The worldwide dissemination of carbapenemase-producing Escherichia coli lineages belonging to high-risk clones poses a challenging public health menace. The aim of this work was to investigate ...genomic features of a colonizing multidrug-resistant strain of Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli from our institution.
Whole-genome sequencing was done by Illumina MiSeq-I, and de novo assembly was achieved using SPAdes. Resistome, mobilome, plasmids, virulome, and integrons were analysed using ResFinder, AMRFinder, ISFinder, PlasmidFinder, MOB-suite, VirulenceFinder, and IntegronFinder. Sequence types (STs) were identified with pubMLST and BIGSdb databases. Conjugation assays were also performed.
Escherichia coli HA25pEc was isolated from a rectal swab sample taken within the framework of the hospital epidemiological surveillance protocol for detection of carbapenemase-producing Enterobacterales. Escherichia coli HA25pEc corresponded to the first report of ST648 co-harbouring blaKPC-2 and blaCTX-M-15 in Latin America from a colonized patient. It had 19 antibiotic resistance genes (ARGs), including blaKPC-2, located on a Tn4401a isoform. Conjugation assays revealed that blaKPC-2 was not transferred by conjugation to E. coli J53 under our experimental conditions.
Escherichia coli ST648 has been detected previously in companion and farm animals as well as in hospital- and community-acquired infections worldwide. Although scarcely reported as KPC-producers, our finding in a culture surveillance with several acquired ARGs, including blaCTX-M-15, alerts the potential of this clone for worldwide unnoticed spreading of extreme drug resistance to β-lactams. These data reinforce the importance of carrying out molecular surveillance to identify reservoirs and warn about the dissemination of new international clones in carbapenemase-bearing patients.
Isolation of colistin- and carbapenem-resistant Klebsiella pneumoniae (CCR-Kp) is increasing in hospital settings worldwide, which is related to increased morbidity, mortality and healthcare costs. ...The aim of this work was to perform whole-genome sequencing (WGS), genomic and phylogenetic analysis, and conjugation assays of an extensively drug-resistant (XDR) CCR-Kp isolate from Argentina.
WGS of strain KpS26 isolated from a bloodstream infection was performed using Illumina MiSeq-I, and de novo assembly was achieved using SPAdes v.3.11. A maximum likelihood tree was created using MEGA7 based on core genome single nucleotide polymorphisms from whole-genome alignment of K. pneumoniae isolates identified in silico as sequence type 15 (ST15). The resistome, plasmids and integrons were analysed using ResFinder, AMRFinderPlus, ISfinder, plasmidSPAdes, PlasmidFinder and IntegronFinder. Standard conjugation was performed.
KpS26 belonged to ST15, which is less common than ST258, ST25 and ST11 that are globally reported as responsible for CCR-Kp outbreaks. Fourteen transferable antimicrobial resistance genes (ARGs), including blaKPC-2 in a novel genetic platform transferable by conjugation, were detected contributing to the XDR phenotype. The amino acid substitution T157P in the protein encoded by the pmrB gene of KpS26, previously reported as being responsible for resistance to colistin in K. pneumoniae lineages globally disseminated, was also identified in this strain.
The XDR CCR-Kp isolate analysed here shows that ST15 is also disseminating blaKPC-2 in Argentina alongside other ARGs, evidencing that KPC epidemiology continues to be shaped by intricate and assorted ways of lateral gene transfer.
•Cu2+ resistant Cryptococcus laurentii are found in tomato rhizosphere.•Cu2+ negatively affects auxin production, carbohydrates and phenolic acids utilization.•Cu2+ increases ammonification, protease ...activity and ligninolytic enzymes activity.
In horticulture copper sulphate is utilized for the inhibition of phytopathogenic fungi. However, copper tends to accumulate in soil with a concomitant effect on soil quality and microbial diversity. As part of the biological diversity of soil and the rhizosphere, yeasts have been relatively less characterized than bacteria or filamentous fungi. In this work, we analyzed the presence of yeasts in the rhizosphere of tomato plants and the effect of copper in fungal biological activities of agronomical and ecological interest. Yeasts isolates that were selected for their higher copper resistance were all identified molecularly as Papiliotrema laurentii. Results show that all were capable of auxin production, and that copper has a detrimental effect on it. In contrast, ammonification was mainly increased by the metal. Copper also inhibits the growth of the yeasts on D-xylose, cellobiose and phenolic acids, suggesting a negative consequence on the recycling of lignocellulosic degradation products. Laccase and catechol oxidase activities were increased by the metal in P. laurentii. Altogether, results presented in this report indicate that P. laurentii presents properties of ecological and agronomical interest. The effect of the metal highlights the importance of the analysis of the consequence of copper utilization as fungicide on microbial activities. At the same time, the variability in the yeast response to copper suggests the concern of not only the characterization of biotechnological properties of a specific strain, but also the effect of copper on them.
