Evaluation of screening algorithms to detect rectal colonization with carbapenemase-producing Enterobacterales in a resource-limited setting.

Objectives: To improve and rationalize the detection of carbapenemase-producing Enterobacterales (CPE) in rectal swabs in a high-prevalence and resource-constrained setting, addressing surveillance challenges typically encountered in laboratories with limited resources. Methods: A point prevalence survey (PPS) was conducted on 15 August 2022, in a provincial children's hospital in northern Vietnam. Rectal swab samples of all admitted children were collected and plated on a selective medium for carbapenem-resistant Enterobacterales (CRE). Species identification and antimicrobial susceptibility testing (AST) were performed by MALDI-TOF, and VITEK2 XL and interpreted according to CLSI breakpoints (2022). Carbapenemases were detected by the carbapenem inactivation method (CIM) and quantitative real-time PCR (qRT-PCR). Results: Rectal swab samples were obtained from 376 patients. Of 178 isolates growing on the CRE screening agar, 140 isolates were confirmed as Enterobacterales of which 118 (84.3%) isolates were resistant to meropenem and/or ertapenem. CIM and PCR showed that 90/118 (76.3%) were carbapenemase producers. Overall, 83/367 (22.6%) were colonized by CPE. Klebsiella pneumoniae, Escherichia coli and Enterobacter cloacae complex were the most common CPE detected, with NDM as the predominant carbapenemase (78/90; 86.7%). Phenotypic resistance to meropenem was the best predictor of CPE production (sensitivity 85.6%, specificity 100%) compared with ertapenem resistance (95.6% sensitivity, 36% specificity). CIM was 100% concordant with PCR in detecting carbapenemases. Conclusions: These findings underscore the effectiveness of meropenem resistance as a robust indicator of the production of carbapenemases and the reliability of the CIM method to detect such carbapenemases in resource-limited settings where the performance of molecular methods is not possible.

Label-free DNA quantification using isothermal amplification on an exposed core optical fiber microfluidic platform.

Isothermal amplification technology has triggered a surge in research due to its compatibility with small and portable equipment, simplicity, and high efficiency, especially in light of the COVID-19 pandemic where reliable widescale testing is critical to outbreak management. In this paper, a label-free isothermal deoxyribonucleic acid (DNA) amplification method based on refractive index (RI) quantification is proposed and demonstrated for the first time by combining optical fiber sensing, microfluidics, and isothermal amplification. A highly RI-sensitive Mach-Zehnder (MZ) interference is formed by splicing a short length of an exposed-core fiber between two lengths of a single-mode fiber while the microfluidic liquid channel on the exposed side of the ECF is filled with target DNA and the amplification solution. Real-time quantitative measurement of the target DNA is then realized by monitoring the change in RI of the solution during the isothermal DNA amplification process. The experimental results show that the platform successfully realizes real-time label-free monitoring of isothermal amplification of 0.16 aM DNA samples. This method is a breakthrough for applications in the fields of DNA detection and quantification where simple operation, rapid detection, portability, small size, high selectivity, and high sensitivity are required.

The effects of pretreatment with Cyclosporin A and Docetaxel before vitrification of porcine immature oocytes on subsequent embryo development.

In the present study, we attempted to improve the developmental competence of vitrified immature porcine oocytes by the preservation of mitochondrial properties using Cyclosporin A (CsA, inhibitor of mitochondrial membrane permeability transition) and Docetaxel (stabilizer of microtubules, hence mitochondrial distribution). In Experiment 1, Mitotracker red staining revealed reduced mitochondrial activity (MA) in vitrified/warmed oocytes at 0 and 22 h of in vitro maturation (IVM) compared with fresh ones. However, by at 46 h of IVM, MA levels in vitrified oocytes were similar to those in fresh control. Treatment of oocytes with CsA or Docetaxel improved MA at 0 h and 22 h of IVM compared with non-treated vitrified oocytes. However, there were no significant differences among groups in percentages of survival, maturation and embryo development after subsequent IVM and parthenogenetic activation. Nevertheless, a pretreatment with a combination of 10 µg/mL CsA and 0.05 µM Docetaxel improved the blastocyst formation of vitrified oocytes compared with non-treatment counterparts (11.2 ± 1.6% vs 5.9 ± 1.6%, P < 0.05). In conclusion, vitrification reduced mitochondrial activity in GV-stage oocytes during 0-22 h of IVM; however, it was normalized by 46 h IVM. Docetaxel or CsA pretreatment alone did not improve development competence of vitrified oocytes. However, pretreatment with a combination of CsA and Docetaxel could improve blastocyst formation rates.

