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Andrews K, Landeryou T, Sicheritz-Pontén T, Nale JY. Diverse Prophage Elements of Salmonella enterica Serovars Show Potential Roles in Bacterial Pathogenicity. Cells 2024; 13:514. [PMID: 38534358 DOI: 10.3390/cells13060514] [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: 12/22/2023] [Revised: 01/26/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
Nontyphoidal salmonellosis is an important foodborne and zoonotic infection that causes significant global public health concern. Diverse serovars are multidrug-resistant and encode several virulence indicators; however, little is known on the role prophages play in driving these traits. Here, we extracted prophages from seventy-five Salmonella genomes which represent the fifteen important serovars in the United Kingdom. We analyzed the intact prophages for the presence of virulence genes and established their genomic relationships. We identified 615 prophages from the Salmonella strains, from which 195 prophages are intact, 332 are incomplete, while 88 are questionable. The average prophage carriage was found to be 'extreme' in S. Heidelberg, S. Inverness, and S. Newport (10.2-11.6 prophages/strain), 'high' in S. Infantis, S. Stanley, S. Typhimurium, and S. Virchow (8.2-9.0 prophages/strain), 'moderate' in S. Agona, S. Braenderup, S. Bovismorbificans, S. Choleraesuis, S. Dublin, and S. Java (6.0-7.8 prophages/strain), and 'low' in S. Javiana and S. Enteritidis (5.8 prophages/strain). Cumulatively, 61 virulence genes (1500 gene copies) were detected from representative intact prophages and linked to Salmonella delivery/secretion system (42.62%), adherence (32.7%), magnesium uptake (3.88%), regulation (5%), stress/survival (1.6%), toxins (10%), and antivirulence (1.6%). Diverse clusters were formed among the intact prophages and with bacteriophages of other enterobacteria, suggesting different lineages and associations. Our work provides a strong body of data to support the contributions diverse prophages make to the pathogenicity of Salmonella, including thirteen previously unexplored serovars.
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Affiliation(s)
- Kirstie Andrews
- Centre for Epidemiology and Planetary Health, School of Veterinary Medicine, Scotland's Rural College, Inverness IV2 5NA, UK
| | - Toby Landeryou
- Centre for Epidemiology and Planetary Health, School of Veterinary Medicine, Scotland's Rural College, Inverness IV2 5NA, UK
| | - Thomas Sicheritz-Pontén
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Janet Yakubu Nale
- Centre for Epidemiology and Planetary Health, School of Veterinary Medicine, Scotland's Rural College, Inverness IV2 5NA, UK
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Duggett N, AbuOun M, Stubberfield E, Turner O, Randall L, Horton R, Nunez-Garcia J, Gates D, Chanter J, Teale C, Anjum MF. Genomic surveillance of extended-spectrum cephalosporin-resistant Escherichia coli isolated from poultry in the UK from 2016 to 2020. Front Microbiol 2024; 14:1335173. [PMID: 38352060 PMCID: PMC10861728 DOI: 10.3389/fmicb.2023.1335173] [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: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 02/16/2024] Open
Abstract
Introduction Surveillance is vital for monitoring the increasing risk of antimicrobial resistance (AMR) in bacteria leading to failures in humans and animals to treat infections. In a One Health context, AMR bacteria from livestock and food can transfer through the food chain to humans, and vice versa, which can be characterized in detail through genomics. We investigated the critical aspects of AMR and the dynamics of AMR in poultry in the UK. Methods In this study, we performed whole genome sequencing for genomic characterization of 761 extended-spectrum cephalosporinases (ESCs) harboring Escherichia coli isolated from poultry caeca and meat through EU harmonized monitoring of AMR in zoonotic and commensal bacteria from 2016 and 2018 and UK national monitoring in 2020. Results The most common ESC in 2016 and 2018 was blaCTX-M-1; however, 2020 had a greater diversity of ESCs with blaCTX-M-55 dominant in chickens and blaCTX-M-15 more prevalent in turkeys. Co-resistance to sulphonamides, tetracycline, and trimethoprim was widespread, and there were several positive correlations between the sequence types (STs) and ESC genes. We identified certain AMR genotypes and STs that were frequent each year but not as successful in subsequent years, e.g., ST350 harboring blaCTX-M-1, sul2, and tetA-v4.Phylogenetic comparison of isolates prevalent in our panel with global ones from the same STs available in public databases showed that isolates from the UK generally clustered together, suggesting greater within-country than between-country transmission. Discussion We conclude that future genomic surveillance of indicator organisms will be invaluable as it will enable detailed comparisons of AMR between and within neighboring countries, potentially identifying the most successful sequence types, plasmids, or emerging threats.
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Affiliation(s)
- Nicholas Duggett
- Animal and Plant Health Agency, Addlestone, United Kingdom
- Animal and Plant Health Agency, Thirsk Veterinary Investigation Centre, Thirsk, United Kingdom
| | - Manal AbuOun
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | | | - Olivia Turner
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Luke Randall
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Robert Horton
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | | | - Daisy Gates
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Jeremy Chanter
- Animal and Plant Health Agency, Starcross Veterinary Investigation Centre, Exeter, United Kingdom
| | - Chris Teale
- Animal and Plant Health Agency, Veterinary Investigation Centre, Shrewsbury, United Kingdom
| | - Muna F. Anjum
- Animal and Plant Health Agency, Addlestone, United Kingdom
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Park S, Choi J, Shin D, Kwon KT, Kim SH, Wi YM, Ko KS. Conversion to colistin susceptibility by tigecycline exposure in colistin-resistant Klebsiella pneumoniae and its implications to combination therapy. Int J Antimicrob Agents 2024; 63:107017. [PMID: 37884228 DOI: 10.1016/j.ijantimicag.2023.107017] [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: 07/29/2023] [Revised: 10/13/2023] [Accepted: 10/21/2023] [Indexed: 10/28/2023]
Abstract
OBJECTIVES This study investigated the effect of tigecycline exposure on susceptibility of colistin-resistant Klebsiella pneumoniae isolates to colistin and explored the possibility of antibiotic combination at low concentrations to treat colistin-resistant K. pneumoniae isolates. METHODS Twelve tigecycline-resistant (TIR) mutants were induced in vitro from wild-type, colistin-resistant, and tigecycline-susceptible K. pneumoniae isolates. Antibiotic susceptibility was determined using the broth microdilution method. The deduced amino acid alterations were identified for genes associated with colistin resistance, lipid A biosynthesis, and tigecycline resistance. Expression levels of genes were compared between wild-type stains and TIR mutants using quantitative real-time polymerase chain reaction (PCR). Lipid A modification was explored using MALDI-TOF mass spectrometry. Time-killing assay was performed to assess the efficiency of combination therapy using low concentrations of colistin and tigecycline. RESULTS All TIR mutants except one were converted to be susceptible to colistin. These TIR mutants had mutations in the ramR gene and increased expression levels of ramA. Three genes associated with lipid A biosynthesis, lpxC, lpxL, and lpxO, were also overexpressed in TIR mutants, although no mutation was observed. Additional polysaccharides found in colistin-resistant, wild-type strains were modified in TIR mutants. Colistin-resistant K. pneumoniae strains were eliminated in vitro by combining tigecycline and colistin at 2 mg/L. In this study, we found that tigecycline exposure resulted in reduced resistance of colistin-resistant K. pneumoniae to colistin. Such an effect was mediated by regulation of lipid A modification involving ramA and lpx genes. CONCLUSION Because of such reduced resistance, a combination of colistin and tigecycline in low concentrations could effectively eradicate colistin-resistant K. pneumoniae strains.
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Affiliation(s)
- Suyeon Park
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Jihyun Choi
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Dongwoo Shin
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Ki Tae Kwon
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Si-Ho Kim
- Division of Infectious Diseases, Department of Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Republic of Korea
| | - Yu Mi Wi
- Division of Infectious Diseases, Department of Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Republic of Korea
| | - Kwan Soo Ko
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea.
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Biswas U, Das S, Barik M, Mallick A. Situation Report on mcr-Carrying Colistin-Resistant Clones of Enterobacterales: A Global Update Through Human-Animal-Environment Interfaces. Curr Microbiol 2023; 81:12. [PMID: 37989899 DOI: 10.1007/s00284-023-03521-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 11/23/2023]
Abstract
In the twenty-first century, antibiotic resistance (ABR) is one of the acute medical emergencies around the globe, overwhelming human-animal-environmental interfaces. Hit-or-mis use of antibiotics exacerbates the crisis of ABR, dispersing transferable resistance traits and challenging treatment regimens based on life-saving drugs such as colistin. Colistin is the highest priority critically important antimicrobials for human medicine, but its long use as a growth promoter in animal husbandry reduces clinical efficacy. Since 2015, the emergence and spread of mobile colistin resistance (mcr)-carrying colistin-resistant clones of Enterobacterales have been markedly sustained in both humans and animals, especially in developing countries. Hospital and community transmissions of mcr clones pose a high risk for infection prevention and outbreaks at the national and international levels. Several public health and limited one health studies have highlighted the genomic insights of mcr clones, clarifying the chromosomal sequence types (STs) and plasmid incompatibility (Inc) types. But this information is segregated into humans and animals, and rarely are environmental sectors complicating the understanding of possibly intercontinental and sectoral transmission of these clones. India is the hotspot for superbugs, including mcr-carrying colistin-resistant isolates that threaten cross-border transmission. The current review provided an up-to-date worldwide scenario of mcr-carrying STs and plasmid Inc types among the Gram-negative bacilli of Enterobacterales across human-animal-environmental interfaces and correlated with the available information from India.
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Affiliation(s)
- Urmy Biswas
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Surojit Das
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India.
| | - Mili Barik
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Abhi Mallick
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
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Archer EW, Chisnall T, Tano-Debrah K, Card RM, Duodu S, Kunadu APH. Prevalence and genomic characterization of Salmonella isolates from commercial chicken eggs retailed in traditional markets in Ghana. Front Microbiol 2023; 14:1283835. [PMID: 38029182 PMCID: PMC10646427 DOI: 10.3389/fmicb.2023.1283835] [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: 08/27/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Salmonella enterica are important foodborne bacterial pathogens globally associated with poultry. Exposure to Salmonella-contaminated eggs and egg-related products is a major risk for human salmonellosis. Presently, there is a huge data gap regarding the prevalence and circulating serovars of Salmonella in chicken eggs sold in Ghana. In this study, 2,304 eggs (pools of six per sample unit) collected from informal markets in Accra, Kumasi and Tamale, representing the three ecological belts across Ghana, were tested for Salmonella. Antimicrobial susceptibility testing and Whole Genome Sequencing (WGS) of the isolates were performed using standard microdilution protocols and the Illumina NextSeq platform, respectively. The total prevalence of Salmonella was 5.5% with a higher rate of contamination in eggshell (4.9%) over egg content (1.8%). The serovars identified were S. Ajiobo (n = 1), S. Chester (n = 6), S. Hader (n = 7), S. enteritidis (n = 2); and S. I 4:b:- (n = 8). WGS analysis revealed varied sequence types (STs) that were serovar specific. The S. I 4:b:- isolates had a novel ST (ST8938), suggesting a local origin. The two S. enteritidis isolates belonged to ST11 and were identified with an invasive lineage of a global epidemic clade. All isolates were susceptible to ampicillin, azithromycin, cefotaxime, ceftazidime, gentamicin, meropenem, and tigecycline. The phenotypic resistance profiles to seven antimicrobials: chloramphenicol (13%), ciprofloxacin (94%), and nalidixic acid (94%), colistin (13%), trimethoprim (50%) sulfamethoxazole (50%) and tetracycline (50%) corresponded with the presence of antimicrobial resistance (AMR) determinants including quinolones (gyrA (D87N), qnrB81), aminoglycosides (aadA1), (aph(3")-Ib aph(6)-Id), tetracyclines (tet(A)), phenicols (catA1), trimethoprim (dfrA14 and dfrA1). The S. enteritidis and S. Chester isolates were multidrug resistant (MDR). Several virulence factors were identified, notably cytolethal distending toxin (cdtB gene), rck, pef and spv that may promote host invasion and disease progression in humans. The findings from this study indicate the presence of multidrug resistant and virulent strains of Salmonella serovars in Ghanaian chicken eggs, with the potential to cause human infections. This is a critical baseline information that could be used for Salmonella risk assessment in the egg food chain to mitigate potential future outbreaks.
