scholarly journals Natural Horizontal Gene Transfer of Antimicrobial Resistance Genes in Campylobacter spp. From Turkeys and Swine

2021 ◽  
Vol 12 ◽  
Author(s):  
Vanina Guernier-Cambert ◽  
Julian Trachsel ◽  
Joel Maki ◽  
Jing Qi ◽  
Matthew J. Sylte ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Resistance Genes ◽  
Genomic Islands ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes ◽  
Horizontal Spread

Antibiotic-resistant Campylobacter constitutes a serious threat to public health. The clonal expansion of resistant strains and/or the horizontal spread of resistance genes to other strains and species can hinder the clinical effectiveness of antibiotics to treat severe campylobacteriosis. Still, gaps exist in our understanding of the risks of acquisition and spread of antibiotic resistance in Campylobacter. While the in vitro transfer of antimicrobial resistance genes between Campylobacter species via natural transformation has been extensively demonstrated, experimental studies have favored the use of naked DNA to obtain transformants. In this study, we used experimental designs closer to real-world conditions to evaluate the possible transfer of antimicrobial resistance genes between Campylobacter strains of the same or different species (Campylobacter coli or Campylobacter jejuni) and originating from different animal hosts (swine or turkeys). This was evaluated in vitro through co-culture experiments and in vivo with dual-strain inoculation of turkeys, followed by whole genome sequencing of parental and newly emerged strains. In vitro, we observed four independent horizontal gene transfer events leading to the acquisition of resistance to beta-lactams (blaOXA), aminoglycosides [aph(2′′)-If and rpsL] and tetracycline [tet(O)]. Observed events involved the displacement of resistance-associated genes by a mutated version, or the acquisition of genomic islands harboring a resistance determinant by homologous recombination; we did not detect the transfer of resistance-carrying plasmids even though they were present in some strains. In vivo, we recovered a newly emerged strain with dual-resistance pattern and identified the replacement of an existing non-functional tet(O) by a functional tet(O) in the recipient strain. Whole genome comparisons allowed characterization of the events involved in the horizontal spread of resistance genes between Campylobacter following in vitro co-culture and in vivo dual inoculation. Our study also highlights the potential for antimicrobial resistance transfer across Campylobacter species originating from turkeys and swine, which may have implications for farms hosting both species in close proximity.

scholarly journals Antimicrobial Drug Resistance Genes Do Not Convey a Secondary Fitness Advantage to Calf-Adapted Escherichia coli

2006 ◽  
Vol 72 (1) ◽  
pp. 443-448 ◽  
Author(s):  
Artashes R. Khachatryan ◽  
Dale D. Hancock ◽  
Thomas E. Besser ◽  
Douglas R. Call
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Null Mutant ◽  
Antimicrobial Drug Resistance ◽  
E Coli ◽  
Fitness Advantage ◽  
Antimicrobial Resistance Genes ◽  
Mutant Strains

ABSTRACT Maintenance of antimicrobial drug resistance in bacteria can be influenced by factors unrelated to direct selection pressure such as close linkage to other selectively advantageous genes and secondary advantage conveyed by antimicrobial resistance genes in the absence of drug selection. Our previous trials at a dairy showed that the maintenance of the antimicrobial resistance genes is not influenced by specific antimicrobial selection and that the most prevalent antimicrobial resistance phenotype of Escherichia coli is specifically selected for in young calves. In this paper we examine the role of secondary advantages conveyed by antimicrobial resistance genes. We tested antimicrobial-susceptible null mutant strains for their ability to compete with their progenitor strains in vitro and in vivo. The null mutant strains were generated by selection for spontaneous loss of resistance genes in broth supplemented with fusaric acid or nickel chloride. On average, the null mutant strains were as competitive as the progenitor strains in vitro and in newborn calves (in vivo). Inoculation of newborn calves at the dairy with antimicrobial-susceptible strains of E. coli did not impact the prevalence of antimicrobial-resistant E. coli. Our results demonstrate that the antimicrobial resistance genes are not responsible for the greater fitness advantage of antimicrobial-resistant E. coli in calves, but the farm environment and the diet clearly exert critical selective pressures responsible for the maintenance of antimicrobial resistance genes. Our current hypothesis is that the antimicrobial resistance genes are linked to other genes responsible for differential fitness in dairy calves.