Whispering gallery mode excitation using exposed-core fiber.

Whispering gallery modes (WGMs) in micro-resonators are of interest due to their high Q-factors. Ultra-thin fiber tapers are widely deployed to couple light into micro-resonators but achieving stable and practical coupling for out-of-lab use remains challenging. Here, a new WGM coupling scheme using an exposed-core silica fiber (ECF) is proposed, which overcomes the challenge of using fragile fiber tapers. Microspheres are deposited onto the exposed channel for excitation via the evanescent field of the fiber's guided modes. The outer jacket of the ECF partially encapsulates the microspheres, protecting them from external physical disturbance. By varying the mode launching conditions in this few-mode ECF, in combination with a Fano resonance effect, we demonstrate a high degree of tunability in the reflection spectrum. Furthermore, we show multi-particle WGM excitation, which could be controlled to occur either simultaneously or separately through controlling the ECF mode launching conditions. This work can bring value towards applications such as optical switches and modulators, multiplexed/distributed biosensing, and multi-point lasing, integrated in a single optical fiber device that avoids fiber post-processing.

In Situ Temperature-Compensated DNA Hybridization Detection Using a Dual-Channel Optical Fiber Sensor.

A multifunction, high-sensitivity, and temperature-compensated optical fiber DNA hybridization sensor combining surface plasmon resonance (SPR) and Mach-Zehnder interference (MZI) has been designed and implemented. We demonstrate, for the first time to our knowledge, the dual-parameter measurement of temperature and refractive index (RI) by simultaneously using SPR and MZI in a simple single-mode fiber (SMF)-no-core fiber (NCF)-SMF structure. The experimental results show RI sensitivities of 930 and 1899 nm/RIU and temperature sensitivities of 0.4 and -1.4 nm/°C for the MZI and SPR, respectively. We demonstrate a sensitivity matrix used to simultaneously detect both parameters, solving the problem of temperature interference of RI variation-based biosensors. In addition, the sensor can also distinguish biological binding events by detecting the localized RI changes at the fiber's surface. We realize label-free sensing of DNA hybridization detection by immobilizing probe DNA (pDNA) onto the fiber as the probe to capture complementary DNA (cDNA). The experimental results show that the sensor can qualitatively detect cDNA after temperature compensation, and the limit of detection (LOD) of the sensor reaches 80 nM. The proposed sensor has advantages of high sensitivity, real time, low cost, temperature compensation, and low detection limit and is suitable for in situ monitoring, high-precision sensing of DNA molecules, and other related fields, such as gene diagnosis, kinship judgment, environmental monitoring, and so on.

Interferometric high temperature sensor using suspended-core optical fibers.

We propose and experimentally demonstrate, for the first time to our knowledge, high temperature fiber sensing using the multimode interference effect within a suspended-core microstructured optical fiber (SCF). Interference fringes were found to red-shift as the temperature increased and vice versa. Temperature sensing up to 1100°C was performed by measuring the wavelength shifts of the fringes after fast Fourier transform (FFT) filtering of the spectra. In addition, phase monitoring at the dominant spatial frequency in the Fourier spectrum was used as an interrogation method to monitor various temperature-change scenarios over a period of 80 hours. Our proposed high temperature fiber sensor is simple, cost-effective, and can operate at temperatures beyond 1000°C.

