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Ott LC, Mellata M. Short-chain fatty acids inhibit bacterial plasmid transfer through conjugation in vitro and in ex vivo chicken tissue explants. Front Microbiol 2024; 15:1414401. [PMID: 38903782 PMCID: PMC11187007 DOI: 10.3389/fmicb.2024.1414401] [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: 04/08/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
The animal gut acts as a potent reservoir for spreading and maintaining conjugative plasmids that confer antimicrobial resistance (AMR), fitness, and virulence attributes. Interventions that inhibit the continued emergence and expansion of AMR and virulent strains in agricultural and clinical environments are greatly desired. This study aims to determine the presence and efficacy of short-chain fatty acids (SCFA) inhibitory effects on the conjugal transfer of AMR plasmids. In vitro broth conjugations were conducted between donor Escherichia coli strains carrying AMP plasmids and the plasmid-less Escherichia coli HS-4 recipient strain. Conjugations were supplemented with ddH2O or SCFAs at 1, 0.1, 0.01, or 0.001 molar final concentration. The addition of SCFAs completely inhibited plasmid transfer at 1 and 0.1 molar and significantly (p < 0.05) reduced transfer at 0.01 molar, regardless of SCFA tested. In explant models for the chicken ceca, either ddH2O or a final concentration of 0.025 M SCFAs were supplemented to the explants infected with donor and recipient E. coli. In every SCFA tested, significant decreases in transconjugant populations compared to ddH2O-treated control samples were observed with minimal effects on donor and recipient populations. Finally, significant reductions in transconjugants for plasmids of each incompatibility type (IncP1ε, IncFIβ, and IncI1) tested were detected. This study demonstrates for the first time the broad inhibition ability of SCFAs on bacterial plasmid transfer and eliminates AMR with minimal effect on bacteria. Implementing interventions that increase the concentrations of SCFAs in the gut may be a viable method to reduce the risk, incidence, and rate of AMR emergence in agricultural and human environments.
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Affiliation(s)
- Logan C. Ott
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
| | - Melha Mellata
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
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Wang L, Li F, Liu T, Ouyang C, Wang X, Li M, Huang Z, Huang J, Wang L, Wang X. Identification of a multidrug resistance genomic island harboring a nonfunctional optrA gene in Campylobacter coli of chicken origin. Vet Microbiol 2024; 293:110083. [PMID: 38593623 DOI: 10.1016/j.vetmic.2024.110083] [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: 10/26/2023] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
Campylobacter spp., such as Campylobacter jejuni and Campylobacter coli, are important zoonotic Gram-negative pathogens that cause acute intestinal diseases in humans. In this study, a retrospective analysis was conducted on previously collected Campylobacter isolates from antimicrobial resistance surveillance. A total of 29 optrA-positive C. coli strains were identified and subjected to second-generation sequencing. Multilocus sequence typing and single nucleotide polymorphism analyses demonstrated that the 29 optrA-positive isolates were genetically homogeneous. Notably, among the 29 isolated strains, the ΔoptrA variants exhibit a nonsense mutation at position 979 where the base C is substituted by T, leading to the formation of a premature termination codon. The alignment of sequences and genetic environmental characteristics suggested that ΔoptrA located on a chromosomally carried multidrug-resistant genomic island. There are other resistant genes on the multidrug resistance genomic island, such as aph(2'')-If, aph(3')-III, aadE, tet(O), tet(L), cat, erm(A), optrA and blaOXA-61. As a result, the 29 ΔoptrA-positive strains displayed susceptibility to both florfenicol and linezolid. The ΔoptrA gene is linked to the erm(A) gene, resulting in the formation of translocatable unit (TU) that are encompassed by two copies of IS1216 mobile elements. Multiple occurrences of similar TUs have been documented in numerous C. coli and provided evidence for the significance of TUs in facilitating the transfer of drug resistance genes in C. coli.
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Affiliation(s)
- Liangliang Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Fan Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Ouyang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyue Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Meifang Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiyu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
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An JU, Lee S, Guk JH, Woo J, Song H, Cho S. Circular intermediate-mediated horizontal transfer of the chromosome-encoded cfr(C) gene in multi-drug resistant Campylobacter coli from swine sources. Front Microbiol 2023; 14:1274245. [PMID: 38188581 PMCID: PMC10770853 DOI: 10.3389/fmicb.2023.1274245] [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: 08/08/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Campylobacter is a major zoonotic pathogen that causes gastrointestinal and, rarely, immune diseases in humans. The antimicrobial-resistance gene cfr(C) carried by Campylobacter and is a cfr-like gene that targets bacterial 23S rRNA through A2503 methylation. cfr(C) confers cross-resistance to five antimicrobial classes (PhLOPSA), including lincosamide, streptogramin A, and pleuromutilin, which are classified as critically important antimicrobials to human by the World Health Organization. To elucidate the genetic variation and horizontal transfer mechanism of cfr(C), we analyzed the genetic background and horizontal transfer unit of Campylobacter-derived cfr(C) through comparative genomic analysis. We identified nine cfr(C)-positive C. coli strains of 157 strains isolated from swine sources. Three novel cfr(C) gene single nucleotide polymorphism (SNP) sites (19delA, 674C > A, and 890 T > C) were identified from nine cfr(C)-positive strains. Among six identified cfr(C) SNP variant types (SNP-I to -VI), five types of randomly inserted cfr(C)-cassettes on chromosome and one type of plasmid-like element were identified, their gene cassette composition differing depending on the cfr(C) variants. Three of six cfr(C) cassette types contained aminoglycoside-streptothricin resistance cluster "aphA3-sat4-aadE." The cfr(C) gene cassette with pcp gene (GC-1, GC-4, and GC-5) formed a pcp-mediated circular intermediate "pcp-hp-cfr(C)-aphA3," which has not been previously reported. Other two cfr(C) cassette-types with ISChh1 formed circular intermediate "ISChh1-aphA3-cfr(C)-lnu (G)-pnp-ant1-hp-ATPase" and "ISChh1-aphA3-cfr(C)-hp." In conjugation assay, the pcp-mediated circular intermediate was naturally transferred to the plasmid of recipient C. coli wild-type strain from swine source, and comparative genomic analysis revealed that cfr(C) encoded in pcp-mediated circular intermediate was inserted into the plasmid of recipient by homologous recombination with pcp and aphA3. This study revealed that novel multidrug resistance gene cfr(C) carried by C. coli from swine sources can be highly genetically diverse and transferable. Moreover, we suggest that the transferability of chromosomal cfr(C) may contribute to the global spread of multidrug resistance against clinically important antimicrobials.
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Affiliation(s)
| | | | | | | | | | - Seongbeom Cho
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
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Sordo M, Grilo T, Freire S, Rodrigues B, Bouvier M, Poirel L, Aires-de-Sousa M. Rapid culture-based LNZ test for detection of linezolid susceptibility/resistance in staphylococci and enterococci. Diagn Microbiol Infect Dis 2023; 107:116058. [PMID: 37657232 DOI: 10.1016/j.diagmicrobio.2023.116058] [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: 06/21/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 09/03/2023]
Abstract
A rapid, easy-to-handle, cost-effective and universal culture-based test was developed for the identification of linezolid resistance among the most clinically relevant enterococcal and staphylococcal species. Our technique was tested using linezolid-resistant (n = 50) and linezolid-susceptible (n = 67) Gram-positive isolates: 34 Enterococcus faecium, 20 Enterococcus faecalis, 20 Staphylococcus aureus, 38 Staphylococcus epidermidis, and 5 Staphylococcus capitis. The susceptibility/resistance phenotype of E. faecium, E. faecalis, S. aureus, and S. epidermidis to linezolid was detected within 4.5 hours, while an extended timeframe was actually required for S. capitis (6.5 hours). The Rapid LNZ test showed a full agreement with the standard broth microdilution method, independently of the molecular resistance mechanism and MIC values, with sensitivities and specificities of 100% for all species.
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Affiliation(s)
- Miguel Sordo
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Teresa Grilo
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Samanta Freire
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal; Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Bruna Rodrigues
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Maxime Bouvier
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Marta Aires-de-Sousa
- Escola Superior de Saúde da Cruz Vermelha Portuguesa-Lisboa (ESSCVP-Lisboa), Lisboa, Portugal; Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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Tang B, Zou C, Schwarz S, Xu C, Hao W, Yan XM, Huang Y, Ni J, Yang H, Du XD, Shan X. Linezolid-Resistant Enterococcus faecalis of Chicken Origin Harbored Chromosome-Borne optrA and Plasmid-Borne cfr, cfr(D), and poxtA2 Genes. Microbiol Spectr 2023; 11:e0274122. [PMID: 36995237 PMCID: PMC10269796 DOI: 10.1128/spectrum.02741-22] [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: 07/18/2022] [Accepted: 02/26/2023] [Indexed: 03/31/2023] Open
Abstract
The aim of this study was to investigate the transferability of acquired linezolid resistance genes and associated mobile genetic elements in an Enterococcus faecalis isolate QZ076, cocarrying optrA, cfr, cfr(D), and poxtA2 genes. MICs were determined by broth microdilution. Whole-genome sequencing (WGS) was performed using the Illumina and Nanopore platforms. The transfer of linezolid resistance genes was investigated by conjugation, using E. faecalis JH2-2 and clinical methicillin-resistant Staphylococcus aureus (MRSA) 109 as recipients. E. faecalis QZ076 harbors four plasmids, designated pQZ076-1 to pQZ076-4, with optrA located in the chromosomal DNA. The gene cfr was located on a novel pseudocompound transposon, designated Tn7515, integrated into the 65,961-bp pCF10-like pheromone-responsive conjugative plasmid pQZ076-1. Tn7515 generated 8-bp direct target duplications (5'-GATACGTA-3'). The genes cfr(D) and poxtA2 were colocated on the 16,397-bp mobilizable broad-host-range Inc18 plasmid pQZ076-4. The cfr-carrying plasmid pQZ076-1 could transfer from E. faecalis QZ076 to E. faecalis JH2-2, along with the cfr(D)- and poxtA2-cocarrying plasmid pQZ076-4, conferring the corresponding resistant phenotype to the recipient. Moreover, pQZ076-4 could also transfer to MRSA 109. To the best of our knowledge, this study presented the first report of four acquired linezolid resistance genes [optrA, cfr, cfr(D), and poxtA2] being simultaneously present in the same E. faecalis isolate. The location of the cfr gene on a pseudocompound transposon in a pheromone-responsive conjugative plasmid will accelerate its rapid dissemination. In addition, the cfr-carrying pheromone-responsive conjugative plasmid in E. faecalis was also able to mobilize the interspecies transfer of the cfr(D)- and poxtA2-cocarrying plasmid between enterococci and staphylococci. IMPORTANCE In this study, the simultaneous occurrence of four acquired oxazolidinone resistance genes [optrA, cfr, cfr(D), and poxtA2] was identified in an E. faecalis isolate of chicken origin. The association of the cfr gene with a novel pseudocompound transposon Tn7515 integrated into a pCF10-like pheromone-responsive conjugative plasmid will accelerate its dissemination. Moreover, the location of the resistance genes cfr(D) and poxtA2 on a mobilizable broad-host-range Inc18 family plasmid represents the basis for their intra- and interspecies dissemination with the aid of a conjugative plasmid and further accelerates the spreading of acquired oxazolidinone resistance genes, such as cfr, cfr(D), and poxtA2, among Gram-positive pathogens.
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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
| | - Chenhui Zou
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Chunyan Xu
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Wenbo Hao
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xiao-Mei Yan
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuting Huang
- 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
| | - Juan Ni
- 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
| | - 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
| | - Xiang-Dang Du
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xinxin Shan
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
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Concha-Toloza M, Lopez-Cantillo M, Molina-Mora JA, Collado L. Genomic Characterization of Antibiotic-Resistant Campylobacterales Isolated from Chilean Poultry Meat. Antibiotics (Basel) 2023; 12:antibiotics12050917. [PMID: 37237819 DOI: 10.3390/antibiotics12050917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
Due to the lack of knowledge about Campylobacterales in the Chilean poultry industry, the objective of this research was to know the prevalence, resistance, and genotypes of Campylobacter, Arcobacter and Helicobacter in 382 samples of chicken meat purchased in Valdivia, Chile. The samples were analyzed using three isolation protocols. Resistance to four antibiotics was evaluated by phenotypic methods. Genomic analyses were performed on selected resistant strains to detect resistance determinants and their genotypes. A total of 59.2% of the samples were positive. Arcobacter butzleri (37.4%) was the most prevalent species, followed by Campylobacter jejuni (19.6%), C. coli (11.3%), A. cryaerophilus (3.7%) and A. skirrowii (1.3%). Helicobacter pullorum (14%) was detected by PCR in a subset of samples. Campylobacter jejuni was resistant to ciprofloxacin (37.3%) and tetracycline (20%), while C. coli and A. butzleri were resistant to ciprofloxacin (55.8% and 2.8%), erythromycin (16.3% and 0.7%) and tetracycline (4.7% and 2.8%), respectively. Molecular determinants were consistent with phenotypic resistance. The genotypes of C. jejuni (CC-21, CC-48, CC-49, CC-257, CC-353, CC-443, CC-446 and CC-658) and C. coli (CC-828) coincided with genotypes of Chilean clinical strains. These findings suggest that besides C. jejuni and C. coli, chicken meat could play a role in the transmission of other pathogenic and antibiotic-resistant Campylobacterales.
