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Felix MA, Sopovski D, Commichaux S, Yoskowitz N, Aljahdali NH, Grim CJ, Abbott CN, Carlton A, Han J, Sanad YM, Zhao S, Wang X, Foley SL, Khajanchi BK. Genetic relatedness and virulence potential of Salmonella Schwarzengrund strains with or without an IncFIB-IncFIC(FII) fusion plasmid isolated from food and clinical sources. Front Microbiol 2024; 15:1397068. [PMID: 38827152 PMCID: PMC11143878 DOI: 10.3389/fmicb.2024.1397068] [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: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 06/04/2024] Open
Abstract
A total of 55 food and clinical S. Schwarzengrund isolates were assayed for plasmid content, among which an IncFIB-IncFIC(FII) fusion plasmid, conferring streptomycin resistance, was detected in 17 isolates. Among the 17 isolates, 9 were food isolates primarily collected from poultry meat, and 8 clinical isolates collected from stool, urine, and gallbladder. SNP-based phylogenetic analyses showed that the isolates carrying the fusion plasmid formed a subclade indicating the plasmid was acquired and is now maintained by the lineage. Phylogenetic analysis of the plasmid suggested it is derived from avian pathogenic plasmids and might confer an adaptive advantage to the S. Schwarzengrund isolates within birds. IncFIB-IncFIC(FII) fusion plasmids from all food and three clinical isolates were self-conjugative and successfully transferred into E. coli J53 by conjugation. Food and clinical isolates had similar virulome profiles and were able to invade human Caco-2 cells. However, the IncFIB-IncFIC(FII) plasmid did not significantly add to their invasion and persistence potential in human Caco-2 cells.
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Affiliation(s)
- Monique A. Felix
- National Center for Toxicological Research, U. S. Food and Drug Administration, Jefferson, AR, United States
- University of Arkansas at Pine Bluff, Pine Bluff, AR, United States
| | - Danielle Sopovski
- National Center for Toxicological Research, U. S. Food and Drug Administration, Jefferson, AR, United States
| | - Seth Commichaux
- Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Noah Yoskowitz
- National Center for Toxicological Research, U. S. Food and Drug Administration, Jefferson, AR, United States
| | - Nesreen H. Aljahdali
- National Center for Toxicological Research, U. S. Food and Drug Administration, Jefferson, AR, United States
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, MD, United States
| | - Carter N. Abbott
- National Center for Toxicological Research, U. S. Food and Drug Administration, Jefferson, AR, United States
| | - Ashlyn Carlton
- National Center for Toxicological Research, U. S. Food and Drug Administration, Jefferson, AR, United States
- University of Arkansas at Pine Bluff, Pine Bluff, AR, United States
| | - Jing Han
- National Center for Toxicological Research, U. S. Food and Drug Administration, Jefferson, AR, United States
| | - Yasser M. Sanad
- University of Arkansas at Pine Bluff, Pine Bluff, AR, United States
- Department of Epidemiology, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Shaohua Zhao
- Center for Veterinary Medicine, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Xiong Wang
- Minnesota Department of Health, St. Paul, MN, United States
| | - Steven L. Foley
- National Center for Toxicological Research, U. S. Food and Drug Administration, Jefferson, AR, United States
| | - Bijay K. Khajanchi
- National Center for Toxicological Research, U. S. Food and Drug Administration, Jefferson, AR, United States
- Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, U. S. Food and Drug Administration, Laurel, MD, United States
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Pan S, Liu S, Tai S, Yu J, Yuan E, Duan Y. Genomic Analysis of an Escherichia coli Sequence Type 167 Isolate Harboring a Multidrug-Resistant Conjugative Plasmid, Suggesting the Potential Transmission of the Type Strains from Animals to Humans. Infect Drug Resist 2023; 16:5077-5084. [PMID: 37576518 PMCID: PMC10422969 DOI: 10.2147/idr.s420635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/22/2023] [Indexed: 08/15/2023] Open
Abstract
Purpose The E. coli ST167 clone is the globally dominant ST among extraintestinal pathogenic E. coli (ExPEC) and is frequently associated with carbapenem resistance. This study reports genomic characterization of a pandrug-resistant E. coli ST167 isolate (ECO3183) and the possibility of the type strains' transmission. Materials and Methods Antibiotic susceptibility testing was performed using disk diffusion and the VITEK 2 automated system. The E. coli ECO3183 genome was sequenced. We used the genome to analyze the phylogenetic relationship, phylogenetic group, sequence type (ST), acquired antibiotic resistance genes (ARGs), IS elements, genomics islands, the replicon type and transferability of the plasmids. The conjugative transfer of plasmids was assessed using filter mating experiments. Results ECO3183 contained a 4.87-Mb chromosome and two plasmids [pECO3183-1 (167.63 Kb) and pECO3183-2 (46.16 Kb)]. It belonged to phylogenetic group A, clonal complex 10 (CC10), and ST167. ECO3183 is a pandrug-resistant strain nonsusceptible to 24 tested antimicrobials representing 8 different antimicrobial classes. Among 55 E. coli isolates phylogenetically related to ECO3183, 47% (26/55) were from humans, while 35% (19/55) were from animals. Further analysis revealed that among 1140 ST167 isolates (in the EnteroBase database), 4% (47/1140) originated from environments, 17% (192/1140) were isolated from humans, and 78% (890/1140) were obtained from animals. The pECO3183-1 contained two identical repeats of a 9633 bp region (IS6100-sul1-ΔaadA16-dfrA27-arr-3-aac(6')-Ib-cr-IS26) and a 17.88-kb resistance island (sul2-aph(3″)-Ib-aph(6)-Id-IS26-Δaph(3')-Ia-IS26-tet(A)-ΔfloR-ΔISVsa3-IS26-Δaac(3)-IId-IS26-mph(A)), and these three regions contained most of ECO3183 carrying ARGs. It was identified as a conjugative plasmid, which confers MDR resistance and has the potential to spread. Conclusion ECO3183 exhibited pandrug-resistance phenotype that was mediated by pECO3183-1 carrying MDR ARGs and pECO3183-2 carrying blaNDM-5. Source analysis of strains indicated that ST167 E. coli might be transmitted between species from animals to humans, which needs continued monitoring.
