Identification of 'Candidatus Liberibacter asiaticus', the Huanglongbing Bacterium, in Citrus from Colombia

'Candidatus Liberibacter' spp. are the most prevalent microorganisms in the citrus plant, associated with citrus huanglongbing, which are transmitted by psyllid vectors. In Colombia, the vector Diaphorina citri Kuwayama has been reported in different regions, but 'Ca. Liberibacter asiaticus' (CLas) has only been detected in insect vectors, not in citrus host plants. To identify the presence and quantify the pathogen in citrus tissues, we employed a combined strategy that involved three techniques based on polymerase chain reaction (PCR). First, we used endpoint PCR with specific primers for CLas (OI1/OI2c) to confirm the infection. Second, we used qPCR with specific primers CIT295a/CIT298 designed on 16S rDNA gene regions to quantify the pathogen load. Finally, we used droplet digital PCR (ddPCR) to determine the copy number of the pathogen in citrus tissues using the β-subunit of the ribonucleotide reductase gene (nrdB) that is specific to CLas. We identified the presence of CLas in citrus plants for the first time in Colombia and quantified its titer in the plant tissue. We employed ddPCR and qPCR to provide crucial information for the country's disease management, control strategies, and general crop health.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Detection of Macrolide and/or Fluoroquinolone Resistance Genes in Mycoplasma genitalium Strains Isolated from Men in the Northwest Region of Croatia in 2018-2023

Mycoplasma genitalium (M. genitalium) poses a significant public health challenge due to its association with non-gonococcal urethritis (particularly in men) and antimicrobial resistance. However, despite the prevalence of M. genitalium infections and the rise in resistance rates, routine testing and surveillance remain limited. This is the first study from Croatia that aimed to assess the prevalence and trends of resistance in M. genitalium strains isolated from male individuals by detecting macrolide and fluoroquinolone resistance genes. The study also aimed to explore the factors associated with resistance and changes in resistance patterns over time. Urine samples collected from male individuals in the Zagreb County and northwest region of Croatia between 2018 and 2023 were tested for M. genitalium with the use of molecular methods. Positive samples were subjected to DNA extraction and multiplex tandem polymerase chain reaction (MT-PCR) targeting genetic mutations associated with macrolide (23S rRNA gene) and fluoroquinolone (parC gene) resistance. Of the 8073 urine samples tested from 6480 male individuals (and following the exclusion of repeated specimens), we found that the prevalence of M. genitalium infection was 2.2%. Macrolide resistance was observed in 60.4% of strains, while fluoroquinolone resistance was found in 19.2%. Co-resistance to both antibiotics was present in 18.2% of cases. A statistically significant increase in fluoroquinolone resistance was noted over the study period (p = 0.010), but this was not evident for azithromycin resistance (p = 0.165). There were no statistically significant differences in resistance patterns between age groups, whereas re-testing of patients revealed dynamic changes in resistance profiles over time. The high burden of macrolide resistance and increasing fluoroquinolone resistance underscore the urgent need for comprehensive resistance testing and surveillance programs. The implementation of resistance-guided treatment strategies, along with enhanced access to molecular diagnostics, is pivotal for effectively managing M. genitalium infections.

Label-Free Citrate-Stabilized Silver Nanoparticles-Based, Highly Sensitive, Cost-Effective, and Rapid Visual Method for the Differential Detection of Mycobacterium tuberculosis and Mycobacterium bovis

Tuberculosis poses a global health challenge, and it demands improved diagnostics and therapies. Distinguishing between Mycobacterium tuberculosis (M. tb) and Mycobacterium bovis (M. bovis) infections holds critical "One Health" significance due to the zoonotic nature of these infections and inherent resistance of M. bovis to pyrazinamide, a key part of the directly observed treatment, short-course (DOTS) regimen. Furthermore, most of the currently used molecular detection methods fail to distinguish between the two species. To address this, our study presents an innovative molecular-biosensing strategy. We developed a label-free citrate-stabilized silver nanoparticle aggregation assay that offers sensitive, cost-effective, and swift detection. For molecular detection, genomic markers unique to M. tb and M. bovis were targeted using species-specific primers. In addition to amplifying species-specific regions, these primers also aid the detection of characteristic deletions in each of the mycobacterial species. Post polymerase chain reaction (PCR), we compared two highly sensitive visual detection methods with respect to the traditional agarose gel electrophoresis. The paramagnetic bead-based bridging flocculation assay successfully discriminates M. tb from M. bovis with a sensitivity of ∼40 bacilli. The second strategy exploits citrate-stabilized silver nanoparticles, which aggregate in the absence of amplified dsDNA on the addition of sodium chloride (NaCl). This technique enables the precise, sensitive, and differential detection of as few as ∼4 bacilli. Our study hence advances tuberculosis detection, overcoming the challenges of M. tb and M. bovis differentiation and offering a quicker alternative to time-consuming methods.

