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Cohen E, Azriel S, Auster O, Gal A, Mikhlin S, Crauwels S, Rahav G, Gal-Mor O. A new Salmonella enterica serovar that was isolated from a wild sparrow presents a distinct genetic, metabolic and virulence profile. Microbes Infect 2024; 26:105249. [PMID: 37956735 DOI: 10.1016/j.micinf.2023.105249] [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: 08/27/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
Salmonella enterica is a ubiquitous and clinically-important bacterial pathogen, able to infect and cause different diseases in a wide range of hosts. Here, we report the isolation and characterization of a new S. enterica serovar (13,23:i:-; S. Tirat-Zvi), belonging to the Havana supper-lineage that was isolated from a wild house sparrow (Passer domesticus) in Israel. Whole genome sequencing and complete assembly of its genome indicated a plasmid-free, 4.7 Mb genome that carries the Salmonella pathogenicity islands 1-6, 9, 19 and an integrative and conjugative element (ICE), encoding arsenic resistance genes. Phenotypically, S. Tirat-Zvi isolate TZ282 was motile, readily formed biofilm, more versatile in carbon source utilization than S. Typhimurium and highly tolerant to arsenic, but impaired in host cell invasion. In-vivo infection studies indicated that while S. Tirat-Zvi was able to infect and cause an acute inflammatory enterocolitis in young chicks, it was compromised in mice colonization and did not cause an inflammatory colitis in mice compared to S. Typhimurium. We suggest that these phenotypes reflect the distinctive ecological niche of this new serovar and its evolutionary adaptation to passerine birds, as a permissive host. Moreover, these results further illuminate the genetic, phenotypic and ecological diversity of S. enterica pathovars.
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Affiliation(s)
- Emiliano Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Shalevet Azriel
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Oren Auster
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
| | - Adiv Gal
- Faculty of Sciences, Kibbutzim College, Tel-Aviv, Israel
| | | | - Sam Crauwels
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Galia Rahav
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel.
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Kopf A, Bunk B, Riedel T, Schröttner P. The zoonotic pathogen Wohlfahrtiimonas chitiniclastica - current findings from a clinical and genomic perspective. BMC Microbiol 2024; 24:3. [PMID: 38172653 PMCID: PMC10763324 DOI: 10.1186/s12866-023-03139-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
The zoonotic pathogen Wohlfahrtiimonas chitiniclastica can cause several diseases in humans, including sepsis and bacteremia. Although the pathogenesis is not fully understood, the bacterium is thought to enter traumatic skin lesions via fly larvae, resulting in severe myiasis and/or wound contamination. Infections are typically associated with, but not limited to, infestation of an open wound by fly larvae, poor sanitary conditions, cardiovascular disease, substance abuse, and osteomyelitis. W. chitiniclastica is generally sensitive to a broad spectrum of antibiotics with the exception of fosfomycin. However, increasing drug resistance has been observed and its development should be monitored with caution. In this review, we summarize the currently available knowledge and evaluate it from both a clinical and a genomic perspective.
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Affiliation(s)
- Anna Kopf
- Clinic for Cardiology, Sana Heart Center, Leipziger Str. 50, 03048, Cottbus, Germany
- 2nd Medical Clinic for Hematology, Oncology, Pneumology and Nephrology, Carl-Thiem Hospital Cottbus gGmbH, Cottbus, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Percy Schröttner
- Institute for Medical Microbiology and Virology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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3
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Kröger C, Lerminiaux NA, Ershova AS, MacKenzie KD, Kirzinger MW, Märtlbauer E, Perry BJ, Cameron ADS, Schauer K. Plasmid-encoded lactose metabolism and mobilized colistin resistance ( mcr-9) genes in Salmonella enterica serovars isolated from dairy facilities in the 1980s. Microb Genom 2023; 9. [PMID: 38031909 DOI: 10.1099/mgen.0.001149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Horizontal gene transfer by plasmids can confer metabolic capabilities that expand a host cell's niche. Yet, it is less understood whether the coalescence of specialized catabolic functions, antibiotic resistances and metal resistances on plasmids provides synergistic benefits. In this study, we report whole-genome assembly and phenotypic analysis of five Salmonella enterica strains isolated in the 1980s from milk powder in Munich, Germany. All strains exhibited the unusual phenotype of lactose-fermentation and encoded either of two variants of the lac operon. Surprisingly, all strains encoded the mobilized colistin resistance gene 9 (mcr-9), long before the first report of this gene in the literature. In two cases, the mcr-9 gene and the lac locus were linked within a large gene island that formed an IncHI2A-type plasmid in one strain but was chromosomally integrated in the other strain. In two other strains, the mcr-9 gene was found on a large IncHI1B/IncP-type plasmid, whereas the lac locus was encoded on a separate chromosomally integrated plasmidic island. The mcr-9 sequences were identical and genomic contexts could not explain the wide range of colistin resistances exhibited by the Salmonella strains. Nucleotide variants did explain phenotypic differences in motility and exopolysaccharide production. The observed linkage of mcr-9 to lactose metabolism, an array of heavy-metal detoxification systems, and other antibiotic resistance genes may reflect a coalescence of specialized phenotypes that improve the spread of colistin resistance in dairy facilities, much earlier than previously suspected.
