scholarly journals Comparative Analysis of AbaR-Type Genomic Islands Reveals Distinct Patterns of Genetic Features in Elements with Different Backbones

mSphere ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Dexi Bi ◽  
Jiayi Zheng ◽  
Ruting Xie ◽  
Yin Zhu ◽  
Rong Wei ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Resistance Genes ◽  
Genomic Islands ◽  
Content Type ◽  
Antimicrobial Resistance Genes ◽  
Genetic Features ◽  
Clonal Distribution ◽  
Structural Modulation

ABSTRACT AbaR-type genomic islands (AbaRs) are prevalent and associated with multiple antimicrobial resistance in Acinetobacter baumannii. AbaRs feature varied structural configurations involving different but closely related backbones with acquisition of diverse mobile genetic elements (MGEs) and antimicrobial resistance genes. This study aimed to understand the structural modulation patterns of AbaRs. A total of 442 intact AbaRs, including nonresistance but closely related islands, were mapped to backbones Tn6019, Tn6022, Tn6172/Tn6173, and AbGRI1-0 followed by alien sequence characterization. Genetic configurations were then examined and compared. The AbaRs fall into 53 genetic configurations, among which 26 were novel, including one Tn6019-type, nine Tn6022-type, three Tn6172/Tn6173-type, nine AbGRI1-type, and four new transposons that could not be mapped to the known backbones. The newly identified genetic configurations involved insertions of novel MGEs like ISAcsp2, ISAba42, ISAba17, and ISAba10, novel structural modulations driven by known MGEs such as ISCR2, Tn2006, and even another AbaR, and different backbone deletions. Recombination events in AbGRI1-type elements were also examined by identifying hybrid sequences from different backbones. Moreover, we found that the content and context features of AbaRs including the profiles of the MGEs driving the plasticity of these elements and the consequently acquired antimicrobial resistance genes, insertion sites, and clonal distribution displayed backbone-specific patterns. This study provides a comprehensive view of the genetic features of AbaRs. IMPORTANCE AbaR-type genomic islands (AbaRs) are well-known elements that can cause antimicrobial resistance in Acinetobacter baumannii. These elements contain diverse and complex genetic configurations involving different but related backbones with acquisition of diverse mobile genetic elements and antimicrobial resistance genes. Understanding their structural diversity is far from complete. In this study, we performed a large-scale comparative analysis of AbaRs, including nonresistance but closely related islands. Our findings offered a comprehensive and interesting view of their genetic features, which allowed us to correlate the structural modulation signatures, antimicrobial resistance patterns, insertion loci, as well as host clonal distribution of these elements to backbone types. This study provides insights into the evolution of these elements, explains the association between their antimicrobial resistance gene profiles and clonal distribution, and could facilitate establishment of a more proper nomenclature than the term “AbaR” that has been variously used.

scholarly journals Salmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Max Laurence Cummins ◽  
Piklu Roy Chowdhury ◽  
Marc Serge Marenda ◽  
Glenn Francis Browning ◽  
Steven Philip Djordjevic
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Genomic Island ◽  
Sequence Type ◽  
Genomic Islands ◽  
Content Type ◽  
E Coli ◽  
Antimicrobial Resistance Genes