Temperature sensing up to 1300°C using suspended-core microstructured optical fibers.

We demonstrate a new approach to high temperature sensing using femtosecond laser ablation gratings within silica suspended-core microstructured optical fibers. The simple geometry of the suspended-core fiber allows for femtosecond laser processing directly through the fiber cladding. Pure silica glass is used, allowing the sensor to be used up to temperatures as high as 1300°C while still allowing the fibre to be spliced to conventional fiber. The sensor can also be wavelength division multiplexed, with three sensors in a single fiber demonstrated.

Genotyping single nucleotide polymorphisms using different molecular beacon multiplexed within a suspended core optical fiber.

We report a novel approach to genotyping single nucleotide polymorphisms (SNPs) using molecular beacons in conjunction with a suspended core optical fiber (SCF). Target DNA sequences corresponding to the wild- or mutant-type have been accurately recognized by immobilizing two different molecular beacons on the core of a SCF. The two molecular beacons differ by one base in the loop-probe and utilize different fluorescent indicators. Single-color fluorescence enhancement was obtained when the immobilized SCFs were filled with a solution containing either wild-type or mutant-type sequence (homozygous sample), while filling the immobilized SCF with solution containing both wild- and mutant-type sequences resulted in dual-color fluorescence enhancement, indicating a heterozygous sample. The genotyping was realized amplification-free and with ultra low-volume for the required DNA solution (nano-liter). This is, to our knowledge, the first genotyping device based on the combination of optical fiber and molecular beacons.

Fabrication, splicing, Bragg grating writing, and polyelectrolyte functionalization of exposed-core microstructured optical fibers.

Femtosecond laser written Bragg gratings have been written in exposed-core microstructured optical fibers with core diameters ranging from 2.7 µm to 12.5 µm and can be spliced to conventional single mode fiber. Writing a Bragg grating on an open core fiber allows for real-time refractive index based sensing, with a view to multiplexed biosensing. Smaller core fibers are shown both experimentally and theoretically to provide a higher sensitivity. A 7.5 µm core diameter fiber is shown to provide a good compromise between sensitivity and practicality and was used for monitoring the deposition of polyelectrolyte layers, an important first step in developing a biosensor.

Molecular beacons immobilized within suspended core optical fiber for specific DNA detection.

We propose and experimentally demonstrate a new class of sensor for specific DNA sequences based on molecular beacons (MB) immobilized on the internal surfaces of suspended core optical fibers (SCF). MBs, a type of hairpin structured DNA probe, are attached on the surface of the SCF core using a fuzzy nanoassembly process used in conjunction with a biotin-streptavidin-biotin surface attachment strategy. The proposed DNA sensor detects complementary DNA sequences (cDNA) while discriminating sequences differing from the target by just one base. This enables the detection of DNA in unprecedentedly small sample volumes (nL scale) and is, to the best of our knowledge, the first specific DNA detection using a DNA probe immobilized within a microstructured optical fiber.

High temperature fiber sensor with high sensitivity based on core diameter mismatch.

We report a simple fiber sensor for measurement of high temperature with high sensitivity. The sensing head is a multimode-single mode-multimode (MM-SM-MM) fiber configuration formed by splicing a section of uncoated single mode fiber (SMF) with two short sections of multimode fibers (MMF) whose core is composed of pure silica. Because of the mode-field mismatch at the splicing points of the SMF with 2 sections of MMFs, as well as index matching between the core of the MMF and the cladding of the SMF, optical power from the lead-in fiber can be partly coupled to the cladding modes of the SMF through the MMF. The cladding modes of the SMF then re-coupled to the lead-out fiber, in the same fashion. Due to the effective index difference between the core and cladding modes, an interference pattern in the transmission spectrum of the proposed device was obtained. The interference pattern was found to shift to the longer wavelength region with respect to temperature variation. The temperature sensor can measure temperature stably up to more than 900 degrees C with sensitivity of 0.088 nm/ degrees C.