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Affiliation(s)
- Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Nicole A Lerminiaux
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
| | - Anna S Ershova
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Keith D MacKenzie
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
| | - Morgan W Kirzinger
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Present address: National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, 85764, Germany
| | - Benjamin J Perry
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Present address: AgResearch, 176 Puddle Alley, Mosgiel 9092, New Zealand
| | - Andrew D S Cameron
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
| | - Kristina Schauer
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, 85764, Germany
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Rebelo A, Almeida A, Peixe L, Antunes P, Novais C. Unraveling the Role of Metals and Organic Acids in Bacterial Antimicrobial Resistance in the Food Chain. Antibiotics (Basel) 2023; 12:1474. [PMID: 37760770 PMCID: PMC10525130 DOI: 10.3390/antibiotics12091474] [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: 07/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial resistance (AMR) has a significant impact on human, animal, and environmental health, being spread in diverse settings. Antibiotic misuse and overuse in the food chain are widely recognized as primary drivers of antibiotic-resistant bacteria. However, other antimicrobials, such as metals and organic acids, commonly present in agri-food environments (e.g., in feed, biocides, or as long-term pollutants), may also contribute to this global public health problem, although this remains a debatable topic owing to limited data. This review aims to provide insights into the current role of metals (i.e., copper, arsenic, and mercury) and organic acids in the emergence and spread of AMR in the food chain. Based on a thorough literature review, this study adopts a unique integrative approach, analyzing in detail the known antimicrobial mechanisms of metals and organic acids, as well as the molecular adaptive tolerance strategies developed by diverse bacteria to overcome their action. Additionally, the interplay between the tolerance to metals or organic acids and AMR is explored, with particular focus on co-selection events. Through a comprehensive analysis, this review highlights potential silent drivers of AMR within the food chain and the need for further research at molecular and epidemiological levels across different food contexts worldwide.
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Affiliation(s)
- Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- ESS, Polytechnic of Porto, 4200-072 Porto, Portugal
| | - Agostinho Almeida
- LAQV/REQUIMTE, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Faculty of Nutrition and Food Sciences (FCNAUP), University of Porto, 4150-180 Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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5
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Rebelo A, Duarte B, Freitas AR, Peixe L, Antunes P, Novais C. Exploring Peracetic Acid and Acidic pH Tolerance of Antibiotic-Resistant Non-Typhoidal Salmonella and Enterococcus faecium from Diverse Epidemiological and Genetic Backgrounds. Microorganisms 2023; 11:2330. [PMID: 37764174 PMCID: PMC10534362 DOI: 10.3390/microorganisms11092330] [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: 07/25/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Acid stress poses a common challenge for bacteria in diverse environments by the presence of inorganic (e.g., mammals' stomach) or organic acids (e.g., feed additives; acid-based disinfectants). Limited knowledge exists regarding acid-tolerant strains of specific serotypes, clonal lineages, or sources in human/animal pathogens: namely, non-typhoidal Salmonella enterica (NTS) and Enterococcus faecium (Efm). This study evaluated the acidic pH (Mueller-Hinton acidified with HCl) and peracetic acid (PAA) susceptibility of Efm (n = 72) and NTS (n = 60) from diverse epidemiological/genetic backgrounds and with multiple antibiotic resistance profiles. Efm minimum growth/survival pH was 4.5-5.0/3.0-4.0, and for NTS it was 4.0-4.5/3.5-4.0. Efm distribution among acidic pH values showed that only isolates of clade-non-A1 (non-hospital associated) or the food chain were more tolerant to acidic pH compared to clade-A1 (hospital-associated clones) or clinical isolates (p < 0.05). In the case of NTS, multidrug-resistant (MDR) isolates survived better in acidic pH (p < 0.05). The PAA MIC/MBC for Efm was 70-120/80-150 mg/L, and for NTS, it was 50-70/60-100 mg/L. The distribution of Efm among PAA concentrations showed that clade-A1 or MDR strains exhibited higher tolerance than clade-non-A1 or non-MDR ones (p < 0.05). NTS distribution also showed higher tolerance to PAA among non-MDR and clinical isolates than food chain ones (p < 0.05) but there were no differences among different serogroups. This unique study identifies specific NTS or Efm populations more tolerant to acidic pH or PAA, emphasizing the need for further research to tailor controlled measures of public health and food safety within a One Health framework.