ABSTRACT Salmonella genomic island 1 (SGI1) is an integrative genetic island first described in Salmonella enterica serovars Typhimurium DT104 and Agona in 2000. Variants of it have since been described in multiple serovars of S. enterica, as well as in Proteus mirabilis, Acinetobacter baumannii, Morganella morganii, and several other genera. The island typically confers resistance to older, first-generation antimicrobials; however, some variants carry blaNDM-1, blaVEB-6, and blaCTX-M15 genes that encode resistance to frontline, clinically important antibiotics, including third-generation cephalosporins. Genome sequencing studies of avian pathogenic Escherichia coli (APEC) identified a sequence type 117 (ST117) isolate (AVC96) with genetic features found in SGI1. The complete genome sequence of AVC96 was assembled from a combination of Illumina and single-molecule real-time (SMRT) sequence data. Analysis of the AVC96 chromosome identified a variant of SGI1-B located 18 bp from the 3′ end of trmE, also known as the attB site, a known hot spot for the integration of genomic islands. This is the first report of SGI1 in wild-type E. coli. The variant, here named SGI1-B-Ec1, was otherwise unremarkable, apart from the identification of ISEc43 in open reading frame (ORF) S023. IMPORTANCE SGI1 and variants of it carry a variety of antimicrobial resistance genes, including those conferring resistance to extended-spectrum β-lactams and carbapenems, and have been found in diverse S. enterica serovars, Acinetobacter baumannii, and other members of the Enterobacteriaceae. SGI1 integrates into Gram-negative pathogenic bacteria by targeting a conserved site 18 bp from the 3′ end of trmE. For the first time, we describe a novel variant of SGI1 in an avian pathogenic Escherichia coli isolate. The presence of SGI1 in E. coli is significant because it represents yet another lateral gene transfer mechanism to enhancing the capacity of E. coli to acquire and propagate antimicrobial resistance and putative virulence genes. This finding underscores the importance of whole-genome sequencing (WGS) to microbial genomic epidemiology, particularly within a One Health context. Further studies are needed to determine how widespread SGI1 and variants of it may be in Australia.

scholarly journals Intercellular Transfer of Chromosomal Antimicrobial Resistance Genes between Acinetobacter baumannii Strains Mediated by Prophages

2019 ◽  
Vol 63 (8) ◽  
Author(s):  
Jun-ichi Wachino ◽  
Wanchun Jin ◽  
Kouji Kimura ◽  
Yoshichika Arakawa
Keyword(s):  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Resistance Genes ◽  
Cell Interaction ◽  
Extracellular Dna ◽  
Content Type ◽  
Intercellular Transfer ◽  
Antimicrobial Resistance Genes ◽  
Direct Cell ◽  
Cell Cell

ABSTRACT The spread of antimicrobial resistance genes (ARGs) among Gram-negative pathogens, including Acinetobacter baumannii, is primarily mediated by transferable plasmids; however, ARGs are frequently integrated into its chromosome. How ARG gets horizontally incorporated into the chromosome of A. baumannii, and whether it functions as a cause for further spread of ARG, remains unknown. Here, we demonstrated intercellular prophage-mediated transfer of chromosomal ARGs without direct cell-cell interaction in A. baumannii. We prepared ARG-harboring extracellular DNA (eDNA) components from the culture supernatant of a multidrug-resistant (MDR) A. baumannii NU-60 strain and exposed an antimicrobial-susceptible (AS) A. baumannii ATCC 17978 strain to the eDNA components. The antimicrobial-resistant (AR) A. baumannii ATCC 17978 derivatives appeared to acquire various ARGs, originating from dispersed loci of the MDR A. baumannii chromosome, along with their surrounding regions, by homologous recombination, with the ARGs including armA (aminoglycoside resistance), blaTEM-1 (β-lactam resistance), tet(B) (tetracycline resistance), and gyrA-81L (nalidixic acid resistance) genes. Notably, the eDNAs conferring antimicrobial resistance were enveloped in specific capsid proteins consisting of phage particles, thereby protecting the eDNAs from detergent and DNase treatments. The phages containing ARGs were likely released into the extracellular space from MDR A. baumannii, thereby transducing ARGs into AS A. baumannii, resulting in the acquisition of AR properties by the recipient. We concluded that the generalized transduction, in which phages were capable of carrying random pieces of A. baumannii genomic DNAs, enabled efficacious intercellular transfer of chromosomal ARGs between A. baumannii strains without direct cell-cell interaction.

scholarly journals Impact of UV and Peracetic Acid Disinfection on the Prevalence of Virulence and Antimicrobial Resistance Genes in Uropathogenic Escherichia coli in Wastewater Effluents

