The aim of this study was to perform an
analysis of the available whole-genome sequencing data to detect syntenic genomic islands (GIs) having homology to
genomic island 1 (SGI1), analyze the genetic ...variations of their backbone, and determine their relatedness. Eighty-nine non-redundant SGI1-related elements (SGI1-REs) were identified among gamma-proteobacteria. With the inclusion of the thirty-seven backbones characterized to date, seven clusters were identified based on integrase homology: SGI1, PGI1, PGI2, AGI1 clusters, and clusters 5, 6, and 7 composed of GIs mainly harbored by waterborne or marine bacteria, such as
,
,
,
,
, and
. The integrase genes and the backbones of SGI1-REs from clusters 6 and 7, and from PGI1, PGI2, and AGI1 clusters differed significantly from those of the SGI1 cluster, suggesting a different ancestor. All backbones consisted of two parts: the part from
to the origin of transfer (
) harbored the DNA recombination, transfer, and mobilization genes, and the part from
to
differed among the clusters. The diversity of SGI1-REs resulted from the recombination events between GIs of the same or other families. The
appeared to be a high recombination site. The multi-drug resistant (MDR) region was located upstream of the resolvase gene. However, most SGI1-REs in
,
, and marine bacteria did not harbor any MDR region. These strains could constitute a reservoir of SGI1-REs that could be potential ancestors of SGI1-REs encountered in pathogenic bacteria. Furthermore, four SGI1-REs did not harbor a resolvase gene and therefore could not acquire an integron. The presence of mobilization genes and AcaCD binding sites indicated that their conjugative transfer could occur with helper plasmids. The plasticity of SGI1-REs contributes to bacterial adaptation and evolution. We propose a more relevant classification to categorize SGI1-REs into different clusters based on their integrase gene similarity.
Bacterial biofilm can occur on all medical implanted devices and lead to infection and/or dysfunction of the device. For all treatments, the optical and scanning electron microscope images showed ...substantial less biofilm biomass remaining on the silicone implant compared to non-treated implant. Depending on the materials used, the biofilm dislodging technique must be adapted. The US procedure was the best technic to dislodge S. epidermidis biofilm on silicone, piccline, peripheral venous catheter but not endotracheal tube. This suggested that scientists should compare themselves different methods before designing a protocol of biofilm study on a given material.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Several groups of integrative mobilizable elements (IMEs) that harbour a class 1 integron carrying antibiotic resistance genes have been found at the 3′-end of the chromosomal trmE gene. Here, a new ...IME, designated SGI0, was found in trmE in the sequenced and assembled genome of a French clinical, multiply antibiotic resistant Proteus mirabilis strain, Pm1LENAR. SGI0 shares the same gene content as the backbones of SGI1 and SGI2 (overall 97.6% and 97.7% nucleotide identity, respectively) but it lacks a class 1 integron. However, SGI0 is a mosaic made up of segments with >98.5% identity to SGI1 and SGI2 interspersed with segments sharing 74–95% identity indicating that further diverged backbone types exist and that recombination between them is occurring. The structure of SGI1-V, here re-named SGI-V, which lacks two SGI1 (S023 and S024) backbone genes and includes a group of additional genes in the backbone, was re-examined. In regions shared with SGI1, the backbones shared 97.3% overall identity with the differences distributed in patches with various levels of identity. The class 1 integron is also in a slightly different position with the target site duplication AAATT instead of ACTTG for SGI1 and variants, indicating that it was acquired independently. The Pm1LENAR resistance genes are in the chromosome, in Tn7 and an ISEcp1-mobilised segment.
•SGI0, a genomic island without class 1 integron, was found in the trmE gene in Proteus mirabilis..•The SGI0 backbone is a mosaic that includes segments of SGI1, SGI2 and SGI1-V backbones.•SGI0 was excised in the presence of an IncC plasmid and could be completely lost.•SGI1-V is independently derived and is re-named SGI-V.•SGI0, SGI1, SGI2 and SGI-V arose independently from an original ancestor.
Achromobacter xylosoxidans is an emerging pathogen in cystic fibrosis patients. The multidrug resistance of these bacteria remains poorly understood. We have characterized in a clinical strain the ...first resistance-nodulation-cell division (RND)-type multidrug efflux pump in this species: AxyABM. The inactivation of the transporter component axyB gene led to decreased MICs of cephalosporins (except cefepime), aztreonam, nalidixic acid, fluoroquinolones, and chloramphenicol.
