1
|
Tsiklauri R, Gabashvili E, Kobakhidze S, Tabatadze L, Bobokhidze E, Dadiani K, Koulouris S, Kotetishvili M. In-silico analyses provide strong statistical evidence for intra-species recombination events of the gyrA and CmeABC operon loci contributing to the continued emergence of resistance to fluoroquinolones in natural populations of Campylobacter jejuni. J Glob Antimicrob Resist 2022; 31:22-31. [PMID: 35985623 DOI: 10.1016/j.jgar.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES The continued emergence of Campylobacter jejuni strains resistant to fluoroquinolones (FQs) has posed a significant threat to global public health, leading frequently to undesirable outcomes of human campylobacteriosis treatment. The molecular genetic mechanisms contributing to the increased retention of resistance to FQs in natural populations of this species, especially in antibiotic-free environments, are not clearly understood. This study aimed to determine whether genetic recombination could be such a mechanism. METHODS We applied a large array of algorithms, imbedded in the SplitsTree and RDP4 software packages, to analyse the DNA sequences of the chromosomal loci, including the gyrA gene and the CmeABC operon, to identify events of their genetic recombination between C. jejuni strains. RESULTS The SplitsTree analyses of the above genetic loci resulted in several parallelograms with the bootstrap values being in a range of 94.7 to 100, with the high fit estimates being 99.3 to 100. These analyses were further strongly supported by the Phi test results (P ≤ 0.02715) and the RDP4-generated statistics (P ≤ 0.04005). The recombined chromosomal regions, along with the gyrA gene and CmeABC operon loci, were also found to contain the genetic loci that included, but were not limited to, the genes encoding for phosphoribosyltransferase, lipoprotein, outer membrane motility protein, and radical SAM domain protein. CONCLUSION These findings strongly suggest that the genetic recombination of the chromosomal regions involving gyrA, CmeABC, and their adjacent loci may be an additional mechanism underlying the constant emergence of epidemiologically successful FQ-resistant strains in natural populations of C. jejuni.
Collapse
Affiliation(s)
- Rusudan Tsiklauri
- Faculty of Medicine, Iv. Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Ekaterine Gabashvili
- Bioinformatics Core, Scientific-Research Center of Agriculture, Tbilisi, Georgia
| | - Saba Kobakhidze
- Division of Risk Assessment, Scientific-Research Center of Agriculture, Tbilisi, Georgia
| | - Leila Tabatadze
- Division of Risk Assessment, Scientific-Research Center of Agriculture, Tbilisi, Georgia
| | - Ekaterine Bobokhidze
- Division of Risk Assessment, Scientific-Research Center of Agriculture, Tbilisi, Georgia
| | - Ketevan Dadiani
- Faculty of Medicine, Iv. Javakhishvili Tbilisi State University, Tbilisi, Georgia; G. Natadze Scientific-Research Institute of Sanitation, Hygiene and Medical Ecology, Tbilisi, Georgia
| | - Stylianos Koulouris
- European Commission, Directorate General for Health and Food Safety, Bruxelles/Brussel, Belgium
| | - Mamuka Kotetishvili
- G. Natadze Scientific-Research Institute of Sanitation, Hygiene and Medical Ecology, Tbilisi, Georgia; School of Science and Technology, Scientific Research Institute of the University of Georgia, Tbilisi, Georgia.
| |
Collapse
|
2
|
Virulence Comparison of Salmonella enterica Subsp. enterica Isolates from Chicken and Whole Genome Analysis of the High Virulent Strain S. Enteritidis 211. Microorganisms 2021; 9:microorganisms9112239. [PMID: 34835366 PMCID: PMC8619400 DOI: 10.3390/microorganisms9112239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 01/28/2023] Open
Abstract
Background: Salmonellaenterica is one of the common pathogens in both humans and animals that causes salmonellosis and threatens public health all over the world. Methods and Results: Here we determined the virulence phenotypes of nine Salmonellaenterica subsp. enterica (S. enterica) isolates in vitro and in vivo, including pathogenicity to chicken, cell infection, biofilm formation and virulence gene expressions. S. Enteritidis 211 (SE211) was highly pathogenic with notable virulence features among the nine isolates. The combination of multiple virulence genes contributed to the conferring of the high virulence in SE211. Importantly, many mobile genetic elements (MGEs) were found in the genome sequence of SE211, including a virulence plasmid, genomic islands, and prophage regions. The MGEs and CRISPR-Cas system might function synergistically for gene transfer and immune defense. In addition, the neighbor joining tree and the minimum spanning tree were constructed in this study. Conclusions: This study provided both the virulence phenotypes and genomic features, which might contribute to the understanding of bacterial virulence mechanisms in Salmonella enterica subsp. enterica. The first completed genomic sequence for the high virulent S. Enteritidis isolate SE211 and the comparative genomics and phylogenetic analyses provided a preliminary understanding of S. enterica genetics and laid the foundation for further study.