2014 ◽  
Vol 80 (12) ◽  
pp. 3656-3666 ◽  
Author(s):  
Basanta Kumar Biswal ◽  
Ramzi Khairallah ◽  
Kareem Bibi ◽  
Alberto Mazza ◽  
Ronald Gehr ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Peracetic Acid ◽  
Content Type ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Municipal Wastewaters ◽  
The Impact

ABSTRACTWastewater discharges may increase the populations of pathogens, includingEscherichia coli, and of antimicrobial-resistant strains in receiving waters. This study investigated the impact of UV and peracetic acid (PAA) disinfection on the prevalence of virulence and antimicrobial resistance genes in uropathogenicEscherichia coli(UPEC), the most abundantE. colipathotype in municipal wastewaters. Laboratory disinfection experiments were conducted on wastewater treated by physicochemical, activated sludge, or biofiltration processes; 1,766E. coliisolates were obtained for the evaluation. The target disinfection level was 200 CFU/100 ml, resulting in UV and PAA doses of 7 to 30 mJ/cm2and 0.9 to 2.0 mg/liter, respectively. The proportions of UPECs were reduced in all samples after disinfection, with an average reduction by UV of 55% (range, 22% to 80%) and by PAA of 52% (range, 11% to 100%). Analysis of urovirulence genes revealed that the decline in the UPEC populations was not associated with any particular virulence factor. A positive association was found between the occurrence of urovirulence and antimicrobial resistance genes (ARGs). However, the changes in the prevalence of ARGs in potential UPECs were different following disinfection, i.e., UV appears to have had no effect, while PAA significantly reduced the ARG levels. Thus, this study showed that both UV and PAA disinfections reduced the proportion of UPECs and that PAA disinfection also reduced the proportion of antimicrobial resistance gene-carrying UPEC pathotypes in municipal wastewaters.

scholarly journals Antimicrobial Susceptibility Testing and Tentative Epidemiological Cutoff Values for FiveBacillusSpecies Relevant for Use as Animal Feed Additives or for Plant Protection

2018 ◽  
Vol 84 (19) ◽  
Author(s):  
Yvonne Agersø ◽  
Birgitte Stuer-Lauridsen ◽  
Karin Bjerre ◽  
Michelle Geervliet Jensen ◽  
Eric Johansen ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Animal Feed ◽  
Bacterial Species ◽  
Feed Additives ◽  
Content Type ◽  
Cutoff Values ◽  
Antimicrobial Resistance Genes ◽  
Species Specific

ABSTRACTBacillus megaterium(n= 29),Bacillus velezensis(n= 26),Bacillus amyloliquefaciens(n= 6),Bacillus paralicheniformis(n= 28), andBacillus licheniformis(n= 35) strains from different sources, origins, and time periods were tested for the MICs for nine antimicrobial agents by the CLSI-recommended method (Mueller-Hinton broth, 35°C, for 18 to 20 h), as well as with a modified CLSI method (Iso-Sensitest [IST] broth, 37°C [35°C forB. megaterium], 24 h). This allows a proposal of species-specific epidemiological cutoff values (ECOFFs) for the interpretation of antimicrobial resistance in these species. MICs determined by the modified CLSI method were 2- to 16-fold higher than with the CLSI-recommended method for several antimicrobials. The MIC distributions differed between species for five of the nine antimicrobials. Consequently, use of the modified CLSI method and interpretation of resistance by use of species-specific ECOFFs is recommended. The genome sequences of all strains were determined and used for screening for resistance genes against the ResFinder database and for multilocus sequence typing. A putative chloramphenicol acetyltransferase (cat) gene was found in oneB. megateriumstrain with an elevated chloramphenicol MIC compared to the otherB. megateriumstrains. InB. velezensisandB. amyloliquefaciens, a putative tetracycline efflux gene,tet(L), was found in all strains (n= 27) with reduced tetracycline susceptibility but was absent in susceptible strains. AllB. paralicheniformisand 23% ofB. licheniformisstrains had elevated MICs for erythromycin and harboredermD. The presence of these resistance genes follows taxonomy suggesting they may be intrinsic rather than horizontally acquired. Reduced susceptibility to chloramphenicol, streptomycin, and clindamycin could not be explained in all species.IMPORTANCEWhen commercializing bacterial strains, likeBacillusspp., for feed applications or plant bioprotection, it is required that the strains are free of acquired antimicrobial resistance genes that could potentially spread to pathogenic bacteria, thereby adding to the pool of resistance genes that may cause treatment failures in humans or animals. Conversely, if antimicrobial resistance is intrinsic to a bacterial species, the risk of spreading horizontally to other bacteria is considered very low. Reliable susceptibility test methods and interpretation criteria at the species level are needed to accurately assess antimicrobial resistance levels. In the present study, tentative ECOFFs for fiveBacillusspecies were determined, and the results showed that the variation in MICs followed the respective species. Moreover, putative resistance genes, which were detected by whole-genome sequencing and suggested to be intrinsic rather that acquired, could explain the resistance phenotypes in most cases.