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Affiliation(s)
- Macarena Concha-Toloza
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Mónica Lopez-Cantillo
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Luis Collado
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile
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Jeremia L, Deprez BE, Dey D, Conn GL, Wuest WM. Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation. RSC Med Chem 2023; 14:624-643. [PMID: 37122541 PMCID: PMC10131624 DOI: 10.1039/d2md00459c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
The rise of multidrug-resistant bacterial infections is a cause of global concern. There is an urgent need to both revitalize antibacterial agents that are ineffective due to resistance while concurrently developing new antibiotics with novel targets and mechanisms of action. Pathogen associated resistance-conferring ribosomal RNA (rRNA) methyltransferases are a growing threat that, as a group, collectively render a total of seven clinically-relevant ribosome-targeting antibiotic classes ineffective. Increasing frequency of identification and their growing prevalence relative to other resistance mechanisms suggests that these resistance determinants are rapidly spreading among human pathogens and could contribute significantly to the increased likelihood of a post-antibiotic era. Herein, with a view toward stimulating future studies to counter the effects of these rRNA methyltransferases, we summarize their prevalence, the fitness cost(s) to bacteria of their acquisition and expression, and current efforts toward targeting clinically relevant enzymes of this class.
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Affiliation(s)
- Learnmore Jeremia
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Benjamin E Deprez
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - William M Wuest
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
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van der Graaf-van Bloois L, Duim B, Looft T, Veldman KT, Zomer AL, Wagenaar JA. Antimicrobial resistance in Campylobacter fetus: emergence and genomic evolution. Microb Genom 2023; 9. [PMID: 36862577 PMCID: PMC10132061 DOI: 10.1099/mgen.0.000934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Campylobacter fetus is a pathogen, which is primarily associated with fertility problems in sheep and cattle. In humans, it can cause severe infections that require antimicrobial treatment. However, knowledge on the development of antimicrobial resistance in C. fetus is limited. Moreover, the lack of epidemiological cut-off values (ECOFFs) and clinical breakpoints for C. fetus hinders consistent reporting about wild-type and non-wild-type susceptibility. The aim of this study was to determine the phenotypic susceptibility pattern of C. fetus and to determine the C. fetus resistome [the collection of all antimicrobial resistance genes (ARGs) and their precursors] to describe the genomic basis of antimicrobial resistance in C. fetus isolates over time. Whole-genome sequences of 295 C. fetus isolates, including isolates that were isolated in the period 1939 till the mid 1940s, before the usage of non-synthetic antimicrobials, were analysed for the presence of resistance markers, and phenotypic antimicrobial susceptibility was obtained for a selection of 47 isolates. C. fetus subspecies fetus (Cff) isolates showed multiple phenotypic antimicrobial resistances compared to C. fetus subspecies venerealis (Cfv) isolates that were only intrinsic resistant to nalidixic acid and trimethoprim. Cff isolates showed elevated minimal inhibitory concentrations for cefotaxime and cefquinome that were observed in isolates from 1943 onwards, and Cff isolates contained gyrA substitutions, which conferred resistance to ciprofloxacin. Resistances to aminoglycosides, tetracycline and phenicols were linked to acquired ARGs on mobile genetic elements. A plasmid-derived tet(O) gene in a bovine Cff isolate in 1999 was the first mobile genetic element observed, followed by detection of mobile elements containing tet(O)-aph(3')-III and tet(44)-ant(6)-Ib genes, and a plasmid from a single human isolate in 2003, carrying aph(3')-III-ant(6)-Ib and a chloramphenicol resistance gene (cat). The presence of ARGs in multiple mobile elements distributed among different Cff lineages highlights the risk for spread and further emergence of AMR in C. fetus. Surveillance for these resistances requires the establishment of ECOFFs for C. fetus.
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Affiliation(s)
- Linda van der Graaf-van Bloois
- Department Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective / WOAH Reference Laboratory for Campylobacteriosis, Utrecht/Lelystad, Netherlands
| | - Birgitta Duim
- Department Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective / WOAH Reference Laboratory for Campylobacteriosis, Utrecht/Lelystad, Netherlands
| | - Torey Looft
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Kees T Veldman
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Aldert L Zomer
- Department Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective / WOAH Reference Laboratory for Campylobacteriosis, Utrecht/Lelystad, Netherlands
| | - Jaap A Wagenaar
- Department Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective / WOAH Reference Laboratory for Campylobacteriosis, Utrecht/Lelystad, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
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Abstract
PURPOSE OF REVIEW Campylobacter is a major foodborne pathogen that infects the human intestinal tract. This review discusses the current status of antibiotic resistance, transmission of antibiotic resistance genes, and strategies to combat the global Campylobacter epidemic. RECENT FINDINGS Over the past 18 months, articles on Campylobacter antibiotic resistance have been published in ∼39 countries. Antibiotic-resistant Campylobacter have been detected in humans, livestock, poultry, wild animals, the environment, and food. Campylobacter spp. are resistant to a wide spectrum of antimicrobial agents, including the antibiotics quinolones, macrolides, tetracyclines, aminoglycosides, and chloramphenicols. Multidrug resistance is a globally emerging problem. Continuous antibiotic pressure promotes the spread of drug-resistant Campylobacter spp. Additionally, Campylobacter is well adapted to acquiring foreign drug resistance genes, including ermB, optrA, fexA, and cfrC, which are usually acquired from gram-positive bacteria. SUMMARY The widespread use of antibiotics has caused a global epidemic of drug-resistant Campylobacter infections. Many countries are actively reducing the use of antibiotics and adopting alternatives in the livestock and poultry industries to control the spread of drug-resistant Campylobacter spp.
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Genomic Insights into the Increased Occurrence of Campylobacteriosis Caused by Antimicrobial-Resistant Campylobacter coli. mBio 2022; 13:e0283522. [PMID: 36472434 PMCID: PMC9765411 DOI: 10.1128/mbio.02835-22] [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] [Indexed: 12/12/2022] Open
Abstract
Campylobacter is the leading bacterial cause of diarrheal illnesses worldwide. Campylobacter jejuni and C. coli are the most common species accounting for campylobacteriosis. Although the proportion of campylobacteriosis caused by C. coli is increasing rapidly in China, the underlying mechanisms of this emergence remain unclear. In this study, we analyzed the whole-genome sequences and associated environments of 1,195 C. coli isolates with human, poultry, or porcine origins from 1980 to 2021. C. coli isolates of human origin were closely related to those from poultry, suggesting that poultry was the main source of C. coli infection in humans. Analysis of antimicrobial resistance determinants indicated that the prevalence of multidrug-resistant C. coli has increased dramatically since the 2010s, coinciding with the shift in abundance from C. jejuni to C. coli in Chinese poultry. Compared with C. jejuni, drug-resistant C. coli strains were better adapted and showed increased proliferation in the poultry production environment, where multiple antimicrobial agents were frequently used. This study provides an empirical basis for the molecular mechanisms that have enabled C. coli to become the dominant Campylobacter species in poultry; we also emphasize the importance of poultry products as sources of campylobacteriosis caused by C. coli in human patients. IMPORTANCE The proportion of campylobacteriosis caused by C. coli is increasing rapidly in China. Coincidentally, the dominant species of Campylobacter occurring in poultry products has shifted from C. jejuni to C. coli. Here, we analyzed the whole-genome sequences of 1,195 C. coli isolates from different origins. The phylogenetic relationship among C. coli isolates suggests that poultry was the main source of C. coli infection in humans. Further analysis indicated that antimicrobial resistance in C. coli strains has increased dramatically since the 2010s, which could facilitate their adaptation in the poultry production environment, where multiple antimicrobial agents are frequently used. Thus, our findings suggest that the judicious use of antimicrobial agents could mitigate the emergence of multidrug-resistant C. coli strains and enhance clinical outcomes by restoring drug sensitivity in Campylobacter.
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Ramamurthy T, Ghosh A, Chowdhury G, Mukhopadhyay AK, Dutta S, Miyoshi SI. Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens. Front Cell Infect Microbiol 2022; 12:952491. [PMID: 36506027 PMCID: PMC9727169 DOI: 10.3389/fcimb.2022.952491] [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: 05/25/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.
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Affiliation(s)
- Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India,*Correspondence: Thandavarayan Ramamurthy,
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K. Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-inchi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR- National Institute of Cholera and Enteric Diseases, Kolkata, India,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Huang Z, Bai Y, Wang Q, Yang X, Zhang T, Chen X, Wang H. Persistence of transferable oxazolidinone resistance genes in enterococcal isolates from a swine farm in China. Front Microbiol 2022; 13:1010513. [PMID: 36299730 PMCID: PMC9589348 DOI: 10.3389/fmicb.2022.1010513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/26/2022] [Indexed: 11/21/2022] Open
Abstract
The appearance of transferable oxazolidinone resistance genes poses a major challenge to public health and environmental safety. These genes not only lead pathogenic bacteria to become resistant to linezolid but also reduce sensitivity to florfenicol, which is widely used in the veterinary field. To verify the dissemination of oxazolidinone resistance genes in enterococcal isolates from pigs at different production stages in a swine farm in China, we collected 355 enterococcal isolates that were resistant to florfenicol from 600 (150 per stage) fresh fecal swabs collected from a swine farm. Through initial PCR screening and whole-genome sequencing, 175 isolates harboring different oxazolidinone resistance genes were identified. All isolates carried the optrA gene. A total of 161 (92%, 161/175) isolates carried only the optrA gene. Three (1.71%, 3/175) isolates carried both the optrA and poxtA genes, and 11 (3.1%, 11/175) isolates contained the optrA gene and poxtA2 and cfr(D) variants. A total of 175 isolates that harbored oxazolidinone resistance genes included 161 E. faecalis, 6 E. faecium, and 8 E. hirae. By sequencing the whole genomes, we found that the 161 isolates of E. faecalis belonged to 28 different STs, including 8 new STs, and the 6 isolates of E. faecium belonged to four different STs, including one new ST. The phylogenetic tree based on SNPs of the core genome showed that both clonal spread and horizontal transfer mediated the diffusion of oxazolidone resistance genes in enterococcal isolates at specific stages in pig farms. Moreover, enterococcal isolates carrying oxazolidone resistance genes could spread from breeding pigs to fattening pigs, while transferable oxazolidone resistance genes in enterococcal isolates could persist on a pig farm throughout all production stages. Representative enterococcal isolates with different oxazolidinone resistance genes were further studied through Nanopore sequencing. We identified a novel plasmid, pM4-80 L4 (15,008 bp), carrying the poxtA2 and cfr(D) genes in enterococcal isolates at different stages. We also found three different plasmids harboring the poxtA gene with high genetic variation, and all poxtA genes were flanked by two copies of IS1216E elements. In addition, four genetically distinct plasmids carrying the optrA gene were identified, and Tn554 was found to mediate chromosome-localized optrA gene transfer. Our study highlighted that transferable oxazolidinone resistance genes in enterococcal isolates could persist throughout all production stages on a pig farm, and the prevalence and dissemination of oxazolidinone resistance genes in enterococcal isolates from animal farms should be continually monitored.