The inactivation of quorum sensing signals, a phenomenon known as quorum quenching, has been described in diverse microorganisms, though it remains almost unexplored in yeasts. Beyond the well-known ...properties of these microorganisms for the industry or as eukaryotic models, the role of yeasts in soil or in the inner tissues of a plant is largely unknown. In this report, the wider survey of quorum quenching activities in yeasts isolated from Antarctic soil and the inner tissues of sugarcane, a tropical crop, is presented. Results show that, independently of their niche, quorum quenching activities are broadly present in unicellular fungi. Although yeasts showing a broad range of quorum quenching activity are present in the two niches, at the same time specific AHL inactivation profiles can also be found. Furthermore, yeasts from both sampling sites show quorum quenching activities compatible with lactonase-like and acylase-like inactivations of AHLs. Interestingly, the characterization of Rhodotorula mucilaginosa 7Apo1 showed that the presence of a particular AHL does not interfere with the quenching of a second molecule. Evidence suggests that yeasts could play a role in the modulation of the quorum sensing activity of bacteria. The relationship among phylogeny, sampling sites and yeast quorum quenching activities of the isolates is analyzed.
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In the rhizosphere, the role of yeasts in microbial interactions and signaling is an open question. To study the influence of fungicides on yeast inactivation of N-acyl homoserine lactone quorum ...sensing signals, we evaluated the resistance of Papiliotrema laurentii strains from tomato rhizosphere to CuSO4 and Cu2(OH)3Cl fungicides, and the copper effect on yeast quorum quenching. Copper resistance profiles and colony morphologies allowed the distinction of two groups of P. laurentii strains: mucoid, green and resistant, and brown-orange and more sensitive. Most of the strains inactivated C6-HSL and C10-HSL QS signals. Inactivation and copper divided the strains in three with weak activity independently of the metal, and 11 with activities affected by copper. The lack of alkalinization allows the hypothesis of an enzymatic inactivation of the signals. These results suggest that yeasts contribute to communications in the rhizosphere, and that copper fungicides can modify their interactions with other rhizosphere microorganisms.
•Copper-resistant Papiliotrema laurentii strains are present in tomato rhizosphere.•Most of Papiliotrema laurentii strains inactivate bacterial quorum sensing signals.•Copper has a negative effect on yeasts quorum quenching activities.•Yeast quorum quenching activity varies with the QS signal in presence of copper.
According to the World Health Organization, carbapenem-resistant
Enterobacteriaceae
(CRE) belong to the highest priority group for the development of new antibiotics. Argentina-WHONET data showed ...that Gram-negative resistance frequencies to imipenem have been increasing since 2010 mostly in two CRE bacteria:
Klebsiella pneumoniae
and
Enterobacter cloacae
Complex (ECC). This scenario is mirrored in our hospital. It is known that
K. pneumoniae
and the ECC coexist in the human body, but little is known about the outcome of these species producing KPC, and colonizing or infecting a patient. We aimed to contribute to the understanding of the rise of the ECC in Argentina, taking as a biological model both a patient colonized with two KPC-producing strains (one
Enterobacter hormaechei
and one
K. pneumoniae
) and
in vitro
competition assays with prevalent KPC-producing ECC (KPC-ECC) versus KPC-producing
K. pneumoniae
(KPC-Kp) high-risk clones from our institution. A KPC-producing
E. hormaechei
and later a KPC-Kp strain that colonized a patient shared an identical novel conjugative IncM1 plasmid harboring
bla
KPC-2
. In addition, a total of 19 KPC-ECC and 58 KPC-Kp strains isolated from nosocomial infections revealed that high-risk clones KPC-ECC ST66 and ST78 as well as KPC-Kp ST11 and ST258 were prevalent and selected for competition assays. The competition assays with KCP-ECC ST45, ST66, and ST78 versus KPC-Kp ST11, ST18, and ST258 strains analyzed here showed no statistically significant difference. These assays evidenced that high-risk clones of KPC-ECC and KPC-Kp can coexist in the same hospital environment including the same patient, which explains from an ecological point of view that both species can exchange and share plasmids. These findings offer hints to explain the worldwide rise of KPC-ECC strains based on the ability of some pandemic clones to compete and occupy a certain niche. Taken together, the presence of the same new plasmid and the fitness results that showed that both strains can coexist within the same patient suggest that horizontal genetic transfer of
bla
KPC-2
within the patient cannot be ruled out. These findings highlight the constant interaction that these two species can keep in the hospital environment, which, in turn, can be related to the spread of KPC.