scholarly journals Conjugal Transfer, Whole-Genome Sequencing, and Plasmid Analysis of Four mcr-1-Bearing Isolates from U.S. Patients

2019 ◽  
Vol 63 (4) ◽  
Author(s):  
Wenming Zhu ◽  
Adrian Lawsin ◽  
Rebecca L. Lindsey ◽  
Dhwani Batra ◽  
Kristen Knipe ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Whole Genome ◽  
Colistin Resistance ◽  
Content Type ◽  
Plasmid Analysis ◽  
Antimicrobial Resistance Genes

ABSTRACT Four Enterobacteriaceae clinical isolates bearing mcr-1 gene-harboring plasmids were characterized. All isolates demonstrated the ability to transfer colistin resistance to Escherichia coli; plasmids were stable in conjugants after multiple passages on nonselective media. mcr-1 was located on an IncX4 (n = 3) or IncN (n = 1) plasmid. The IncN plasmid harbored 13 additional antimicrobial resistance genes. Results indicate that the mcr-1-bearing plasmids in this study were highly transferable in vitro and stable in the recipients.

scholarly journals Exploring Antibiotic Susceptibility, Resistome and Mobilome Structure of Planctomycetes from Gemmataceae Family

2021 ◽  
Vol 13 (9) ◽  
pp. 5031
Author(s):  
Anastasia A. Ivanova ◽  
Kirill K. Miroshnikov ◽  
Igor Y. Oshkin
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Resistance Genes ◽  
Antibiotic Susceptibility ◽  
Large Genome ◽  
Antimicrobial Resistance Genes ◽  
The Family ◽  
Terrestrial Environments ◽  
Environmental Bacteria

The family Gemmataceae accomodates aerobic, chemoorganotrophic planctomycetes with large genome sizes, is mostly distributed in freshwater and terrestrial environments. However, these bacteria have recently also been found in locations relevant to human health. Since the antimicrobial resistance genes (AMR) from environmental resistome have the potential to be transferred to pathogens, it is essential to explore the resistant capabilities of environmental bacteria. In this study, the reconstruction of in silico resistome was performed for all nine available gemmata genomes. Furthermore, the genome of the newly isolated yet-undescribed strain G18 was sequenced and added to all analyses steps. Selected genomes were screened for the presence of mobile genetic elements. The flanking location of mobilizable genomic milieu around the AMR genes was of particular interest since such colocalization may appear to promote the horizontal gene transfer (HGT) events. Moreover the antibiotic susceptibility profile of six phylogenetically distinct strains of Gemmataceae planctomycetes was determined.

scholarly journals Staphylococcus epidermidis Phages Transduce Antimicrobial Resistance Plasmids and Mobilize Chromosomal Islands

mSphere ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Lenka Fišarová ◽  
Tibor Botka ◽  
Xin Du ◽  
Ivana Mašlaňová ◽  
Pavol Bárdy ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Resistance Genes ◽  
Staphylococcus Epidermidis ◽  
Content Type ◽  
Antimicrobial Resistance Genes ◽  
Evolutionary Relatedness ◽  
Resistance Plasmids