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Affiliation(s)
- Zheren Huang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yilin Bai
- College of Veterinary Medicine, Northwest A&F University, Yanglin, China
| | - Qin Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xue Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tiejun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xuan Chen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Hongning Wang,
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Brenciani A, Morroni G, Schwarz S, Giovanetti E. Oxazolidinones: mechanisms of resistance and mobile genetic elements involved. J Antimicrob Chemother 2022; 77:2596-2621. [PMID: 35989417 DOI: 10.1093/jac/dkac263] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The oxazolidinones (linezolid and tedizolid) are last-resort antimicrobial agents used for the treatment of severe infections in humans caused by MDR Gram-positive bacteria. They bind to the peptidyl transferase centre of the bacterial ribosome inhibiting protein synthesis. Even if the majority of Gram-positive bacteria remain susceptible to oxazolidinones, resistant isolates have been reported worldwide. Apart from mutations, affecting mostly the 23S rDNA genes and selected ribosomal proteins, acquisition of resistance genes (cfr and cfr-like, optrA and poxtA), often associated with mobile genetic elements [such as non-conjugative and conjugative plasmids, transposons, integrative and conjugative elements (ICEs), prophages and translocatable units], plays a critical role in oxazolidinone resistance. In this review, we briefly summarize the current knowledge on oxazolidinone resistance mechanisms and provide an overview on the diversity of the mobile genetic elements carrying oxazolidinone resistance genes in Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China.,Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Jalal K, Khan K, Hayat A, Ahmad D, Alotaibi G, Uddin R, Mashraqi MM, Alzamami A, Aurongzeb M, Basharat Z. Mining therapeutic targets from the antibiotic-resistant Campylobacter coli and virtual screening of natural product inhibitors against its riboflavin synthase. Mol Divers 2022; 27:793-810. [PMID: 35699868 DOI: 10.1007/s11030-022-10455-z] [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: 02/11/2022] [Accepted: 04/29/2022] [Indexed: 11/29/2022]
Abstract
Campylobacter coli resides in the intestine of several commonly consumed animals, as well as water and soil. It leads to campylobacteriosis when humans eat raw/undercooked meat or come into contact with infected animals. A common manifestation of the infection is fever, nausea, headache, and diarrhea. Increasing antibiotic resistance is being observed in this pathogen. The increased incidence of C. coli infection, and post-infection complications like Guillain-Barré syndrome, make it an important pathogen. It is essential to find novel therapeutic targets and drugs against it, especially with the emergence of antibiotic-resistant strains. In the current study, genomes of 89 antibiotic-resistant strains of C. coli were downloaded from the PATRIC database. Potent drug targets (n = 36) were prioritized from the core genome (n = 1,337 genes) of this species. Riboflavin synthase was selected as a drug target and pharmacophore-based virtual screening was performed to predict its inhibitors from the NPASS (n = ~ 30,000 compounds) natural product library. The top three docked compounds (NPC115144, NPC307895, and NPC470462) were selected for dynamics simulation (for 50 ns) and ADMET profiling. These identified compounds appear safe for targeting this pathogen and can be further validated by experimental analysis before clinical trials.
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Affiliation(s)
- Khurshid Jalal
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Ajmal Hayat
- Department of Pharmacy, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Diyar Ahmad
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Ghallab Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Al-Dawadmi Campus, Shaqra University, Shaqra, Saudi Arabia
| | - Reaz Uddin
- Computational Biology Unit, Lab 103 PCMD ext. Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, 61441, Saudi Arabia
| | - Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Science, Shaqra University, AlQuwayiyah, 11961, Saudi Arabia
| | - Muhammad Aurongzeb
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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Promising Colloidal Rhenium Disulfide Nanosheets: Preparation and Applications for In Vivo Breast Cancer Therapy. NANOMATERIALS 2022; 12:nano12111937. [PMID: 35683791 PMCID: PMC9182237 DOI: 10.3390/nano12111937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 11/20/2022]
Abstract
Photothermal therapy (PTT) has become an important therapeutic strategy in the treatment of cancer. However, exploring novel photothermal nanomaterials with satisfactory biocompatibility, high photothermal conversion efficiency, and efficient theranostic outcomes, remains a major challenge for satisfying clinical application. In this study, poly-ethylene glycol modified rhenium disulfide (PEG-ReS2) nanosheets are constructed by a simple-liquid phase exfoliation method. The PEG-ReS2 nanosheets were demonstrated to have good solubility, good biocompatibility, low toxicity, and strong capability of accumulating near-infrared (NIR) photons. Under 808 nm laser irradiation, the PEG-ReS2 nanosheets were found to have an excellent photothermal conversion efficiency (PTCE) of 42%. Moreover, the PEG-ReS2 nanosheets were demonstrated to be ideal photothermal transduction agents (PTAs), which promoted rapid cancer cell death in vitro and efficiently ablated tumors in vivo. Interestingly, the potential utility of up-regulation or down-regulation of miRNAs was proposed to evaluate the therapeutic outcomes of PEG-ReS2 nanosheets. The expression levels of a set of miRNAs in tumor-bearing mice were restored to normal levels after PTT therapy with PEG-ReS2 nanosheets. Both down-regulation miRNAs (miR-125a-5p, miR-34a-5p, miR-132-3p, and miR-148b-3p) and up-regulation miRNAs (miR-133a-3p, miR-200c-5p, miR-9-3p, and miR-150-3p) were suggested to be important clinical biomarkers for evaluating therapeutic outcomes of breast cancer-related PTT. This work highlights the great significance of PEG-ReS2 nanosheets as therapeutic nanoagents for cancer therapy.
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Wang T, Zhao W, Li S, Yao H, Zhang Q, Yang L. Characterization of erm(B)-carrying Campylobacter spp. of retail chicken meat origin. J Glob Antimicrob Resist 2022; 30:173-177. [PMID: 35660664 DOI: 10.1016/j.jgar.2022.05.029] [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: 11/17/2021] [Revised: 04/12/2022] [Accepted: 05/29/2022] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES The erm(B) gene in Campylobacter, conferring resistance to macrolides, poses a great concern worldwide. In this study, the prevalence of erm(B) in Campylobacter of retail chicken meat origin was investigated and the characterization of erm(B)-harboring Campylobacter isolates was also analyzed. METHODS The antimicrobial susceptibility testing was performed to determine the susceptibility of Campylobacter isolates. Whole genome sequencing and analysis were used to characterize ST type and genetic context of erm(B). Natural transformation was conducted to evaluate transferability of the erm(B) gene. RESULTS A total of 16 (11.8%) Campylobacter isolates were obtained from 136 samples collected from retail chicken meat, among which 5 erm(B)-positive isolates were identified as C. coli belonging to ST3753 (n=4) and ST825 (n=1). Furthermore, a total of 22 Campylobacter spp. were erm(B)-positive in GenBank database, all except one C. jejuni isolate were collected in China. Diverse ST types were involved in these erm(B)-carrying isolates. Comparison analysis indicated that 11 types for genetic environment of erm(B) were identified, mostly associated with multidrug-resistance genomic islands (MDRGIs). The genetic context of erm(B) in C. coli of retail chicken meat origin showed highly nucleotide sequence identity to that in C. coli from human. CONCLUSION This is the first report of prevalence and characterization for erm(B) in Campylobacter of retail chicken meat origin. Highly homologous of genetic context of erm(B) in C. coli isolates from retail meat and human, implying the possibility of zoonotic transmission of erm(B) in Campylobacter, which poses a great threat to public health.
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Affiliation(s)
- Tao Wang
- School of Pharmaceutical Sciences, & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Wenbo Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Shihong Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Hong Yao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Qiurong Zhang
- School of Pharmaceutical Sciences, & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, People's Republic of China.
| | - Longhua Yang
- School of Pharmaceutical Sciences, & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, People's Republic of China.
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The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2019–2020. EFSA J 2022; 20:e07209. [PMID: 35382452 PMCID: PMC8961508 DOI: 10.2903/j.efsa.2022.7209] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Data on antimicrobial resistance (AMR) in zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs), jointly analysed by the EFSA and the ECDC and reported in a yearly EU Summary Report. The annual monitoring of AMR in animals and food within the EU is targeted at selected animal species corresponding to the reporting year. The 2020 monitoring specifically focussed on poultry and their derived carcases/meat, while the monitoring performed in 2019 specifically focused on fattening pigs and calves under 1 year of age, as well as their derived carcases/meat. Monitoring and reporting of AMR in 2019–2020 included data regarding Salmonella, Campylobacter and indicator E. coli isolates, as well as data obtained from the specific monitoring of presumptive ESBL‐/AmpC‐/carbapenemase‐producing E. coli isolates. Additionally, some MSs reported voluntary data on the occurrence of methicillin‐resistant Staphylococcus aureus in animals and food, with some countries also providing data on antimicrobial susceptibility. This report provides an overview of the main findings of the 2019–2020 harmonised AMR monitoring in the main food‐producing animal populations monitored, in carcase/meat samples and in humans. Where available, monitoring data obtained from pigs, calves, broilers, laying hens and turkeys, as well as from carcase/meat samples and humans were combined and compared at the EU level, with particular emphasis on multidrug resistance, complete susceptibility and combined resistance patterns to critically important antimicrobials, as well as Salmonella and E. coli isolates possessing ESBL‐/AmpC‐/carbapenemase phenotypes. The key outcome indicators for AMR in food‐producing animals, such as complete susceptibility to the harmonised panel of antimicrobials in E. coli and the prevalence of ESBL‐/AmpC‐producing E. coli have been specifically analysed over the period 2014–2020.
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Plasmid Fusion and Recombination Events That Occurred during Conjugation of poxtA-Carrying Plasmids in Enterococci. Microbiol Spectr 2022; 10:e0150521. [PMID: 35044200 PMCID: PMC8768628 DOI: 10.1128/spectrum.01505-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Linezolid plays a crucial role in the treatment of infections caused by multiresistant Gram-positive bacteria. The poxtA gene not only confers oxazolidinone and phenicol resistance but also decreases susceptibility to tetracycline. In this study, we investigated structural changes in mobilizable poxtA-carrying plasmids in enterococci which occurred during conjugation experiments using S1-PFGE (pulsed-field gel electrophoresis), Southern blot hybridization, and whole-genome sequencing (WGS) analysis. Two poxtA-carrying strains were identified in Enterococcus faecalis E006 and Enterococcus lactis E843, respectively. E. faecalis E006 contains the 121,520-bp conjugative plasmid pE006-121 and the 19,832-bp mobilizable poxtA-carrying plasmid pE006-19, while E. lactis E843 contains the 171,930-bp conjugative plasmid pE843-171 and the 27,847-bp mobilizable poxtA-carrying plasmid pE843-27. Moreover, both poxtA-carrying plasmids were mobilized by their respective conjugative plasmid in enterococci by plasmid fusion; one was generated by homologous recombination in E. faecalis through an identical 864-bp homologous region in the plasmids of the parental strain, while another was generated by an IS1216E-mediated plasmid integration in E. lactis, involving a replicative transposition. IMPORTANCE Until now, all the poxtA genes described in enterococci, including E. faecalis, E. faecium, and E. hirae, are plasmid-borne, suggesting that plasmids play an important role in the dissemination of the poxtA gene among enterococci. This study showed that the mobilizable poxtA-carrying plasmid could transfer with the help of conjugative plasmid in enterococci via plasmid fusion, with one generated by homologous recombination in E. faecalis, and another by replicative transposition in E. lactis. During both the fusion events, the poxtA-carrying plasmids changed from nonconjugative to conjugative, leading to the generation and enhanced dissemination of the larger phenicol-oxazolidinone-tetracycline resistance-encoding plasmids in enterococci.
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Genome sequence of a multidrug-resistant Campylobacter coli strain isolated from a newborn with severe diarrhea in Lebanon. Folia Microbiol (Praha) 2022; 67:319-328. [PMID: 34997523 DOI: 10.1007/s12223-021-00921-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 09/18/2021] [Indexed: 11/04/2022]
Abstract
A multidrug-resistant (MDR) Campylobacter coli (C. coli) strain was isolated from a 2-month-old newborn who suffered from severe diarrhea in Lebanon. Here, whole-genome sequencing (WGS) analysis was deployed to determine the genetic basis of antimicrobial resistance and virulence in the C. coli isolate and to identify its epidemiological background (sequence type). The identity of the isolate was confirmed using API® Campy, MALDI-TOF, and 16S rRNA gene sequencing analysis. The antimicrobial susceptibility phenotype was determined using the disk diffusion assay. Our analysis showed that resistance to macrolide and quinolone was potentially associated with the presence of multiple point mutations in antibiotic targets on the chromosomal DNA. Furthermore, tetracycline and aminoglycoside resistance were encoded by genes on a pTet plasmid. The blaOXA-61, which is associated with beta-lactam resistance, was also detected in the C. coli genome. A set of 30 genes associated with the virulence in C. coli was detected using WGS analysis. MLST analysis classified the isolate as belonging to a new sequence type (ST-9588), a member of ST-828 complex which is mainly associated with humans and chickens. Taking together, this study provides the first WGS analysis of Campylobacter isolated from Lebanon. The detection of a variety of AMR and virulence determinants strongly emphasizes the need for studying the burden of Campylobacter in Lebanon and the Middle East and North Africa (MENA) region, where information on campylobacteriosis is scant.
