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Shymialevich D, Błażejak S, Średnicka P, Cieślak H, Ostrowska A, Sokołowska B, Wójcicki M. Biological Characterization and Genomic Analysis of Three Novel Serratia- and Enterobacter-Specific Virulent Phages. Int J Mol Sci 2024; 25:5944. [PMID: 38892136 PMCID: PMC11172527 DOI: 10.3390/ijms25115944] [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: 04/29/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Due to the high microbiological contamination of raw food materials and the increase in the incidence of multidrug-resistant bacteria, new methods of ensuring microbiological food safety are being sought. One solution may be to use bacteriophages (so-called phages) as natural bacterial enemies. Therefore, the aim of this study was the biological and genomic characterization of three newly isolated Serratia- and Enterobacter-specific virulent bacteriophages as potential candidates for food biocontrol. Serratia phage KKP_3708 (vB_Sli-IAFB_3708), Serratia phage KKP_3709 (vB_Sma-IAFB_3709), and Enterobacter phage KKP_3711 (vB_Ecl-IAFB_3711) were isolated from municipal sewage against Serratia liquefaciens strain KKP 3654, Serratia marcescens strain KKP 3687, and Enterobacter cloacae strain KKP 3684, respectively. The effect of phage addition at different multiplicity of infection (MOI) rates on the growth kinetics of the bacterial hosts was determined using a Bioscreen C Pro growth analyzer. The phages retained high activity in a wide temperature range (from -20 °C to 60 °C) and active acidity values (pH from 3 to 12). Based on transmission electron microscopy (TEM) imaging and whole-genome sequencing (WGS), the isolated bacteriophages belong to the tailed bacteriophages from the Caudoviricetes class. Genomic analysis revealed that the phages have linear double-stranded DNA of size 40,461 bp (Serratia phage KKP_3708), 67,890 bp (Serratia phage KKP_3709), and 113,711 bp (Enterobacter phage KKP_3711). No virulence, toxins, or antibiotic resistance genes were detected in the phage genomes. The lack of lysogenic markers indicates that all three bacteriophages may be potential candidates for food biocontrol.
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Affiliation(s)
- Dziyana Shymialevich
- Culture Collection of Industrial Microorganisms—Microbiological Resources Center, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland; (D.S.); (H.C.)
| | - Stanisław Błażejak
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS–SGGW), Nowoursynowska 166 Str., 02-776 Warsaw, Poland;
| | - Paulina Średnicka
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland;
| | - Hanna Cieślak
- Culture Collection of Industrial Microorganisms—Microbiological Resources Center, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland; (D.S.); (H.C.)
| | - Agnieszka Ostrowska
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences (WULS–SGGW), Ciszewskiego 8 Str., 02-786 Warsaw, Poland;
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland;
| | - Michał Wójcicki
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland;
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Cooper AL, Wong A, Tamber S, Blais BW, Carrillo CD. Analysis of Antimicrobial Resistance in Bacterial Pathogens Recovered from Food and Human Sources: Insights from 639,087 Bacterial Whole-Genome Sequences in the NCBI Pathogen Detection Database. Microorganisms 2024; 12:709. [PMID: 38674654 PMCID: PMC11051753 DOI: 10.3390/microorganisms12040709] [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: 03/05/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Understanding the role of foods in the emergence and spread of antimicrobial resistance necessitates the initial documentation of antibiotic resistance genes within bacterial species found in foods. Here, the NCBI Pathogen Detection database was used to query antimicrobial resistance gene prevalence in foodborne and human clinical bacterial isolates. Of the 1,843,630 sequence entries, 639,087 (34.7%) were assigned to foodborne or human clinical sources with 147,788 (23.14%) from food and 427,614 (76.88%) from humans. The majority of foodborne isolates were either Salmonella (47.88%), Campylobacter (23.03%), Escherichia (11.79%), or Listeria (11.3%), and the remaining 6% belonged to 20 other genera. Most foodborne isolates were from meat/poultry (95,251 or 64.45%), followed by multi-product mixed food sources (29,892 or 20.23%) and fish/seafood (6503 or 4.4%); however, the most prominent isolation source varied depending on the genus/species. Resistance gene carriage also varied depending on isolation source and genus/species. Of note, Klebsiella pneumoniae and Enterobacter spp. carried larger proportions of the quinolone resistance gene qnrS and some clinically relevant beta-lactam resistance genes in comparison to Salmonella and Escherichia coli. The prevalence of mec in S. aureus did not significantly differ between meat/poultry and multi-product sources relative to clinical sources, whereas this resistance was rare in isolates from dairy sources. The proportion of biocide resistance in Bacillus and Escherichia was significantly higher in clinical isolates compared to many foodborne sources but significantly lower in clinical Listeria compared to foodborne Listeria. This work exposes the gaps in current publicly available sequence data repositories, which are largely composed of clinical isolates and are biased towards specific highly abundant pathogenic species. We also highlight the importance of requiring and curating metadata on sequence submission to not only ensure correct information and data interpretation but also foster efficient analysis, sharing, and collaboration. To effectively monitor resistance carriage in food production, additional work on sequencing and characterizing AMR carriage in common commensal foodborne bacteria is critical.