ABSTRACT Staphylococcus epidermidis is a leading opportunistic pathogen causing nosocomial infections that is notable for its ability to form a biofilm and for its high rates of antibiotic resistance. It serves as a reservoir of multiple antimicrobial resistance genes that spread among the staphylococcal population by horizontal gene transfer such as transduction. While phage-mediated transduction is well studied in Staphylococcus aureus, S. epidermidis transducing phages have not been described in detail yet. Here, we report the characteristics of four phages, 27, 48, 456, and 459, previously used for S. epidermidis phage typing, and the newly isolated phage E72, from a clinical S. epidermidis strain. The phages, classified in the family Siphoviridae and genus Phietavirus, exhibited an S. epidermidis-specific host range, and together they infected 49% of the 35 strains tested. A whole-genome comparison revealed evolutionary relatedness to transducing S. aureus phietaviruses. In accordance with this, all the tested phages were capable of transduction with high frequencies up to 10−4 among S. epidermidis strains from different clonal complexes. Plasmids with sizes from 4 to 19 kb encoding resistance to streptomycin, tetracycline, and chloramphenicol were transferred. We provide here the first evidence of a phage-inducible chromosomal island transfer in S. epidermidis. Similarly to S. aureus pathogenicity islands, the transfer was accompanied by phage capsid remodeling; however, the interfering protein encoded by the island was distinct. Our findings underline the role of S. epidermidis temperate phages in the evolution of S. epidermidis strains by horizontal gene transfer, which can also be utilized for S. epidermidis genetic studies. IMPORTANCE Multidrug-resistant strains of S. epidermidis emerge in both nosocomial and livestock environments as the most important pathogens among coagulase-negative staphylococcal species. The study of transduction by phages is essential to understanding how virulence and antimicrobial resistance genes spread in originally commensal bacterial populations. In this work, we provide a detailed description of transducing S. epidermidis phages. The high transduction frequencies of antimicrobial resistance plasmids and the first evidence of chromosomal island transfer emphasize the decisive role of S. epidermidis phages in attaining a higher pathogenic potential of host strains. To date, such importance has been attributed only to S. aureus phages, not to those of coagulase-negative staphylococci. This study also proved that the described transducing bacteriophages represent valuable genetic modification tools in S. epidermidis strains where other methods for gene transfer fail.

scholarly journals Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis

2019 ◽  
Author(s):  
Juan Feng ◽  
Yiqin Deng ◽  
Haidong Xu ◽  
Youlu Su ◽  
Songlin Liu ◽  
...  
Keyword(s):  
Climate Change ◽  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Complete Genome ◽  
Genomic Islands

Abstract Background Horizontal gene transfer (HGT), which is affected by environmental pollution and climate change, promotes genetic communication, changing bacterial pathogenicity and drug resistance. However, few studies have been conducted on the effect of HGT on the high pathogenicity and drug resistance of the opportunistic pathogen Vibrio harveyi.Results V. harveyi 345 that was multidrug resistant and infected Epinephelus oanceolutus was isolated from a diseased organism in Shenzhen, Southern China, an important and contaminated aquaculture area. Analysis of the entire genome sequence predicted 5,678 genes including 487 virulence genes contributing to bacterial pathogenesis and 25 antibiotic-resistance genes (ARGs) contributing to antimicrobial resistance. Five ARGs ( tetm , tetb , qnrs , dfra17 , and sul2 ) and one virulence gene (CU052_28670) on the pAQU-type plasmid p345-185, provided direct evidence for HGT. Comparative genome analysis of 31 V. harveyi strains indicated that 217 genes and 7 gene families, including a class C beta-lactamase gene, a virulence-associated protein D gene, and an OmpA family protein gene were specific to strain V. harveyi 345. These genes could contribute to HGT or be horizontally transferred from other bacteria to enhance the virulence or antibiotic resistance of 345. Mobile genetic elements in 71 genomic islands encoding virulence factors for three type III secretion proteins and 13 type VI secretion system proteins, and two incomplete prophage sequences were detected that could be HGT transfer tools. Evaluation of the complete genome of V. harveyi 345 and comparative genomics indicated genomic exchange, especially exchange of pathogenic genes and drug-resistance genes by HGT contributing to pathogenicity and drug resistance. Climate change and continued environmental deterioration are expected to accelerate the HGT of V. harveyi , increasing its pathogenicity and drug resistance.Conclusion This study provides timely information for further analysis of V. harveyi pathogenesis and antimicrobial resistance and developing pollution control measurements for coastal areas.

