgraff C, Robertson J, Pollari F, Parker S, Nadon C, Gannon VPJ, Johnson R, Nash J. Distribution of heavy metal resistance elements in Canadian Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype. PLoS One 2020; 15:e0236436. [PMID: 32716946 PMCID: PMC7384650 DOI: 10.1371/journal.pone.0236436] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/06/2020] [Indexed: 12/02/2022] Open
Abstract
Salmonella 4,[5],12:i:- are monophasic S. Typhimurium variants incapable of producing the second-phase flagellar antigen. They have emerged since the mid-1990s to become one of the most prevalent Salmonella serotypes causing human disease world-wide. Multiple genetic events associated with different genetic elements can result in the monophasic phenotype. Several jurisdictions have reported the emergence of a Salmonella 4,[5],12:i:- clone with SGI-4 and a genetic element (MREL) encoding a mercury resistance operon and antibiotic resistance loci that disrupts the second phase antigen region near the iroB locus in the Salmonella genome. We have sequenced 810 human and animal Canadian Salmonella 4,[5],12:i:- isolates and determined that isolates with SGI-4 and the mercury resistance element (MREL; also known as RR1&RR2) constitute several global clades containing various proportions of Canadian, US, and European isolates. Detailed analysis of the data provides a clearer picture of how these heavy metal elements interact with bacteria within the Salmonella population to produce the monophasic phenotype. Insertion of the MREL near iroB is associated with several deletions and rearrangements of the adjacent flaAB hin region, which may be useful for defining human case clusters that could represent outbreaks. Plasmids carrying genes encoding silver, copper, mercury, and antimicrobial resistance appear to be derived from IS26 mediated acquisition of these genes from genomes carrying SGI-4 and the MREL. Animal isolates with the mercury and As/Cu/Ag resistance elements are strongly associated with porcine sources in Canada as has been shown previously for other jurisdictions. The data acquired in these investigations, as well as from the extensive literature on the subject, may aid source attribution in outbreaks of the organism and interventions to decrease the prevalence of this clone and reduce its impact on human disease.
Collapse
Affiliation(s)
- Clifford G Clark
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chrystal Landgraff
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - James Robertson
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Frank Pollari
- FoodNet Canada, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Stephen Parker
- FoodNet Canada, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Celine Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- PulseNet Canada, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Victor P J Gannon
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Canada
| | - Roger Johnson
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - John Nash
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| |
Collapse
|
35
|
Giachino A, Waldron KJ. Copper tolerance in bacteria requires the activation of multiple accessory pathways. Mol Microbiol 2020; 114:377-390. [DOI: 10.1111/mmi.14522] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Andrea Giachino
- Biosciences Institute Faculty of Medical Sciences Newcastle University Newcastle upon Tyne UK
| | - Kevin J. Waldron
- Biosciences Institute Faculty of Medical Sciences Newcastle University Newcastle upon Tyne UK
| |
Collapse
|
36
|
Mourão J, Rebelo A, Ribeiro S, Peixe L, Novais C, Antunes P. Tolerance to arsenic contaminant among multidrug‐resistant and copper‐tolerant
Salmonella
successful clones is associated with diverse
ars
operons and genetic contexts. Environ Microbiol 2020; 22:2829-2842. [DOI: 10.1111/1462-2920.15016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/13/2020] [Accepted: 04/08/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Joana Mourão
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Center for Innovative Biomedicine and BiotechnologyUniversity of Coimbra Coimbra Portugal
- Center for Neuroscience and Cell BiologyUniversity of Coimbra Coimbra Portugal
- Institute for Interdisciplinary Research, University of Coimbra Coimbra Portugal
| | - Andreia Rebelo
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Scientific Area of Environmental HealthSchool of Health, Polytechnic Institute of Porto Porto Portugal
| | - Sofia Ribeiro
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Carla Novais
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Patrícia Antunes
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Faculty of Nutrition and Food SciencesUniversity of Porto Porto Portugal
| |
Collapse
|
37
|
Biswas S, Li Y, Elbediwi M, Yue M. Emergence and Dissemination of mcr-Carrying Clinically Relevant Salmonella Typhimurium Monophasic Clone ST34. Microorganisms 2019; 7:E298. [PMID: 31466338 PMCID: PMC6780495 DOI: 10.3390/microorganisms7090298] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 02/07/2023] Open
Abstract
Antibiotic resistance in bacteria is one of the urgent threats to both public and global health. The Salmonella Typhimurium monophasic sequence type 34 (ST34) clone, with its rapid dissemination and resistance to numerous critical antimicrobials, has raised global concerns. Here, we present an updated overview on the emerging infections caused by mobile colistin resistance (mcr)-carrying colistin-resistant ST34 isolates, covering their global dissemination and virulence-associated efficacy. The higher rates of mcr-1-positive ST34 in children in China highlights the increasing threat caused by this pathogen. Most of the ST34 isolates carrying the mcr-1 gene were isolated from animals and food products, indicating the role of foodborne transmission of mcr-1. The emergence of multidrug resistance genes along with various virulence factors and many heavy metal resistance genes on the chromosome and plasmid from ST34 isolates will challenge available therapeutic options. The presence of the colistin resistance gene (mcr-1, mcr-3, and mcr-5) with the multidrug-resistant phenotype in ST34 has spread across different countries, and most of the mcr-1 genes in ST34 isolates were detected in plasmid type IncHI2 followed by IncI2, and IncX4. Together, mcr-carrying S. Typhimurium ST34 may become a new pandemic clone. The fast detection and active surveillance in community, hospital, animal herds, food products and environment are urgently warranted.
Collapse
Affiliation(s)
- Silpak Biswas
- CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yan Li
- CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Mohammed Elbediwi
- CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Min Yue
- CATG Microbiology & Food Safety Laboratory, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou 310058, China.
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China.
| |
Collapse
|