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Affiliation(s)
- Andreia Rebelo
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- ESS, Polytechnic of Porto, 4200-072 Porto, Portugal
| | - Bárbara Duarte
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ana R. Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, 4150-180 Porto, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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Zhou L, Zhang TJ, Zhang W, Xie C, Yang Y, Chen X, Wang Q, Wang HN, Lei CW. Prevalence and genetic diversity of multidrug-resistant Salmonella Typhimurium monophasic variant in a swine farm from China. Front Microbiol 2023; 14:1200088. [PMID: 37396383 PMCID: PMC10311412 DOI: 10.3389/fmicb.2023.1200088] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/25/2023] [Indexed: 07/04/2023] Open
Abstract
Salmonella 4,[5],12:i:-, a monophasic variant of S. Typhimurium, has become a global serovar causing animal and human infections since its first emergence in the late 1980's. Several previous studies showed the increasing prevalence of S. 4,[5],12:i:- in China, most of which were from swine with multidrug resistance (MDR) profiles. However, the molecular characteristic and evolution of S. 4,[5],12:i:- in the same swine farm are still unknown. In this study, a total of 54 S. enterica strains were isolated from different fattening pigs aged 1, 3, and 6 months, most of which belonged to S. 4,[5],12:i:-. Whole-genome sequencing revealed that all 45 S. 4,[5],12:i:- strains belonged to ST34 and were further divided into two different ribosomal STs and nine different core-genome STs. Phylogenetic analysis of 286 S. 4,[5],12:i:- strains in China, including 241 from the EnteroBase Salmonella database, revealed the genetic diversity of S. 4,[5],12:i:- and indicated that S. 4,[5],12:i:- in this swine farm might have multiple origins. Three different IncHI2 plasmids carrying various resistance genes were characterized by nanopore sequencing and could be conjugated to Escherichia coli. The colistin resistance gene mcr-1 and ESBLs gene blaCTX - M-14 were co-located on the chromosome of one strain. The dynamic changes in antimicrobial resistance regions and transferability of IncHI2 plasmids, as well as the chromosomal location of resistance genes, facilitated the diversity of the antimicrobial resistance characteristics in S. 4,[5],12:i:-. Since the swine farm is regarded as the important reservoir of MDR S. 4,[5],12:i:-, the prevalence and evolution of S. 4,[5],12:i:- from swine farms to pig products and humans should be continually monitored.
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Spread of blaCTX-M-9 and Other Clinically Relevant Resistance Genes, Such as mcr-9 and qnrA1, Driven by IncHI2-ST1 Plasmids in Clinical Isolates of Monophasic Salmonella enterica Serovar Typhimurium ST34. Antibiotics (Basel) 2023; 12:antibiotics12030547. [PMID: 36978414 PMCID: PMC10044134 DOI: 10.3390/antibiotics12030547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
The monophasic 4,[5],12:i:-variant of Salmonella enterica serovar Typhimurium with sequence type ST34 has become one of the most prevalent non-typhoidal salmonellae worldwide. In the present study, we thoroughly characterized seven isolates of this variant detected in a Spanish hospital and selected based on cefotaxime resistance and cefoxitin susceptibility, mediated by blaCTX-M-9. For this, conventional microbiological techniques, together with whole genome sequencing performed with the Illumina platform, were applied. All selected isolates carried the resistance region RR or variants therein, and most also contained the SGI-4 genomic island. These chromosomal elements, typically associated with monophasic S. Typhimurium ST34, confer resistance to traditional antibiotics (ampicillin, streptomycin, sulfonamides, and tetracycline) and tolerance to heavy metals (mercury, silver, and copper). In addition, each isolate carried a large IncHI2-ST1 conjugative plasmid containing additional or redundant resistance genes. All harbored the blaCTX-M-9 gene responsible for cefotaxime resistance, whereas the qnrA1 gene mediating fluoroquinolone resistance was detected in two of the plasmids. These genes were embedded in ISCR1-bearing complex class 1 integrons, specifically In60-like and In36-like. The mcr-9 gene was present in all but one of the IncHI2-ST1 plasmids found in the analyzed isolates, which were nevertheless susceptible to colistin. Most of the resistance genes of plasmid origin clustered within a highly complex and variable region. The observed diversity results in a wide range of resistance phenotypes, enabling bacterial adaptation to selective pressure posed by the use of antimicrobials.