Rapid Minimum Inhibitory Concentration (MIC) Analysis Using Lyophilized Reagent Beads in a Novel Multiphase, Single-Vessel Assay

Antimicrobial resistance (AMR) is a global threat fueled by incorrect (and overuse) of antibiotic drugs, giving rise to the evolution of multi- and extreme drug-resistant bacterial strains. The longer time to antibiotic administration (TTA) associated with the gold standard bacterial culture method has been responsible for the empirical usage of antibiotics and is a key factor in the rise of AMR. While polymerase chain reaction (PCR) and other nucleic acid amplification methods are rapidly replacing traditional culture methods, their scope has been restricted mainly to detect genotypic determinants of resistance and provide little to no information on phenotypic susceptibility to antibiotics. The work presented here aims to provide phenotypic antimicrobial susceptibility testing (AST) information by pairing short growth periods (~3-4 h) with downstream PCR assays to ultimately predict minimum inhibitory concentration (MIC) values of antibiotic treatment. To further simplify the dual workflows of the AST and PCR assays, these reactions are carried out in a single-vessel format (PCR tube) using novel lyophilized reagent beads (LRBs), which store dried PCR reagents along with primers and enzymes, and antibiotic drugs separately. The two reactions are separated in space and time using a melting paraffin wax seal, thus eliminating the need to transfer reagents across different consumables and minimizing user interactions. Finally, these two-step single-vessel reactions are multiplexed by using a microfluidic manifold that allows simultaneous testing of an unknown bacterial sample against different antibiotics at varying concentrations. The LRBs used in the microfluidic system showed no interference with the bacterial growth and PCR assays and provided an innovative platform for rapid point-of-care diagnostics (POC-Dx).

An Overview of Systematic Reviews of Polymerase Chain Reaction (PCR) for the Diagnosis of Invasive Aspergillosis in Immunocompromised People: A Report of the Fungal PCR Initiative (FPCRI)-An ISHAM Working Group

This overview of reviews (i.e., an umbrella review) is designed to reappraise the validity of systematic reviews (SRs) and meta-analyses related to the performance of Aspergillus PCR tests for the diagnosis of invasive aspergillosis in immunocompromised patients. The methodological quality of the SRs was assessed using the AMSTAR-2 checklist; the quality of the evidence (QOE) within each SR was appraised following the GRADE approach. Eight out of 12 SRs were evaluated for qualitative and quantitative assessment. Five SRs evaluated Aspergillus PCR on bronchoalveolar lavage fluid (BAL) and three on blood specimens. The eight SRs included 167 overlapping reports (59 evaluating PCR in blood specimens, and 108 in BAL), based on 107 individual primary studies (98 trials with a cohort design, and 19 with a case-control design). In BAL specimens, the mean sensitivity and specificity ranged from 0.57 to 0.91, and from 0.92 to 0.97, respectively (QOE: very low to low). In blood specimens (whole blood or serum), the mean sensitivity ranged from 0.57 to 0.84, and the mean specificity from 0.58 to 0.95 (QOE: low to moderate). Across studies, only a low proportion of AMSTAR-2 critical domains were unmet (1.8%), demonstrating a high quality of methodological assessment. Conclusions. Based on the overall methodological assessment of the reviews included, on average we can have high confidence in the quality of results generated by the SRs.

An updated systemic review and meta-analysis on human papillomavirus in breast carcinogenesis

Background

Breast Cancer (BC) stands out as the widely prevalent malignancy among all the types of cancer affecting women worldwide. There is significant evidence that the pathogenicity of BC may be altered by Human Papillomavirus (HPV) infection; however, conclusive data are not yet available.

Methods

By searching five databases, including EMBASE, IBECS, PubMed, Scopus, Science Direct, Google Scholar, and Web of Science, a thorough systematic analysis was conducted on the prevalence of HPV in BC patients from 1990 to June 30, 2022. After applying extensive eligibility criteria, we selected 74 publications for further analysis based on the prevalence of HPV infections in breast tissues. All of the data were analyzed using a random-effects meta-analysis, Cochran Q test and I2 statistic were used to calculate the heterogeneity of the prevalence among these studies using subgroup analysis. Variations in the HPV prevalence estimates in different subgroups were evaluated by subgroup meta-analysis.