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Affiliation(s)
- Edward W. Archer
- Nutrition and Food Science Department, University of Ghana, Accra, Ghana
- Food and Drug Authority, Food Safety Management Department, Accra, Ghana
| | - Tom Chisnall
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Kwaku Tano-Debrah
- Nutrition and Food Science Department, University of Ghana, Accra, Ghana
| | | | - Samuel Duodu
- Biochemistry Cell and Molecular Biology Department, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
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Petrin S, Orsini M, Massaro A, Olsen JE, Barco L, Losasso C. Phenotypic and genotypic antimicrobial resistance correlation and plasmid characterization in Salmonella spp. isolates from Italy reveal high heterogeneity among serovars. Front Public Health 2023; 11:1221351. [PMID: 37744490 PMCID: PMC10513437 DOI: 10.3389/fpubh.2023.1221351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction The spread of antimicrobial resistance among zoonotic pathogens such as Salmonella is a serious health threat, and mobile genetic elements (MGEs) carrying antimicrobial resistance genes favor this phenomenon. In this work, phenotypic antimicrobial resistance to commonly used antimicrobials was studied, and the antimicrobial resistance genes (ARGs) and plasmid replicons associated with the resistances were determined. Methods Eighty-eight Italian Salmonella enterica strains (n = 88), from human, animal and food sources, isolated between 2009 and 2019, were selected to represent serovars with different frequency of isolation in human cases of salmonellosis. The presence of plasmid replicons was also investigated. Results and discussion Resistances to sulphonamides (23.9%), ciprofloxacin (27.3%), ampicillin (29.5%), and tetracycline (32.9%) were the most found phenotypes. ARGs identified in the genomes correlated with the phenotypical results, with blaTEM-1B, sul1, sul2, tetA and tetB genes being frequently identified. Point mutations in gyrA and parC genes were also detected, in addition to many different aminoglycoside-modifying genes, which, however, did not cause phenotypic resistance to aminoglycosides. Many genomes presented plasmid replicons, however, only a limited number of ARGs were predicted to be located on the contigs carrying these replicons. As an expectation of this, multiple ARGs were identified on contigs with IncQ1 plasmid replicon in strains belonging to the monophasic variant of Salmonella Typhimurium. In general, high variability in ARGs and plasmid replicons content was observed among isolates, highlighting a high level of heterogeneity in Salmonella enterica. Irrespective of the serovar., many of the ARGs, especially those associated with critically and highly important antimicrobials for human medicine were located together with plasmid replicons, thus favoring their successful dissemination.
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Affiliation(s)
- Sara Petrin
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Massimiliano Orsini
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
| | - Andrea Massaro
- Applied Chemistry Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicenza, Italy
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lisa Barco
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
| | - Carmen Losasso
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
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Tada T, Oshiro S, Watanabe S, Tohya M, Hishinuma T, Htoon TT, Tin HH, Kirikae T. Klebsiella pneumoniae co-harbouring bla NDM-1 , armA and mcr-10 isolated from blood samples in Myanmar. J Med Microbiol 2023; 72. [PMID: 37706679 DOI: 10.1099/jmm.0.001750] [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: 09/15/2023] Open
Abstract
Background. The spread of Enterobacteriaceae coproducing carbapenemases, 16S rRNA methylase and mobile colistin resistance proteins (MCRs) has become a serious public health problem worldwide. This study describes two clinical isolates of Klebsiella pneumoniae coharbouring bla IMP-1, armA and mcr-10.Methods. Two clinical isolates of K. pneumoniae resistant to carbapenems and aminoglycosides were obtained from two patients at a hospital in Myanmar. Their minimum inhibitory concentrations (MICs) were determined by broth microdilution methods. The whole-genome sequences were determined by MiSeq and MinION methods. Drug-resistant factors and their genomic environments were determined.Results. The two K. pneumoniae isolates showed MICs of ≥4 and ≥1024 µg ml-1 for carbapenems and aminoglycosides, respectively. Two K. pneumonaie harbouring mcr-10 were susceptible to colistin, with MICs of ≤0.015 µg ml-1 using cation-adjusted Mueller-Hinton broth, but those for colistin were significantly higher (0.5 and 4 µg ml-1) using brain heart infusion medium. Whole-genome analysis revealed that these isolates coharboured bla NDM-1, armA and mcr-10. These two isolates showed low MICs of 0.25 µg ml-1 for colistin. Genome analysis revealed that both bla NDM-1 and armA were located on IncFIIs plasmids of similar size (81 kb). The mcr-10 was located on IncM2 plasmids of sizes 220 or 313 kb in each isolate. These two isolates did not possess a qseBC gene encoding a two-component system, which is thought to regulate the expression of mcr genes.Conclusion. This is the first report of isolates of K. pneumoniae coharbouring bla NDM-1, armA and mcr-10 obtained in Myanmar.
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Affiliation(s)
- Tatsuya Tada
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Satoshi Oshiro
- Juntendo Advanced Research Institute for Health Science, Juntendo University, Tokyo, Japan
| | - Shin Watanabe
- Department of Microbiome Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mari Tohya
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Tomomi Hishinuma
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | | | | | - Teruo Kirikae
- Juntendo Advanced Research Institute for Health Science, Juntendo University, Tokyo, Japan
- Department of Microbiome Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Talat A, Miranda C, Poeta P, Khan AU. Farm to table: colistin resistance hitchhiking through food. Arch Microbiol 2023; 205:167. [PMID: 37014461 DOI: 10.1007/s00203-023-03476-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023]
Abstract
Colistin is a high priority, last-resort antibiotic recklessly used in livestock and poultry farms. It is used as an antibiotic for treating multi-drug resistant Gram-negative bacterial infections as well as a growth promoter in poultry and animal farms. The sub-therapeutic doses of colistin exert a selection pressure on bacteria leading to the emergence of colistin resistance in the environment. Colistin resistance gene, mcr are mostly plasmid-mediated, amplifying the horizontal gene transfer. Food products such as chicken, meat, pork etc. disseminate colistin resistance to humans through zoonotic transfer. The antimicrobial residues used in livestock and poultry often leaches to soil and water through faeces. This review highlights the recent status of colistin use in food-producing animals, its association with colistin resistance adversely affecting public health. The underlying mechanism of colistin resistance has been explored. The prohibition of over-the-counter colistin sales and as growth promoters for animals and broilers has exhibited effective stewardship of colistin resistance in several countries.
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Affiliation(s)
- Absar Talat
- Medical and Molecular Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Carla Miranda
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Department of Sciences, University Institute of Health Sciences (IUCS), CESPU, CRL, Gandra, Portugal
- Toxicology Research Unit (TOXRUN), IUCS, CESPU, CRL, Gandra, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, Caparica, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-Os-Montes and Alto Douro (UTAD)UTAD, Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
| | - Asad U Khan
- Medical and Molecular Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Zhang E, Zong S, Zhou W, Zhou J, Han J, Qu D. Characterization and comparative genomics analysis of RepA_N multi-resistance plasmids carrying optrA from Enterococcus faecalis. Front Microbiol 2023; 13:991352. [PMID: 36777024 PMCID: PMC9911807 DOI: 10.3389/fmicb.2022.991352] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/01/2022] [Indexed: 01/28/2023] Open
Abstract
Introduction This research aimed to investigate the antibiotic resistance of Enterococcus faecalis from swine farms in Zhejiang Province and the prevalence and transmission mechanism of oxazolidone resistance gene optrA. Method A total of 226 Enterococcus faecalis were isolated and their resistance to 14 antibiotics was detected by broth microdilution. The resistance genes were detected by PCR. Results The antibiotic resistance rate of 226 isolates to nearly 57% (8/14) of commonly used antibiotics was higher than 50%. The resistance rate of tiamulin was highest (98.23%), that of tilmicosin, erythromycin, tetracycline and florfenicol was higher than 80%, and that of oxazolidone antibiotic linezolid was 38.49%. The overall antibiotics resistance in Hangzhou, Quzhou and Jinhua was more serious than that in the coastal cities of Ningbo and Wenzhou. The result of PCR showed that optrA was the main oxazolidinone and phenicols resistance gene, with a detection rate of 71.68%, and optrA often coexisted with fexA in the isolates. Through multi-locus sequence typing, conjugation transfer, and replicon typing experiments, it was found that the horizontal transmission mediated by RepA_N plasmid was the main mechanism of optrA resistance gene transmission in E. faecalis from Zhejiang Province. Two conjugative multi-resistance plasmids carrying optrA, RepA_N plasmid pHZ318-optrA from Hangzhou and Rep3 plasmid from Ningbo, were sequenced and analyzed. pHZ318-optrA contain two multidrug resistance regions (MDR), which contributed to the MDR profile of the strains. optrA and fexA resistance genes coexisted in IS1216E-fexA-optrA-ferr-erm(A)-IS1216E complex transposon, and there was a partial sequence of Tn554 transposon downstream. However, pNB304-optrA only contain optrA, fexA and an insertion sequence ISVlu1. The presence of mobile genetic elements at the boundaries can possibly facilitate transfer among Enterococcus through inter-replicon gene transfer. Discussion This study can provide theoretical basis for ensuring the quality and safety of food of animal origin, and provide scientific guidance for slowing down the development of multi-antibiotic resistant Enterococcus.
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Affiliation(s)
- Enbao Zhang
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Shuaizhou Zong
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Wei Zhou
- Zhejiang Provincial Center for Animal Disease Prevention and Control, Hangzhou, China
| | - Jinzhi Zhou
- Zhejiang Provincial Center for Animal Disease Prevention and Control, Hangzhou, China
| | - Jianzhong Han
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Daofeng Qu
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China,*Correspondence: Daofeng Qu, ✉
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Food for Thought: Proteomics for Meat Safety. Life (Basel) 2023; 13:life13020255. [PMID: 36836616 PMCID: PMC9966529 DOI: 10.3390/life13020255] [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: 12/08/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
Foodborne bacteria interconnect food and human health. Despite significant progress in food safety regulation, bacterial contamination is still a serious public health concern and the reason for significant commercial losses. The screening of the microbiome in meals is one of the main aspects of food production safety influencing the health of the end-consumers. Our research provides an overview of proteomics findings in the field of food safety made over the last decade. It was believed that proteomics offered an accurate snapshot of the complex networks of the major biological machines called proteins. The proteomic methods for the detection of pathogens were armed with bioinformatics algorithms, allowing us to map the data onto the genome and transcriptome. The mechanisms of the interaction between bacteria and their environment were elucidated with unprecedented sensitivity, specificity, and depth. Using our web-based tool ScanBious for automated publication analysis, we analyzed over 48,000 scientific articles on antibiotic and disinfectant resistance and highlighted the benefits of proteomics for the food safety field. The most promising approach to studying safety in food production is the combination of classical genomic and metagenomic approaches and the advantages provided by proteomic methods with the use of panoramic and targeted mass spectrometry.
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Tang B, Elbediwi M, Nambiar RB, Yang H, Lin J, Yue M. Genomic Characterization of Antimicrobial-Resistant Salmonella enterica in Duck, Chicken, and Pig Farms and Retail Markets in Eastern China. Microbiol Spectr 2022; 10:e0125722. [PMID: 36047803 PMCID: PMC9603869 DOI: 10.1128/spectrum.01257-22] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/17/2022] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial-resistant Salmonella enterica poses a significant public health concern worldwide. However, the dissemination of Salmonella enterica among food animals in eastern China has not been fully addressed. Here, we demonstrated the antimicrobial resistance (AMR) patterns and the whole-genome characterization of 105 S. enterica isolates from 1,480 fecal samples and anal swabs collected from 22 different farms (chickens, ducks, and pigs) and two live animal markets located in Zhejiang and Fujian Provinces in eastern China in 2019. The prevalence of isolates in duck farms (19.17%, 23/120) was statistically significantly higher (P < 0.001) than that in chicken farms (6.61%, 37/523) and pig farms (3.50%, 7/200). Among these isolates, 75.26% (79/105) were multidrug resistant, with the highest rates of resistance to tetracycline (76.20%) and ampicillin (67.62%) and the lowest resistance rate to meropenem (0.00%). The serotypes were consistent with sequence types and were closely related to the sampling animal species and sites. S. enterica serotype Kentucky (20.95%, 22/105) was the most frequent serotype and harbored more AMR patterns and genes than others. Furthermore, IncFII(S) and IncHI2 were the most prevalent replicons. A total of 44 acquired AMR genes were found. Among those genes, aac(6')-Iaa, blaTEM-1B, floR, dfrA14, fosA7, mph(A), qnrS1, sul1, tet(A), and ARR-3 were the dominant AMR genes mediating the AMR toward aminoglycosides, β-lactams, phenicol, trimethoprim, fosfomycin, macrolide, quinolone, sulfonamides, tetracycline, and rifampin, respectively. The consistency of acquired AMR genes with AMR phenotypes for ampicillin, ceftiofur, ceftazidime, meropenem, sulfamethoxazole-trimethoprim, and tetracycline was >90%. Together, our study highlights the application of whole-genome sequencing to assess veterinary public health threats. IMPORTANCE Public health is a significant concern in China, and the foodborne pathogen Salmonella, which is spread via the animal-borne food chain, plays an important role in the overall disease burden in China annually. The development of advanced sequencing technologies has introduced a new way of understanding emerging pathogens. However, the routine surveillance application of this method in China remains in its infancy. Here, we applied a pool of all isolates from the prevalence data in Zhejiang and Fujian for whole-genome sequencing and combined these data with the cutting-edge bioinformatic analysis pipeline for one-step determination of the complete genetic makeup for all 105 genomes. The illustrated method could provide a cost-effective approach, without labor-intensive laboratory characterization, for predicting serotypes, genotypes, plasmid types, antimicrobial resistance genes, and virulence genes, and thus would provide essential knowledge for emerging pathogens. Our findings and perspectives are essential for delivering updated knowledge on foodborne pathogens in an understudied region in China.