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Vázquez X, García V, Fernández J, Bances M, de Toro M, Ladero V, Rodicio R, Rodicio MR. Colistin Resistance in Monophasic Isolates of Salmonella enterica ST34 Collected From Meat-Derived Products in Spain, With or Without CMY-2 Co-production. Front Microbiol 2022; 12:735364. [PMID: 35069462 PMCID: PMC8770973 DOI: 10.3389/fmicb.2021.735364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/17/2021] [Indexed: 12/02/2022] Open
Abstract
Colistin is a last-resort antibiotic in fighting severe infections caused by multidrug resistant Gram negative pathogens in hospitals. Zoonotic bacteria acquire colistin resistance in animal reservoirs and mediate its spread along the food chain. This is the case of non-typhoid serovars of Salmonella enterica. Colistin-resistant S. enterica in foods represents a threat to human health. Here, we assessed the prevalence of colistin-resistance in food-borne isolates of S. enterica (2014–2019; Asturias, Spain), and established the genetic basis and transferability of this resistance. Five out of 231 isolates tested (2.2%) were resistant to colistin. Four of them, belonging to the European monophasic ST34 clone of S. Typhimurium, were characterized in the present study. They were collected from pork or pork and beef meat-derived products, either in 2015 (three isolates) or 2019 (one isolate). Molecular typing with XbaI-PFGE and plasmid profiling revealed distinct patterns for each isolate, even though two of the 2015 isolates derived from the same sample. The MICs of colistin ranged from 8 to 16 mg/L. All isolates carried the mcr-1.1 gene located on conjugative plasmids of the incompatibility groups IncX4 (2015 isolates) or IncHI2 (2019 isolate). Apart from colistin resistance, the four isolates carried chromosomal genes conferring resistance to ampicillin, streptomycin, sulfonamides and tetracycline [blaTEM–1, strA-strB, sul2, and tet(B)] and heavy metals, including copper and silver (silESRCFBAGP and pcoGE1ABCDRSE2), arsenic (arsRSD2A2BCA1D1) ± mercury (merEDACPTR), which are characteristically associated with the European ST34 monophasic clone. The 2019 isolate was also resistant to other antibiotics, comprising third generation cephalosporins and cephamycins. The latter phenotype was conferred by the blaCMY–2 gene located on an IncI1-I(α)-ST2 plasmid. Results in the present study identified meat-derived products as a reservoir of a highly successful clone harboring transferable plasmids which confer resistance to colistin and other clinically important antibiotics. An important reduction in the number of food-borne S. enterica detected during the period of the study, together with the low frequency of colistin resistance, underlines the success of One Health initiatives, such as those implemented at the UE, to control zoonotic bacteria along the food chain and to halt the spread of antimicrobial resistance.