Results

In total, 3156 studies were initially screened, resulting in 93 full-text studies reviewed, with 74 meeting inclusion criteria. Among a total of 7156 BC biopsies, the pool prevalence of HPV was 25.6% (95% CI= 0.24-0.33, τ2 = 0.0369 with significant heterogeneity between estimates (I 2 = 97% and p< 0.01). Consequently, 45 studies with available controls were further studied, and the prevalence of HPV in case-control studies was 26.2% with overall odds 5.55 (95% CI= 3.67-8.41, I 2 = 38%, τ2 = 1.4878, p< 0.01). Further subgroup analysis of HPV revealed HPV-16 had a maximum prevalence of 9.6% (95% CI= 3.06-11.86, I 2 = 0%, τ2 = 0.6111, p< 0.01). Among different geographical regions, Europe reported the maximum prevalence of HPV, i.e., 39.2% (95% CI=1.29-7.91, I 2 = 18%, τ2 = 1.2911, p< 0.01). Overall distribution showed HPV-18 was a frequent HPV subtype reported in Australia.

Conclusion

Current study provides a global estimate of HPV prevalence in BC patients and demonstrates a significant association between this virus and BC etiology. Nevertheless, we recommend further investigation into the underlying mechanism is essential to validate this hypothesis.

Low-Cost, Real-Time Polymerase Chain Reaction System with Integrated RNA Extraction

Rapid, easy-to-use, and low-cost systems for biological sample testing are important for point-of-care diagnostics and various other health applications. The recent pandemic of Coronavirus Disease 2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed an urgent need to rapidly and accurately identify the genetic material of SARS-CoV-2, an enveloped ribonucleic acid (RNA) virus, in upper respiratory specimens from people. In general, sensitive testing methods require genetic material extraction from the specimen. Unfortunately, current commercially available extraction kits are expensive and involve time-consuming and laborious extraction procedures. To overcome the difficulties associated with common extraction methods, we propose a simple enzymatic assay for the nucleic acid extraction step using heat mediation to improve the polymerase chain reaction (PCR) reaction sensitivity. Our protocol was tested on Human Coronavirus 229E (HCoV-229E) as an example, which comes from the large coronaviridae family of viruses that affect birds, amphibians, and mammals, of which SARS-CoV-2 is a member. The proposed assay was performed using a low-cost, custom-made, real-time PCR system that incorporates thermal cycling and fluorescence detection. It had fully customizable reaction settings to allow versatile biological sample testing for various applications, including point-of-care medical diagnosis, food and water quality testing, and emergency health situations. Our results show that heat-mediated RNA extraction is a viable extraction method when compared to commercial extraction kits. Further, our study showed that extraction has a direct impact on purified laboratory samples of HCoV-229E, but no direct impact on infected human cells. This is clinically relevant, as it allows us to circumvent the extraction step on clinical samples when using PCR.

Analysis of differentially expressed genes on human X chromosome harboring large deletion induced by X-rays

We examined here normal human cells with large deletions encompassing the hypoxanthine-phosphoribosyltransferase 1 (HPRT1) gene on X chromosome. Expression levels of genes on X chromosome were analyzed by microarray and RT-qPCR method, and differentially expressed genes (DEGs) were extracted. We found that DEGs were not limited to the genes flanking deleted regions but spread over the entire X chromosome. Interestingly, the gene regulation patterns were similar to a large extent among independent clones that have similar-sized large deletions involving the HPRT1 gene. Thus, it is indicated that an impact of large deletion on possible epigenetic transcriptional regulation is not limited to the regions proximal to the deletion region.

Genetic Determinants of Macrolide and Fluoroquinolone Resistance in Mycoplasma genitalium and Their Prevalence in Moscow, Russia

Macrolide (MLR) and fluoroquinolone (FQR) resistance in Mycoplasma genitalium (MG) has recently become a major problem worldwide. The available data on the prevalence of MLR and FQR in MG in Russia are limited. In this study, we aimed to evaluate the prevalence and pattern of mutations in 213 MG-positive urogenital swabs from patients in Moscow between March 2021 and March 2022. MLR- and FQR-associated mutations were searched in 23S rRNA as well as in the parC and gyrA genes using Sanger sequencing. The prevalence of MLR was 55/213 (26%), with A2059G and A2058G substitutions being the two most common variants (36/55, 65%, and 19/55, 35%, respectively). FQR detection showed 17% (37/213); two major variants were D84N (20/37, 54%) and S80I (12/37, 32.4%) and three minor variants were S80N (3/37, 8.1%), D84G (1/37, 2.7%), and D84Y (1/37, 2.7%). Fifteen of the fifty-five MLR cases (27%) simultaneously harbored FQR. This study revealed the high frequency of MLR and FQR. We conclude that the improvement of patient examination algorithms and therapeutic approaches should be combined with the routine monitoring of antibiotic resistance based on the sensitivity profiles presented. Such a complex approach will be essential for restraining the development of treatment resistance in MG.