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Affiliation(s)
- Sijia Pan
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Shuangqing Liu
- Department of Clinical Laboratory, The Second Hospital of Tianjin Medical University, Tianjin, People’s Republic of China
| | - Shuhong Tai
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Jing Yu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Enwu Yuan
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Yitao Duan
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
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Phuadraksa T, Wichit S, Songtawee N, Tantimavanich S, Isarankura-Na-Ayudhya C, Yainoy S. Emergence of plasmid-mediated colistin resistance mcr-3.5 gene in Citrobacter amalonaticus and Citrobacter sedlakii isolated from healthy individual in Thailand. Front Cell Infect Microbiol 2023; 12:1067572. [PMID: 36683683 PMCID: PMC9846275 DOI: 10.3389/fcimb.2022.1067572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023] Open
Abstract
Citrobacter spp. are Gram-negative bacteria commonly found in environments and intestinal tracts of humans and animals. They are generally susceptible to third-generation cephalosporins, carbapenems and colistin. However, several antibiotic resistant genes have been increasingly reported in Citrobacter spp., which leads to the postulation that Citrobacter spp. could potentially be a reservoir for spreading of antimicrobial resistant genes. In this study, we characterized two colistin-resistant Citrobacter spp. isolated from the feces of a healthy individual in Thailand. Based on MALDI-TOF and ribosomal multilocus sequence typing, both strains were identified as Citrobacter sedlakii and Citrobacter amalonaticus. Genomic analysis and S1-nuclease pulsed field gel electrophoresis/DNA hybridization revealed that Citrobacter sedlakii and Citrobacter amalonaticus harbored mcr-3.5 gene on pSY_CS01 and pSY_CA01 plasmids, respectively. Both plasmids belonged to IncFII(pCoo) replicon type, contained the same genetic context (Tn3-IS1-ΔTnAs2-mcr-3.5-dgkA-IS91) and exhibited high transferring frequencies ranging from 1.03×10-4 - 4.6×10-4 CFU/recipient cell Escherichia coli J53. Colistin-MICs of transconjugants increased ≥ 16-fold suggesting that mcr-3.5 on these plasmids can be expressed in other species. However, beside mcr, other major antimicrobial resistant determinants in multidrug resistant Enterobacterales were not found in these two isolates. These findings indicate that mcr gene continued to evolve in the absence of antibiotics selective pressure. Our results also support the hypothesis that Citrobacter could be a reservoir for spreading of antimicrobial resistant genes. To the best of our knowledge, this is the first report that discovered human-derived Citrobacter spp. that harbored mcr but no other major antimicrobial resistant determinants. Also, this is the first report that described the presence of mcr gene in C. sedlakii and mcr-3 in C. amalonaticus.