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Affiliation(s)
- Xenia Vázquez
- Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain.,Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Javier Fernández
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
| | - Margarita Bances
- Laboratorio de Salud Pública (LSP), Consejería de Sanidad del Principado de Asturias, Oviedo, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | - Víctor Ladero
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain.,Grupo de Microbiología Molecular, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Rosaura Rodicio
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - M Rosario Rodicio
- Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain.,Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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9
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Pardo-Esté C, Lorca D, Castro-Severyn J, Krüger G, Alvarez-Thon L, Zepeda P, Sulbaran-Bracho Y, Hidalgo A, Tello M, Molina F, Molina L, Remonsellez F, Castro-Nallar E, Saavedra C. Genetic Characterization of Salmonella Infantis with Multiple Drug Resistance Profiles Isolated from a Poultry-Farm in Chile. Microorganisms 2021; 9:2370. [PMID: 34835497 PMCID: PMC8621671 DOI: 10.3390/microorganisms9112370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 11/30/2022] Open
Abstract
Salmonella comprises over 2500 serotypes and foodborne contamination associated with this pathogen remains an important health concern worldwide. During the last decade, a shift in serotype prevalence has occurred as traditionally less prevalent serotypes are increasing in frequency of infections, especially those related to poultry meat contamination. S. Infantis is one of the major emerging serotypes, and these strains commonly display antimicrobial resistance and can persist despite cleaning protocols. Thus, this work aimed to isolate S. Infantis strains from a poultry meat farm in Santiago, Chile and to characterize genetic variations present in them. We determined their genomic and phenotypic profiles at different points along the production line. The results indicate that the strains encompass 853 polymorphic sites (core-SNPs) with isolates differing from one another by 0-347 core SNPs, suggesting variation among them; however, we found discrete correlations with the source of the sample in the production line. Furthermore, the pan-genome was composed of 4854 total gene clusters of which 2618 (53.9%) corresponds to the core-genome and only 181 (3.7%) are unique genes (those present in one particular strain). This preliminary analysis will enrich the surveillance of Salmonella, yet further studies are required to assess their evolution and phylogeny.
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Affiliation(s)
- Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
| | - Diego Lorca
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile; (J.C.-S.); (F.R.)
| | - Gabriel Krüger
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
| | - Luis Alvarez-Thon
- Facultad de Ingeniería y Arquitectura, Universidad Central de Chile, Santa Isabel 1186, Santiago 8330601, Chile;
| | - Phillippi Zepeda
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
| | - Yoelvis Sulbaran-Bracho
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
| | - Alejandro Hidalgo
- Escuela de Química y Farmacia, Facultad de Medicina, Universidad Andres Bello, Santiago 8370071, Chile;
| | - Mario Tello
- Laboratorio de Metagenomica Bacteriana, Centro de Biotecnología Acuicola, Universidad de Santiago, Alameda, Estación Central, Santiago 9170002, Chile;
| | - Franck Molina
- Sys2Diag, UMR9005 CNRS ALCEDIAG, 34184 Montpellier, France; (F.M.); (L.M.)
| | - Laurence Molina
- Sys2Diag, UMR9005 CNRS ALCEDIAG, 34184 Montpellier, France; (F.M.); (L.M.)
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile; (J.C.-S.); (F.R.)
- Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta 1240000, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile;
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Claudia Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile; (C.P.-E.); (D.L.); (G.K.); (P.Z.); (Y.S.-B.)
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10
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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.
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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
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11
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Li M, Wang K, Tang A, Tang A, Chen A, Huang Z. Investigation of the Genes Involved in the Outbreaks of Escherichia coli and Salmonella spp. in the United States. Antibiotics (Basel) 2021; 10:1274. [PMID: 34680854 PMCID: PMC8532668 DOI: 10.3390/antibiotics10101274] [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: 09/10/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022] Open
Abstract
Salmonella spp. and Escherichiacoli (E. coli) are two of the deadliest foodborne pathogens in the US. Genes involved in antimicrobial resistance, virulence, and stress response, enable these pathogens to increase their pathogenicity. This study aims to examine the genes detected in both outbreak and non-outbreak Salmonella spp. and E. coli by analyzing the data from the National Centre for Biotechnology Information (NCBI) Pathogen Detection Isolates Browser database. A multivariate statistical analysis was conducted on the genes detected in isolates of outbreak Salmonella spp., non-outbreak Salmonella spp., outbreak E. coli, and non-outbreak E. coli. The genes from the data were projected onto a two-dimensional space through principal component analysis. Hierarchical clustering was then used to quantify the relationship between the genes in the dataset. Most of the outlier genes identified in E. coli isolates are virulence genes, while outlier genes identified in Salmonella spp. are mainly involved in stress response. Gene epeA, which encodes a high-molecular-weight serine protease autotransporter of Enterobacteriaceae (SPATE) protein, along with subA and subB that encode cytotoxic activity, may contribute to the pathogenesis of outbreak E. coli. The iro operon and ars operon may play a role in the ecological success of the epidemic clones of Salmonella spp. Concurrent relationships between esp and ter operons in E. coli and pco and sil operons in Salmonella spp. are found. Stress-response genes (asr, golT, golS), virulence gene (sinH), and antimicrobial resistance genes (mdsA and mdsB) in Salmonella spp. also show a concurrent relationship. All these findings provide helpful information for experiment design to combat outbreaks of E. coli and Salmonella spp.