α- and β-Globin Gene Mutations in Individuals with Hemoglobinopathies in the Chattogram and Sylhet Regions of Bangladesh

Hemoglobinopathies, including α- and β-thalassemias and sickle cell disease, are among the most widely disseminated hereditary blood disorders worldwide. Bangladesh is considered a hotspot for hemoglobinopathies, and these diseases cause a significant health concern in the country. However, the country has a dearth of knowledge on the molecular etiology and carrier frequency of thalassemias, primarily due to a lack of diagnostic facilities, limited access to information, and the absence of efficient screening programs. This study sought to investigate the spectrum of mutations underlying hemoglobinopathies in Bangladesh. We developed a set of polymerase chain reaction (PCR)-based techniques to detect mutations in α- and β-globin genes. We recruited 63 index subjects with previously diagnosed thalassemia. Along with age- and sex-matched control subjects, we assessed several hematological and serum indices and genotyped them using our PCR-based methods. We identified that parental consanguinity was associated with the occurrence of these hemoglobinopathies. Our PCR-based genotyping assays identified 23 HBB genotypes, with the codons 41/42 (-TTCT) (HBB: c.126_129delCTTT) mutation leading the spectrum. We also observed the presence of cooccurring HBA conditions, of which the participants were not aware. All index participants in this study were on iron chelation therapies, yet we found they had very high serum ferritin (SF) levels, indicating inefficient management of the individuals undergoing such treatments. Overall, this study provides essential information on the hemoglobinopathy mutation spectrum in Bangladesh and highlights the need for nationwide screening programs and an integrated policy for diagnosing and managing individuals with hemoglobinopathies.

Ultrafast Nucleic Acid Detection Equipment with Silicon-Based Microfluidic Chip

Recently, infectious diseases, such as COVID-19, monkeypox, and Ebola, are plaguing human beings. Rapid and accurate diagnosis methods are required to preclude the spread of diseases. In this paper, an ultrafast polymerase chain reaction (PCR) equipment is designed to detect virus. The equipment consists of a silicon-based PCR chip, a thermocycling module, an optical detection module, and a control module. Silicon-based chip, with its thermal and fluid design, is used to improve detection efficiency. A thermoelectric cooler (TEC), together with a computer-controlled proportional-integral-derivative (PID) controller, is applied to accelerate the thermal cycle. A maximum of four samples can be tested simultaneously on the chip. Two kinds of fluorescent molecules can be detected by optical detection module. The equipment can detect viruses with 40 PCR amplification cycles in 5 min. The equipment is portable, easily operated, and low equipment cost, which shows great potential in epidemic prevention.

Occurrence, Role, and Challenges of MicroRNA in Human Breast Milk: A Scoping Review

MicroRNAs are non-coding segments of RNA involved in the epigenetic modulation of various biological processes. Their occurrence in biological fluids, such as blood, saliva, tears, and breast milk, has drawn attention to their potential influence on health and disease development. Hundreds of microRNAs have been isolated from breast milk, yet the evidence on their function remains inconsistent and inconclusive. The rationale for the current scoping review is to map the evidence on the occurrence, characterization techniques, and functional roles of microRNAs in breast milk. The review of the sources of this evidence highlights the need to address methodological challenges to achieve future advances in understanding microRNAs in breast milk, particularly their role in conditions such as neoplasms. Nonetheless, remarkable progress has been made in characterizing the microRNA profiles of human breast milk.