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Affiliation(s)
- Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Mohammed Elbediwi
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Reshma B. Nambiar
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiahui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Min Yue
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- Hainan Institute of Zhejiang University, Sanya, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
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12
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Mmatli M, Mbelle NM, Osei Sekyere J. Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update. Front Cell Infect Microbiol 2022; 12:941358. [PMID: 36093193 PMCID: PMC9462459 DOI: 10.3389/fcimb.2022.941358] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/01/2022] [Indexed: 12/28/2022] Open
Abstract
Background Mobile colistin resistance (mcr) genes modify Lipid A molecules of the lipopolysaccharide, changing the overall charge of the outer membrane. Results and discussion Ten mcr genes have been described to date within eleven Enterobacteriaceae species, with Escherichia coli, Klebsiella pneumoniae, and Salmonella species being the most predominant. They are present worldwide in 72 countries, with animal specimens currently having the highest incidence, due to the use of colistin in poultry for promoting growth and treating intestinal infections. The wide dissemination of mcr from food animals to meat, manure, the environment, and wastewater samples has increased the risk of transmission to humans via foodborne and vector-borne routes. The stability and spread of mcr genes were mediated by mobile genetic elements such as the IncHI2 conjugative plasmid, which is associated with multiple mcr genes and other antibiotic resistance genes. The cost of acquiring mcr is reduced by compensatory adaptation mechanisms. MCR proteins are well conserved structurally and via enzymatic action. Thus, therapeutics found effective against MCR-1 should be tested against the remaining MCR proteins. Conclusion The dissemination of mcr genes into the clinical setting, is threatening public health by limiting therapeutics options available. Combination therapies are a promising option for managing and treating colistin-resistant Enterobacteriaceae infections whilst reducing the toxic effects of colistin.
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Affiliation(s)
- Masego Mmatli
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, United States
- Department of Dermatology, School of Medicine, University of Pretoria, Pretoria, South Africa
- *Correspondence: John Osei Sekyere, ;
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13
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Al Mana H, Johar AA, Kassem II, Eltai NO. Transmissibility and Persistence of the Plasmid-Borne Mobile Colistin Resistance Gene, mcr-1, Harbored in Poultry-Associated E. coli. Antibiotics (Basel) 2022; 11:antibiotics11060774. [PMID: 35740180 PMCID: PMC9220209 DOI: 10.3390/antibiotics11060774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
Colistin, a last-resort antibiotic, is used to treat infections caused by multi-drug-resistant Gram-negative bacteria. Colistin resistance can emerge by acquiring the mobile colistin gene, mcr-1, usually plasmid borne. Studies on mcr-1 and its transmissibility are limited in the Middle East and North Africa (MENA) region. Here, we investigated the occurrence of mcr-1 in 18 previously collected Escherichia coli isolates collected from chicken samples in Qatar; whole-genome sequencing was performed to determine the location (plasmid-borne and chromosomal) of mcr-1 in the isolates. Additionally, we assessed the transmissibility of plasmid-borne mcr-1 and its cost on fitness in E. coli biofilms. Our results showed that the E. coli isolates belonged to different sequence types, indicating that mcr-1 was occurring in strains with diverse genetic backgrounds. In silico analysis and transformation assays showed that all the isolates carried mcr-1 on plasmids that were mainly IncI2 types. All the mcr-1 plasmids were found to be transmissible by conjugation. In biofilms, a significant reduction in the number of CFU (≈0.055 logs CFU/mL) and colistin resistance (≈2.19 log CFU/mL) was observed; however, the reduction in resistance was significantly larger, indicating that the plasmids incur a high fitness cost. To our knowledge, this is the first study that investigates mcr-1 transmissibility and persistence in Qatar. Our findings highlight that mcr has the potential to spread colistin resistance to potentially disparate strains and niches in Qatar, posing a risk that requires intervention.
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Affiliation(s)
- Hassan Al Mana
- Biomedical Research Centre, Microbiology Department, Qatar University, Doha 2713, Qatar;
| | - Alreem A. Johar
- Research and Development Department, Barzan Holdings, Doha 7178, Qatar;
| | - Issmat I. Kassem
- GA Centre for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA 30609, USA;
| | - Nahla O. Eltai
- Biomedical Research Centre, Microbiology Department, Qatar University, Doha 2713, Qatar;
- Correspondence: ; Tel.: +974-44-037-705
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14
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Smoglica C, Angelucci S, Farooq M, Antonucci A, Marsilio F, Di Francesco CE. Microbial community and antimicrobial resistance in fecal samples from wild and domestic ruminants in Maiella National Park, Italy. One Health 2022; 15:100403. [PMID: 35647256 PMCID: PMC9136667 DOI: 10.1016/j.onehlt.2022.100403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 01/04/2023] Open
Abstract
This study aimed to provide new insights about antimicrobial resistance genes abundance and microbial communities of wild and domestic ruminants in wildlife-livestock interface. In total, 88 fecal samples were recovered from Apennine chamois, red deer, goat, cattle and sheep, and were collected in pools. The populations under study were selected based on ecological data useful to define sympatric and non-sympatric populations. Samples were screened for commonly used in farms under study or critically important antimicrobial resistance genes (aadA2, TetA, TetB, TetK, TetM, mcr-1). The microbial community composition was found to be different based on the species and land use of animals under study. Indeed, it was mostly characterized by phyla Firmicutes in bovine, Bacteroidota in chamois and Proteobacteria in red deer. Additionally, positive correlations between antibiotic resistance genes and microbial taxa (e.g., Tet genes correlated with Firmicutes and Patescibacteria) were described. Of the antimicrobials investigated, the abundance of mcr-1 gene suggests the importance of monitoring the wildlife in order to detect the emerging resistance genes contamination in environment. This study provides new data that highlight the importance of multidisciplinary and uncultured study in order to describe the spreading of antimicrobial resistance and related contamination in the environment. Multidisciplinary approach including ecological data, real time PCRs and 16S rRNA analysis Microbial communities composition of rare species as Apennine chamois Evaluation of antibiotic resistance genes abundance in feces of wild and domestic ruminants Detection of mcr-1 resistance gene relevant for Public Health
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15
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Conjugative transfer of mcr-1-bearing plasmid from Salmonella to Escherichia coli in vitro on chicken meat and in mouse gut. Food Res Int 2022; 157:111263. [DOI: 10.1016/j.foodres.2022.111263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 11/23/2022]
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16
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Fan Z, Feng Y, Xu W, Feng J, Yan C, Fu T, Zhao H, Cui J, Gan L, Liu S, Du S, Zhang R, Xu Z, Li N, Xue G, Yuan J. Rapid Detection of Multi-Resistance Strains Carrying mcr-1 Gene Using Recombinase-Aided Amplification Directly on Clinical Samples. Front Microbiol 2022; 13:852488. [PMID: 35432248 PMCID: PMC9009391 DOI: 10.3389/fmicb.2022.852488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
With the increasingly severe problem of bacterial resistance, colistin, as the last line of defense, has attracted attention again. Mobile colistin resistance (mcr-1) gene is involved in the horizontal transmission of colistin resistance in Gram-negative bacteria (GNB), which is a serious threat to human health. Therefore, rapid detection of mcr-1 gene presence in clinical samples is crucial. In this study, a Recombinase-aided amplification(RAA) method for mcr-1 was successfully constructed, with sensitivity of 20 copies/reaction. In addition, amplification signal could only be detected in the strain containing mcr-1 gene among 14 different bacterial species. The method was then used to test a total of 672 clinical samples from a pediatric hospital in Beijing. Five strains harbored mcr-1 genes were isolated from mcr-1-positive clinical samples and identified as Escherichia coli. Multi-locus sequence typing (MLST) analysis showed that the five E. coli belonged to different ST types. Notably, the mcr-1 gene from the isolates could be transferred conjugately to the recipient strain E. coli J53, with highest transfer efficiency up to 57–58%, suggesting that the mcr-1 gene was located on the plasmid. These findings showed that the RAA assay has potential to be a rapid and sensitive mcr-1 gene screening test for clinical samples, and mcr-1 could be transmitted vertically and horizontally between and within bacterial species in a plasmid-mediated manner.
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Affiliation(s)
- Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Wenjian Xu
- Children’s Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Tongtong Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shiyu Liu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Nannan Li
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- *Correspondence: Guanhua Xue,
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- Jing Yuan,
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17
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Niu SH, Liu S, Deng WK, Wu RT, Cai YF, Liao XD, Xing SC. A sustainable and economic strategy to reduce risk antibiotic resistance genes during poultry manure bioconversion by black soldier fly Hermetia illucens larvae: Larval density adjustment. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 232:113294. [PMID: 35152113 DOI: 10.1016/j.ecoenv.2022.113294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/27/2022] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
Black soldier fly (Hermetia illucens) larvae (BSFL) are common insects that are known for bioconversion of organic waste into a sustainable utilization resource. However, a strategy to increase antibiotic resistance gene (ARG) elimination in sustainable and economic ways through BSFL is lacking. In the present study, different larval densities were employed to assess the mcr-1 and tetX elimination abilities, and potential mechanisms were investigated. The application and economic value of each larval density were also analyzed. The results showed that the 100 larvae cultured in 100 g of manure group had the best density because the comprehensive disadvantage evaluation ratio was the lowest (14.97%, good bioconversion manure quality, low ARG deposition risk and reasonable larvae input cost). Further investigation showed that mcr-1 could be significantly decreased by BSFL bioconversion (4.42 ×107 copies/g reduced to 4.79 ×106-2.14 ×105 copies/g)(P<0.05); however, mcr-1 was increasingly deposited in the larval gut with increasing larval density. The tetX abundance was stabilized by BSFL bioconversion, except that the abundance at the lowest larval density increased (1.22 ×1010 copies/g increase, 34-fold). Escherichia was the host of mcr-1 and tetX in all samples, especially in fresh manure; Alcaligenes was the host of tetX in bioconversion manure; and the abundance of Alcaligenes was highly correlated with the pH of bioconversion manure. The pH of bioconversion manure was extremely correlated with the density of larvae. Klebsiella and Providencia were both hosts of tetX in the BSF larval gut, and Providencia was also the host of mcr-1 in the BSF larval gut. The density of larvae influenced the bioconversion manure quality and caused the ARG host abundance to change to control the abundance of ARGs, suggesting that larval density adjustment was a useful strategy to manage the ARG risk during BSFL manure bioconversion.
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Affiliation(s)
- Shi-Hua Niu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Shuo Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Wei-Kang Deng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Rui-Ting Wu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Ying-Feng Cai
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Di Liao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou 510642, Guangdong, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Si-Cheng Xing
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou 510642, Guangdong, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China.
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18
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Lu J, Yang Y, Wu Y, Liu C, Zeng Y, Lei L, Song H, Zhang R. Escherichia coli carrying IncI2 plasmid-mediated mcr-1 genes in crested ibis (Nipponia nippon). J Infect Public Health 2022; 15:558-561. [DOI: 10.1016/j.jiph.2022.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 11/26/2022] Open
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19
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Storey N, Cawthraw S, Turner O, Rambaldi M, Lemma F, Horton R, Randall L, Duggett NA, AbuOun M, Martelli F, Anjum MF. Use of genomics to explore AMR persistence in an outdoor pig farm with low antimicrobial usage. Microb Genom 2022; 8:000782. [PMID: 35344479 PMCID: PMC9176276 DOI: 10.1099/mgen.0.000782] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Food animals may be reservoirs of antimicrobial resistance (AMR) passing through the food chain, but little is known about AMR prevalence in bacteria when selective pressure from antimicrobials is low or absent. We monitored antimicrobial-resistant Escherichia coli over 1 year in a UK outdoor pig farm with low antimicrobial usage (AMU) compared to conventional pig farms in the United Kingdom. Short and selected long-read whole-genome sequencing (WGS) was performed to identify AMR genes, phylogeny and mobile elements in 385 E. coli isolates purified mainly from pig and some seagull faeces. Generally, low levels of antimicrobial-resistant E. coli were present, probably due to low AMU. Those present were likely to be multi-drug resistant (MDR) and belonging to particular Sequence Types (STs) such as ST744, ST88 or ST44, with shared clones (<14 Single Nucleotide Polymorphisms (SNPs) apart) isolated from different time points indicating epidemiological linkage within pigs of different ages, and between pig and the wild bird faeces. Although importance of horizontal transmission of AMR is well established, there was limited evidence of plasmid-mediated dissemination between different STs. Non-conjugable MDR plasmids or large AMR gene-bearing transposons were stably integrated within the chromosome and remained associated with particular STs/clones over the time period sampled. Heavy metal resistance genes were also detected within some genetic elements. This study highlights that although low levels of antimicrobial-resistant E. coli correlates with low AMU, a basal level of MDR E. coli can still persist on farm potentially due to transmission and recycling of particular clones within different pig groups. Environmental factors such as wild birds and heavy metal contaminants may also play important roles in the recycling and dissemination, and hence enabling persistence of MDR E. coli. All such factors need to be considered as any rise in AMU on low usage farms, could in future, result in a significant increase in their AMR burden.