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Affiliation(s)
| | | | | | | | | | - Zuyi Huang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA; (M.L.); (K.W.); (A.T.); (A.T.); (A.C.)
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12
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Rebelo A, Mourão J, Freitas AR, Duarte B, Silveira E, Sanchez-Valenzuela A, Almeida A, Baquero F, Coque TM, Peixe L, Antunes P, Novais C. Diversity of metal and antibiotic resistance genes in Enterococcus spp. from the last century reflects multiple pollution and genetic exchange among phyla from overlapping ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 787:147548. [PMID: 34000557 DOI: 10.1016/j.scitotenv.2021.147548] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 04/26/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Arsenic (As), mercury (Hg), and copper (Cu) are among the major historical and contemporary metal pollutants linked to global anthropogenic activities. Enterococcus have been considered indicators of fecal pollution and antibiotic resistance for years, but its largely underexplored metallome precludes understanding their role as metal pollution bioindicators as well. Our goal was to determine the occurrence, diversity, and phenotypes associated with known acquired genes/operons conferring tolerance to As, Hg or Cu among Enterococcus and to identify their genetic context (381 field isolates from diverse epidemiological and genetic backgrounds; 3547 enterococcal genomes available in databases representing a time span during 1900-2019). Genes conferring tolerance to As (arsA), Hg (merA) or Cu (tcrB) were used as biomarkers of widespread metal tolerance operons. Different variants of metal tolerance (MeT) genes (13 arsA, 6 merA, 1 tcrB) were more commonly recovered from the food-chain (arsA, tcrB) or humans (merA), and were shared with 49 other bacterial taxa. Comparative genomics analysis revealed that MeT genes occurred in heterogeneous operons, at least since the 1900s, with an increasing accretion of antibiotic resistance genes since the 1960's, reflecting diverse antimicrobial pollution. Multiple MeT genes were co-located on the chromosome or conjugative plasmids flanked by elements with high potential for recombination, often along with antibiotic resistance genes. Phenotypic analysis of some isolates carrying MeT genes revealed up to 128× fold increase in the minimum inhibitory concentrations to metals. The main distribution of functional MeT genes among Enterococcus faecium and Enterococcus faecalis from different sources, time spans, and clonal lineages, and their ability to acquire diverse genes from multiple taxa bacterial communities places these species as good candidates to be used as model organisms in future projects aiming at the identification and quantification of bioindicators of metal polluted environments by anthropogenic activities.
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Affiliation(s)
- Andreia Rebelo
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal; Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal; Área Técnico-científica de Saúde Ambiental, Escola Superior de Saúde, Instituto Politécnico do Porto, Portugal
| | - Joana Mourão
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal; Centro de Neurociências e Biologia Celular, Universidade de Coimbra, Portugal; Centro de Inovação em Biomedicina e Biotecnologia, Universidade de Coimbra, Portugal; Instituto de Investigação Interdisciplinar, Universidade de Coimbra, Portugal
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Bárbara Duarte
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Eduarda Silveira
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal; Centro de Investigação Vasco da Gama (CIVG), Departamento de Ciências Veterinárias, Escola Universitária Vasco da Gama, Coimbra, Portugal; Faculdade de Farmácia, Universidade de Coimbra, Portugal
| | - Antonio Sanchez-Valenzuela
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal; Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Agostinho Almeida
- LAQV/REQUIMTE, Laboratório de Química Aplicada, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Fernando Baquero
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Teresa M Coque
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Patrícia Antunes
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal; Faculdade de Ciências da Nutrição e Alimentação, Universidade do Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal.