Quorum Sensing (QS) signaling, which allows the coordination of the microbial physiology, can be influenced by environmental factors. However, the impact of copper-based fungicides on the QS of ...rhizosphere microorganisms is currently unknown. The simultaneous presence of other microorganisms may also alter the QS signaling. In this work we report that the fungicide CuSO4 modifies the expression from the promoter of ppuI, ppoR and rsaL, components of Pseudomonas capeferrum WCS358 QS system. ppuI and ppoR promoters showed a biphasic behavior reducing their activities as CuSO4 concentrations increased up to 1 mmol l−1, but with increased values at higher metal concentrations. rsaL promoter attained a minimal activity with 1 mmol l−1, though higher concentrations did not modify its expression. The impact of CuSO4 on biofilm formation by WCS358 was dependent on the bacterial QS activity. Dual biofilms with Papiliotrema laurentii YL2 yeast were also affected by the bacterial QS and the metal. CuSO4 was detrimental for the bacterial colonization, but YL2 exerted a protective effect in dual colonies, an effect that depended on the QS activity. These results suggest the importance of the WCS358 QS systems in the rhizosphere, where copper-based fungicides and concomitant microorganisms conform a complex system.
•CuSO4 has a negative impact on P. capeferrum QS activity.•P.capeferrum colonization and biofilm formation capacities are affected by copper sulfate.•Pa. laurentii shows a protective effect on these rhizobacteria.•Copper-based fungicides and neighboring microorganisms constitute a complex system.
The worldwide dissemination of carbapenemase-producing Escherichia coli lineages belonging to high-risk clones poses a challenging public health menace. The aim of this work was to investigate ...genomic features of a colonizing multidrug-resistant strain of Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli from our institution.
Whole-genome sequencing was done by Illumina MiSeq-I, and de novo assembly was achieved using SPAdes. Resistome, mobilome, plasmids, virulome, and integrons were analysed using ResFinder, AMRFinder, ISFinder, PlasmidFinder, MOB-suite, VirulenceFinder, and IntegronFinder. Sequence types (STs) were identified with pubMLST and BIGSdb databases. Conjugation assays were also performed.
Escherichia coli HA25pEc was isolated from a rectal swab sample taken within the framework of the hospital epidemiological surveillance protocol for detection of carbapenemase-producing Enterobacterales. Escherichia coli HA25pEc corresponded to the first report of ST648 co-harbouring bla
and bla
in Latin America from a colonized patient. It had 19 antibiotic resistance genes (ARGs), including bla
, located on a Tn4401a isoform. Conjugation assays revealed that bla
was not transferred by conjugation to E. coli J53 under our experimental conditions.
Escherichia coli ST648 has been detected previously in companion and farm animals as well as in hospital- and community-acquired infections worldwide. Although scarcely reported as KPC-producers, our finding in a culture surveillance with several acquired ARGs, including bla
, alerts the potential of this clone for worldwide unnoticed spreading of extreme drug resistance to β-lactams. These data reinforce the importance of carrying out molecular surveillance to identify reservoirs and warn about the dissemination of new international clones in carbapenemase-bearing patients.
Isolation of colistin- and carbapenem-resistant Klebsiella pneumoniae (CCR-Kp) is increasing in hospital settings worldwide, which is related to increased morbidity, mortality and healthcare costs. ...The aim of this work was to perform whole-genome sequencing (WGS), genomic and phylogenetic analysis, and conjugation assays of an extensively drug-resistant (XDR) CCR-Kp isolate from Argentina.
WGS of strain KpS26 isolated from a bloodstream infection was performed using Illumina MiSeq-I, and de novo assembly was achieved using SPAdes v.3.11. A maximum likelihood tree was created using MEGA7 based on core genome single nucleotide polymorphisms from whole-genome alignment of K. pneumoniae isolates identified in silico as sequence type 15 (ST15). The resistome, plasmids and integrons were analysed using ResFinder, AMRFinderPlus, ISfinder, plasmidSPAdes, PlasmidFinder and IntegronFinder. Standard conjugation was performed.
KpS26 belonged to ST15, which is less common than ST258, ST25 and ST11 that are globally reported as responsible for CCR-Kp outbreaks. Fourteen transferable antimicrobial resistance genes (ARGs), including bla
in a novel genetic platform transferable by conjugation, were detected contributing to the XDR phenotype. The amino acid substitution T157P in the protein encoded by the pmrB gene of KpS26, previously reported as being responsible for resistance to colistin in K. pneumoniae lineages globally disseminated, was also identified in this strain.
The XDR CCR-Kp isolate analysed here shows that ST15 is also disseminating bla
in Argentina alongside other ARGs, evidencing that KPC epidemiology continues to be shaped by intricate and assorted ways of lateral gene transfer.
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