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Affiliation(s)
- Nathaniel Storey
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- Great Ormond Street Hospital for Children, London WC1N 3JH, UK
| | - Shaun Cawthraw
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Olivia Turner
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Margherita Rambaldi
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- University of Bologna, Via Zamboni, 33, 40126 Bologna BO, Italy
| | - Fabrizio Lemma
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Robert Horton
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Luke Randall
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Nicholas A. Duggett
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- Teeside University, Campus Heart, Middlesbrough TS1 3BX, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Francesca Martelli
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Muna F. Anjum
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- *Correspondence: Muna F. Anjum,
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20
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Clinically healthy household dogs and cats as carriers of multidrug-resistant Salmonella enterica with variable R plasmids. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Introduction. Antimicrobial resistance (AMR) is a One Health issue concerning humans, animals and the environment and a unified One Health approach is required to contain this problematic issue. Dogs and cats are popular pet animals and are known to carry many bacterial pathogens that are of public health importance, including
Salmonella
. However, data on AMR in companion animals is limited.
Gap statement. Scant AMR data from bacteria originating from companion animals limits an accurate assessment of the impacts of pet-animal-related AMR on public health.
Purpose. This study aimed to phenotypically and genetically investigate AMR in
Salmonella
isolated from pet dogs and cats in Thailand.
Methodology.
Salmonella enterica
were isolated from pet dogs (n=159) and cats (n=19) in Thailand between 2016 and 2019. All isolates were serotyped. Phenotypic and genotypic antimicrobial resistance was examined. PCR-based replicon typing, replicon sequence typing and plasmid multilocus sequence typing were conducted to characterize plasmids.
Results. Seventy-seven serovars were identified, with serovars Weltevreden (9.6%) and Stockholm (9.0%) the most common. Most of the isolates (34.3%) were multidrug-resistant. The serovar Stockholm was an ESBL-producer and carried the β-lactamase genes bla
TEM-1 and bla
CTX-M-55. The plasmid-mediated quinolone resistance (PMQR) gene, qnrS, was also detected (10.1%). Class 1 integrons carrying the dfrA12-aadA2 cassette array were most frequent (45.9%). Five plasmid replicon types as IncA/C (0.6%), N (1.1%), IncFIIA (28.7%), IncHI1 (2.2%), and IncI1 (3.4%) were identified. Based on the pMLST typing scheme (n=9), plasmids were assigned into five different STs including IncA/C-ST6 (n=1), IncH1-ST16 (n=4), IncI1-ST3 (n=1), IncI1-ST60 (n=1) and IncI1-ST136 (n=1). The ST 16 of IncHI1 plasmid was a novel plasmid ST. Subtyping F-type plasmids using the RST scheme (n=9) revealed four different combinations of replicons including S1:A-:B- (n=4), S1:A-:B22 (n=2), S3:A-:B- (n=1) and S-:A-:B47 (n=1).
Conclusions. Our findings highlight the role of clinically healthy household dogs and cats as carriers of AMR
Salmonella
strains with different R plasmid. The implementation of AMR phenotypes instigation and genotypic monitoring and surveillance programmes in companion animals are imperative as integral components of the One Health framework.
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21
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Valdez C, Costa C, Simões M, de Carvalho CCCR, Baptista T, Campos MJ. Detection of mcr-1 Gene in Undefined Vibrio Species Isolated from Clams. Microorganisms 2022; 10:microorganisms10020394. [PMID: 35208850 PMCID: PMC8876837 DOI: 10.3390/microorganisms10020394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/24/2022] [Accepted: 02/03/2022] [Indexed: 01/27/2023] Open
Abstract
The increase of antimicrobial resistant strains is leading to an emerging threat to public health. Pathogenic Vibrio are responsible for human and animal illness. The Enterobacteriaceae family includes microorganisms that affect humans, causing several infections. One of the main causes of human infection is related to the ingestion of undercooked seafood. Due to their filter-feeding habit, marine invertebrates, such as clams, are known to be a natural reservoir of specific microbial communities. In the present study, Vibrionaceae and coliforms microorganisms were isolated from clams. A microbial susceptibility test was performed using the disk diffusion method. From 43 presumptive Vibrio spp. and 17 coliforms, three Vibrio spp. with MICs to colistin >512 mg L−1 were found. From the 23 antimicrobial resistance genes investigated, only the three isolates that showed phenotypic resistance to colistin contained the mcr-1 gene. Genotypic analysis for virulence genes in EB07V indicated chiA gene presence. The results from the plasmid cure and transformation showed that the resistance is chromosomally mediated. Biochemical analysis and MLSA, on the basis of four protein-coding gene sequences (recA, rpoB, groEL and dnaJ), grouped the isolates into the genus Vibrio but distinguished them as different from any known Vibrio spp.
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Affiliation(s)
- Christian Valdez
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Cátia Costa
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Marco Simões
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Carla C. C. R. de Carvalho
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Teresa Baptista
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Maria J. Campos
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
- Correspondence:
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22
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Rodríguez-Santiago J, Rodríguez-Medina N, Tamayo-Legorreta EM, Silva-Sánchez J, Téllez-Sosa J, Duran-Bedolla J, Aguilar-Vera A, Lecona-Valera AN, Garza-Ramos U, Alpuche-Aranda C. Molecular and Genomic Insights of mcr-1-Producing Escherichia coli Isolates from Piglets. Antibiotics (Basel) 2022; 11:antibiotics11020157. [PMID: 35203760 PMCID: PMC8868104 DOI: 10.3390/antibiotics11020157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
The use of colistin in food-producing animals favors the emergence and spread of colistin-resistant strains. Here, we investigated the occurrence and molecular mechanisms of colistin resistance among E. coli isolates from a Mexican piglet farm. A collection of 175 cephalosporin-resistant colonies from swine fecal samples were recovered. The colistin resistance phenotype was identified by rapid polymyxin test and the mcr-type genes were screened by PCR. We assessed the colistin-resistant strains by antimicrobial susceptibility test, pulse-field gel electrophoresis, plasmid profile, and mating experiments. Whole-Genome Sequencing data was used to explore the resistome, virulome, and mobilome of colistin-resistant strains. A total of four colistin-resistant E. coli were identified from the cefotaxime-resistant colonies. All harbored the plasmid-borne mcr-1 gene, which was located on conjugative 170-kb IncHI-2 plasmid co-carrying ESBLs genes. Thus, high antimicrobial resistance rates were observed for several antibiotic families. In the RC2-007 strain, the mcr-1 gene was located as part of a prophage carried on non-conjugative 100-kb-plasmid, which upon being transformed into K. variicola strain increased the polymyxin resistance 2-fold. The genomic analysis showed a broad resistome and virulome. Our findings suggest that colistin resistance followed independent acquisition pathways as clonal and non-genetically related mcr-1-harboring strains were identified. These E. coli isolates represent a reservoir of antibiotic resistance and virulence genes in animals for human consumption which could be potentially propagated into other interfaces.
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Affiliation(s)
- Jonathan Rodríguez-Santiago
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Nadia Rodríguez-Medina
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Elsa María Tamayo-Legorreta
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Jesús Silva-Sánchez
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Josefina Duran-Bedolla
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Alejandro Aguilar-Vera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62100, Morelos, Mexico;
| | - Alba Neri Lecona-Valera
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Ulises Garza-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
- Correspondence: (U.G.-R.); (C.A.-A.)
| | - Celia Alpuche-Aranda
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
- Correspondence: (U.G.-R.); (C.A.-A.)
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23
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Development of a Phage Cocktail to Target Salmonella Strains Associated with Swine. Pharmaceuticals (Basel) 2022; 15:ph15010058. [PMID: 35056115 PMCID: PMC8777603 DOI: 10.3390/ph15010058] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 02/06/2023] Open
Abstract
Infections caused by multidrug resistant Salmonella strains are problematic in swine and are entering human food chains. Bacteriophages (phages) could be used to complement or replace antibiotics to reduce infection within swine. Here, we extensively characterised six broad host range lytic Salmonella phages, with the aim of developing a phage cocktail to prevent or treat infection. Intriguingly, the phages tested differed by one to five single nucleotide polymorphisms. However, there were clear phenotypic differences between them, especially in their heat and pH sensitivity. In vitro killing assays were conducted to determine the efficacy of phages alone and when combined, and three cocktails reduced bacterial numbers by ~2 × 103 CFU/mL within two hours. These cocktails were tested in larvae challenge studies, and prophylactic treatment with phage cocktail SPFM10-SPFM14 was the most efficient. Phage treatment improved larvae survival to 90% after 72 h versus 3% in the infected untreated group. In 65% of the phage-treated larvae, Salmonella counts were below the detection limit, whereas it was isolated from 100% of the infected, untreated larvae group. This study demonstrates that phages effectively reduce Salmonella colonisation in larvae, which supports their ability to similarly protect swine.
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24
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Bennani H, Cornelsen L, Stärk KDC, Häsler B. Evaluating Integrated Surveillance for Antimicrobial Use and Resistance in England: A Qualitative Study. Front Vet Sci 2021; 8:743857. [PMID: 34805336 PMCID: PMC8596565 DOI: 10.3389/fvets.2021.743857] [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: 07/19/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
Integrated surveillance systems for antimicrobial use (AMU) and antimicrobial resistance (AMR) require regular evaluation to ensure the effectiveness and efficiency of the system. An important step in the evaluation is to choose an appropriate tool for the purpose of the evaluation. The “Integrated Surveillance System Evaluation” (ISSE) framework is a conceptual framework that was developed to evaluate One Health (OH) integration in surveillance system for AMU/AMR. This study aimed to evaluate the performance and value of integrated surveillance system for AMU/AMR in England by applying the ISSE framework, which was used to develop data collection protocols and define the study design. A qualitative study using semi-structured interviews was conducted to collect the data and analyse it thematically. Eighteen stakeholders from human, animal, food and environment sectors that are involved in AMU/AMR surveillance were interviewed. Four main themes emerged from the analysis: (1) Cross-sectoral integration in the surveillance system for AMU/AMR; (2) Production of OH outputs and outcomes; (3) Drivers and barriers to cross-sectoral collaboration; and 4) Need for more cross-sectoral collaboration. The findings showed that there were links between integrated surveillance information, decision making and interventions. However, there were only few OH examples, such as the UK AMR contingency plan, where the potential of cross-sectoral collaboration was fully exploited. A lot of the benefits described were related to the generation of information and increase in knowledge and understanding without links to how the information generated was used. While these intangible benefits have a value on their own, being able to link surveillance information and mitigation measures would help to enhance the value of integrated surveillance. In terms of improvement, the main areas identified were the development of more harmonised methods for data collection and analysis, provision of resources dedicated to cross-sectoral collaboration, improved coordination, and collection of surveillance data from the environment and from companion animals. By identifying links between OH surveillance information produced and various outputs and outcomes; this study helped to understand the wider benefits of integrated surveillance for AMU/AMR in England and provided insights on how the system could be improved and efficiency increased.
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Affiliation(s)
- Houda Bennani
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Laura Cornelsen
- Department of Public Health, Environments and Society, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Katharina D C Stärk
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom.,Department of Animal Health, Federal Food Safety and Veterinary Office, Bern, Switzerland
| | - Barbara Häsler
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
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25
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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.
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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.
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26
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Mori N, Tada T, Oshiro S, Kuwahara-Arai K, Kirikae T, Uehara Y. A transferrable IncL/M plasmid harboring a gene encoding IMP-1 metallo-β-lactamase in clinical isolates of Enterobacteriaceae. BMC Infect Dis 2021; 21:1061. [PMID: 34645409 PMCID: PMC8513173 DOI: 10.1186/s12879-021-06758-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 10/04/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The worldwide spread of carbapenemase-producing Enterobacteriaceae (CPE) has reduced the clinical utility of carbapenems. Plasmids often play an important role in the spread of genes encoding drug-resistance factors, especially in the horizontal transfer of these genes among species of Enterobacteriaceae. This study describes a patient infected with three species of CPE carrying an identical transferrable IncL/M plasmid. METHODS Clinical isolates of CPE were collected at St. Luke's International Hospital, Tokyo, Japan, from 2015 to 2019. Three species of CPE isolates, Enterobacter cloacae, Klebsiella aerogenes and Serratia marcescens, were isolated from a patient who developed severe gallstone pancreatitis associated with bloodstream infection, with all three isolates producing IMP-1 metallo-β-lactamase. The complete sequences of the plasmids of the three isolates were determined by both MiSeq and MinION. The medical chart of this patient was retrospectively reviewed conducted to obtain relevant clinical information. RESULTS The three CPE species carried an IncL/M plasmid, pSL264, which was 81,133 bp in size and harbored blaIMP-1. The genetic environment surrounding blaIMP-1 consisted of int1-blaIMP-1-aac(6')-IIc-qacL-qacEdelta1-sul1-istB-IS21. Conjugation experiments showed that S. marcescens could transmit the plasmid to E. cloacae and K. aerogenes. In contrast, pSL264 could not transfer from E. cloacae or K. aerogenes to S. marcescens. CONCLUSION The IncL/M plasmid pSL264 harboring blaIMP-1 was able to transfer among different species of Enterobacteriaceae in a patient receiving long-term antimicrobial treatment. The worldwide emergence and spread of IncL/M plasmids harboring carbapenemase-encoding genes among species of Enterobacteriaceae is becoming a serious public health hazard.