The burden of extended-spectrum β-lactamases producing
(ESBL-
), has increased over several decades. Freshwater ecosystems are suspected to play an important ecological and evolutionary role in ...driving the dissemination of antimicrobial resistance. The aim of our study was to decipher the occurrence of ESBL-
in a small watershed (Ouche river, Burgundy, France), targeting environmental matrices and fishes. Among cefotaxime resistant
(ctxR
) isolates, we detected and characterized 36 ESBL-
from water, biofilm and fish guts. ctxR
and ESBL-
were found in samples from sites near the first small town, located downstream from the watershed which was studied. Treatment of urban wastewater by waste water treatment plants (WWTP), might therefore be a major potential source of ctxR
and thus of ESBL-
. Prevalence of total
and ctxR
in fish guts ranged between 0 to 92% and 0 to 85%; respectively, depending on the sampling site and the fish species. The diet of fish (predator or omnivore) seems to strongly influence the prevalence of total
and ESBL-
. Extended spectrum beta-lactamases produced by the isolates from this study belonged to the CTX-M family (CTX-M group 1 and 9). Moreover, some environmental ESBL-
proved to share genotypic features (MLST types) with isolates which originated from 8 WWTP effluents discharged in the Ouche river and with the sequence type ST131, which is widely described in clinical isolates. Ninety-seven % (97%) of ESBL-
from the study harbored additional antibiotic resistances and can thus be considered as multi drug resistant (MDR) bacteria. Finally, 53% of the ESBL-
strains harbored class 1 integron-integrase (
). These results are discussed with the perspective of defining indicators of antibiotic resistance contamination in freshwater ecosystems.
CTX-M a major type of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli are increasingly involved in human infections worldwide. The aim of this study was to investigate potential ...reservoirs for such strains: soils, cattle, and farm environment. The prevalence of bla(CTX-M) genes was determined directly from soil DNA extracts obtained from 120 sites in Burgundy (France) using real-time PCR. bla(CTX-M) targets were found in 20% of the DNA extracts tested. Samples of cattle feces (n = 271) were collected from 182 farms in Burgundy. Thirteen ESBL-producing isolates were obtained from 12 farms and further characterized for the presence of bla genes. Of the 13 strains, five and eight strains carried bla(TEM-71) genes and bla(CTX-M-1) genes respectively. Ten strains of CTX-M-1 producing E. coli were isolated from cultivated and pasture soils as well as from composted manure within two of these farms. The genotypic analysis revealed that environmental and animal strains were clonally related. Our study confirms the occurrence of CTX-M producing E. coli in cattle and reports for the first time the occurrence of such strains in cultivated soils. The environmental competence of such strains has to be determined and might explain their long term survival since CTX-M isolates were recovered from a soil that was last amended with manure 1 year before sampling.
Abstract
Objectives
To characterize the structure of Salmonella genomic islands 1 (SGI1s) from two clinical Proteus mirabilis isolates: one producing an ESBL and the other a penicillinase.
Methods
...WGS completed by PCR and Sanger sequencing was performed to determine sequences of SGI1s from Pm2CHAMA and Pm37THOMI strains.
Results
Two new variants of SGI1 named SGI1-Pm2CHAMA (53.6 kb) and SGI1-K7 (55.1 kb) were identified. The backbone of SGI1-Pm2CHAMA shared 99.9% identity with that of SGI1. Its MDR region (26.3 kb) harboured two class 1 integrons (an In2-type integron and an In4-type integron) containing in particular a qacH cassette (encoding a quaternary ammonium compound efflux pump). These two integrons framed a complex region (harbouring among others blaCARB-4) resulting from transposon insertions mediated by IS26 and successive transposition events of ISs (ISAba14 isoform and the new ISPmi2). The second variant (SGI1-K7) had the same backbone as SGI1-K. Its MDR region (29.7 kb) was derived from that of SGI1-K and was generated by three events. The two main events were mediated by IS26: inversion of a large portion of the MDR region of SGI1-K and insertion of a structure previously reported on plasmids carried by prevalent and successful MDR clones of Enterobacteriaceae. This last event led to the insertion of the blaCTX-M-15 gene into SGI1-K7.
Conclusions
This study confirmed the great plasticity of the MDR region of SGI1 and its potential key role for the dissemination of clinically significant antibiotic resistance among Enterobacteriaceae.
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