scholarly journals Merging Metagenomics and Spatial Epidemiology To Understand the Distribution of Antimicrobial Resistance Genes from Enterobacteriaceae in Wild Owls

2020 ◽  
Vol 86 (20) ◽  
Author(s):  
Elizabeth A. Miller ◽  
Julia B. Ponder ◽  
Michelle Willette ◽  
Timothy J. Johnson ◽  
Kimberly L. VanderWaal
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Spatial Epidemiology ◽  
Anthropogenic Sources ◽  
Resistant Bacteria ◽  
Metagenomic Sequencing ◽  
Wild Animals ◽  
Natural Ecosystems ◽  
Content Type ◽  
Antimicrobial Resistance Genes

ABSTRACT Antimicrobial resistance (AMR) is a well-documented phenomenon in bacteria from many natural ecosystems, including wild animals. However, the specific determinants and spatial distribution of resistant bacteria and antimicrobial resistance genes (ARGs) in the environment remain incompletely understood. In particular, information regarding the importance of anthropogenic sources of AMR relative to that of other biological and ecological influences is lacking. We conducted a cross-sectional study of AMR in great horned owls (Bubo virginianus) and barred owls (Strix varia) admitted to a rehabilitation center in the midwestern United States. A combination of selective culture enrichment and shotgun metagenomic sequencing was used to identify ARGs from Enterobacteriaceae. Overall, the prevalence of AMR was comparable to that in past studies of resistant Enterobacteriaceae in raptors, with acquired ARGs being identified in 23% of samples. Multimodel regression analyses identified seasonality and owl age to be important predictors of the likelihood of the presence of ARGs, with birds sampled during warmer months being more likely to harbor ARGs than those sampled during cooler months and with birds in their hatch year being more likely to harbor β-lactam ARGs than adults. Beyond host-specific determinants, ARG-positive owls were also more likely to be recovered from areas of high agricultural land cover. Spatial clustering analyses identified a significant high-risk cluster of tetracycline resistance gene-positive owls in the southern sampling range, but this could not be explained by any predictor variables. Taken together, these results highlight the complex distribution of AMR in natural environments and suggest that both biological and anthropogenic factors play important roles in determining the emergence and persistence of AMR in wildlife. IMPORTANCE Antimicrobial resistance (AMR) is a multifaceted problem that poses a worldwide threat to human and animal health. Recent reports suggest that wildlife may play an important role in the emergence, dissemination, and persistence of AMR. As such, there have been calls for better integration of wildlife into current research on AMR, including the use of wild animals as biosentinels of AMR contamination in the environment. A One Health approach can be used to gain a better understanding of all AMR sources and pathways, particularly those at the human-animal-environment interface. Our study focuses on this interface in order to assess the effect of human-impacted landscapes on AMR in a wild animal. This work highlights the value of wildlife rehabilitation centers for environmental AMR surveillance and demonstrates how metagenomic sequencing within a spatial epidemiology framework can be used to address questions surrounding AMR complexity in natural ecosystems.