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Affiliation(s)
- Nobuyoshi Mori
- grid.430395.8Department of Infectious Diseases, St. Luke’s International Hospital, Tokyo, Japan ,grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan
| | - Tatsuya Tada
- grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan
| | - Satoshi Oshiro
- grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan
| | - Kyoko Kuwahara-Arai
- grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan
| | - Teruo Kirikae
- grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan
| | - Yuki Uehara
- grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan ,grid.430395.8Department of Clinical Laboratory, St. Luke’s International Hospital, Tokyo, Japan
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27
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AbuOun M, Jones H, Stubberfield E, Gilson D, Shaw LP, Hubbard ATM, Chau KK, Sebra R, Peto TEA, Crook DW, Read DS, Gweon HS, Walker AS, Stoesser N, Smith RP, Anjum MF, On Behalf Of The Rehab Consortium. A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage. Microb Genom 2021; 7. [PMID: 34609275 PMCID: PMC8627209 DOI: 10.1099/mgen.0.000630] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Enterobacterales from livestock are potentially important reservoirs for antimicrobial resistance (AMR) to pass through the food chain to humans, thereby increasing the AMR burden and affecting our ability to tackle infections. In this study 168 isolates from four genera of the order Enterobacterales, primarily Escherichia coli, were purified from livestock (cattle, pigs and sheep) faeces from 14 farms in the United Kingdom. Their genomes were resolved using long- and short-read sequencing to analyse AMR genes and their genetic context, as well as to explore the relationship between AMR burden and on-farm antimicrobial usage (AMU), in the three months prior to sampling. Although E. coli isolates were genomically diverse, phylogenetic analysis using a core-genome SNP tree indicated pig isolates to generally be distinct from sheep isolates, with cattle isolates being intermediates. Approximately 28 % of isolates harboured AMR genes, with the greatest proportion detected in pigs, followed by cattle then sheep; pig isolates also harboured the highest number of AMR genes per isolate. Although 90 % of sequenced isolates harboured diverse plasmids, only 11 % of plasmids (n=58 out of 522) identified contained AMR genes, with 91 % of AMR plasmids being from pig, 9 % from cattle and none from sheep isolates; these results indicated that pigs were a principle reservoir of AMR genes harboured by plasmids and likely to be involved in their horizontal transfer. Significant associations were observed between AMU (mg kg−1) and AMR. As both the total and the numbers of different antimicrobial classes used on-farm increased, the risk of multi-drug resistance (MDR) in isolates rose. However, even when AMU on pig farms was comparatively low, pig isolates had increased likelihood of being MDR; harbouring relatively more resistances than those from other livestock species. Therefore, our results indicate that AMR prevalence in livestock is not only influenced by recent AMU on-farm but also livestock-related factors, which can influence the AMR burden in these reservoirs and its plasmid mediated transmission.
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Affiliation(s)
- Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Hannah Jones
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Daniel Gilson
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Liam P Shaw
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alasdair T M Hubbard
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Kevin K Chau
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert Sebra
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mt Sinai, Mt Sinai, New York, USA
| | - Tim E A Peto
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick W Crook
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in partnership with Public Health England (PHE), Oxford, UK
| | - Daniel S Read
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford, UK
| | - H Soon Gweon
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford, UK.,School of Biological Sciences, University of Reading, UK
| | - A Sarah Walker
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in partnership with Public Health England (PHE), Oxford, UK
| | - Nicole Stoesser
- Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in partnership with Public Health England (PHE), Oxford, UK
| | - Richard P Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Surrey, UK
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28
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Liu G, Qian H, Lv J, Tian B, Bao C, Yan H, Gu B. Emergence of mcr-1-Harboring Salmonella enterica Serovar Sinstorf Type ST155 Isolated From Patients With Diarrhea in Jiangsu, China. Front Microbiol 2021; 12:723697. [PMID: 34603249 PMCID: PMC8483771 DOI: 10.3389/fmicb.2021.723697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Background: This study analyzed the antimicrobial resistance phenotypes and mechanisms of quinolone, cephalosporins, and colistin resistance in nontyphoidal Salmonella from patients with diarrhea in Jiangsu, China. Methods: A total of 741 nontyphoidal Salmonella isolates were collected from hospitals in major cities of Jiangsu Province, China between 2016 and 2017. Their susceptibility to commonly used antibiotics was evaluated by broth micro-dilution and sequencing analysis of resistance genes screened by a PCR method. For mcr-1 positive isolates, genetic relationship study was carried out by pulsed-field gel electrophoresis and multiloci sequence typing analysis. The transferability of these plasmids was measured with conjugation experiments and the genetic locations of mcr-1 were analyzed by pulsed-field gel electrophoresis profiles of S1-digested genomic DNA and subsequent Southern blot hybridization. Results: Among 741 nontyphoidal Salmonella isolates, the most common serotypes identified were S. Typhimurium (n=257, 34.7%) and S. Enteritidis (n=127, 17.1%), and the isolates showed 21.7, 20.6, and 5.0% resistance to cephalosporins, ciprofloxacin, and colistin, respectively. Among the 335 nalidixic acid-resistant Salmonella, 213 (63.6%) and 45 (13.4%) had at least one mutation in gyrA and parC. Among the plasmid-borne resistance, qnrS1 (85; 41.9%) and aac(6')-Ib-cr4 (75; 36.9%) were the most common quinolone resistance (PMQR) genes, while bla CTX-M-14 (n=35) and bla CTX-M-55 (n=46) were found to be dominant extended-spectrum beta-lactamase (ESBL) genes in nontyphoidal Salmonella. In addition, eight mcr-1-harboring strains were detected since 2016 and they were predominate in children under the age of 7years. Conjugation assays showed the donor Salmonella strain has functional and transferable colistin resistance and Southern blot hybridization revealed that mcr-1 was located in a high molecular weight plasmid. Conclusion: In nontyphoidal Salmonella, there is a rapidly increasing trend of colistin resistance and this is the first report of patients harboring mcr-1-positive Salmonella with a new ST type ST155 and new serotype S. Sinstorf. These findings demonstrate the necessity for cautious use and the continuous monitoring of colistin in clinical applications.
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Affiliation(s)
- Guoye Liu
- Department of Clinical Laboratory, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Huimin Qian
- Department of Acute Infectious Disease Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - Jingwen Lv
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Benshun Tian
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Changjun Bao
- Department of Acute Infectious Disease Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - Hong Yan
- Laboratory Medicine Center, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Bing Gu
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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29
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Portes AB, Rodrigues G, Leitão MP, Ferrari R, Conte Junior CA, Panzenhagen P. Global distribution of plasmid-mediated colistin resistance mcr gene in Salmonella: A systematic review. J Appl Microbiol 2021; 132:872-889. [PMID: 34480840 DOI: 10.1111/jam.15282] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 08/04/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022]
Abstract
This systematic review focuses on obtaining the most relevant information from multiple studies that detected a mobilized colistin resistance mcr gene in Salmonella for a better comprehension of its global distribution. A group of strategic and systematic keywords were combined to retrieve research data on the detection frequency of the mcr gene globally from four database platforms (Google Scholar, Science Direct, PubMed and Scielo). Forty-eight studies attended all the eligibility criteria and were selected. China was the country with the highest frequency of Salmonella strains with the mcr gene, and Europe exhibited a wide diversity of countries with positive mcr strains. In addition, animals and humans carried the highest frequency of positive strains for the mcr gene. Salmonella Typhimurium was the most frequent serovar carrying the mcr gene. Apparently, colistin overuse in animal husbandry has increased the selective pressure of antimicrobial resistance, resulting in the emergence of a plasmid-mediated colistin resistance mcr gene in China. The mcr-positive Salmonella strains are recently predominant worldwide, which is probably due to the capacity of this gene to be swiftly horizontally transmissible. The transmission ability of mcr-positive Salmonella strains to humans through the consumption of contaminated animal-based food is a public health concern.
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Affiliation(s)
- Ana Beatriz Portes
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Grazielle Rodrigues
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Mylenna Palma Leitão
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Rafaela Ferrari
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Carlos Adam Conte Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói, RJ, Brazil.,Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil.,Graduate Program in Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
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The First Report of mcr-1-Carrying Escherichia coli Originating from Animals in Serbia. Antibiotics (Basel) 2021; 10:antibiotics10091063. [PMID: 34572647 PMCID: PMC8467794 DOI: 10.3390/antibiotics10091063] [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: 07/23/2021] [Revised: 08/16/2021] [Accepted: 08/30/2021] [Indexed: 01/08/2023] Open
Abstract
The aim of this study was continuous monitoring of the presence of mcr-1 to mcr-5 genes in Enterobacterales isolated from cattle, pigs, and domestic poultry at intensive breeding facilities in Northern Vojvodina, Serbia, from 1 January 1 to 1 October 2020. Out of 2167 examined samples, mcr-1 was observed in five E. coli isolates originating from healthy turkeys. Four isolates belonged to the phylogenetic group B1, and one isolate to the phylogenetic group A. Detected E. coli serogenotypes (somatic O and flagellar H antigens) were O8:H25 and O29:H25. Core-genome multi-locus sequence typing (cgMLST) revealed three ST58 isolates clustering together in Clonal Complex (CC) 155 and two singletons of ST641-CC86 and ST410-CC23, respectively. Clonotyping revealed CH4-32 (n = 3), CH6-53 (n = 1) and CH4-24 (n = 1). In all isolates, the mcr-1 gene was located on a large IncX4 replicon type plasmid. Eight virulence-associated genes (VAGs) typical of avian pathogenic E. coli (APEC) (fyuA, fimH, hlyF, iss, ompT, sitA, traT, iroN) were detected in four isolates. These isolates were investigated for susceptibility to four biocides and revealed MIC values of 0.125% for glutardialdehyde, of 0.00003–0.00006% for chlorohexidine, of 4–6% for isopropanol and of 0.001–0.002% for benzalkonium chloride. All obtained MIC values of the tested biocides were comparable to the reference strain, with no indication of possible resistance. This is the first report of mcr-1.1-carrying E. coli from Serbia. Although only samples from turkeys were mcr-positive in this study, continuous monitoring of livestock samples is advised to prevent a spill-over from animals to humans.
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Wakabayashi Y, Sekizuka T, Yamaguchi T, Fukuda A, Suzuki M, Kawahara R, Taguchi M, Kuroda M, Semba K, Shinomiya H, Kawatsu K. Isolation and plasmid characterisation of Salmonella enterica serovar Albany harbouring mcr-5 from retail chicken meat in Japan. FEMS Microbiol Lett 2021; 367:5881302. [PMID: 32756977 DOI: 10.1093/femsle/fnaa127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/28/2020] [Indexed: 11/13/2022] Open
Abstract
The emergence of plasmid-mediated colistin resistance genes (mcr), which is occurring in numerous countries, is a worldwide concern, primarily because colistin is a last-resort antibiotic. Compared to E. coli, prevalence of mcr genes in Salmonella is unclear in Japan. Here we screened for mcr-1-5 genes in our collection of Salmonella strains isolated from retail meat products collected in Japan from 2012 through 2016. We found that Salmonella Albany strain 27A-368 encodes mcr-5 and that mcr genes were undetectable among the remaining 202 isolates. The resistance plasmid p27A-368 was transferred by conjugation to S. Infantis and was stably retained as a transconjugant. Whole-genome sequencing revealed that mcr-5 resided on a 115 kb plasmid (p27A-368). The plasmid backbone of p27A-368 is more similar to that of pCOV27, an ESBL-encoding plasmid recovered from avian pathogenic E. coli, rather than pSE13-SA01718 of S. Paratyphi B that encodes mcr-5. Further, mcr-5 is located on a transposon, and its sequence is similar to that of pSE13-SA01718. A phylogenetic tree based on single nucleotide variants implies a relationship between 27A-368 and S. Albany isolated in Southeast Asian countries.