Closed-Loop Microreactor on PCB for Ultra-Fast DNA Amplification: Design and Thermal Validation

Polymerase chain reaction (PCR) is the most common method used for nucleic acid (DNA) amplification. The development of PCR-performing microfluidic reactors (μPCRs) has been of major importance, due to their crucial role in pathogen detection applications in medical diagnostics. Closed loop (CL) is an advantageous type of μPCR, which uses a circular microchannel, thus allowing the DNA sample to pass consecutively through the different temperature zones, in order to accomplish a PCR cycle. CL μPCR offers the main advantages of the traditional continuous-flow μPCR, eliminating at the same time most of the disadvantages associated with the long serpentine microchannel. In this work, the performance of three different CL μPCRs designed for fabrication on a printed circuit board (PCB) was evaluated by a computational study in terms of the residence time in each thermal zone. A 3D heat transfer model was used to calculate the temperature distribution in the microreactor, and the residence times were extracted by this distribution. The results of the computational study suggest that for the best-performing microreactor design, a PCR of 30 cycles can be achieved in less than 3 min. Subsequently, a PCB chip was fabricated based on the design that performed best in the computational study. PCB constitutes a great substrate as it allows for integrated microheaters inside the chip, permitting at the same time low-cost, reliable, reproducible, and mass-amenable fabrication. The fabricated chip, which, at the time of this writing, is the first CL μPCR chip fabricated on a PCB, was tested by measuring the temperatures on its surface with a thermal camera. These results were then compared with the ones of the computational study, in order to evaluate the reliability of the latter. The comparison of the calculated temperatures with the measured values verifies the accuracy of the developed model of the microreactor. As a result of that, a total power consumption of 1.521 W was experimentally measured, only ~7.3% larger than the one calculated (1.417 W). Full validation of the realized CL μPCR chip will be demonstrated in future work.

Identification of Fish Species and Targeted Genetic Modifications Based on DNA Analysis: State of the Art

Food adulteration is one of the most serious problems regarding food safety and quality worldwide. Besides misleading consumers, it poses a considerable health risk associated with the potential non-labeled allergen content. Fish and fish products are one of the most expensive and widely traded commodities, which predisposes them to being adulterated. Among all fraud types, replacing high-quality or rare fish with a less valuable species predominates. Because fish differ in their allergen content, specifically the main one, parvalbumin, their replacement can endanger consumers. This underlines the need for reliable, robust control systems for fish species identification. Various methods may be used for the aforementioned purpose. DNA-based methods are favored due to the characteristics of the target molecule, DNA, which is heat resistant, and the fact that through its sequencing, several other traits, including the recognition of genetic modifications, can be determined. Thus, they are considered to be powerful tools for identifying cases of food fraud. In this review, the major DNA-based methods applicable for fish meat and product authentication and their commercial applications are discussed, the possibilities of detecting genetic modifications in fish are evaluated, and future trends are highlighted, emphasizing the need for comprehensive and regularly updated online database resources.

High incidence of Pneumocystis jirovecii pneumonia in oncological patients: a 19-year study

AIM

In the past, Pneumocystis jirovecii belonged to the Protozoa group, but is currently taxonomically included in the kingdom Fungi. P. jirovecii is an opportunistic pathogen, responsible for pneumocystis pneumonia with frequent complications of immunocompromised patients. Delayed initiation of appropriate therapy increases the risk of death in immunocompromised patient. The aim of this work was to determine and evaluate the reliability of methods of laboratory diagnosis of pneumocystosis used in routine laboratories as well as the occurrence of this disease in patients from Slovakia during 19 years.

MATERIAL AND METHODS

The diagnosis is based on microscopic examination (Giemsa- and Gram-Weigert-staining) and detection of parasite DNA by classical or real-time PCR in bronchoalveolar lavage and sputum.

RESULTS

Pneumocysts were detected in 190 persons (5.7%) from the whole group of patients. Cancer patients represented the riskiest group in terms of pneumocystosis, which was confirmed by the highest percentage (57.9%) of individuals infected with P. jirovecii. Compared with the PCR, 33.7% sensitivity and 100% specificity of microscopy was calculated by using a binary classification test. Molecular methods are more sensitive in the detection of P. jirovecii compared to microscopic evidence and currently represent a reliable detection system in the diagnosis of pneumocystosis.

CONCLUSION

In view of the increasing number of immunocompromised persons, diagnostics of P. jirovecii in patients with pulmonary complications is essential. This was also confirmed in our study, where the number of examinations and detection of this opportunistic pathogen increased over the years.

Analysis of Salivary Bacterial Community by Direct PCR and High Resolution Melting Curve and Its Forensic Applications

OBJECTIVES

To develop a rapid test for salivary bacterial community based on direct PCR (dPCR) and high resolution melting (HRM) curve analysis, to evaluate its application value in forensic medicine.

