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The rate of emulsification in surfactant/oil/water systems is influenced by transport of chemicals and mixing of the fluid phases. In porous media applications, complex flow regimes ...are generated due to three-dimensional connectivity and irregular cross-sections of the pores facilitating the mixing for emulsification. The properties of the resulting emulsified phase depend on the interplay of flow, mixing and emulsification kinetics of the surfactant/oil/water system. Emulsification can be relatively quick. Direct visualization of the process and compositional gradients in three-dimensional pore space during flow requires imaging at few seconds time intervals.
In this study, a flow unit was integrated in a synchrotron beamline-based fast X-ray computed micro-tomography set-up. Non-destructive three-dimensional visualization of multi phase flow inside a porous rock at flow conditions became viable. An oil saturated rock sample was first flooded with water, followed by surfactant solution to mobilize the remaining oil by miscible displacement. The sample was continuously imaged during injection; the scans were made at time intervals of 7–60 s.
The presence of an emulsified phase in addition to the oil and the aqueous phases required a more advanced image processing workflow compared to the workflows used for the immiscible fluid systems. A newly developed image processing technique was adopted; the grey levels in the images were correlated with the local oil content in the emulsified fluid regions. The visual extractions of the pore space showed that the emulsification occurred within seconds. Compositional gradients were observed in the emulsified phase as the injected surfactant solution reached the remote locations in the pore space. While a significant fraction of the oil was displaced within few seconds, the compositional gradients persisted over several millimeter length for several minutes, illustrating a sequence of mobilization and solubilization of the oil phase. The ability to interpret such compositional gradients in real time in porous space brings capability to study interfacial phenomena in applications where in situ emulsification occurs under flow.
CTX-M-producing
are spreading since 1999 both in clinical and in community settings. Environmental samples such as rivers have also been pointed out as being vectors for ESBL producers. In this ...report, we have investigated the presence and the diversity of CTX-M-producing
isolates in two samplings of the Seine River (next to Notre Dame), Paris France, performed in June 2016 and 2017. The total number of bacteria growing on the selective ChromID ESBL agar was 3.1 × 10
cfu/L (23.8% of all growing bacteria) in 2016, whereas it was 100-fold lower in 2017 (3 × 10
cfu/L; 8.3% of all growing bacteria). However, among them, the prevalence of ESBL-producing
increased from <0.1 to 1.1% in one-year. ESBLs were exclusively of the CTX-M-type: CTX-M-1 (
= 5), CTX-M-15 (
= 7), CTX-M-14 (
= 1), and CTX-M-27 (
= 2). The isolates belonged to several multi locus sequence types, and a wide diversity of incompatibility groups of plasmids were identified in those
isolates. The occurrence and diversity of
isolates belonging to many clones and producing many CTX-M-variants have been identified in our study. The presence of these bacteria in rivers that are open again for recreational usage (swimming) is worrying as it may contribute to further dissemination of ESBL producers in the community.
Highlights • The 5HT system starts to develop early and plays a crucial role in brain maturation. • Alterations in the serotonergic tone during development can change neural networks. • The s and l ...alleles of the SERT gene are associated with different vulnerabilities. • Developmental exposure to SSRIs can affect the biobehavioral outcome. • The interaction of genes, environment and SSRI exposure determines risk or resilience.
Abstract
Background
Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-Kp) has emerged globally over the last decade as a major nosocomial pathogen that threatens patient care. ...These highly resistant bacteria are mostly associated with a single Kp clonal group, CG258, but the reasons for its host and hospital adaptation remain largely unknown.
Methods
We analyzed the in vivo evolution of a colistin-resistant KPC-Kp CG258 strain that contaminated a patient following an endoscopy and was responsible for a fatal bacteremia 4.5 years later. Whole-genome sequencing was performed on 17 KPC-Kp isolates from this patient; single-nucleotide polymorphisms were analyzed and their implication in antimicrobial resistance and bacterial host adaptation investigated.
Results
The patient KPC-Kp strain diversified over 4.5 years at a rate of 7.5 substitutions per genome per year, resulting in broad phenotypic modifications. After 2 years of carriage, all isolates restored susceptibility to colistin. Higher expression of the fimbriae conferred the ability to produce more biofilm, and the isolate responsible for a bacteremia grew in human serum. The convergent mutations occurring in specific pathways, such as the respiratory chain and the cell envelope, revealed a complex long-term adaptation of KPC-Kp.