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Affiliation(s)
- Yuki Wakabayashi
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Centre, National Institute of Infectious Diseases, 1-3-21 Toyama Shinjuku-ku, Tokyo, Japan
| | - Takahiro Yamaguchi
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Japan
| | - Akira Fukuda
- Microbiology Section, Division of Microbiology, Osaka Institute of Public Health, 8-34 Toujyo-cho, Tennouji-ku, Osaka, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Centre, National Institute of Infectious Diseases, 4-2-1 Aoba-cho, Higashimurayama-shi, Tokyo, Japan
| | - Ryuji Kawahara
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Japan
| | - Masumi Taguchi
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Japan
| | - Makoto Kuroda
- Pathogen Genomics Centre, National Institute of Infectious Diseases, 1-3-21 Toyama Shinjuku-ku, Tokyo, Japan
| | - Keiko Semba
- Ehime Prefectural Institute of Public Health and Environmental Science, 8-234 Sanban-cho, Matsuyama-shi, Ehime, Japan
| | - Hiroto Shinomiya
- Ehime Prefectural Institute of Public Health and Environmental Science, 8-234 Sanban-cho, Matsuyama-shi, Ehime, Japan
| | - Kentaro Kawatsu
- Bacteriology Section, Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Japan
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De Lucia A, Card RM, Duggett N, Smith RP, Davies R, Cawthraw SA, Anjum MF, Rambaldi M, Ostanello F, Martelli F. Reduction in antimicrobial resistance prevalence in Escherichia coli from a pig farm following withdrawal of group antimicrobial treatment. Vet Microbiol 2021; 258:109125. [PMID: 34033985 DOI: 10.1016/j.vetmic.2021.109125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
An important element in the control of antimicrobial resistance (AMR) is reduction in antimicrobial usage. In the veterinary sector individual antimicrobial treatment of livestock, rather than the use of group treatment, can help achieve this goal. The aim of this study was to investigate how cessation of group antimicrobial treatment impacted the prevalence of AMR in commensal Escherichia coli in pigs at one farm over an 11-month period. Minimum inhibitory concentrations of eight antimicrobials were determined for 259 E. coli isolates collected during the study. A significant reduction in the prevalence of multidrug resistance and a significant increase in the proportion of full susceptibility to the panel of nine antimicrobials tested was seen after 11 months. Whole genome sequencing of 48 multidrug resistant isolates revealed E. coli clones that persisted across multiple visits and provided evidence for the presence of plasmids harbouring AMR genes shared across multiple E. coli lineages. E. coli were also isolated from on-farm environmental samples. Whole genome sequencing of one multidrug resistant isolate obtained from cleaning tools showed it was clonal to pig-derived E. coli that persisted on the farm for 11 months. In this study we provide evidence that withdrawal of group antimicrobial use leads to significant reductions in key indicators for AMR prevalence and the importance of the farm environment as a reservoir of resistant bacteria. These findings support policy makers and producers in the implementation of measures to control AMR and reduce antimicrobial use.
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Affiliation(s)
- A De Lucia
- Dipartimento di Scienze Mediche Veterinarie Università di Bologna, Italy; Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - R M Card
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - N Duggett
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - R P Smith
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - R Davies
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - S A Cawthraw
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - M F Anjum
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
| | - M Rambaldi
- Dipartimento di Scienze Mediche Veterinarie Università di Bologna, Italy.
| | - F Ostanello
- Dipartimento di Scienze Mediche Veterinarie Università di Bologna, Italy.
| | - F Martelli
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.
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Mthembu TP, Zishiri OT, El Zowalaty ME. Genomic Characterization of Antimicrobial Resistance in Food Chain and Livestock-Associated Salmonella Species. Animals (Basel) 2021; 11:ani11030872. [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] [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
Simple Summary In the era of the COVID-19 global pandemic, antimicrobial resistance is looming as an imminent threat and challenge to human public health. Antimicrobial resistance is a major global threat of increasing concern to human and animal health. It also has implications for both food safety and food security and the economic well-being of millions of humans. Among other zoonotic infectious diseases, antimicrobial resistance in food chain and livestock-associated pathogens such as Salmonella is of great concern. In the present study, the genomic characterization of antimicrobial resistance in food chain and livestock-associated Salmonella was summarized. Several antimicrobial resistance determinants were reported in Salmonella isolated from food chain animals and livestock. Monitoring of antimicrobial resistance in Salmonella in livestock and food chain animals through genomic characterization is significant to control and protect humans from the threat of antimicrobial resistance. Salmonella, a foodborne zoonotic enterobacterium species can transmit antimicrobial resistance from the microbiome of animals to humans. This study summarizes the genomic characterization of antimicrobial resistance in Salmonella species with special focus on resistance against carbapenems and colistin which are the last resort antibiotics used against infections caused by multidrug resistant bacteria. The present review aims to draw attention to prudent use of antibiotics, a good example of the One Health concept. 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.
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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
- Correspondence:
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Jiang Z, Anwar TM, Peng X, Biswas S, Elbediwi M, Li Y, Fang W, Yue M. Prevalence and antimicrobial resistance of Salmonella recovered from pig-borne food products in Henan, China. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107535] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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35
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Moon DC, Kim SJ, Mechesso AF, Kang HY, Song HJ, Choi JH, Yoon SS, Lim SK. Mobile Colistin Resistance Gene mcr- 1 Detected on an IncI2 Plasmid in Salmonella Typhimurium Sequence Type 19 from a Healthy Pig in South Korea. Microorganisms 2021; 9:398. [PMID: 33671955 PMCID: PMC7919004 DOI: 10.3390/microorganisms9020398] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 01/21/2023] Open
Abstract
Colistin is considered the last resort for the treatment of multi-drug resistant Gram-negative bacterial infections. We studied colistin resistance and the mcr-1 gene carriage in Salmonella isolates recovered from food animals in South Korea between 2010 and 2018. Colistin resistance was found in 277 isolates, predominantly in Salmonella Enteritidis (57.1%) and Salmonella Gallinarum (41.9%). However, the mcr-1 gene was identified in only one colistin-resistant Salmonella Typhimurium (MIC = 16 µg/mL) isolated from a healthy pig. The mcr-1 carrying isolate presented additional resistance to multiple antimicrobials. The strain belonged to sequence type (ST)19 and carried various virulence factor genes that are associated with adhesion and invasion of Salmonella into intestinal epithelial cells, as well as its survival in macrophages. The mcr-1 gene was identified on an IncI2 plasmid and it was also transferred to the E. coli J53 recipient strain. The mcr-1-carrying plasmid (pK18JST013) in this study was closely related to that previously reported in S. Indiana (pCFSA664-3) from chicken in China. This is the first report of mcr-1 carrying S. Typhimurium in South Korea. The finding indicates the importance of regular screening for the presence of the mcr-1 gene in S. Typhimurium in food animals to prevent the spread to humans.
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Affiliation(s)
| | | | | | | | | | | | | | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si 39660, Korea; (D.C.M.); (S.-J.K.); (A.F.M.); (H.Y.K.); (H.-J.S.); (J.-H.C.); (S.-S.Y.)
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Ewbank AC, Esperón F, Sacristán C, Sacristán I, Krul R, Cavalcante de Macedo E, Calatayud O, Bueno I, de Francisco Strefezzi R, Catão-Dias JL. Seabirds as anthropization indicators in two different tropical biotopes: A One Health approach to the issue of antimicrobial resistance genes pollution in oceanic islands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142141. [PMID: 32920402 DOI: 10.1016/j.scitotenv.2020.142141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/12/2023]
Abstract
Antimicrobial resistance is a quintessential One Health issue, among the most serious 21st century global threats to human health. Seabirds may act as sentinels of natural and anthropogenic changes in the marine ecosystem health, including pollution by antimicrobial resistance genes (ARGs). We used real time PCR to identify and quantify 22 plasmid-mediated ARGs in the gastrointestinal microbiome of six wild seabird species, comparing an anthropized (Fernando de Noronha Archipelago - FNA) and a pristine biotope (Rocas Atoll - ROA), Brazil. Of 257 birds, 218 (84.8%) were positive to at least one ARG. ARG classes encoding resistance to tetracyclines (75.1%), quinolones (10.5%) and phenicols (10.5%) were the most prevalent, with tetracyclines significantly greater than the remaining classes (p < 0.05). Genes tet(S) (29.2%), tet(A) (28.8%), and tet(B) (24.9%) were the most commonly found and had a significantly greater prevalence when compared to the remaining ARGs (p < 0.05). The anthropized biotope presented statistically significant higher prevalence of sulfonamide- and quinolone-encoding ARGs in comparison with the pristine (respectively, p = 0.01 and p = 0.03), and higher sulII gene prevalence (p = 0.04), consistent with anthropogenic pressure. Migratory species (only present in ROA) showed statistically significant higher mcr-1 (polymyxins) and blaTEM (betalactam) prevalences (respectively, p = 0.009 and p = 0.02), and mcr-1 percentage load (p = 0.0079) in comparison with non-migratory. To our knowledge, this is the largest ARGs survey based on direct detection and quantification in seabirds worldwide, and the first to evaluate non-synanthropic species in oceanic islands. This is the first detection of mcr-1 in wild free-ranging seabirds in Brazil and in free-ranging migratory non-synanthropic seabirds worldwide. Our findings show the importance of biological and ecological factors, highlighting the role of seabirds as anthropization sentinels and ARGs-pollution environmental indicators (even in a pristine biotope), and their involvement in the One Health epidemiological chain of ARGs.
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Affiliation(s)
- Ana Carolina Ewbank
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
| | - Fernando Esperón
- Group of Epidemiology and Environmental Health, Animal Health Research Centre (INIA-CISA), Madrid, Spain.
| | - Carlos Sacristán
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
| | - Irene Sacristán
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Ricardo Krul
- Ornithology Laboratory, Center for Studies of the Sea, Paraná State University, Paraná State, Brazil.
| | - Eduardo Cavalcante de Macedo
- Chico Mendes Institute for Biodiversity Conservation (ICMBio) - Brazilian Ministry of the Environment, Rocas Atol Biological Reserve, Rio Grande do Norte, Brazil.
| | - Olga Calatayud
- Group of Epidemiology and Environmental Health, Animal Health Research Centre (INIA-CISA), Madrid, Spain.
| | - Irene Bueno
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, United States.
| | - Ricardo de Francisco Strefezzi
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil.
| | - José Luiz Catão-Dias
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
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Liu M, Zhang W, Yao J, Niu J. Production, purification, characterization, and biological properties of Rhodosporidium paludigenum polysaccharide. PLoS One 2021; 16:e0246148. [PMID: 33513164 PMCID: PMC7845956 DOI: 10.1371/journal.pone.0246148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 01/14/2021] [Indexed: 11/18/2022] Open
Abstract
The yield of marine red yeast polysaccharide (MRYP) obtained from Rhodosporidium paludigenum was increased by optimizing fermentation conditions, and the pure polysaccharide was extracted by column chromatography. The molecular weight of pure MRYP and the ratio of mannose to glucose in components of MRYP were determined. Antioxidant and antibacterial abilities of MRYP were investigated in vitro and in vivo. The optimal fermentation parameters were as follows: Medium 4, pH = 6.72, temperature = 30.18°C, blades speed = 461.36 r/min; the optimized yield reached 4323.90 mg/L, which was 1.31 times the original yield. The sequence of factors that affected the MRYP yield was the blades speed>pH>temperature. The main components of MRYP were MYH-1 and MYH-2. The molecular weights of MYH-1 and MYH-2 were 246.92 kDa and 21.88 kDa, respectively; they accounted for 53.60% and 28.75% of total polysaccharide. In MYH-1 and MYH-2, the proportion of glucose and mannose accounted for 46.94%, 38.46%, and 67.10%, 7.17%, respectively. In vitro, the ability of scavenging DPPH•, •OH, and •O2− radical was 32.26%, 24.34%, and 22.09%; the minimum inhibitory concentration (MIC) of MRYP was 480 μg/mg. In vivo, MRYP improved the lambs’ body weight, antioxidant enzyme activity, and the number of probiotics, but it reduced the feed/gain (F/G) ratio and the number of pathogenic bacteria in 60-days-old lambs.