scholarly journals Emergence of XDR high-risk Pseudomonas aeruginosa ST309 in South America: a global comparative genomic analysis

2021 ◽  
Author(s):  
Érica L. Fonseca ◽  
Sérgio M. Morgado ◽  
Raquel V. Caldart ◽  
Fernanda Freitas ◽  
Ana Carolina P. Vicente
Keyword(s):  
Pseudomonas Aeruginosa ◽  
High Risk ◽  
Antimicrobial Resistance ◽  
South America ◽  
Resistance Genes ◽  
Genomic Islands ◽  
Intrinsic Resistance ◽  
Heterogeneous Distribution ◽  
Antimicrobial Resistance Genes ◽  
Genomic Analyses

ABSTRACTPseudomonas aeruginosa has been considered one of the major nosocomial pathogens associated with elevated morbidity and mortality worldwide. Outbreaks have been associated with few high-risk pandemic P. aeruginosa lineages, presenting a remarkable antimicrobial resistance. However, the biological features involved with the persistence and spread of such lineages among clinical settings remain to be unravel. This study reports the emergence of the ST309 P. aeruginosa lineage in South America/Brazil, more precisely, in the Amazon region. Global genomic analyses were performed with the Brazilian strain (PA834) and more 41 complete and draft ST309 genomes publicly available, giving insights about ST309 epidemiology and its resistome and mobilome. Antimicrobial susceptibility tests revealed that the Brazilian PA834 strain presented the XDR phenotype, which was mainly due to intrinsic resistance mechanisms. Genomic analyses revealed a heterogeneous distribution of acquired antimicrobial resistance genes among ST309 genomes, which included blaVIM-2, blaIMP-15 and qnrVC1, all of them associated with class 1 integrons. The mobilome mining showed the presence of Integrative and Conjugative Elements, transposons and genomic islands harbouring a huge arsenal of hevy metal resistance genes. Moreover, these elements also carried genes involved with virulence and adaptive traits. Therefore, the presence of such genes in ST309 lineage possibly accounted for the global spread and persistence of this emerging clone, and for its establishment as a pandemic lineage of clinical importance.

scholarly journals Complete Genome Sequence of an mcr-10- Possessing Enterobacter roggenkampii Strain Isolated from a Dog in Japan

2021 ◽  
Vol 10 (30) ◽  
Author(s):  
Toyotaka Sato ◽  
Masaru Usui ◽  
Kazuki Harada ◽  
Yukari Fukushima ◽  
Chie Nakajima ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Content Type ◽  
Antimicrobial Resistance Genes

The complete genome sequence of mcr-10 -possessing Enterobacter roggenkampii En37, isolated from a dog in Japan was determined. mcr-10 was located on a 70,277-bp IncFIB plasmid without any additional antimicrobial resistance genes.

scholarly journals Whole-Genome Sequences of 35 Incompatibility Group I1 Plasmid-Carrying Salmonella enterica Isolates from Food Animal and Clinical Sources

2019 ◽  
Vol 8 (35) ◽  
Author(s):  
Nesreen H. Aljahdali ◽  
Pravin R. Kaldhone ◽  
Steven L. Foley ◽  
Bijay K. Khajanchi
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Whole Genome ◽  
Genome Sequences ◽  
Incompatibility Group ◽  
Content Type ◽  
Food Animal ◽  
Antimicrobial Resistance Genes ◽  
Genotypic Characteristics

We sequenced 35 Salmonella enterica isolates carrying incompatibility group I1 (IncI1) plasmids from different serotypes to study their genotypic characteristics. The isolates originated from food animals (n = 32) and human patients (n = 3). All isolates carried IncI1 plasmids, and many had additional plasmids detected along with virulence and antimicrobial resistance genes.

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.

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