Virulence and antimicrobial resistance genes associated with the in-vivo pathogenicity of avian pathogenic E. coli isolates

2021 ◽  
Vol 1 (1) ◽  
pp. 17-20
Author(s):  
Ahmed Abd El-Mawgoud ◽  
Azza El-Sawah ◽  
Soad Nasef ◽  
Al-Hussien Dahshan ◽  
Ahmed Ali
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Broiler Chickens ◽  
Virulence Genes ◽  
Virulence Gene ◽  
Health Concern ◽  
Pathogenicity Test ◽  
E Coli ◽  
Antimicrobial Resistance Genes

In the current study, ten avian pathogenic E. coli (APEC) isolates of the most predominant APEC serogroups isolated from broiler chickens in Egypt were screened for their virulence and antimicrobial resistance genes pattern using PCR. Five selected virulence gene patterns were further investigated for their in-vivo pathogenicity test. Results showed a 100% prevalence of the β-lactams and tetracyclines resistance genes. However, aminoglycoside and quinolone resistance genes were not detected. Also, 80% of the tested isolates harbored mcr-1 gene, colistin resistance gene. In-vivo pathogenic strains consistently harbored the virulence gene pattern of fimH, fimA, papC, iutA, and tsh. Additionally, the tsh gene was consistently detected with lethal APEC isolates in day-old chicks. These results highlighted the high prevalence of antimicrobial and virulence genes in APEC that potentially represent a public health concern. In this study, the virulence genes fimH, fimA, papC, iutA, and tsh were the most common virulence gene patterns associated with pathogenicity in day-old chicks.

scholarly journals Frequency of Antimicrobial Resistance Genes in Salmonella From Brazil by in silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades

2020 ◽  
Vol 11 ◽  
Author(s):  
Grazielle Lima Rodrigues ◽  
Pedro Panzenhagen ◽  
Rafaela Gomes Ferrari ◽  
Anamaria dos Santos ◽  
Vania Margaret Flosi Paschoalin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
In Silico ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Antimicrobial Resistance Genes

scholarly journals Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella

2016 ◽  
Vol 60 (9) ◽  
pp. 5515-5520 ◽  
Author(s):  
Patrick F. McDermott ◽  
Gregory H. Tyson ◽  
Claudine Kabera ◽  
Yuansha Chen ◽  
Cong Li ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
The United States ◽  
Whole Genome ◽  
Content Type ◽  
Structural Resistance ◽  
Retail Meat

ABSTRACTLaboratory-basedin vitroantimicrobial susceptibility testing is the foundation for guiding anti-infective therapy and monitoring antimicrobial resistance trends. We used whole-genome sequencing (WGS) technology to identify known antimicrobial resistance determinants among strains of nontyphoidalSalmonellaand correlated these with susceptibility phenotypes to evaluate the utility of WGS for antimicrobial resistance surveillance. Six hundred fortySalmonellaof 43 different serotypes were selected from among retail meat and human clinical isolates that were tested for susceptibility to 14 antimicrobials using broth microdilution. The MIC for each drug was used to categorize isolates as susceptible or resistant based on Clinical and Laboratory Standards Institute clinical breakpoints or National Antimicrobial Resistance Monitoring System (NARMS) consensus interpretive criteria. Each isolate was subjected to whole-genome shotgun sequencing, and resistance genes were identified from assembled sequences. A total of 65 unique resistance genes, plus mutations in two structural resistance loci, were identified. There were more unique resistance genes (n =59) in the 104 human isolates than in the 536 retail meat isolates (n =36). Overall, resistance genotypes and phenotypes correlated in 99.0% of cases. Correlations approached 100% for most classes of antibiotics but were lower for aminoglycosides and beta-lactams. We report the first finding of extended-spectrum β-lactamases (ESBLs) (blaCTX-M1andblaSHV2a) in retail meat isolates ofSalmonellain the United States. Whole-genome sequencing is an effective tool for predicting antibiotic resistance in nontyphoidalSalmonella, although the use of more appropriate surveillance breakpoints and increased knowledge of new resistance alleles will further improve correlations.

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