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Affiliation(s)
- Mengjian Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - WenJu Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
- * E-mail:
| | - Jun Yao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Junli Niu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
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Nale JY, Vinner GK, Lopez VC, Thanki AM, Phothaworn P, Thiennimitr P, Garcia A, AbuOun M, Anjum MF, Korbsrisate S, Galyov EE, Malik DJ, Clokie MRJ. An Optimized Bacteriophage Cocktail Can Effectively Control Salmonella in vitro and in Galleria mellonella. Front Microbiol 2021; 11:609955. [PMID: 33552020 PMCID: PMC7858669 DOI: 10.3389/fmicb.2020.609955] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/07/2020] [Indexed: 12/14/2022] Open
Abstract
Salmonella spp. is a leading cause of gastrointestinal enteritis in humans where it is largely contracted via contaminated poultry and pork. Phages can be used to control Salmonella infection in the animals, which could break the cycle of infection before the products are accessible for consumption. Here, the potential of 21 myoviruses and a siphovirus to eliminate Salmonella in vitro and in vivo was examined with the aim of developing a biocontrol strategy to curtail the infection in poultry and swine. Together, the phages targeted the twenty-three poultry and ten swine prevalent Salmonella serotype isolates tested. Although individual phages significantly reduced bacterial growth of representative isolates within 6 h post-infection, bacterial regrowth occurred 1 h later, indicating proliferation of resistant strains. To curtail bacteriophage resistance, a novel three-phage cocktail was developed in vitro, and further investigated in an optimized Galleria mellonella larva Salmonella infection model colonized with representative swine, chicken and laboratory strains. For all the strains examined, G. mellonella larvae given phages 2 h prior to bacterial exposure (prophylactic regimen) survived and Salmonella was undetectable 24 h post-phage treatment and throughout the experimental time (72 h). Administering phages with bacteria (co-infection), or 2 h post-bacterial exposure (remedial regimen) also improved survival (73-100% and 15-88%, respectively), but was less effective than prophylaxis application. These pre-livestock data support the future application of this cocktail for further development to effectively treat Salmonella infection in poultry and pigs. Future work will focus on cocktail formulation to ensure stability and incorporation into feeds and used to treat the infection in target animals.
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Affiliation(s)
- Janet Y Nale
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Gurinder K Vinner
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Viviana C Lopez
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Anisha M Thanki
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Preeda Phothaworn
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Angela Garcia
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Edouard E Galyov
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Danish J Malik
- Department of Chemical Engineering, Loughborough University, Loughborough, United Kingdom
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Plasmid-borne colistin resistance gene mcr-1 in a multidrug resistant Salmonella enterica serovar Typhimurium isolate from an infant with acute diarrhea in China. Int J Infect Dis 2020; 103:13-18. [PMID: 33212253 DOI: 10.1016/j.ijid.2020.11.150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/21/2020] [Accepted: 11/09/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Antimicrobial resistance of Salmonella enterica is a major global concern. Recent findings suggest that colistin as a last resort treatment for multidrug-resistant gram-negative bacteria is seriously threatened by the report of plasmid-mediated colistin resistance gene mcr-1 in China. METHODS A total of 827 S. Typhimurium isolates were recovered from 4 cities of China, including Henan, Shanghai, Zhejiang, and Hubei provinces. Subsequently, mcr-1 presence was identified by PCR screening. Antimicrobial susceptibility testing was performed by broth microdilution using a 96-well microtiter plate. Plasmid conjugation transfer experiments were conducted using Escherichia coli J53 as the recipient. RESULTS Only one mcr-1 positive strain from the stool sample of an infant with acute diarrhea was isolated. Apart from colistin, the mcr-1-positive isolate showed co-resistance to the third-generation cephalosporins, ampicillin, nalidixic acid, tetracycline, chloramphenicol, sulfisoxazole, gentamicin, and cefotaxime revealing a multidrug-resistant phenotype. This strain harbored mcr-1 on a 227 kb IncHI2 plasmid, termed pJZ26, which could be transferred to E. coli J53. In addition to mcr-1, pJZ26 coharbored other resistance genes, including aph(4)-Ia, aac(3)-IVa, fosA, floR, sul2, and blaCTX-M-14. Compared with p2474-MCR1 and pHYEC7-IncHI2, pJZ26 contains an additional 4.6 kb fragment harboring the resistance gene tet(A) and its regulator tetR located on TnAs1 transposable element, which could mediate resistance to tetracycline. CONCLUSIONS These findings highlight that the fact the mcr-1-harboring plasmid pJZ26 has a high potential to disseminate the mcr-1 gene and further challenge the clinical treatment.
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The importance of using whole genome sequencing and extended spectrum beta-lactamase selective media when monitoring antimicrobial resistance. Sci Rep 2020; 10:19880. [PMID: 33199763 PMCID: PMC7670430 DOI: 10.1038/s41598-020-76877-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
To tackle the problem of antimicrobial resistance (AMR) surveillance programmes are in place within Europe applying phenotypic methods, but there are plans for implementing whole genome sequencing (WGS). We tested the benefits of WGS using Escherichia coli collected from pig surveillance performed between 2013 to 2017. WGS was performed on 498 E. coli producing ESBL and AmpC enzymes, recovered from pig caeca on MacConkey + cefotaxime (McC + CTX) agar, as recommended by the European Commission, or ESBL agar, used additionally by United Kingdom. Our results indicated WGS was extremely useful for monitoring trends for specific ESBL genes, as well as a plethora of AMR genotypes, helping to establish their prevalence and co-linkage to certain plasmids. Recovery of isolates with multi-drug resistance (MDR) genotypes was lower from McC + CTX than ESBL agar. The most widespread ESBL genes belonged to the blaCTX-M family. blaCTX-M-1 dominated all years, and was common in two highly stable IncI1 MDR plasmids harbouring (blaCTX-M-1,sul2, tetA) or (blaCTX-M-1, aadA5, sul2, dfrA17), in isolates which were phylogenetically dissimilar, suggesting plasmid transmission. Therefore, WGS provided a wealth of data on prevalence of AMR genotypes and plasmid persistence absent from phenotypic data and, also, demonstrated the importance of culture media for detecting ESBL E. coli.
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Colistin Update on Its Mechanism of Action and Resistance, Present and Future Challenges. Microorganisms 2020; 8:microorganisms8111716. [PMID: 33147701 PMCID: PMC7692639 DOI: 10.3390/microorganisms8111716] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023] Open
Abstract
Colistin has been extensively used since the middle of the last century in animals, particularly in swine, for the control of enteric infections. Colistin is presently considered the last line of defense against human infections caused by multidrug-resistant Gram-negative organisms such as carbapenemase-producer Enterobacterales, Acinetobacter baumanni, and Pseudomonas aeruginosa. Transferable bacterial resistance like mcr-genes was reported in isolates from both humans and animals. Researchers actively seek strategies to reduce colistin resistance. The definition of guidelines for colistin therapy in veterinary and human medicine is thus crucial. The ban of colistin use in swine as a growth promoter and for prophylactic purposes, and the implementation of sustainable measures in farm animals for the prevention of infections, would help to avoid resistance and should be encouraged. Colistin resistance in the human-animal-environment interface stresses the relevance of the One Health approach to achieve its effective control. Such measures should be addressed in a cooperative way, with efforts from multiple disciplines and with consensus among doctors, veterinary surgeons, and environment professionals. A revision of the mechanism of colistin action, resistance, animal and human use, as well as colistin susceptibility evaluation is debated here.
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Moon DC, Mechesso AF, Kang HY, Kim SJ, Choi JH, Kim MH, Song HJ, Yoon SS, Lim SK. First Report of an Escherichia coli Strain Carrying the Colistin Resistance Determinant mcr-1 from a Dog in South Korea. Antibiotics (Basel) 2020; 9:E768. [PMID: 33147688 PMCID: PMC7694106 DOI: 10.3390/antibiotics9110768] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 01/02/2023] Open
Abstract
We studied the presence of the mobile colistin resistance gene mcr-1 in Escherichia coli isolates recovered from fecal and urine samples of companion animals, that were collected from South Korea in 2018 and 2019. The mcr-1 gene was detected in one colistin-resistant E. coli isolated from a diarrheic dog. The isolate exhibited additional resistance to multiple antimicrobials, including fluoroquinolones and third-generation cephalosporins. The mcr-1 carrying isolate belonged to ST160. The pulsed-field gel electrophoresis pattern of our strain differed from those ST160 E. coli strains previously identified from chickens in Korea. The mcr-1 gene was identified in the IncI2 plasmid. It was also transferred to E. coli J53 recipient strain, with a conjugation efficiency of 2.8 × 10-4. Average nucleotide identity analysis demonstrated that the mcr-1-carrying plasmid in this study was closely related to those from patients in Korea. To the best of our knowledge, this is the first report of mcr-1 carrying E. coli from a companion animal in South Korea. Our findings support One Health approach is necessary to prevent the dissemination of this high-risk gene.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Korea; (D.C.M.); (A.F.M.); (H.Y.K.); (S.-J.K.); (J.-H.C.); (M.H.K.); (H.-J.S.); (S.-S.Y.)
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Du C, Feng Y, Wang G, Zhang Z, Hu H, Yu Y, Liu J, Qiu L, Liu H, Guo Z, Huang J, Qiu J. Co-Occurrence of the mcr-1.1 and mcr-3.7 Genes in a Multidrug-Resistant Escherichia coli Isolate from China. Infect Drug Resist 2020; 13:3649-3655. [PMID: 33116684 PMCID: PMC7585518 DOI: 10.2147/idr.s268787] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/19/2020] [Indexed: 12/15/2022] Open
Abstract
Objective A colistin-resistant Escherichia coli strain isolated from dog feces was characterized in this study. Methods and Results A multiplex PCR assay was used to detect the presence of colistin-resistant mcr genes; it was found that E. coli QDFD216 co-harbored the mcr-1 and mcr-3 genes. Whole-genome sequencing and further bioinformatics analysis revealed that E. coli QDFD216 belonged to serotype O176:H11, fimH1311 type and ST132. The resistance genes blaCTX-M-14, mdfA, dfrA3, acrA, acrB, tolc, and sul3 were present in the chromosome. The mcr-1.1 and mcr-3.7 genes were located in two plasmids of different incompatibility groups. mcr-1.1 was carried by a IncX4-type plasmid within an typical IS26-parA-mcr-1.1-pap2 cassette, while mcr-3.7 was encoded by an IncP1-type plasmid with a genetic structure of TnAs2-mcr-3.7-dgkA-IS26. No additional antibiotic resistance genes were carried by either plasmid. Conclusion This is the first report of an E. coli isolate co-harboring a mcr-1.1-carrying IncX4 plasmid and a mcr-3.7-carrying IncP1 plasmid. The evolution and mechanism of mcr gene co-existence need further study to assess its impact on public health.
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Affiliation(s)
- Chongtao Du
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Yuyang Feng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Guizhen Wang
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, People's Republic of China
| | - Zhiyuan Zhang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Huimin Hu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Yu Yu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Jiayang Liu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Lihao Qiu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Hongtao Liu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Zhimin Guo
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun 130021, People's Republic of China
| | - Jing Huang
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun 130021, People's Republic of China
| | - Jiazhang Qiu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
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Kumar H, Chen BH, Kuca K, Nepovimova E, Kaushal A, Nagraik R, Bhatia SK, Dhanjal DS, Kumar V, Kumar A, Upadhyay NK, Verma R, Kumar D. Understanding of Colistin Usage in Food Animals and Available Detection Techniques: A Review. Animals (Basel) 2020; 10:ani10101892. [PMID: 33081121 PMCID: PMC7602861 DOI: 10.3390/ani10101892] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
Progress in the medical profession is determined by the achievements and effectiveness of new antibiotics in the treatment of microbial infections. However, the development of multiple-drug resistance in numerous bacteria, especially Gram-negative bacteria, has limited the treatment options. Due to this resistance, the resurgence of cyclic polypeptide drugs like colistin remains the only option. The drug, colistin, is a well-known growth inhibitor of Gram-negative bacteria like Acinetobacter baumanni, Enterobacter cloacae, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Technological advancements have uncovered the role of the mcr-1(mobilized colistin resistance) gene, which is responsible for the development of resistance in Gram-negative bacteria, which make them distinct from other bacteria without this gene. Additionally, food animals have been determined to be the reservoir for colistin resistance microbes, from which they spread to other hosts. Due to the adverse effects of colistin, many developed countries have prohibited its usage in animal foods, but developing countries are still using colistin in animal food production, thereby imposing a major risk to the public health. Therefore, there is a need for implementation of sustainable measures in livestock farms to prevent microbial infection. This review highlights the negative effects (increased resistance) of colistin consumption and emphasizes the different approaches used for detecting colistin in animal-based foods as well as the challenges associated with its detection.
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Affiliation(s)
- Harsh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India; (H.K.); (R.N.); (A.K.)
| | - Bing-Huei Chen
- Department of Food Science, Fu Jen Catholic University, New Taipei City 24205, Taiwan;
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
- Biomedical Research Center, University Hospital Hradec Kralove, 50003 Hradec Kralove, Czech Republic
- Correspondence: (K.K.); (D.K.); Tel.: +420-603-289-166 (K.K.)
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
| | - Ankur Kaushal
- Centre of Nanotechnology, Amity University, Manesar, Gurugram-122413, Haryana, India;
| | - Rupak Nagraik
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India; (H.K.); (R.N.); (A.K.)
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Korea;
| | - Daljeet Singh Dhanjal
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India;
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield MK430AL, UK;
| | - Anil Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India; (H.K.); (R.N.); (A.K.)
| | - Navneet Kumar Upadhyay
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India;
| | - Rachna Verma
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India;
| | - Dinesh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India; (H.K.); (R.N.); (A.K.)