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Affiliation(s)
- Ashley L. Cooper
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada;
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Sandeep Tamber
- Microbiology Research Division, Bureau of Microbial Hazards, Health Canada, Ottawa, ON K1A0K9, Canada;
| | - Burton W. Blais
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada;
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Catherine D. Carrillo
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada;
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
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Zhou J, Wu H, Wu Z, Shi L, Shen Y, Tian S, Hou LA. Erythromycin fermentation residue exposure induces a short-term wave of antibiotic resistance in a soil-lettuce system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166081. [PMID: 37544437 DOI: 10.1016/j.scitotenv.2023.166081] [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: 06/25/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
The pattern of antibiotic resistance assembly and their unclear transfer in a soil-lettuce system render the treated erythromycin fermentation residue (EFR) land application risky. Herein, the antibiotic resistance genes (ARGs), mobile gene elements, and microbial communities were examined under erythromycin stress at three stages of lettuce growth. Erythromycin exhibited degradation rates of 99.4 % in soils for 60 d, with little uptake in the seedling tissues, reaching a 0.11-0.71 bioconcentration factor range. The EFR application rate must be limited <1 % to avoid human exposure risk. The diversity, biotic networks complexity, and edaphic ARG abundances of the rhizospheric microbial communities increased at the early stage, but returned to the control levels at the mature stage. The Planomicrobium and Pseudomonas bacterial genera were important biotic factors for erythromycin variation. Thirty-three MLSB genes (macrolide, lincosamide, and streptogramin B) conferring resistance to erythromycin were detected in soil, but only two endophytic ARGs (mphA-01 and ermX) were identified, with members of the Microvirga genus being the potential hosts. Partial least-squares path modeling suggested that erythromycin concentration was the main factor for endophytic ARGs evolution. This study highlighted the leaf endophytic ARG emergence and potential exposure human risks majorly caused by the drug traces in antibiotic fermentation residues.
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Affiliation(s)
- Jieya Zhou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Hao Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Zongru Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Lihu Shi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yunpeng Shen
- State Environmental Protection Engineering Center for Harmless Treatment and Resource Utilization of Antibiotic Residues, Khorgos 835007, China
| | - Shulei Tian
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Li-An Hou
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China; High Tech Inst Beijing, Beijing 100085, China.