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Aleksić E, Miljković-Selimović B, Tambur Z, Aleksić N, Biočanin V, Avramov S. Resistance to Antibiotics in Thermophilic Campylobacters. Front Med (Lausanne) 2021; 8:763434. [PMID: 34859016 PMCID: PMC8632019 DOI: 10.3389/fmed.2021.763434] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022] Open
Abstract
Campylobacter jejuni (C. jejuni) is one of the most frequent causes of bacterial enterocolitis globally. The disease in human is usually self-limiting, but when complications arise antibiotic therapy is required at a time when resistance to antibiotics is increasing worldwide. Mechanisms of antibiotic resistance in bacteria are diverse depending on antibiotic type and usage and include: enzymatic destruction or drug inactivation; alteration of the target enzyme; alteration of cell membrane permeability; alteration of ribosome structure and alteration of the metabolic pathway(s). Resistance of Campylobacter spp. to antibiotics, especially fluoroquinolones is now a major public health problem in developed and developing countries. In this review the mechanisms of resistance to fluoroquinolones, macrolides, tetracycline, aminoglycoside and the role of integrons in resistance of Campylobacter (especially at the molecular level) are discussed, as well as the mechanisms of resistance to β-lactam antibiotics, sulphonamides and trimethoprim. Multiple drug resistance is an increasing problem for treatment of campylobacter infections and emergence of resistant strains and resistance are important One Health issues.
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Affiliation(s)
- Ema Aleksić
- Faculty of Stomatology Pancevo, University Business Academy in Novi Sad, Pančevo, Serbia
| | | | - Zoran Tambur
- Faculty of Stomatology Pancevo, University Business Academy in Novi Sad, Pančevo, Serbia
| | - Nikola Aleksić
- Faculty of Stomatology Pancevo, University Business Academy in Novi Sad, Pančevo, Serbia.,Institute for Cardiovascular Disease "Dedinje, "Belgrade, Serbia
| | - Vladimir Biočanin
- Faculty of Stomatology Pancevo, University Business Academy in Novi Sad, Pančevo, Serbia
| | - Stevan Avramov
- Faculty of Stomatology Pancevo, University Business Academy in Novi Sad, Pančevo, Serbia.,Institute for Biological Research "Siniša Stanković," University of Belgrade, Belgrade, Serbia
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Antimicrobial resistance in Campylobacter coli and Campylobacter jejuni from human campylobacteriosis in Taiwan, 2016-2019. Antimicrob Agents Chemother 2021; 66:e0173621. [PMID: 34748382 DOI: 10.1128/aac.01736-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter coli and C. jejuni are highly resistant to most therapeutic antimicrobials in Taiwan, rapid diagnostics of resistance in bacterial isolates is crucial for the treatment of campylobacteriosis. We characterized 219 (40 C. coli and 179 C. jejuni) isolates recovered from humans between 2016 and 2019 using whole-genome sequencing to investigate the genetic diversity among isolates and the genetic resistance determinants associated with antimicrobial resistance. Susceptibility testing with 8 antimicrobials was conducted to assess the concordance between phenotypic resistance and genetic determinants. The conventional and core genome multilocus sequence typing analysis revealed diverse clonality among the isolates. Mutations in gyrA (T86I, D90N), rpsL (K43R, K88R), and 23S rRNA (A2075G) were found in 91.8%, 3.2%, and 6.4% of the isolates, respectively. Horizontally transferable resistance genes ant(6)-I, aad9, aph(3')-IIIa, aph(2"), blaOXA, catA/fexA, cfr(C), erm(B), lnu, sat4, and tet were identified in 24.2%, 21.5%, 33.3%, 11.9%, 96.3%, 10.0%, 0.9%, 6.8%, 3.2%, 13.2%, and 96.3%, respectively. High-level resistance to 8 antimicrobials in isolates was 100% predictable by the known resistance determinants, whereas low-level resistance to azithromycin, clindamycin, nalidixic acid, ciprofloxacin, and florfenicol in isolates was associated with sequence variations in CmeA and CmeB of the CmeABC efflux pump. Resistance-enhancing CmeB variants were identified in 62.1% (136/219) of isolates. In conclusion, an extremely high proportion of C. coli (100%) and C. jejuni (88.3%) were multidrug-resistant and a high proportion (62.5%) of C. coli isolates had been resistant to azithromycin, erythromycin, and clindamycin that would complicate the treatment of invasive campylobacteriosis in this country.
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Lei CW, Chen X, Liu SY, Li TY, Chen Y, Wang HN. Clonal spread and horizontal transfer mediate dissemination of phenicol-oxazolidinone-tetracycline resistance gene poxtA in enterococci isolates from a swine farm in China. Vet Microbiol 2021; 262:109219. [PMID: 34500344 DOI: 10.1016/j.vetmic.2021.109219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/29/2021] [Indexed: 11/16/2022]
Abstract
The emergence of the phenicol-oxazolidinone-tetracycline resistance gene poxtA becomes a significant challenge for public health, since it confers a decreased susceptibility not only to the last resort drug linezolid, but also to florfenicol and doxycycline widely used in veterinary medicine. To determine the dissemination mechanism of poxtA in enterococci isolates from different healthy pigs in the swine farm, a total of 178 florfenicol-resistant enterococci isolates were collected from 400 fresh faecal swabs in a swine farm in China. The poxtA gene was detected in 11 (6.18 %) enterococci isolates, including 8 E. faecium, 2 E. hirae and 1 E. casseliflavus isolates. Whole genome sequencing indicated that the eight poxtA-harbouring E. faecium strains belonged to four different sequence types, including ST156 and three new STs, ST1818, ST1819 and ST1820. Five out of the 11 poxtA-positive enterococci isolates also harboured optrA gene. Moreover, E. casseliflavus strain DY31 co-harboured poxtA, optrA and cfr. Seven different poxtA-harbouring plasmids were obtained through Nanopore combined with Illumina sequencing. The poxtA-harbouring plasmids exhibited high genetic variation, six out of which belonged to rep2 plasmid of Inc18 family. The poxtA gene was flanked by IS1216E in the left and/or right ends.The optrA and cfr genes were located on different plasmids, respectively, but those genes could be co-transferred with poxtA gene into the recipient E. faecalis strain by electrotransformation. Our study highlights that both clonal spread and horizontal transfer mediated by Inc18 plasmid and IS1216E promote the dissemination of poxtA in enterococci isolates from different healthy pigs in the swine farm.
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Affiliation(s)
- Chang-Wei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Xuan Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Si-Yi Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Tian-Yi Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Yanpeng Chen
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Hong-Ning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China.
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Shan X, Li XS, Wang N, Schwarz S, Zhang SM, Li D, Du XD. Studies on the role of IS1216E in the formation and dissemination of poxtA-carrying plasmids in an Enterococcus faecium clade A1 isolate. J Antimicrob Chemother 2021; 75:3126-3130. [PMID: 32772071 DOI: 10.1093/jac/dkaa325] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES To analyse the role of IS1216E in the dissemination of the phenicol-oxazolidinone-tetracycline resistance gene poxtA in an Enterococcus faecium clade A1 isolate. METHODS MICs were determined by broth microdilution. The poxtA-positive isolate was typed by MLST. The two plasmids were characterized by PCR, conjugation, S1-PFGE, Southern blot hybridization and WGS analysis. The presence of translocatable units (TUs) was examined by PCR and sequencing. RESULTS Isolate E1077 contains the 217661 bp conjugative plasmid pE1077-217 and the 23710 bp mobilizable plasmid pE1077-23. pE1077-217 harbours erm(B), aac(A)-aph(D), aadE, spw, lsa(E), lnu(B), aphA3 and dfrG, whereas pE1077-23 carries a Tn6657-like transposon containing poxtA and fexB. pE1077-23 was apparently formed by an IS1216E-mediated composite transposon-plasmid fusion event, involving a replicative transposition process. Conjugation experiments showed that pE1077-23 is mobilizable by pE1077-217. Moreover, a novel 31742 bp plasmid, pT-E1077-31, was found in a transconjugant. WGS analysis indicated that pT-E1077-31 was formed by the integration of a Tn6657-derived, IS1216E-based translocatable unit, which carried fexB and poxtA, into a copy of pE1077-23. CONCLUSIONS This study showed the presence of two cointegrate formation events in the formation and spread of a poxtA/fexB-carrying plasmid in E. faecium. One was the integration of a transposon into a plasmid while the other was the integration of a TU into a different site of the same type of plasmid-borne transposon from which it originated. In both events, IS1216E played a major role, suggesting that IS1216E-mediated transposition and translocation processes aid the dissemination and persistence of important antimicrobial resistance genes, such as poxtA, among enterococci.
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Affiliation(s)
- Xinxin Shan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Xin-Sheng Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Nannan Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Su-Mei Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Dexi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Xiang-Dang Du
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
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Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria. Clin Microbiol Rev 2021; 34:e0018820. [PMID: 34076490 DOI: 10.1128/cmr.00188-20] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Seven mobile oxazolidinone resistance genes, including cfr, cfr(B), cfr(C), cfr(D), cfr(E), optrA, and poxtA, have been identified to date. The cfr genes code for 23S rRNA methylases, which confer a multiresistance phenotype that includes resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds. The optrA and poxtA genes code for ABC-F proteins that protect the bacterial ribosomes from the inhibitory effects of oxazolidinones. The optrA gene confers resistance to oxazolidinones and phenicols, while the poxtA gene confers elevated MICs or resistance to oxazolidinones, phenicols, and tetracycline. These oxazolidinone resistance genes are most frequently found on plasmids, but they are also located on transposons, integrative and conjugative elements (ICEs), genomic islands, and prophages. In these mobile genetic elements (MGEs), insertion sequences (IS) most often flanked the cfr, optrA, and poxtA genes and were able to generate translocatable units (TUs) that comprise the oxazolidinone resistance genes and occasionally also other genes. MGEs and TUs play an important role in the dissemination of oxazolidinone resistance genes across strain, species, and genus boundaries. Most frequently, these MGEs also harbor genes that mediate resistance not only to antimicrobial agents of other classes, but also to metals and biocides. Direct selection pressure by the use of antimicrobial agents to which the oxazolidinone resistance genes confer resistance, but also indirect selection pressure by the use of antimicrobial agents, metals, or biocides (the respective resistance genes against which are colocated on cfr-, optrA-, or poxtA-carrying MGEs) may play a role in the coselection and persistence of oxazolidinone resistance genes.
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Abstract
Florfenicol is widely used for the treatment of respiratory infections and as a feed additive in food animal production. As a foodborne pathogen, Campylobacter is constantly exposed to florfenicol, and resistance to this antimicrobial agent has increased in recent years. Previous studies indicated that Campylobacter has developed several mechanisms that confer resistance to florfenicol, which is used in food animal production. This study describes the coexistence of optrA and fexA in Campylobacter jejuni and Campylobacter coli isolates from pigs and poultry. Moreover, whole-genome sequencing data showed that the two genes are located in various multidrug resistance genomic islands within different regions of the Campylobacter genomes. The emergence of optrA and fexA may support the spread of florfenicol-resistant Campylobacter strains of animal origin. IMPORTANCE Florfenicol is widely used for the treatment of respiratory infections and as a feed additive in food animal production. As a foodborne pathogen, Campylobacter is constantly exposed to florfenicol, and resistance to this antimicrobial agent has increased in recent years. Previous studies indicated that Campylobacter has developed several mechanisms that confer resistance to florfenicol. This study describes for the first time the coexistence of the florfenicol exporter FexA and the ribosomal protective protein OptrA in Campylobacter jejuni isolated from pigs. The two genes were located in various multidrug resistance genomic islands within different regions of the Campylobacter genomes. Although phenicols are not commonly used for the treatment of Campylobacter infections, the extensive use of florfenicol in food animals may play a role in the coselection of multidrug resistance genomic island (MDRGI)-carrying Campylobacter isolates which also exhibited resistance to critically important antimicrobial agents (macrolides, aminoglycosides, and tetracyclines) commonly used for the treatment of human campylobacteriosis.