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Yang Y, Feye KM, Shi Z, Pavlidis HO, Kogut M, J. Ashworth A, Ricke SC. A Historical Review on Antibiotic Resistance of Foodborne Campylobacter. Front Microbiol 2019; 10:1509. [PMID: 31402900 PMCID: PMC6676416 DOI: 10.3389/fmicb.2019.01509] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 06/17/2019] [Indexed: 01/06/2023] Open
Abstract
Campylobacter is one of the most commonly reported foodborne human bacterial gastrointestinal pathogens. Campylobacter is the etiological agent of campylobacteriosis, which is generally a self-limited illness and therefore does not require treatment. However, when patients are immunocompromised or have other co-morbidities, antimicrobial treatment may be necessary for clinical treatment of campylobacteriosis, macrolides and fluoroquinolones are the drugs of choices. However, the increase in antimicrobial resistance of Campylobacter to clinically important antibiotics may become insurmountable. Because of the transmission between poultry and humans, the poultry industry must now allocate resources to address the problem by reducing Campylobacter as well as antimicrobial use, which may reduce resistance. This review will focus on the incidence of antibiotic-resistant Campylobacter in poultry, the clinical consequences of this resistance, and the mechanisms of antibiotic resistance associated with Campylobacter.
Collapse
Affiliation(s)
- Yichao Yang
- Department of Poultry Science, University of Arkansas Fayetteville, Fayetteville, AR, United States
| | - Kristina M. Feye
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
| | - Zhaohao Shi
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR, United States
| | | | - Michael Kogut
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
| | - Amanda J. Ashworth
- Poultry Production and Product Safety Research Unit (USDA-ARS), Fayetteville, AR, United States
| | - Steven C. Ricke
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
| |
Collapse
|
5
|
Fani F, Aminshahidi M, Firoozian N, Rafaatpour N. Prevalence, antimicrobial resistance, and virulence-associated genes of Campylobacter isolates from raw chicken meat in Shiraz, Iran. IRANIAN JOURNAL OF VETERINARY RESEARCH 2019; 20:283-288. [PMID: 32042293 PMCID: PMC6983316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/13/2019] [Accepted: 04/22/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Campylobacter is recognized as a major cause of foodborne gastroenteritis in humans in many countries and may be transferred from animals to humans. The consumption of chicken meat is identified as a major cause of Campylobacter infection in humans. AIMS To find out the contamination rate of chicken meat with Campylobacter, the antimicrobial resistance (AMR) pattern, and the virulence-associated genes of the isolates. METHODS Ninety packed chicken meat from 7 main poultry slaughterhouses in Shiraz were analyzed for Campylobacter spp. isolation through microbiological methods. Specific primers were used for the identification of the Campylobacter isolates on species level by polymerase chain reaction (PCR). Antibiotic resistant profiles were determined using the disc diffusion method based on Clinical and Laboratory Standards Institute (CLSI) standards. All the isolates were screened for 7 virulence-associated genes, namely cdtA, cdtB, cdtC, cadF, pldA, cgtB, and virB11 by PCR. RESULTS Out of 90 chicken meats, 26 (28.9%) Campylobacter spp. have been isolated. Resistance to ciprofloxacin (CIP), nalidixic acid (NA), and cefixime (CFM) was observed in all the isolates. Resistance to trimethoprim/sulfamethoxazole (SXT), tetracycline (TET), ampicillin (AMP), and chloramphenicol (CHO) was 80.8%, 88.5%, 76.9%, and 30.8%, respectively. Multidrug resistance (MDR) phenotype was observed in 80.8% of the Campylobacter isolates. All the isolates were positive for cdtA, cdtB, cdtC, and cadF genes. pldA and cgtB were detected in 65.4% and 15.4% of the isolates, respectively. CONCLUSION In this study, the presence of several virulence genes and an alarming level of MDR in Campylobacter spp. isolates were reported. Particularly, resistance to CIP and TET should be highlighted, since both are key drugs for the treatment of human campylobacteriosis.