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Kon H, Lurie-Weinberger M, Cohen A, Metsamber L, Keren-Paz A, Schwartz D, Carmeli Y, Schechner V. Occurrence, Typing, and Resistance Genes of ESBL/AmpC-Producing Enterobacterales in Fresh Vegetables Purchased in Central Israel. Antibiotics (Basel) 2023; 12:1528. [PMID: 37887229 PMCID: PMC10604292 DOI: 10.3390/antibiotics12101528] [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: 09/03/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
Beta-lactam resistance can lead to increased mortality, higher healthcare expenses, and limited therapeutic options. The primary mechanism of beta-lactam resistance is the production of extended-spectrum beta-lactamases (ESBL) and AmpC beta-lactamases. The spread of beta-lactamase-producing Enterobacterales via the food chain may create a resistance reservoir. The aims of this study were to determine the prevalence of ESBL/AmpC-producing Enterobacterales in vegetables, to examine the association between EBSL/AmpC-producing bacteria and types of vegetables, packaging, and markets, and to investigate the genetic features of ESBL-producing isolates. The antibiotic susceptibilities were determined using VITEK. Phenotypic ESBL/AmpC production was confirmed using disk diffusion. ESBL-producing isolates were subjected to Fourier-transform infrared (FT-IR) spectroscopy and to whole genome sequencing using Oxford Nanopore sequencing technology. Of the 301 vegetable samples, 20 (6.6%) were positive for ESBL producers (16 Klebsiella pneumoniae and 4 Escherichia coli), and 63 (20.9%) were positive for AmpC producers (56 Enterobacter cloacae complex, 4 Enterobacter aerogenes/cancerogenus, and 3 Pantoea spp., Aeromonas hydrophila, and Citrobacter braakii). The blaCTX-M and blaSHV genes were most common among ESBL-producing isolates. The beta-lactamase genes of the ESBL producers were mainly carried on plasmids. Multilocus sequence typing and FT-IR typing revealed high diversity among the ESBL producers. AmpC producers were significantly more common in leafy greens and ESBL producers were significantly less common in climbing vegetables. The presence of ESBL/AmpC-producing Enterobacterales in raw vegetables may contribute to the dissemination of resistance genes in the community.
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Affiliation(s)
- Hadas Kon
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv 6423906, Israel; (H.K.); (M.L.-W.); (A.C.); (A.K.-P.); (D.S.); (Y.C.)
| | - Mor Lurie-Weinberger
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv 6423906, Israel; (H.K.); (M.L.-W.); (A.C.); (A.K.-P.); (D.S.); (Y.C.)
| | - Adi Cohen
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv 6423906, Israel; (H.K.); (M.L.-W.); (A.C.); (A.K.-P.); (D.S.); (Y.C.)
| | - Liat Metsamber
- School of Public Health, Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel;
| | - Alona Keren-Paz
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv 6423906, Israel; (H.K.); (M.L.-W.); (A.C.); (A.K.-P.); (D.S.); (Y.C.)
| | - David Schwartz
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv 6423906, Israel; (H.K.); (M.L.-W.); (A.C.); (A.K.-P.); (D.S.); (Y.C.)
| | - Yehuda Carmeli
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv 6423906, Israel; (H.K.); (M.L.-W.); (A.C.); (A.K.-P.); (D.S.); (Y.C.)
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Vered Schechner
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel-Aviv 6423906, Israel; (H.K.); (M.L.-W.); (A.C.); (A.K.-P.); (D.S.); (Y.C.)
- School of Public Health, Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel;
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The conjugative transfer of plasmid-mediated mobile colistin resistance gene, mcr-1, to Escherichia coli O157:H7 and Escherichia coli O104:H4 in nutrient broth and in mung bean sprouts. Food Microbiol 2023; 111:104188. [PMID: 36681389 DOI: 10.1016/j.fm.2022.104188] [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: 08/28/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/27/2022]
Abstract
The emergence of mobile colistin resistant gene (mcr-1) in Enterobacteriaceae has become a global public health concern. Dissemination of the mcr-1 gene through conjugation of bacteria associated with food may occur. This research investigated the transfer frequency of the mcr-1 gene among Escherichia coli in liquid media and during growth of mung bean sprouts. The donor strain E. coli NCTC 13846 (mcr-1 positive) and recipient strains of E. coli O157:H7 and E. coli O104:H4 were used. Mating experiments in vitro were conducted at 4, 25, and 37 °C for up to 36 h. The in vivo mating experiments (growing sprouts) were conducted in a sprout growth chamber with irrigation of 1 min/h over 6 days following inoculation of mung bean seeds with the donor and a recipient. The highest transfer frequencies in TSB media, 2.86E-07 and 3.24E-07, occurred at 37 °C after mating for 24 h for E. coli O104:H4 and E. coli O157:H7, respectively. Transconjugants were not detected in liquid media at 4 °C. Moreover, transfer frequency (5.68E-05 per recipient) of mcr-1 was greater during mung bean sprout growth for E. coli O104:H4 compared to E. coli O157:H7 (1.02E-05 per recipient) Day 3 to Day 6. This study indicates that the transfer of antibiotic resistant gene(s) among bacteria during mung bean sprout production may facilitate the spread of antibiotic resistant bacteria in the environment and to humans.