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Linezolid Resistance Genes in Enterococci Isolated from Sediment and Zooplankton in Two Italian Coastal Areas. Appl Environ Microbiol 2021; 87:AEM.02958-20. [PMID: 33608287 DOI: 10.1128/aem.02958-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/08/2021] [Indexed: 12/19/2022] Open
Abstract
Linezolid is a last-resort antibiotic for the treatment of severe infections caused by multidrug-resistant Gram-positive organisms; although linezolid resistance remains uncommon, the number of linezolid-resistant enterococci has increased in recent years due to worldwide spread of acquired resistance genes (cfr, optrA, and poxtA) in clinical, animal, and environmental settings. In this study, we investigated the occurrence of linezolid-resistant enterococci in marine samples from two coastal areas in Italy. Isolates grown on florfenicol-supplemented Slanetz-Bartley agar plates were investigated for their carriage of optrA, poxtA, and cfr genes; optrA was found in one Enterococcus faecalis isolate, poxtA was found in three Enterococcus faecium isolates and two Enterococcus hirae isolates, and cfr was not found. Two of the three poxtA-carrying E. faecium isolates and the two E. hirae isolates showed related pulsed-field gel electrophoresis (PFGE) profiles. Two E. faecium isolates belonged to the new sequence type 1710, which clustered in clonal complex 94, encompassing nosocomial strains. S1 PFGE/hybridization assays showed a double (chromosome and plasmid) location of poxtA and a plasmid location of optrA Whole-genome sequencing revealed that poxtA was contained in a Tn6657-like element carried by two plasmids (pEfm-EF3 and pEh-GE2) of similar size, found in different species, and that poxtA was flanked by two copies of IS1216 in both plasmids. In mating experiments, all but one strain (E. faecalis EN3) were able to transfer the poxtA gene to E. faecium 64/3. The occurrence of linezolid resistance genes in enterococci from marine samples is of great concern and highlights the need to improve practices aimed at limiting the transmission of linezolid-resistant strains to humans from environmental reservoirs.IMPORTANCE Linezolid is one of the few antimicrobials available to treat severe infections due to drug-resistant Gram-positive bacteria; therefore, the emergence of linezolid-resistant enterococci carrying transferable resistance determinants is of great concern for public health. Linezolid resistance genes (cfr, optrA, and poxtA), often plasmid located, can be transmitted via horizontal gene transfer and have the potential to spread globally. This study highlights the detection of enterococci carrying linezolid resistance genes from sediment and zooplankton samples from two coastal urban areas in Italy. The presence of clinically relevant resistant bacteria, such as linezolid-resistant enterococci, in marine environments could reflect their spillover from human and/or animal reservoirs and could indicate that coastal seawaters also might represent a source of these resistance genes.
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The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2018/2019. EFSA J 2021; 19:e06490. [PMID: 33868492 PMCID: PMC8040295 DOI: 10.2903/j.efsa.2021.6490] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Data on antimicrobial resistance (AMR) in zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs), jointly analysed by the EFSA and the ECDC and reported in a yearly EU Summary Report. The annual monitoring of AMR in animals and food within the EU is targeted at selected animal species corresponding to the reporting year. The 2018 monitoring specifically focussed on poultry and their derived carcases/meat, while the monitoring performed in 2019 specifically focused on pigs and calves under 1 year of age, as well as their derived carcases/meat. Monitoring and reporting of AMR in 2018/2019 included data regarding Salmonella, Campylobacter and indicator Escherichia coli isolates, as well as data obtained from the specific monitoring of presumptive ESBL-/AmpC-/carbapenemase-producing E. coli isolates. Additionally, some MSs reported voluntary data on the occurrence of meticillin-resistant Staphylococcus aureus in animals and food, with some countries also providing data on antimicrobial susceptibility. This report provides an overview of the main findings of the 2018/2019 harmonised AMR monitoring in the main food-producing animal populations monitored, in related carcase/meat samples and in humans. Where available, data monitoring obtained from pigs, calves, broilers, laying hens and turkeys, as well as from carcase/meat samples and humans were combined and compared at the EU level, with particular emphasis on multidrug resistance, complete susceptibility and combined resistance patterns to critically important antimicrobials, as well as Salmonella and E. coli isolates possessing ESBL-/AmpC-/carbapenemase phenotypes. The outcome indicators for AMR in food-producing animals such as complete susceptibility to the harmonised panel of antimicrobials in E. coli and the prevalence of ESBL-/AmpC-producing E. coli have been also specifically analysed over the period 2015-2019.
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Truccollo B, Whyte P, Burgess C, Bolton D. Genetic characterisation of a subset of Campylobacter jejuni isolates from clinical and poultry sources in Ireland. PLoS One 2021; 16:e0246843. [PMID: 33690659 PMCID: PMC7943001 DOI: 10.1371/journal.pone.0246843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/26/2021] [Indexed: 01/09/2023] Open
Abstract
Campylobacter spp. is a significant and prevalent public health hazard globally. Campylobacter jejuni is the most frequently recovered species from human cases and poultry are considered the most important reservoir for its transmission to humans. In this study, 30 Campylobacter jejuni isolates were selected from clinical (n = 15) and broiler (n = 15) sources from a larger cohort, based on source, virulence, and antimicrobial resistance profiles. The objective of this study was to further characterise the genomes of these isolates including MLST types, population structure, pan-genome, as well as virulence and antimicrobial resistance determinants. A total of 18 sequence types and 12 clonal complexes were identified. The most common clonal complex was ST-45, which was found in both clinical and broiler samples. We characterised the biological functions that were associated with the core and accessory genomes of the isolates in this study. No significant difference in the prevalence of virulence or antimicrobial resistance determinants was observed between clinical and broiler isolates, although genes associated with severe illness such as neuABC, wlaN and cstIII were only detected in clinical isolates. The ubiquity of virulence factors associated with motility, invasion and cytolethal distending toxin (CDT) synthesis in both clinical and broiler C. jejuni genomes and genetic similarities between groups of broiler and clinical C. jejuni reaffirm that C. jejuni from poultry remains a significant threat to public health.
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Affiliation(s)
- Brendha Truccollo
- Food Safety Department, Teagasc Food Research Centre, Dublin, Republic of Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Republic of Ireland
| | - Paul Whyte
- School of Veterinary Medicine, University College Dublin, Dublin, Republic of Ireland
| | - Catherine Burgess
- Food Safety Department, Teagasc Food Research Centre, Dublin, Republic of Ireland
| | - Declan Bolton
- Food Safety Department, Teagasc Food Research Centre, Dublin, Republic of Ireland
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Abstract
Thermophilic Campylobacter, in particular Campylobacter jejuni, C. coli and C. lari are the main relevant Campylobacter species for human infections. Due to their high capacity of genetic exchange by horizontal gene transfer (HGT), rapid adaptation to changing environmental and host conditions contribute to successful spreading and persistence of these foodborne pathogens. However, extensive HGT can exert dangerous side effects for the bacterium, such as the incorporation of gene fragments leading to disturbed gene functions. Here we discuss mechanisms of HGT, notably natural transformation, conjugation and bacteriophage transduction and limiting regulatory strategies of gene transfer. In particular, we summarize the current knowledge on how the DNA macromolecule is exchanged between single cells. Mechanisms to stimulate and to limit HGT obviously coevolved and maintained an optimal balance. Chromosomal rearrangements and incorporation of harmful mutations are risk factors for survival and can result in drastic loss of fitness. In Campylobacter, the restricted recognition and preferential uptake of free DNA from relatives are mediated by a short methylated DNA pattern and not by a classical DNA uptake sequence as found in other bacteria. A class two CRISPR-Cas system is present but also other DNases and restriction-modification systems appear to be important for Campylobacter genome integrity. Several lytic and integrated bacteriophages have been identified, which contribute to genome diversity. Furthermore, we focus on the impact of gene transfer on the spread of antibiotic resistance genes (resistome) and persistence factors. We discuss remaining open questions in the HGT field, supposed to be answered in the future by current technologies like whole-genome sequencing and single-cell approaches.
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Affiliation(s)
- Julia Carolin Golz
- Department of Biological Safety, National Reference Laboratory for Campylobacter, German Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Kerstin Stingl
- Department of Biological Safety, National Reference Laboratory for Campylobacter, German Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, 12277, Berlin, Germany.
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30
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Fioriti S, Morroni G, Coccitto SN, Brenciani A, Antonelli A, Di Pilato V, Baccani I, Pollini S, Cucco L, Morelli A, Paniccià M, Magistrali CF, Rossolini GM, Giovanetti E. Detection of Oxazolidinone Resistance Genes and Characterization of Genetic Environments in Enterococci of Swine Origin, Italy. Microorganisms 2020; 8:E2021. [PMID: 33348682 PMCID: PMC7766396 DOI: 10.3390/microorganisms8122021] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 11/16/2022] Open
Abstract
One hundred forty-five florfenicol-resistant enterococci, isolated from swine fecal samples collected from 76 pig farms, were investigated for the presence of optrA, cfr, and poxtA genes by PCR. Thirty florfenicol-resistant Enterococcus isolates had at least one linezolid resistance gene. optrA was found to be the most widespread linezolid resistance gene (23/30), while cfr and poxtA were detected in 6/30 and 7/30 enterococcal isolates, respectively. WGS analysis also showed the presence of the cfr(D) gene in Enterococcus faecalis (n = 2 isolates) and in Enterococcus avium (n = 1 isolate). The linezolid resistance genes hybridized both on chromosome and plasmids ranging from ~25 to ~240 kb. Twelve isolates were able to transfer linezolid resistance genes to enterococci recipient. WGS analysis displayed a great variability of optrA genetic contexts identical or related to transposons (Tn6628 and Tn6674), plasmids (pE035 and pWo27-9), and chromosomal regions. cfr environments showed identities with Tn6644-like transposon and a region from p12-2300 plasmid; cfr(D) genetic contexts were related to the corresponding region of the plasmid 4 of Enterococcus faecium E8014; poxtA was always found on Tn6657. Circular forms were obtained only for optrA- and poxtA-carrying genetic contexts. Clonality analysis revealed the presence of E. faecalis (ST16, ST27, ST476, and ST585) and E. faecium (ST21) clones previously isolated from humans. These results demonstrate a dissemination of linezolid resistance genes in enterococci of swine origin in Central Italy and confirm the spread of linezolid resistance in animal settings.
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Affiliation(s)
- Simona Fioriti
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy; (S.F.); (G.M.); (S.N.C.)
| | - Gianluca Morroni
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy; (S.F.); (G.M.); (S.N.C.)
| | - Sonia Nina Coccitto
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy; (S.F.); (G.M.); (S.N.C.)
| | - Andrea Brenciani
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy; (S.F.); (G.M.); (S.N.C.)
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Florence, Italy; (A.A.); (I.B.); (S.P.); (G.M.R.)
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50139 Florence, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, 16126 Genoa, Italy;
| | - Ilaria Baccani
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Florence, Italy; (A.A.); (I.B.); (S.P.); (G.M.R.)
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Florence, Italy; (A.A.); (I.B.); (S.P.); (G.M.R.)
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50139 Florence, Italy
| | - Lucilla Cucco
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, 06126 Perugia, Italy; (L.C.); (A.M.); (M.P.); (C.F.M.)
| | - Alessandra Morelli
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, 06126 Perugia, Italy; (L.C.); (A.M.); (M.P.); (C.F.M.)
| | - Marta Paniccià
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, 06126 Perugia, Italy; (L.C.); (A.M.); (M.P.); (C.F.M.)
| | - Chiara Francesca Magistrali
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, 06126 Perugia, Italy; (L.C.); (A.M.); (M.P.); (C.F.M.)
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Florence, Italy; (A.A.); (I.B.); (S.P.); (G.M.R.)
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50139 Florence, Italy
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60121 Ancona, Italy;
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Emergence of a Novel tet(L) Variant in Campylobacter spp. of Chicken Origin in China. Antimicrob Agents Chemother 2020; 65:AAC.01622-20. [PMID: 33046498 DOI: 10.1128/aac.01622-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/06/2020] [Indexed: 12/30/2022] Open
Abstract
Tetracyclines are widely used in veterinary medicine and food animal production. Campylobacter members are major foodborne pathogens, and their resistance to tetracycline has been widely reported in different countries. To date, Tet(O), a ribosomal protection protein, is the only confirmed Tet resistance determinant in Campylobacter spp. Here, we reported the detection and characterization of a novel Tet resistance element in Campylobacter spp. of chicken origin. This gene is identified to be a variant of tet(L), which encodes an efflux pump for Tet resistance. The variant was detected in 14 of the 82 tetracycline-resistant Campylobacter isolates collected from chickens in Henan, China. Cloning of the tet(L) variant into tetracycline-susceptible Campylobacter jejuni NCTC 11168 confirmed its function in conferring resistance to tetracycline and doxycycline. In addition, this tet(L) variant elevated the MIC (4-fold increase) of tigecycline in the heterologous Escherichia coli host. Sequencing analysis indicated the tet(L) variant was located within a multidrug-resistance genomic island (MDRGI) containing tet(L) variant IS1216E-ORF1-fexA-Δtnp-IS1216E-tet(O)-tnpV-repA This MDRGI is inserted into conserved gene potB on the chromosome. Multilocus sequence type (MLST) analysis revealed that both clonal expansion and horizontal transfer were involved in the dissemination of the tet(L) variant. These findings reveal the emergence of a new Tet resistance determinant in Campylobacter spp., which may facilitate their adaptation to the antimicrobial selection pressure in chickens.