- Correspondence: (K.K.); (D.K.); Tel.: +420-603-289-166 (K.K.)
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Liu X, Geng S, Chan EWC, Chen S. Increased prevalence of Escherichia coli strains from food carrying bla NDM and mcr-1-bearing plasmids that structurally resemble those of clinical strains, China, 2015 to 2017. ACTA ACUST UNITED AC 2020; 24. [PMID: 30940314 PMCID: PMC6446510 DOI: 10.2807/1560-7917.es.2019.24.13.1800113] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Introduction Emergence of resistance determinants of blaNDM and mcr-1 has undermined the antimicrobial effectiveness of the last line drugs carbapenems and colistin. Aim This work aimed to assess the prevalence of blaNDM and mcr-1 in E. coli strains collected from food in Shenzhen, China, during the period 2015 to 2017. Methods Multidrug-resistant E. coli strains were isolated from food samples. Plasmids encoding mcr-1 or blaNDM genes were characterised and compared with plasmids found in clinical isolates. Results Among 1,166 non-repeated cephalosporin-resistant E. coli strains isolated from 2,147 food samples, 390 and 42, respectively, were resistant to colistin and meropenem, with five strains being resistant to both agents. The rate of resistance to colistin increased significantly (p < 0.01) from 26% in 2015 to 46% in 2017, and that of meropenem resistance also increased sharply from 0.3% in 2015 to 17% in 2017 (p < 0.01). All meropenem-resistant strains carried a plasmid-borne blaNDM gene. Among the colistin-resistant strains, three types of mcr-1-bearing plasmids were determined. Plasmid sequencing indicated that these mcr-1 and blaNDM-bearing plasmids were structurally similar to those commonly recovered from clinical isolates. Interestingly, both mcr-1-bearing and blaNDM-bearing plasmids were transferrable to E. coli strain J53 under selection by meropenem, yet only mcr-1-bearing plasmids were transferrable under colistin selection. Conclusion These findings might suggest that mobile elements harbouring mcr-1 and blaNDM have been acquired by animal strains and transmitted to our food products, highlighting a need to prevent a spike in the rate of drug resistant food-borne infections.
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Affiliation(s)
- Xiaobo Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China.,Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, China
| | - Shu Geng
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Edward Wai-Chi Chan
- The State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR.,Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, China
| | - Sheng Chen
- The State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR.,Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, China
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AbuOun M, O'Connor HM, Stubberfield EJ, Nunez-Garcia J, Sayers E, Crook DW, Smith RP, Anjum MF. Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain. Front Microbiol 2020; 11:861. [PMID: 32523560 PMCID: PMC7261845 DOI: 10.3389/fmicb.2020.00861] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 04/09/2020] [Indexed: 12/18/2022] Open
Abstract
Combatting antimicrobial resistant (AMR) using a One-Health approach is essential as various bacteria, including Escherichia coli, a common bacteria, are becoming increasingly resistant and livestock may be a reservoir. The AMR gene content of 492 E. coli, isolated from 56 pig farms across Great Britain in 2014–2015, and purified on antibiotic selective and non-selective plates, was determined using whole genome sequencing (WGS). The E. coli were phylogenetically diverse harboring a variety of AMR profiles with widespread resistance to “old” antibiotics; isolates harbored up to seven plasmid Inc-types. None showed concurrent resistance to third-generation cephalosporins, fluoroquinolones and clinically relevant aminoglycosides, although ∼3% harbored AMR genes to both the former two. Transferable resistance to carbapenem and colistin were absent, and six of 117 E. coli STs belonged to major types associated with human disease. Prevalence of genotypically MDR E. coli, gathered from non-selective media was 35% and that of extended-spectrum-beta-lactamase E. coli was low (∼2% from non-selective). Approximately 72.6% of E. coli from ciprofloxacin plates and only 8.5% from the other plates harbored fluoroquinolone resistance due to topoisomerase mutations; the majority were MDR. In fact, multivariable analysis confirmed E. coli purified from CIP enrichment plates were more likely to be MDR, and suggested MDR isolates were also more probable from farms with high antibiotic usage, specialist finisher farms, and farms emptying their manure pits only after each batch. Additionally, farms from the South East were more likely to have MDR E. coli, whereas farms in Yorkshire and the Humber were less likely. Future investigations will determine whether suggested improvements such as better biosecurity or lower antimicrobial use decreases MDR E. coli on pig farms. Although this study focuses on pig farms, we believe the methodology and findings can be applied more widely to help livestock farmers in the United Kingdom and elsewhere to tackle AMR.
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Affiliation(s)
- Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom
| | - Heather M O'Connor
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Emma J Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Javier Nunez-Garcia
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Ellie Sayers
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Derick W Crook
- National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom.,Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Richard P Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom
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de Alcântara Rodrigues I, Ferrari RG, Panzenhagen PHN, Mano SB, Conte-Junior CA. Antimicrobial resistance genes in bacteria from animal-based foods. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:143-183. [PMID: 32762867 DOI: 10.1016/bs.aambs.2020.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Antimicrobial resistance is a worldwide public health threat. Farm animals are important sources of bacteria containing antimicrobial resistance genes (ARGs). Although the use of antimicrobials in aquaculture and livestock has been reduced in several countries, these compounds are still routinely applied in animal production, and contribute to ARGs emergence and spread among bacteria. ARGs are transmitted to humans mainly through the consumption of products of animal origin (PAO). Bacteria can present intrinsic resistance, and once antimicrobials are administered, this resistance may be selected and multiply. The exchange of genetic material is another mechanism used by bacteria to acquire resistance. Some of the main ARGs found in bacteria present in PAO are the bla, mcr-1, cfr and tet genes, which are directly associated to antibiotic resistance in the human clinic.
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Affiliation(s)
- Isadora de Alcântara Rodrigues
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói, Brazil
| | - Rafaela Gomes Ferrari
- Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | - Sergio Borges Mano
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói, Brazil
| | - Carlos Adam Conte-Junior
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói, Brazil; Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; National Institute of Health Quality Control, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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48
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Oluwadare M, Lee MD, Grim CJ, Lipp EK, Cheng Y, Maurer JJ. The Role of the Salmonella spvB IncF Plasmid and Its Resident Entry Exclusion Gene traS on Plasmid Exclusion. Front Microbiol 2020; 11:949. [PMID: 32499773 PMCID: PMC7242723 DOI: 10.3389/fmicb.2020.00949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/21/2020] [Indexed: 11/30/2022] Open
Abstract
Salmonella enterica cause significant illnesses worldwide. There has been a marked increase in resistance to fluoroquinolones and β-lactams/cephalosporins, antibiotics commonly used to treat salmonellosis. However, S. enterica serovars vary in their resistance to these and other antibiotics. The systemic virulence of some Salmonella serovars is due to a low copy number, IncF plasmid (65–100 kb) that contains the ADP-ribosylating toxin, SpvB. This virulence plasmid is present in only nine Salmonella serovars. It is possible that the spvB-virulence plasmid excludes other plasmids and may explain why antibiotic resistance is slow to develop in certain Salmonella serovars such as S. Enteritidis. The distribution of plasmid entry exclusion genes traS/traT and traY/excA are variable in Salmonella IncF and IncI plasmids, respectively and may account for differences in emergent antimicrobial resistance for some Salmonella serovars. The goal of this study is to determine the contribution of the Salmonella spvB-virulence plasmid in F-plasmid exclusion. From conjugation experiments, S. Typhimurium exhibited lower conjugation frequency with incFI and incFII plasmids when the spvB-virulence plasmid is present. Furthermore, introduction of cloned incFI traS into a “plasmidless” S. Typhimurium LT2 strain and Escherichia coli DH5α excluded incFI plasmid. However, deletion of the virulence plasmid traS did not affect plasmid exclusion significantly compared to a spvB control deletion. In addition, differences in F plasmid conjugation in natural Salmonella isolates did not correlate with IncF or SpvB-virulence plasmid genotype. There appear to be other plasmid or chromosomal genes at play in plasmid exclusion that may be responsible for the slow development of antibiotic resistance in certain serovars.
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Affiliation(s)
- Mopelola Oluwadare
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Margie D Lee
- Department of Population Health, University of Georgia, Athens, GA, United States.,Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Christopher J Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, United States
| | - Erin K Lipp
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Ying Cheng
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - John J Maurer
- Department of Population Health, University of Georgia, Athens, GA, United States.,Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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Duff JP, AbuOun M, Bexton S, Rogers J, Turton J, Woodford N, Irvine R, Anjum M, Teale C. Resistance to carbapenems and other antibiotics in Klebsiella pneumoniae found in seals indicates anthropogenic pollution. Vet Rec 2020; 187:154. [PMID: 32327551 DOI: 10.1136/vr.105440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/10/2019] [Accepted: 01/29/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND The beta-lactamase enzyme OXA-48 has spread widely in recent years in Enterobacteriaceae associated with man, disseminated primarily on incompatibility group L/M plasmids. OXA-48 confers resistance to carbapenems, important antimicrobials for treating highly resistant bacterial infections in humans. This enzyme has rarely been detected in bacteria from animals. Furthermore, the use of carbapenem compounds is not permitted in food-producing animals in Europe and to our knowledge has not been reported in food-producing animals globally. METHODS Bacterial isolates from lesions in stranded, free-living, juvenile common seals (Phoca vitulina) were identified. Antimicrobial susceptibility testing and whole genome sequencing analysis were used to characterise antimicrobial resistance genes carried by the bacteria. RESULTS Here, we report the detection of Klebsiella pneumoniae subspecies pneumoniae carrying the bla OXA-48 gene on an incompatibility group L/M plasmid from an infection in a common seal. CONCLUSION Evidence is accruing that marine mammals may be infected with bacteria originating from anthropogenic sources, such as human sewage, contaminating the environment.
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Affiliation(s)
- James Paul Duff
- Animal Plant and Health Agency (APHA), Diseases of Wildlife Scheme, APHA Penrith Veterinary Investigation Centre, Penrith, UK
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | | | - Jon Rogers
- Animal and Plant Health Agency Bury St Edmunds Veterinary Investigation Centre, Bury St Edmunds, UK
| | - Jane Turton
- National Infection Service, Public Health England, London, UK
| | - Neil Woodford
- National Infection Service, Public Health England, London, UK
| | - Richard Irvine
- Surveillance Intelligence Unit, Animal and Plant Health Agency, Weybridge, UK
| | - Muna Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - Christopher Teale
- Animal Plant and Health Agency Shrewsbury Veterinary Investigation Centre, Shrewsbury, UK
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Schages L, Wichern F, Kalscheuer R, Bockmühl D. Winter is coming - Impact of temperature on the variation of beta-lactamase and mcr genes in a wastewater treatment plant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:136499. [PMID: 31945531 DOI: 10.1016/j.scitotenv.2020.136499] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/18/2019] [Accepted: 01/01/2020] [Indexed: 05/29/2023]
Abstract
Wastewater treatment plants (WWTP) play a key role in the dissemination of antibiotic resistance and analyzing the abundance of antibiotic resistance genes (ARGs) and resistant bacteria is necessary to evaluate the risk of proliferation caused by WWTPs. Since few studies investigated the seasonal variation of antibiotic resistance, this study aimed to determine the abundance of beta-lactamase and mcr genes and to characterize phenotypic resistant strains in a WWTP in Germany over the seasons. Wastewater, sewage sludge and effluent samples were collected over a one year period and analyzed using quantitative real-time PCR. Resistant strains were isolated, followed by identification and antibiotic susceptibility testing using VITEK 2. The results show a significantly higher occurrence of nearly all investigated ARGs in the wastewater compared to sewage sludge and effluent. ARG abundance and temperature showed a negative correlation in wastewater and significant differences between ARG abundance during warmer and colder seasons were determined, indicating a seasonal effect. Co-occurrence of mcr-1 and carbapenemase genes in a multi-drug resistant Enterobacter cloacae and Escherichia coli producing extended-spectrum beta-lactamase (ESBL) was determined. To the best of our knowledge, this is the first detection of mcr-1, blaVIM and blaOXA-48 in an ESBL-producing E. coli. Although wastewater treatment reduced the abundance of ARGs and resistant strains, a dissemination into the river might be possible because carbapenemase-, CTX-M- and mcr-1-gene harboring strains were still present in the effluent.
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Affiliation(s)
- Laura Schages
- Rhine-Waal University of Applied Sciences, Faculty of Life Sciences, Kleve, Germany; Heinrich-Heine University Düsseldorf, Institute of Pharmaceutical Biology and Biotechnology, Germany
| | - Florian Wichern
- Rhine-Waal University of Applied Sciences, Faculty of Life Sciences, Kleve, Germany
| | - Rainer Kalscheuer
- Heinrich-Heine University Düsseldorf, Institute of Pharmaceutical Biology and Biotechnology, Germany
| | - Dirk Bockmühl
- Rhine-Waal University of Applied Sciences, Faculty of Life Sciences, Kleve, Germany.
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