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First detection of tet(X4)-positive Enterobacterales in retail vegetables and clonal spread of Escherichia coli ST195 producing Tet(X4) in animals, foods, and humans across China and Thailand. Int J Food Microbiol 2023; 391-393:110145. [PMID: 36841076 DOI: 10.1016/j.ijfoodmicro.2023.110145] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/19/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023]
Abstract
The mobile tigecycline-resistant gene tet(X4), which confers resistance to all tetracyclines, has been identified in bacterial isolates from various sources. However, there are no reports on the occurrence of tet(X4) in bacterial isolates of ready-to-eat fresh vegetables. In this study, 113 vegetable samples from farmers' markets were screened for tigecycline-resistant strains. Ten Escherichia coli (two ST195, two ST48, and one ST10, ST58, ST88, ST394, ST641, and ST101) and one Klebsiella pneumoniae (ST327) recovered from nine vegetable samples (7.96 %) were identified as carrying tet(X4). The core genome sequences of the two E. coli ST195 isolates showed a close relationship (14-41 single-nucleotide polymorphisms) with 31 tet(X4)-bearing E. coli ST195 isolates from humans, pigs, pork, and bird in China and Thailand, and the 33 E. coli ST195 isolates producing Tet(X4) shared similar resistance genes and plasmid replicons. Nanopore sequencing and conjugation experiments confirmed that the tet(X4) genes were located on the hybrid plasmids IncFIA-HI1A-HI1B (n = 6), IncX1 (n = 3), and IncFII2 (n = 1) in E. coli, and IncFII plasmid in K. pneumoniae. IncFIA-HI1A-HI1B and IncX1 plasmids shared highly similar structures with plasmids from various sources in the GenBank database. This is the first study to report the observation of tet(X4)-positive bacteria in retail vegetables. The epidemic clones and plasmids contribute to tet(X4) dissemination in vegetables. The clonal spread of Tet(X4)-producing E. coli ST195 across multiple niches and countries could pose a potential threat to public health.
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Detection of beta-lactam and colistin resistant Enterobacterales in ready-to-eat fresh products. J Verbrauch Lebensm 2023. [DOI: 10.1007/s00003-023-01428-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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Occurrence of Extended Spectrum Cephalosporin-, Carbapenem- and Colistin-Resistant Gram-Negative Bacteria in Fresh Vegetables, an Increasing Human Health Concern in Algeria. Antibiotics (Basel) 2022; 11:antibiotics11080988. [PMID: 35892378 PMCID: PMC9332692 DOI: 10.3390/antibiotics11080988] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 02/06/2023] Open
Abstract
The aim of this study was to screen for extended spectrum cephalosporin-, carbapenem- and colistin-resistant Gram-negative bacteria in fresh vegetables in Batna, Algeria. A total of 400 samples of fresh vegetables were collected from different retail stores. Samples were immediately subjected to selective isolation, then the representative colonies were identified using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF–MS). Phenotypic and genotypic analyses were carried out in terms of species identification and relative antibiotic resistance. Transferability of the carbapenemase and mcr-bearing plasmids was verified by conjugation. The clonal relationships of carbapenemase and mcr-positive Escherichia coli isolates were studied by multi-locus sequence typing (MLST). Sixty-seven isolates were characterised and were mostly isolated from green leafy vegetables, where the dominant species identified included Citrobacter freundii, Klebsiella pneumoniae, Enterobacter cloacae, Stenotrophomona maltophilia, E. coli and Citrobacter braakii. PCR and sequencing results showed that E. coli was the bacterial species presenting the highest antibiotic resistance level in parallel to blaTEM (n = 16) and blaCTX-M-15 (n = 11), which were the most detected genes. Moreover, five isolates carried carbapenemase genes, including the blaOXA-48 and/or blaVIM-4 genes. The mcr-1 gene was detected in two E. coli isolates. MLST analysis revealed three different E. coli sequence types: ST101 (n = 1), ST216 (n = 1) and ST2298 (n = 1). Conjugation assays confirmed the transferability of the blaOXA-48 and mcr-1 genes. In this study we report, for the first time, the detection of the blaOXA-48 gene in E. coli and C. braakii isolates and the blaVIM-4 gene in vegetables. To the best of our knowledge, this is the first report on the detection of mcr-1 genes from vegetables in Algeria.
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