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32
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Skarżyńska M, Leekitcharoenphon P, Hendriksen RS, Aarestrup FM, Wasyl D. A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more. PLoS One 2020; 15:e0242987. [PMID: 33270717 PMCID: PMC7714112 DOI: 10.1371/journal.pone.0242987] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is a complex subject, why one need to look at this phenomenon from a wider and holistic perspective. The extensive use of the same antimicrobial classes in human and veterinary medicine as well as horticulture is one of the main drivers for the AMR selection. Here, we applied shotgun metagenomics to investigate the AMR epidemiology in several animal species including farm animals, which are often exposed to antimicrobial treatment opposed to an unique set of wild animals that seems not to be subjected to antimicrobial pressure. The comparison of the domestic and wild animals allowed to investigate the possible anthropogenic impact on AMR spread. Inclusion of animals with different feeding behaviors (carnivores, omnivores) enabled to further assess which AMR genes that thrives within the food chain. We tested fecal samples not only of intensively produced chickens, turkeys, and pigs, but also of wild animals such as wild boars, red foxes, and rodents. A multi-directional approach mapping obtained sequences to several databases provided insight into the occurrence of the different AMR genes. The method applied enabled also analysis of other factors that may influence AMR of intestinal microbiome such as diet. Our findings confirmed higher levels of AMR in farm animals than in wildlife. The results also revealed the potential of wildlife in the AMR dissemination. Particularly in red foxes, we found evidence of several AMR genes conferring resistance to critically important antimicrobials like quinolones and cephalosporins. In contrast, the lowest abundance of AMR was observed in rodents originating from natural environment with presumed limited exposure to antimicrobials. Shotgun metagenomics enabled us to demonstrate that discrepancies between AMR profiles found in the intestinal microbiome of various animals probably resulted from the different antimicrobial exposure, habitats, and behavior of the tested animal species.
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Affiliation(s)
- Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
- * E-mail:
| | - Pimlapas Leekitcharoenphon
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens, Food and Agriculture Organization Reference Laboratory for Antimicrobial Resistance, and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rene S. Hendriksen
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens, Food and Agriculture Organization Reference Laboratory for Antimicrobial Resistance, and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens, Food and Agriculture Organization Reference Laboratory for Antimicrobial Resistance, and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
- Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
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Kreling V, Falcone FH, Kehrenberg C, Hensel A. Campylobacter sp.: Pathogenicity factors and prevention methods-new molecular targets for innovative antivirulence drugs? Appl Microbiol Biotechnol 2020; 104:10409-10436. [PMID: 33185702 PMCID: PMC7662028 DOI: 10.1007/s00253-020-10974-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 08/24/2020] [Accepted: 10/21/2020] [Indexed: 02/08/2023]
Abstract
Infections caused by bacterial species from the genus Campylobacter are one of the four main causes of strong diarrheal enteritis worldwide. Campylobacteriosis, a typical food-borne disease, can range from mild symptoms to fatal illness. About 550 million people worldwide suffer from campylobacteriosis and lethality is about 33 million p.a. This review summarizes the state of the current knowledge on Campylobacter with focus on its specific virulence factors. Using this knowledge, multifactorial prevention strategies can be implemented to reduce the prevalence of Campylobacter in the food chain. In particular, antiadhesive strategies with specific adhesion inhibitors seem to be a promising concept for reducing Campylobacter bacterial load in poultry production. Antivirulence compounds against bacterial adhesion to and/or invasion into the host cells can open new fields for innovative antibacterial agents. Influencing chemotaxis, biofilm formation, quorum sensing, secretion systems, or toxins by specific inhibitors can help to reduce virulence of the bacterium. In addition, the unusual glycosylation of the bacterium, being a prerequisite for effective phase variation and adaption to different hosts, is yet an unexplored target for combating Campylobacter sp. Plant extracts are widely used remedies in developing countries to combat infections with Campylobacter. Therefore, the present review summarizes the use of natural products against the bacterium in an attempt to stimulate innovative research concepts on the manifold still open questions behind Campylobacter towards improved treatment and sanitation of animal vectors, treatment of infected patients, and new strategies for prevention. KEY POINTS: • Campylobacter sp. is a main cause of strong enteritis worldwide. • Main virulence factors: cytolethal distending toxin, adhesion proteins, invasion machinery. • Strong need for development of antivirulence compounds.
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Affiliation(s)
- Vanessa Kreling
- Institute of Pharmaceutical Biology and Phytochemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany
| | - Franco H Falcone
- Institute of Parasitology, University of Gießen, Schubertstraße 81, 35392, Gießen, Germany
| | - Corinna Kehrenberg
- Institute of Veterinary Food Science, University of Gießen, Frankfurterstraße 81, 35392, Gießen, Germany
| | - Andreas Hensel
- Institute of Pharmaceutical Biology and Phytochemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany.
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Tang Y, Lai Y, Wang X, Lei C, Li C, Kong L, Wang Y, Wang H. Novel insertion sequence ISChh1-like mediating acquisition of optrA gene in foodborne pathogen Campylobacter coli of swine origin. Vet Microbiol 2020; 252:108934. [PMID: 33249367 DOI: 10.1016/j.vetmic.2020.108934] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
The optrA gene encodes an ABC-F protein which confers cross-resistance to oxazolidinones and phenicols, and its transmission has so far been associated with multiple transposable elements, including IS1216E, prophages, ICEs and Tn558. Here, we identified an optrA gene flanked by two copies of a novel insertion sequence ISChh1-like in the same direction in Campylobacter coli. Seven optrA-positive C. coli were identified from 263 Campylobacter isolates obtained from one swine farm and two slaughterhouses in Sichuan province of China. The optrA genes in 6 isolates were directly flanked by two copies of ISChh1-like elements in the same orientation, in the remaining one isolate, optrA was co-located with fexA and flanked by two copies of IS1216E and inserted in the downstream of the aadE-sat4-aphA3 gene cluster on chromosome. Cloning of optrA into C. jejuni NCTC 11,168 confirmed its role in elevated MICs to oxazolidinones and phenicols. Translocatable units (TUs) and natural transformants were only detected from the isolate with optrA bracketed by IS1216E, not from these with optrA bracketed by ISChh1-like. ISChh1-like in all isolates inserts specifically either next to or between adjacent GG nucleotides, neither have terminal inverted repeats nor generate target site duplications. Interestingly, ISChh1-like were also found mediating integration of other antibiotic resistance genes in Campylobacter, including tet(O), aphA3 and aadE-sat4-aphA3 gene cluster. Taken together, these results identify ISChh1-like as a novel transposon mediating acquisition of multiple antibiotic resistance genes in Campylobacter, including the very important optrA gene, suggesting that it plays an essential role in the transmission of antibiotic resistance genes to Campylobacter.
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Affiliation(s)
- Yizhi Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Yan Lai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Xingyuan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Changwei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Chao Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Linghan Kong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Yulong Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, 610064, People's Republic of China.
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Liu D, Li X, Liu W, Yao H, Liu Z, Feßler AT, He J, Zhou Y, Shen Z, Wu Z, Schwarz S, Zhang Q, Wang Y. Characterization of multiresistance gene cfr(C) variants in Campylobacter from China. J Antimicrob Chemother 2020; 74:2166-2170. [PMID: 31081013 DOI: 10.1093/jac/dkz197] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/26/2019] [Accepted: 04/08/2019] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES To investigate the occurrence, the genetic environment and the functionality of novel variants of the MDR gene cfr(C) in Campylobacter from China. METHODS A total of 370 Campylobacter isolates of porcine and chicken origin collected from three regions of China in 2015 were screened for cfr(C) by PCR. The phenotypes and genotypes of cfr(C)-positive isolates were investigated by antimicrobial susceptibility testing, PFGE, MLST, S1-PFGE, Southern blotting and WGS. Quantitative RT-PCR was used to compare the expression levels of the cfr(C) variants in their original isolate and clone constructs in Campylobacter jejuni NCTC 11168. RESULTS Four (1.1%) porcine Campylobacter coli isolates were positive for cfr(C). They failed to show elevated MICs of phenicols. The deduced Cfr(C) sequences identified exhibited 2-6 amino acid changes compared with the original Cfr(C) reported in the USA. Cloning of the cfr(C) variant genes into C. jejuni NCTC 11168 resulted in ≥32-fold increases in the MICs of phenicols, indicating that the cfr(C) variant genes are functional. The cfr(C)-carrying isolates belonged to three genotypes and WGS analysis revealed the cfr(C) genes were chromosomally located in MDR genomic islands, which contained multiple antibiotic resistance genes of Gram-positive origin. CONCLUSIONS This study identified chromosomal cfr(C) genes in C. coli isolates from China. They appeared functionally dormant in the original isolates but were fully functional when cloned and expressed in C. jejuni. The cfr(C) genes were co-transferred with other antibiotic resistance genes, possibly from Gram-positive bacteria. These findings reveal new insights into the function and transmission of cfr(C) in Campylobacter.
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Affiliation(s)
- Dejun Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,The State Key Laboratory of Agro-Biotechnology, College of Biological Science, China Agricultural University, Beijing, China
| | - Xing Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Weiwen Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hong Yao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhihai Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Junjia He
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yuqing Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zuowei Wu
- College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Stefan Schwarz
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Qijing Zhang
- College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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Cheng C, Ying Y, Zhou D, Zhu L, Lu J, Li A, Bao Q, Zhu M. RamA, a transcriptional regulator conferring florfenicol resistance in Leclercia adecarboxylata R25. Folia Microbiol (Praha) 2020; 65:1051-1060. [PMID: 32857336 PMCID: PMC7716942 DOI: 10.1007/s12223-020-00816-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 08/19/2020] [Indexed: 12/11/2022]
Abstract
Due to the inappropriate use of florfenicol in agricultural practice, florfenicol resistance has become increasingly serious. In this work, we studied the novel florfenicol resistance mechanism of an animal-derived Leclercia adecarboxylata strain R25 with high-level florfenicol resistance. A random genomic DNA library was constructed to screen the novel florfenicol resistance gene. Gene cloning, gene knockout, and complementation combined with the minimum inhibitory concentration (MIC) detection were conducted to determine the function of the resistance-related gene. Sequencing and bioinformatics methods were applied to analyze the structure of the resistance gene-related sequences. Finally, we obtained a regulatory gene of an RND (resistance-nodulation-cell division) system, ramA, that confers resistance to florfenicol and other antibiotics. The ramA-deleted variant (LA-R25ΔramA) decreased the level of resistance against florfenicol and several other antibiotics, while a ramA-complemented strain (pUCP24-prom-ramA/LA-R25ΔramA) restored the drug resistance. The whole-genome sequencing revealed that there were five RND efflux pump genes (mdtABC, acrAB, acrD, acrEF, and acrAB-like) encoded over the chromosome, and ramA located upstream of the acrAB-like genes. The results of this work suggest that ramA confers resistance to florfenicol and other structurally unrelated antibiotics, presumably by regulating the RND efflux pump genes in L. adecarboxylata R25.
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Affiliation(s)
- Cong Cheng
- Vocational and Technical College, Lishui University, Lishui, 323000, China
| | - Yuanyuan Ying
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Taizhou, 317000, Zhejiang, China
| | - Danying Zhou
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Licheng Zhu
- Vocational and Technical College, Lishui University, Lishui, 323000, China
| | - Junwan Lu
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Taizhou, 317000, Zhejiang, China
| | - Aifang Li
- The Fifth Affiliated Hospital, Wenzhou Medical University, Lishui, 323000, Zhejiang, China
| | - Qiyu Bao
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Taizhou, 317000, Zhejiang, China
| | - Mei Zhu
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, 310013, Zhejiang, China.