Collapse
Affiliation(s)
- F. Fani
- Division of Bacteriology, Professor Alborzi Clinical Microbiology Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - M. Aminshahidi
- MSc in Microbiology, Division of Bacteriology, Professor Alborzi Clinical Microbiology Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - N. Firoozian
- MSc in Biotechnology, Division of Bacteriology, Professor Alborzi Clinical Microbiology Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - N. Rafaatpour
- BSc in Medical Technology, Division of Bacteriology, Professor Alborzi Clinical Microbiology Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
6
|
Shabbir MAB, Tang Y, Xu Z, Lin M, Cheng G, Dai M, Wang X, Liu Z, Yuan Z, Hao H. The Involvement of the Cas9 Gene in Virulence of Campylobacter jejuni. Front Cell Infect Microbiol 2018; 8:285. [PMID: 30177957 PMCID: PMC6109747 DOI: 10.3389/fcimb.2018.00285] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 07/26/2018] [Indexed: 12/28/2022] Open
Abstract
Campylobacter jejuni is considered as the leading cause of gastroenteritis all over the world. This bacterium has the CRISPR–cas9 system, which is used as a gene editing technique in different organisms. However, its role in bacterial virulence has just been discovered; that discovery, however, is just the tip of the iceberg. The purpose of this study is to find out the relationship between cas9 and virulence both phenotypically and genotypically in C. jejuni NCTC11168. Understanding both aspects of this relationship allows for a much deeper understanding of the mechanism of bacterial pathogenesis. The present study determined virulence in wild and mutant strains by observing biofilm formation, motility, adhesion and invasion, intracellular survivability, and cytotoxin production, followed by the transcriptomic analysis of both strains. The comparative gene expression profile of wild and mutant strains was determined on the basis of De-Seq transcriptomic analysis, which showed that the cas9 gene is involved in enhancing virulence. Differential gene expression analysis revealed that multiple pathways were involved in virulence, regulated by the CRISPR-cas9 system. Our findings help in understanding the potential role of cas9 in regulating the other virulence associated genes in C. jejuni NCTC11168. The findings of this study provide critical information about cas9's potential involvement in enhancing the virulence of C. jejuni, which is a major public health threat.
Collapse
Affiliation(s)
- Muhammad A B Shabbir
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Yanping Tang
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Zihui Xu
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Mingyue Lin
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Guyue Cheng
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Menghong Dai
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Xu Wang
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Zhengli Liu
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Zonghui Yuan
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China.,National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Haihong Hao
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China.,National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
7
|
Hussain HI, Iqbal Z, Seleem MN, Huang D, Sattar A, Hao H, Yuan Z. Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken. Sci Rep 2017; 7:8335. [PMID: 28827616 PMCID: PMC5567091 DOI: 10.1038/s41598-017-07798-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/03/2017] [Indexed: 02/01/2023] Open
Abstract
Numerous studies have examined the prevalence of pathogenic Escherichia coli in poultry and poultry products; however, limited data are available regarding their resistance- and virulence-associated gene expression profiles. This study was designed to examine the resistance and virulence of poultry E. coli strains in vitro and in vivo via antibiotic susceptibility, biofilm formation and adhesion, and invasion and intracellular survivability assays in Caco-2 and Raw 264.7 cell lines as well as the determination of the median lethal dose in two-day old chickens. A clinical pathogenic multidrug-resistant isolate, E. coli 381, isolated from broilers, was found to be highly virulent in cell culture and 1000-fold more virulent in a chicken model than other strains; accordingly, the isolate was subsequently selected for transcriptome analysis. The comparative gene expression profile of MDR E. coli 381 and the reference human strain E. coli ATCC 25922 was completed with Illumina HiSeq. 2500 transcriptome analysis. Differential gene expression analysis indicates that there are multiple pathways involved in the resistance and virulence of this highly virulent strain. The results garnered from this study provide critical information about the highly virulent MDR E. coli strain of poultry origin and warrant further investigation due to its significant threat to public health.
Collapse
Affiliation(s)
- Hafiz I Hussain
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Zahid Iqbal
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
- University College of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Deyu Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Adeel Sattar
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China.
| | - Zonghui Yuan
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China.
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China.
| |
Collapse
|