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Affiliation(s)
- Thanawat Phuadraksa
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Sineewanlaya Wichit
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Napat Songtawee
- Department of Clinical Chemistry, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Srisurang Tantimavanich
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | | | - Sakda Yainoy
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
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Zeng Y, Deng L, Zhou X, Zhang C, Hu Z, Chen Y, Zheng W. Prevalence and risk factors of tet(X4)-positive Enterobacteriaceae in human gut microbiota. J Glob Antimicrob Resist 2022; 31:15-21. [PMID: 35850430 DOI: 10.1016/j.jgar.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/12/2022] [Accepted: 07/12/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES This work is aimed to investigate the prevalence of tet(X4) in healthy individuals and patients and assess risk factors associated with tet(X4)-positive populations. METHODS A total of 662 patients and 120 healthy individuals from three municipal hospitals during August 2021 to September 2021 were selected to investigate the prevalence of tet(X4) in gut microbiota. A further case-control study was conducted to identify the risk factors associated with tet(X4)-positive populations. The tet(X4)-positive isolates were characterised by antimicrobial susceptibility testing, multilocus sequence typing (MLST), whole genome sequencing, and bioinformatics analyses. RESULTS The prevalence of tet(X4)-positive Enterobacteriaceae in healthy individuals and patients (19.1%, 95% CI: 16.3%-21.8%) was substantially higher than previous studies in China (less than 1%). Patients ranging from 19 to 45 years of age had significantly higher odds of tet(X4)-positive bacterial colonization (OR = 2.545, 95% CI: 1.106-5.856). All tet(X4)-positive Enterobacteriaceae were resistant to tigecycline. In addition, tet(X4)-positive Escherichia coli were highly diverse, with CC10 belonging to the dominant clone. Genome analysis showed that tet(X4) was adjacent to ISVsa3 on the plasmids. CONCLUSION Data from this study suggested that geographic region may partly explain the high prevalence of tet(X4)-positive Enterobacteriaceae in healthy individuals and patients. Young and middle-aged populations were associated with the colonization of tet(X4)-positive isolates.
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Affiliation(s)
- Yu Zeng
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen City, China
| | - Li Deng
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen City, China
| | - Xianyuan Zhou
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen City, China
| | - Chi Zhang
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen City, China
| | - Zhen Hu
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen City, China
| | - Yunsheng Chen
- Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen City, China
| | - Weidong Zheng
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen City, China.
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Co-occurrence of mcr-2 and mcr-3 genes on chromosome of multidrug-resistant Escherichia coli isolated from healthy individuals in Thailand. Int J Antimicrob Agents 2022; 60:106662. [PMID: 36007781 DOI: 10.1016/j.ijantimicag.2022.106662] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/08/2022] [Accepted: 08/11/2022] [Indexed: 11/22/2022]
Abstract
The aim of this study was to characterize three strains of colistin-resistant E. coli isolated from feces samples of healthy individuals in Thailand. The three strains, namely, SY_EC03, SY_EC07, and SY_EC10 were identified as ST165, ST1602, and ST34. All isolates exhibited multidrug-resistant phenotype, which is mediated by accumulation of various antimicrobial resistance genes. SY_EC03 contained mcr-1.1 while SY_EC07 co-harbored mcr-2.3 and mcr-3.4, and SY_EC10 co-harbored mcr-1.1 and mcr-3.5. Genomic analysis revealed that mcr-1.1 of the two strains were located on IncI2 plasmid with genetic environment of ISApl1-mcr-1.1-PAP2, which is a composite transposon Tn6330 with single-ended. Regarding mcr-2.3, the gene was identified within the composite transposon of ISKpn71-mcr-2.3-ISSpu2-ISKpn71, which was located on a novel mobile genetic element (MGE) that was integrated into the chromosome by phage integrase. For mcr-3.4 and mcr-3.5, the genes were confirmed to locate on the chromosome by S1-PFGE/DNA hybridization. Hence, to the best of our knowledge, this is the first report on co-occurrence of mcr-2 and mcr-3 on chromosome of E. coli. More interestingly, mcr-2 was found to locate on a novel MGE, which had never been described. In addition, we also report the co-occurrence of plasmidic mcr-1.1 and chromosomal mcr-3.5 which is extremely rare. Since all these bacteria were isolated from healthy individuals and the identified STs have been found in a variety of origins, all these clones may serve as reservoir for horizontal and vertical transmission of mcr genes. Strategic action plans to control and prevent the spread of mcr genes are urgently needed.
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Ott LC, Mellata M. Models for Gut-Mediated Horizontal Gene Transfer by Bacterial Plasmid Conjugation. Front Microbiol 2022; 13:891548. [PMID: 35847067 PMCID: PMC9280185 DOI: 10.3389/fmicb.2022.891548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence of new antimicrobial resistant and virulent bacterial strains may pose a threat to human and animal health. Bacterial plasmid conjugation is a significant contributor to rapid microbial evolutions that results in the emergence and spread of antimicrobial resistance (AR). The gut of animals is believed to be a potent reservoir for the spread of AR and virulence genes through the horizontal exchange of mobile genetic elements such as plasmids. The study of the plasmid transfer process in the complex gut environment is limited due to the confounding factors that affect colonization, persistence, and plasmid conjugation. Furthermore, study of plasmid transfer in the gut of humans is limited to observational studies, leading to the need to identify alternate models that provide insight into the factors regulating conjugation in the gut. This review discusses key studies on the current models for in silico, in vitro, and in vivo modeling of bacterial conjugation, and their ability to reflect the gut of animals. We particularly emphasize the use of computational and in vitro models that may approximate aspects of the gut, as well as animal models that represent in vivo conditions to a greater extent. Directions on future research studies in the field are provided.
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Affiliation(s)
- Logan C. Ott
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Melha Mellata
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- *Correspondence: Melha Mellata,
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