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Campylobacter jejuni from Canine and Bovine Cases of Campylobacteriosis Express High Antimicrobial Resistance Rates against (Fluoro)quinolones and Tetracyclines. Pathogens 2020; 9:pathogens9090691. [PMID: 32842457 PMCID: PMC7558055 DOI: 10.3390/pathogens9090691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 11/17/2022] Open
Abstract
Campylobacter (C.) spp. from poultry is the main source of foodborne human campylobacteriosis, but diseased pets and cattle shedding Campylobacter spp. may contribute sporadically as a source of human infection. As fluoroquinolones are one of the drugs of choice for the treatment of severe human campylobacteriosis, the resistance rates of C. jejuni and C. coli from poultry against antibiotics, including fluoroquinolones, are monitored within the European program on antimicrobial resistance (AMR) in livestock. However, much less is published on the AMR rates of C.jejuni and C. coli from pets and cattle. Therefore, C. jejuni and C. coli isolated from diseased animals were tested phenotypically for AMR, and associated AMR genes or mutations were identified by whole genome sequencing. High rates of resistance to (fluoro)quinolones (41%) and tetracyclines (61.1%) were found in C. jejuni (n = 29/66). (Fluoro)quinolone resistance was associated with the known point mutation in the quinolone resistance-determining region (QRDR) of gyrA, and tetracycline resistance was mostly caused by the tet(O) gene. These high rates of resistance, especially to critically important antibiotics in C. jejuni and C. coli, are worrisome not only in veterinary medicine. Efforts to preserve the efficacy of important antimicrobial treatment options in human and veterinary medicine have to be strengthened in the future.
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Huang J, Wang M, Gao Y, Chen L, Wang L. Emergence of plasmid-mediated oxazolidinone resistance gene poxtA from CC17 Enterococcus faecium of pig origin. J Antimicrob Chemother 2020; 74:2524-2530. [PMID: 31236590 DOI: 10.1093/jac/dkz250] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 05/13/2019] [Accepted: 05/20/2019] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES To characterize the oxazolidinone resistance gene poxtA on broad-host-range Inc18 plasmids from CC17 Enterococcus faecium of pig origin. METHODS Oxazolidinone-resistant E. faecium isolates were screened for the presence of poxtA. The poxtA-carrying isolates were characterized by antimicrobial susceptibility testing, conjugation, S1-PFGE and hybridization. The poxtA-carrying plasmids were completely sequenced and their instability was verified. RESULTS Two individual CC17 E. faecium strains were positive for poxtA. S1-PFGE and hybridization revealed the presence of a poxtA-carrying plasmid of ∼62 kb in both WZ27-2 and the transconjugant, while poxtA-carrying plasmids of different sizes were observed in QF25-1 and the transconjugant. The two poxtA-carrying plasmids, pC25-1 and pC27-2, belonged to the broad-host-range plasmids of the Inc18 family and carried dfrG, aadE, Δsat4, aph(3')-III, erm(B), tet(M), tet(L) and fexB. Plasmid pC27-2 was virtually identical to pC25-1, with minor differences. The calculated transfer frequency was ∼0.87 × 10-8 and ∼1.03 × 10-7 per recipient to plasmids pC25-1 and pC27-2, respectively. Instability assays of the region with four adjacent IS1216Es, which forms three IS1216E translocatable units, revealed the formation of a series of mosaic circular intermediates. CONCLUSIONS We report the emergence of the plasmid-mediated oxazolidinone resistance gene poxtA in E. faecium from different farms in China. Comparison of the poxtA genetic context suggests that IS1216E elements play an important role in the dissemination of poxtA. The co-occurrence of poxtA with other antimicrobial and heavy metal resistance genes on the broad-host-range plasmids of the Inc18 family may lead to the co-selection of poxtA, contributing to its persistence and accelerating its dissemination.
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Affiliation(s)
- Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengli Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Gao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
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Li P, Yang Y, Ding L, Xu X, Lin D. Molecular Investigations of Linezolid Resistance in Enterococci OptrA Variants from a Hospital in Shanghai. Infect Drug Resist 2020; 13:2711-2716. [PMID: 32801805 PMCID: PMC7414921 DOI: 10.2147/idr.s251490] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/05/2020] [Indexed: 12/22/2022] Open
Abstract
Purpose The OptrA protein is a member of ATP-binding cassette (ABC) transporters, a transporter family which can confer resistance to oxazolidinone antibiotics by transferring plasmid. We aim to describe the distribution of optrA-harbored Enterococcus in Huashan hospital in 2017 and to address the effects of optrA mutations on the susceptibility of linezolid antibiotic drug. Methods Linezolid-resistance-related genes were tested for Enterococcus by polymerase chain reaction (PCR) and then sequenced for amino acid substitution site analysis. Broth microdilution and agar dilution test were applied to determine the minimal inhibitory concentration (MIC) of linezolid for Enterococcus containing optrA. Pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to evaluate the genotypes of optrA-positive isolates. To verify the functions of two main optrA variants, optrA over-expressing strains were constructed. Results Among 20 optrA-positive strains, only two were resistant to linezolid. No amino acid substitution existed in 23S rRNA V domain among Enterococcus faecalis. None had cfr, cfr(B) or cfr(C) genes. F101L and G4D/K/R or T150A were the main substitutions of ribosomal protein L4, L3, respectively. We found one Enterococcus faecium isolate co-contained optrA and poxtA and another E. faecalis isolate co-contained optrA and cfr(D), but they were not resistant to linezolid. Among 20 optrA-positive strains, ST-16 was the main type. Two main optrA variants KD (T112K, Y176D) and RDK (I104R, Y176D, E256K) slightly raised enterococci's MIC of linezolid. Conclusion OptrA exists in linezolid non-resistant enterococci with diverse amino acid substitutions. The variants play different roles in changing the MIC of linezolid.
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Affiliation(s)
- Pei Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Yang Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Li Ding
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Dongfang Lin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
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Genetic environments and related transposable elements of novel cfr(C) variants in Campylobacter coli isolates of swine origin. Vet Microbiol 2020; 247:108792. [DOI: 10.1016/j.vetmic.2020.108792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 01/05/2023]
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Emergence of fexA in Mediating Resistance to Florfenicols in Campylobacter. Antimicrob Agents Chemother 2020; 64:AAC.00260-20. [PMID: 32366706 PMCID: PMC7317992 DOI: 10.1128/aac.00260-20] [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] [Received: 02/09/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Florfenicol belongs to a class of phenicol antimicrobials widely used as feed additives and for the treatment of respiratory infections. In recent years, increasing resistance to florfenicol has been reported in Campylobacter spp., the leading foodborne enteric pathogens causing diarrheal diseases worldwide. Here, we reported the identification of fexA, a novel mobile florfenicol resistance gene in Campylobacter. Of the 100 Campylobacter jejuni strains isolated from poultry in Zhejiang, China, 9 were shown to be fexA positive, and their whole-genome sequences were further determined by integration of Illumina short-read and MinION long-read sequencing. Florfenicol belongs to a class of phenicol antimicrobials widely used as feed additives and for the treatment of respiratory infections. In recent years, increasing resistance to florfenicol has been reported in Campylobacter spp., the leading foodborne enteric pathogens causing diarrheal diseases worldwide. Here, we reported the identification of fexA, a novel mobile florfenicol resistance gene in Campylobacter. Of the 100 Campylobacter jejuni strains isolated from poultry in Zhejiang, China, 9 were shown to be fexA positive, and their whole-genome sequences were further determined by integration of Illumina short-read and MinION long-read sequencing. The fexA gene was found in the plasmid of one strain and chromosomes of eight strains, and its location was verified by S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern blotting. Based on comparative analysis, the fexA gene was located within a region with the tet(L)-fexA-catA-tet(O) gene arrangement, demonstrated to be successfully transferable among C. jejuni strains. Functional cloning indicated that acquisition of the single fexA gene significantly increased resistance to florfenicol, whereas its inactivation resulted in increased susceptibility to florfenicol in Campylobacter. Taken together, these results indicated that the emerging fexA resistance is horizontally transferable, which might greatly facilitate the adaptation of Campylobacter in food production environments where florfenicols are frequently used.
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Zhang L, Li Y, Shao Y, Hu Y, Lou H, Chen X, Wu Y, Mei L, Zhou B, Zhang X, Yao W, Fang L, Zhang Y. Molecular Characterization and Antibiotic Resistant Profiles of Campylobacter Species Isolated From Poultry and Diarrheal Patients in Southeastern China 2017-2019. Front Microbiol 2020; 11:1244. [PMID: 32655522 PMCID: PMC7324532 DOI: 10.3389/fmicb.2020.01244] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 05/15/2020] [Indexed: 01/02/2023] Open
Abstract
Campylobacter is a zoonotic pathogen that causes foodborne diarrheal illness globally. To better understand health risks in Southeastern China, Campylobacter spp. were surveyed in humans and representative poultry products over 3 years. One hundred and ninety-five representative isolates (n = 148, Campylobacter jejuni; n = 45, Campylobacter coli; n = 2 Campylobacter hyointestinalis) were examined for genetic relatedness and antimicrobial susceptibility. Nearly all Campylobacter isolates (99.0%, 193/195) were resistant to at least one class of antimicrobials, and 45.6% (89/195) of the isolates exhibited multidrug resistance. Genotypic analysis revealed high diversity among tested strains. Multilocus sequence typing (MLST) displayed 120 sequence types (STs) including 42 novel STs being added to the PubMLST international database. Sixty-two STs belonged to 16 previously characterized clonal complexes (CCs), of which CC-21, CC-45, CC-464, CC-574, CC-353, and CC-828 were most frequently identified. In addition, pulsed-field gel electrophoresis (PFGE) fingerprinting resulted in 66 PFGE SmaI patterns among the 125 isolates, with eight patterns shared between human and poultry sources. Subtyping data did not correlate with antimicrobial resistance phenotypes. Taken together, this large-scale surveillance study highlights high antimicrobial resistance and molecular features of Campylobacter isolates in Southeastern China.
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Affiliation(s)
- Leyi Zhang
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China
| | - Yi Li
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China
| | - Yongqiang Shao
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China
| | - Yuqin Hu
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China
| | - Huihuang Lou
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China
| | - Xiaonan Chen
- Ouhai Center for Disease Control and Prevention, Ouhai, China
| | - Yuejin Wu
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China
| | - Lingling Mei
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Biao Zhou
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | | | - Wenwu Yao
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Lei Fang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
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Genomic Epidemiology and Evolution of Diverse Lineages of Clinical Campylobacter jejuni Cocirculating in New Hampshire, USA, 2017. J Clin Microbiol 2020; 58:JCM.02070-19. [PMID: 32269101 PMCID: PMC7269400 DOI: 10.1128/jcm.02070-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/28/2020] [Indexed: 12/26/2022] Open
Abstract
Campylobacter jejuni is one of the leading causes of bacterial gastroenteritis worldwide. In the United States, New Hampshire was one of the 18 states that reported cases in the 2016 to 2018 multistate outbreak of multidrug-resistant C. jejuni. Here, we aimed to elucidate the baseline diversity of the wider New Hampshire C. jejuni population during the outbreak. We used genome sequences of 52 clinical isolates sampled in New Hampshire in 2017, including 1 of the 2 isolates from the outbreak. Campylobacter jejuni is one of the leading causes of bacterial gastroenteritis worldwide. In the United States, New Hampshire was one of the 18 states that reported cases in the 2016 to 2018 multistate outbreak of multidrug-resistant C. jejuni. Here, we aimed to elucidate the baseline diversity of the wider New Hampshire C. jejuni population during the outbreak. We used genome sequences of 52 clinical isolates sampled in New Hampshire in 2017, including 1 of the 2 isolates from the outbreak. Results revealed a remarkably diverse population composed of at least 28 sequence types, which are mostly represented by 1 or a few strains. A comparison of our isolates with 249 clinical C. jejuni from other states showed frequent phylogenetic intermingling, suggesting a lack of geographical structure and minimal local diversification within the state. Multiple independent acquisitions of resistance genes from 5 classes of antibiotics characterize the population, with 47/52 (90.4%) of the genomes carrying at least 1 horizontally acquired resistance gene. Frequently recombining genes include those associated with heptose biosynthesis, colonization, and stress resistance. We conclude that the diversity of clinical C. jejuni in New Hampshire in 2017 was driven mainly by the coexistence of phylogenetically diverse antibiotic-resistant lineages, widespread geographical mixing, and frequent recombination. This study provides an important baseline census of the standing pangenomic variation and drug resistance to aid the development of a statewide database for epidemiological studies and clinical decision making. Continued genomic surveillance will be necessary to accurately assess how the population of C. jejuni changes over the long term.