Conclusions
Broad genomic and phenotypic diversification and the parallel selection of pathoadaptive mutations might contribute to long-term carriage and virulence of KPC-Kp CG258 strains and to the dissemination of this clone.
KPC-producing Klebsiella pneumoniae (KPC-Kp) has emerged as a major nosocomial pathogen. This study emphasizes long-term in vivo genomic evolution along with the selection of pathoadaptive mutations in a KPC-Kp strain that might have contributed to its long-term carriage, virulence, and dissemination.
Bacterial evolution is affected by mobile genetic elements like phages and conjugative plasmids, offering new adaptive traits while incurring fitness costs. Their infection is affected by the ...bacterial capsule. Yet, its importance has been difficult to quantify because of the high diversity of confounding mechanisms in bacterial genomes such as anti-viral systems and surface receptor modifications. Swapping capsule loci between Klebsiella pneumoniae strains allowed us to quantify their impact on plasmid and phage infection independently of genetic background. Capsule swaps systematically invert phage susceptibility, revealing serotypes as key determinants of phage infection. Capsule types also influence conjugation efficiency in both donor and recipient cells, a mechanism shaped by capsule volume and conjugative pilus structure. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The least capsule-sensitive pili (F-like) are the most frequent in the species' plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.
With the dissemination of carbapenemase-producing
(CPE) strains worldwide, carbapenem-hydrolyzing enzymes are increasingly reported among isolates of
, the first hospital and community-acquired ...opportunistic pathogen. Here, we have performed an epidemiological survey of carbapenemase-producing
(CP-
) isolates received at the French National Reference Centre (F-NRC) in 2012 and 2013. Antimicrobial susceptibilities for last-resort antibiotics and antimicrobial compounds commonly used to treat urinary tract infections were determined by broth microdilution. Clonal relationship was assessed using repetitive sequence-based PCR (rep-PCR) and multilocus sequence typing (MLST). From this collection of 140 carbapenemase-producing
isolates, 74% produced an OXA-48-like carbapenemase and 21% produced an NDM carbapenemase. A link with a foreign country was suspected for 37% of infected/colonized patients. Most of the isolates were from screening (56%) and from urine samples (26%). Colistin, fosfomycin, and nitrofurantoin possessed the most consistent activity, with 100%, 95%, and 96% isolates susceptible, respectively. A wide diversity of carbapenemase-producing
isolates has been found (50 different sequence types STs). The most prevalent clones were (i)
sequence type 38 (ST38) producing OXA-48 (
= 21), a clone linked to Turkey and North African countries, (ii)
ST-90 producing OXA-204 (
= 9), which was responsible for an outbreak related to a contaminated duodenoscope, and (iii)
ST-410 producing OXA-181 (
= 5), which was recovered from patients of different geographical origins. These specific clones might be considered high-risk clones for the dissemination of carbapenemases in
The wide diversity of STs, combined with the increasing number of CP-
isolates received by the F-NRC, suggests a likely dissemination of CP-
isolates in the community.
There is an urgent need for accurate and rapid diagnostic tests to identify carbapenemase producing enterobacteria (CPE). Here, we have evaluated the Carbapenem Inactivation Method (CIM) test to ...detect CPEs from cultured colonies.
A total of 256 enterobacterial isolates were used to evaluate the performance of the CIM in comparison to Carba NP test and molecular detection used a reference method. Ninety three well-characterized isolates (including 29 non-CPE and 63 CPEs of worldwide origin) with decreased susceptibility to at least one carbapenem were used to (i) evaluate the efficacy of CIM test and (ii) to compare it to the Carba NP test. We also tested different carbapenems to determine the best substrate for this test. Finally, the CIM test was then evaluated prospectively against 164 isolates referred to the French National Reference Center (NRC) for Antimicrobial Resistance from may 2016 to july 2016.
Based on the results of this retrospective study, sensitivity and specificity of the CIM and the Carba NP test were 92.1% and 100%, respectively. We demonstrated that the meropenem was the best substrate to perform the CIM test since sensitivity and specificity were 81.1% and 100% using ertapenem disk, and 100% and 65,6% using imipenem disk, and respectively. Taking in account the results of retrospective and prospective studies, CIM and Carba NP tests have similar sensitivity, specificity, positive predictive value and negative predictive values being 96.3%, 98.9%, 99.0% and 98.4% for the CIM test versus 96.9%, 100%, 100% and 100% for the Carba NP test.