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13
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Ribeiro S, Mourão J, Novais Â, Campos J, Peixe L, Antunes P. From farm to fork: Colistin voluntary withdrawal in Portuguese farms reflected in decreasing occurrence of mcr-1-carrying Enterobacteriaceae from chicken meat. Environ Microbiol 2021; 23:7563-7577. [PMID: 34327794 DOI: 10.1111/1462-2920.15689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/27/2021] [Indexed: 11/27/2022]
Abstract
Expansion of mcr-carrying Enterobacteriaceae (MCR-E) is a well-recognized problem affecting animals, humans and the environment. Ongoing global control actions involve colistin restrictions among food-animal production, but their impact on poultry-derived products is largely unknown, justifying comprehensive farm-to-fork studies. Occurrence of MCR-E among 53 chicken-meat batches supplied from 29 Portuguese farms shortly after colistin withdrawal was evaluated. Strains (FT-IR/MLST/WGS), mcr plasmids and their adaptive features were characterized by cultural, molecular and genomic approaches. We found high rates of chicken-meat batches (80%-100% - 4 months; 12% - the last month) with multiple MDR + mcr-1-carrying Escherichia coli (Ec-including ST117 and ST648-Cplx) and Klebsiella pneumoniae (Kp-ST147-O5:K35) clones, some of them persisting over time. The mcr-1 was located in the chromosome (Ec-ST297/16-farms) or dispersed IncX4 (Ec-ST602/ST6469/5-farms), IncHI2-ST2/ST4 (Ec-ST533/ST6469/5 farms and Kp-ST147/6-farms) or IncI2 (Ec-ST117/1-farm) plasmids. WGS revealed high load and diversity in virulence, antibiotic resistance and metal tolerance genes. This study supports colistin withdrawal potential efficacy in poultry production and highlights both poultry-production chain as a source of mcr-1 and the risk of foodborne transmission to poultry-meat consumers. Finally, in the antibiotic reduction/replacement context, other potential co-selective pressures (e.g., metals-Cu as feed additives) need to be further understood to guide concerted, effective and durable actions under 'One Health' perspective.
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Affiliation(s)
- Sofia Ribeiro
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Joana Mourão
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ângela Novais
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Joana Campos
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,INEB-Institute of Biomedical Engineering, i3S-Institute for Research & Innovation in Health, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Patrícia Antunes
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Faculty of Nutrition and Food Sciences, University of Porto, Porto, 4150-180, Portugal
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14
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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.
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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.)
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15
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Mourão J, Rebelo A, Ribeiro S, Peixe L, Novais C, Antunes P. Atypical Non-H 2S-Producing Monophasic Salmonella Typhimurium ST3478 Strains from Chicken Meat at Processing Stage Are Adapted to Diverse Stresses. Pathogens 2020; 9:pathogens9090701. [PMID: 32859122 PMCID: PMC7557518 DOI: 10.3390/pathogens9090701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 01/23/2023] Open
Abstract
Poultry products are still an important cause of Salmonella infections worldwide, with an increasingly reported expansion of less-frequent serotypes or atypical strains that are frequently multidrug-resistant. Nevertheless, the ability of Salmonella to survive antimicrobials promoted in the context of antibiotic reducing/replacing and farming rethinking (e.g., organic acids and copper in feed/biocides) has been scarcely explored. We investigated Salmonella occurrence (conventional and molecular assays) among chicken meat at the processing stage (n = 53 batches/29 farms) and characterized their tolerance to diverse stress factors (antibiotics, copper, acid pH, and peracetic acid). Whole-genome sequencing was used to assess adaptive features and to perform comparative analysis. We found a low Salmonella occurrence (4%) and identified S. Enteritidis/ST11 plus atypical non-H2S-producing S. 1,4,[5],12:i:-/ST3478. The ST3478 presented the ability to grow under diverse stresses (antibiotics, copper, and acid-pH). Comparative genomics among ST3478 isolates showed similar antibiotic/metal resistance gene repertoires and identical nonsense phsA thiosulfate reductase mutations (related to H2S-negative phenotype), besides their close phylogenetic relationship by cgMLST and SNPs. This study alerts for the ongoing national and international spread of an emerging monophasic Salmonella Typhimurium clonal lineage with an enlarged ability to survive to antimicrobials/biocides commonly used in poultry production, being unnoticed by conventional Salmonella detection approaches due to an atypical non-H2S-producing phenotype.
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Affiliation(s)
- Joana Mourão
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Andreia Rebelo
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- Scientific Area of Environmental Health, School of Health, Polytechnic Institute of Porto, 4200-465 Porto, Portugal
| | - Sofia Ribeiro
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- ESCMID Food- and Water-borne Infections Study Group (EFWISG), 4010 Basel, Switzerland
| | - Carla Novais
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- ESCMID Food- and Water-borne Infections Study Group (EFWISG), 4010 Basel, Switzerland
| | - Patrícia Antunes
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- ESCMID Food- and Water-borne Infections Study Group (EFWISG), 4010 Basel, Switzerland
- Faculty of Nutrition and Food Sciences, University of Porto, 4150-180 Porto, Portugal
- Correspondence: ; Tel.: +351-507-4320
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