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Detection of the enterococcal oxazolidinone/phenicol resistance gene optrA in Campylobacter coli. Vet Microbiol 2020; 246:108731. [PMID: 32605743 DOI: 10.1016/j.vetmic.2020.108731] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/12/2020] [Accepted: 05/19/2020] [Indexed: 11/22/2022]
Abstract
The transferable optrA gene encodes an ABC-F protein which confers resistance to oxazolidinones and phenicols, and has so far been detected exclusively in Gram-positive bacteria, including enterococci, staphylococci and streptococci. Here, we identified for the first time the presence of optrA in naturally occurring Gram-negative bacteria. Seven optrA-positive Campylobacter coli were identified from 563 Campylobacter isolates of animal origin from Guangdong (n = 1, chicken) and Shandong (n = 6, duck) provinces of China in 2017-2018. The detected optrA genes were functionally active and mediated resistance or elevated minimal inhibitory concentrations of linezolid, florfenicol and chloramphenicol in the respective C. coli isolates. The optrA gene, together with other transferable resistance genes, such as fexA, catA9, tet(O), tet(L), erm(A)-like, spc, or aadE, was located in two different chromosome-borne multidrug resistance genomic islands (MDRGIs). In both MDRGIs, complete or truncated copies of the insertion sequence IS1216E were present in the vicinity of optrA. The IS1216E-bracketed genetic environment of optrA was almost identical to the optrA regions on enterococcal plasmids, suggesting that the optrA in Campylobacter probably originated from Enterococcus spp.. Moreover, the formation of an optrA-carrying translocatable unit by recombination of IS1216E indicated that this IS element may play an important role in the horizontal transfer of optrA in Campylobacter. Although optrA was only found in a small number of C. coli isolates, enhanced surveillance is needed to monitor the distribution and the potential emergence of optrA in Campylobacter.
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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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Guerin F, Sassi M, Dejoies L, Zouari A, Schutz S, Potrel S, Auzou M, Collet A, Lecointe D, Auger G, Cattoir V. Molecular and functional analysis of the novel cfr(D) linezolid resistance gene identified in Enterococcus faecium. J Antimicrob Chemother 2020; 75:1699-1703. [DOI: 10.1093/jac/dkaa125] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/08/2020] [Accepted: 03/10/2020] [Indexed: 12/17/2022] Open
Abstract
Abstract
Objectives
To characterize the novel cfr(D) gene identified in an Enterococcus faecium clinical isolate (15-307.1) collected from France.
Methods
The genome of 15-307.1 was entirely sequenced using a hybrid approach combining short-read (MiSeq, Illumina) and long-read (GridION, Oxford Nanopore Technologies) technologies in order to analyse in detail the genetic support and environment of cfr(D). Transfer of linezolid resistance from 15-307.1 to E. faecium BM4107 was attempted by filter-mating experiments. The recombinant plasmid pAT29Ωcfr(D), containing cfr(D) and its own promoter, was transferred to E. faecium HM1070, Enterococcus faecalis JH2-2 and Escherichia coli AG100A.
Results
As previously reported, 15-307.1 belonged to ST17 and was phenotypically resistant to linezolid (MIC, 16 mg/L), vancomycin and teicoplanin. A hybrid sequencing approach confirmed the presence of several resistance genes including vanA, optrA and cfr(D). Located on a 103 kb plasmid, cfr(D) encoded a 357 amino acid protein, which shared 64%, 64%, 48% and 51% amino acid identity with Cfr, Cfr(B), Cfr(C) and Cfr(E), respectively. Both optrA and cfr(D) were successfully co-transferred to E. faecium BM4107. When expressed in E. faecium HM1070 and E. faecalis JH2-2, pAT29Ωcfr(D) did not confer any resistance, whereas it was responsible for an expected PhLOPSA resistance phenotype in E. coli AG100A. Analysis of the genetic environment of cfr(D) showed multiple IS1216 elements, putatively involved in its mobilization.
Conclusions
Cfr(D) is a novel member of the family of 23S rRNA methyltransferases. While only conferring a PhLOPSA resistance phenotype when expressed in E. coli, enterococci could constitute an unknown reservoir of cfr(D).
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Affiliation(s)
- François Guerin
- CHU de Caen, Service de Microbiologie, Caen, France
- Université de Caen Normandie, EA4655 Caen, France
| | - Mohamed Sassi
- Université de Rennes 1, Inserm U1230, Rennes, France
| | - Loren Dejoies
- Université de Rennes 1, Inserm U1230, Rennes, France
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
| | - Asma Zouari
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
- CNR de la Résistance aux Antibiotiques (laboratoire associé ‘Entérocoques’), Rennes, France
| | - Sacha Schutz
- CHU de Rennes, Service de Génétique moléculaire et Génomique médicale, Rennes, France
| | - Sophie Potrel
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
- CNR de la Résistance aux Antibiotiques (laboratoire associé ‘Entérocoques’), Rennes, France
| | - Michel Auzou
- CHU de Caen, Service de Microbiologie, Caen, France
| | - Anaïs Collet
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
- CNR de la Résistance aux Antibiotiques (laboratoire associé ‘Entérocoques’), Rennes, France
| | - Didier Lecointe
- Unité Fonctionnelle d’Hygiène Hospitalière et de Lutte contre les Infections Nosocomiales, Centre Hospitalier Sud Francilien, Corbeil-Essonnes, France
| | - Gabriel Auger
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
- CNR de la Résistance aux Antibiotiques (laboratoire associé ‘Entérocoques’), Rennes, France
| | - Vincent Cattoir
- Université de Rennes 1, Inserm U1230, Rennes, France
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
- CNR de la Résistance aux Antibiotiques (laboratoire associé ‘Entérocoques’), Rennes, France
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The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2017/2018. EFSA J 2020; 18:e06007. [PMID: 32874244 PMCID: PMC7448042 DOI: 10.2903/j.efsa.2020.6007] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Data on antimicrobial resistance (AMR) in zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs), jointly analysed by EFSA and ECDC and reported in a yearly EU Summary Report. The annual monitoring of AMR in animals and food within the EU is targeted at selected animal species corresponding to the reporting year. The 2017 monitoring specifically focussed on pigs and calves under 1 year of age, as well as their derived carcases/meat, while the monitoring performed in 2018 specifically focussed on poultry and their derived carcases/meat. Monitoring and reporting of AMR in 2017/2018 included data regarding Salmonella, Campylobacter and indicator Escherichia coli isolates, as well as data obtained from the specific monitoring of ESBL-/AmpC-/carbapenemase-producing E. coli isolates. Additionally, some MSs reported voluntary data on the occurrence of meticillin-resistant Staphylococcus aureus in animals and food, with some countries also providing data on antimicrobial susceptibility. This report provides, for the first time, an overview of the main findings of the 2017/2018 harmonised AMR monitoring in the main food-producing animal populations monitored, in related carcase/meat samples and in humans. Where available, data monitoring obtained from pigs, calves/cattle, broilers, laying hens and turkeys, as well as from carcase/meat samples and humans were combined and compared at the EU level, with particular emphasis on multiple drug resistance, complete susceptibility and combined resistance patterns to critically important antimicrobials, as well as Salmonella and E. coli isolates exhibiting presumptive ESBL-/AmpC-/carbapenemase-producing phenotypes. The outcome indicators for AMR in food-producing animals, such as complete susceptibility to the harmonised panel of antimicrobials in E. coli and the prevalence of ESBL-/AmpC-producing E. coli have been also specifically analysed over the period 2014-2018.
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In Vitro Susceptibility and Florfenicol Resistance in Citrobacter Isolates and Whole-Genome Analysis of Multidrug-Resistant Citrobacter freundii. Int J Genomics 2019; 2019:7191935. [PMID: 31828082 PMCID: PMC6885840 DOI: 10.1155/2019/7191935] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/17/2019] [Indexed: 01/06/2023] Open
Abstract
The genus Citrobacter is an opportunistic pathogen causing infections in animals, and the published data for its resistance to florfenicol are scarce. In this study, we investigated the antimicrobial susceptibility and molecular characteristics of florfenicol resistance genes among Citrobacter isolates from animal and relevant environmental samples and conducted a comparative analysis of a multidrug-resistant Citrobacter freundii strain isolated from a rabbit. Among 20 Citrobacter strains isolated from animal samples, resistance was most commonly observed to ampicillin (100%), tetracycline (75%), streptomycin (65%), florfenicol (60%), chloramphenicol (60%), and aztreonam (50%), while all the strains found in environmental samples were resistant to few antibiotics. The florfenicol resistance gene floR was detected in 12 isolates (48%, 12/25) from animal samples, and all of the floR-positive isolates were resistant to florfenicol with minimum inhibitory concentration (MIC) values ≥256 μg/mL. Sequencing and comparative analysis of the plasmids from a multidrug-resistant C. freundii isolate named R47 showed that the floR-containing region in the plasmid pR47-54 was a truncated transposon-like structure and could be found on both plasmids and chromosomes of bacteria of either animal or human origin. Furthermore, a range of antimicrobial and metal resistance genes associated with mobile genetic elements could be identified in pR47-54 and the other plasmid pR47-309 of C. freundii R47. These results provide in-depth views into the phenotypic and molecular characteristics of Citrobacter isolates recovered from animal and relevant environmental samples, as well as highlight the role horizontal gene transfer plays in the dissemination of plasmid-encoded resistance genes.
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Comparative genomics analysis of Raoultella planticola S25 isolated from duck in China, with florfenicol resistance. Comp Immunol Microbiol Infect Dis 2019; 68:101398. [PMID: 31775114 DOI: 10.1016/j.cimid.2019.101398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/09/2019] [Accepted: 11/14/2019] [Indexed: 12/29/2022]
Abstract
To characterize the florfenicol resistance gene and analyze the structure of the resistance gene-related sequence of an Raoultella planticola strain S25 isolated from a duck fecal sample from a farm in South China. Molecular cloning was performed to clone the resistance genes such as mdfA, floR and so on, and the minimum inhibitory concentrations (MICs) were quantified to determine the resistance levels generated by the cloned genes and the related strains. Sequencing and comparative genomics methods were used to analyze the structure of the resistance gene-related sequence. The result showed that the genome of R. planticola S25 consists of a 5.47 Mb chromosome encoding 4962 predicted coding sequence (CDS) and a 68,566 bp plasmid, pS25-68, encoding 84 ORFs. The plasmid sharing the greatest sequence identity with the floR-carrying plasmid pS25-68 is plasmid1 in Klebsiella pneumoniae strain blaNDM-1, which was isolated from a patient in Canada. The mdfA1 gene encoded on the chromosome generated resistance to florfenicol in addition to chloramphenicol. Comparative genomic analysis of the floR-related transposon-like fragment of pS25-68 showed that an approximately 3 kb sequence encoding IS91-virD2-floR-lysR was conserved and presented in the majority of the sequences (84.5 %, 169/200) collected from the database. The results of this work demonstrated that horizontal transfer of the florfenicol resistance gene floR occurred widely between the bacteria of different species and with different origins and that additional florfenicol resistance genes may be present in the bacterial population.
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Analysis of combined resistance to oxazolidinones and phenicols among bacteria from dogs fed with raw meat/vegetables and the respective food items. Sci Rep 2019; 9:15500. [PMID: 31664106 PMCID: PMC6820769 DOI: 10.1038/s41598-019-51918-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/08/2019] [Indexed: 12/30/2022] Open
Abstract
The gene optrA is the first gene that confers resistance to the oxazolidinone tedizolid, a last resort antimicrobial agent in human medicine. In this study we investigated the presence of optrA and the multi-resistance genes poxtA and cfr in enterococci and staphylococci from (i) pet animals known to be fed raw meat and vegetables and (ii) the respective food items. We examined 341 bacterial isolates from cats and dogs, 195 bacterial isolates from supermarket food items and only one E. faecium collected from industrial food in Beijing during 2016. Thirty-five (6.5%) of the 537 isolates, including 31/376 (8.2%) enterococci and 4/161 (2.5%) staphylococci, were positive for optrA, while all isolates were negative for poxtA and cfr. S1-nuclease pulsed-field gel electrophoresis (PFGE) and Southern blotting confirmed that optrA was located in the chromosomal DNA of 19 isolates and on a plasmid in the remaining 16 isolates. Whole genome sequencing revealed several different genetic environments of optrA in plasmid- or chromosome-borne optrA genes. PFGE, multilocus sequence typing (MLST) and/or SNP analysis demonstrated that the optrA-carrying Staphylococcus and Enterococcus isolates were genetically heterogeneous. However, in single cases, groups of related isolates were identified which might suggest a transfer of closely related optrA-positive E. faecalis isolates between food items and dogs.
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