Our results confirm that the CIM test may be a useful tool for the reliable confirmation of carbapenemase-activity in enterobacterial isolates, especially in clinical microbiological laboratories with limited resources, no trained personnel, and no specialized equipment.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
There is an urgent need for accurate and fast diagnostic tests capable of identifying carbapenemase producers. Here, we assessed the performance of a new multiplex lateral flow assay (OKN K -SeT) for ...the rapid detection of OXA-48-like, KPC and NDM carbapenemase-producing Enterobacteriaceae from culture colonies.
Two hundred collection isolates with characterized β-lactamase content and 183 non-duplicate consecutive isolates referred to two National Reference Centres over a 2 month period in 2016 were used to evaluate the OKN K -SeT assay.
The assay correctly detected all 42 OXA-48-like-, 27 KPC- and 30 NDM-producing isolates from the collection panel, including 7 isolates that co-produced NDM and OXA-181 carbapenemases. No cross-reactivity was observed with non-targeted carbapenemases ( n = 41) or with non-carbapenemase producers ( n = 60). Prospectively, all OXA-48-like ( n = 69), KPC ( n = 9) and NDM ( n = 19) carbapenemase-producing Enterobacteriaceae isolates were correctly detected, while 11 carbapenemase producers not targeted by the assay went undetected VIM ( n = 8) and OXA-23/OXA-58-like ( n = 3). Overall, the sensitivity and specificity of the assay were 100%.
The OKN assay is efficient, rapid and easy to implement in the workflow of a clinical microbiology laboratory for the confirmation of OXA-48, NDM and KPC carbapenemases. This test represents a powerful diagnostic tool as it enables the rapid detection of the most clinically important carbapenemases without the need for more costly and less frequently available molecular assays.
Carbapenemase-producing
have increasingly been reported worldwide, with an ever-increasing heterogeneity of carbapenem resistance mechanisms, depending on the bacterial species and the geographical ...location. OXA-198 is a plasmid-encoded class D β-lactamase involved in carbapenem resistance in one
isolate from Belgium. In the setting of a multicenter survey of carbapenem resistance in
strains in Belgian hospitals in 2013, three additional OXA-198-producing
isolates originating from patients hospitalized in one hospital were detected. To reveal the molecular mechanism underlying the reduced susceptibility to carbapenems, MIC determinations, whole-genome sequencing, and PCR analyses to confirm the genetic organization were performed. The plasmid harboring the
gene was characterized, along with the genetic relatedness of the four
isolates. The
gene was harbored on a class 1 integron carried by an ∼49-kb IncP-type plasmid proposed as IncP-11. The same plasmid was present in all four
isolates. Multilocus sequence typing revealed that the isolates all belonged to sequence type 446, and single-nucleotide polymorphism analysis revealed only a few differences between the isolates. This report describes the structure of a 49-kb plasmid harboring the
gene and presents the first description of OXA-198-producing
isolates associated with a hospital-associated cluster episode.
The emergence of colistin-resistant
(CoR
) is a public health concern, since this antibiotic has become the last line of treatment for infections caused by multidrug-resistant (MDR) Gram negatives. ...In this study, we have investigated the molecular basis of colistin resistance in 13 MDR
strains isolated from 12 patients in a teaching hospital in Sousse, Tunisia. Whole-genome sequencing (WGS) was used to decipher the molecular mechanism of colistin resistance and to identify the resistome of these CoR
isolates. It revealed a genome of ca. 5.5 Mbp in size with a G+C content of 57%, corresponding to that commonly observed for
These isolates belonged to the 5 different sequence types (ST11, ST15, ST101, ST147, and ST392), and their resistome was composed of acquired β-lactamases, including extended-spectrum beta-lactamase and carbapenemase genes (
,
,
, and
genes), aminoglycoside resistance genes
(
')
,
(
″)-
,
(
)-
, and
(
)-
, and fosfomycin (
), fluoroquinolone (
-like), chloramphenicol, trimethoprim, and tetracycline resistance genes. All of the isolates were identified as having a mutated
gene. Mapping reads with reference sequences of the most common genes involved in colistin resistance revealed several modifications in
,
, and
operons (deletions, insertions, and substitutions) likely affecting the function of these proteins. It is worth noting that among the 12 patients, 10 were treated with colistin before the isolation of CoR
No plasmid encoding
to
genes was found in these isolates. This study corresponds to the first molecular characterization of a collection of CoR
strains in Tunisia and highlights that the small-transmembrane protein MgrB is a main mechanism for colistin resistance in
.
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