METHODS

The salivary bacteria were collected by centrifugation and then resuspended in Tris-EDTA (TE) buffer, and directly used as the template for amplification and HRM curve analysis (dPCR-HRM) of the 16S rDNA V4 region. The genotype confidence percentage (GCP) of the HRM profiles compared with the reference profile was calculated. The template DNA was extracted by traditional kit and then PCR-HRM (namely kPCR-HRM) was used as reference to validate the feasibility of dPCR-HRM. The gradient dilution templates, population samples and simulated salivary stains were analyzed by dPCR-HRM to evaluate its sensitivity, typing ability and adaptability.

RESULTS

Using dPCR-HRM method, the HRM profiles of salivary bacterial community were obtained within 90 minutes. The GCP between dPCR-HRM and kPCR-HRM was greater than 95.85%. For general individuals, the HRM type of bacterial community could be determined with 0.29 nL saliva by dPCR-HRM. The 61 saliva samples could be divided into 10 types. The typing of salivary stains deposited within 8 h was the same as those of fresh saliva (GCP>90.83%).

CONCLUSIONS

dPCR-HRM technology can be used for rapid typing of salivary bacterial community, and has the advantage of low cost and simple operation.

Antimicrobial Susceptibility and Genetic Prevalence of Extended-Spectrum β-Lactamases in Gram-Negative Rods Isolated from Clinical Specimens in Pakistan

The prevalence of extended-spectrum β-lactamase (ESBL) genes has increased remarkably, resulting in multidrug-resistant gram-negative rods (GNRs) in clinical specimens. This cross-sectional study aimed to determine the antimicrobial susceptibility of ESBL-producing GNRs and its correlation with corresponding genes. Two hundred and seventy-two (n = 272) samples were evaluated for the molecular identification of ESBL genes by polymerase chain reaction after confirmation with the modified double-disc synergy test. E. coli 64.0% (n = 174) was the most prevalent ESBL producer, followed by Klebsiella species 27.2% (n = seventy-four), Acinetobacter species 6.6% (n = eighteen) and others 2.2% (n = six). These ESBL-producing isolates showed resistance to β-lactam antibiotics, i.e., sulbactam/cefoperazone (41.5%), piperacillin/tazobactam (39.3%), meropenem (36.0%), imipenem (34.2%) and non- β-lactam antibiotics, i.e., nalidixic acid (89.0%), co-trimoxazole (84.9%), ciprofloxacin (82.4%), gentamicin (46.3%), nitrofurantoin (24.6%), amikacin (19.9%) and fosfomycin (19.9%). The incidences of the ESBLs-producing genes bla_CTX-M, bla_TEM, bla_OXA and bla_SHV were 91.2%, 61.8%, 39.3% and 17.6%, respectively. Among nine multiple-gene combinations, bla_CTX-M + bla_TEM (30.5%) was the most prevalent combination, followed by bla_CTX-M + bla_OXA + bla_TEM (14.0%), bla_CTX-M + bla_OXA (13.6%), bla_CTX-M + bla_TEM + bla_SHV (7.0%), bla_CTX-M + bla_SHV (2.2%), bla_CTX-M + bla_OXA + bla_SHV (2.2%) and bla_OXA + bla_TEM (1.8%). ESBLs producing GNRs carrying bla_CTX-M, bla_TEM, bla_OXA and bla_SHV showed resistances to β-lactam antibiotics, i.e., ampicillin, amoxillin-clavulanic acid, cefotaxime and ceftazidime but were susceptible to carbapenems (meropenem and imipenem), β-lactam-β-lactamase inhibitor combination (piperacillin/tazobactam) and non-β-lactam antibiotics i.e., aminoglycoside (amikacin and gentamicin), nitrofurantoin and fosfomycin. These antibiotics that demonstrated activity may be used to treat infections in clinical settings.

Pipette Olympics: An Engaging Exercise for Undergraduate Laboratory Training

Pipetting is an important technique used in almost every molecular neuroscience method including but not limited to, PCR, reverse transcription, immunohistochemistry, chromatin immunoprecipitation, and cell culture. The COVID-19 pandemic has robbed the undergraduate population of time to practice in person laboratory techniques. In response, we have devised a standardized, quick, and fun way to instruct students on the fundamentals of pipetting, serial dilutions, and basic statistical analysis. Here, we offer a standardized protocol for instructors to use to teach undergraduates valuable skills while providing friendly competition. We also offer an example of an undergraduate performing the steps of this protocol with example results and the results from three separate undergrads' first two attempts. This exercise provides laboratories with a method to reintroduce undergraduates to lab basics while standardizing the training thereby saving time lost to the pandemic.

Application of Microfluidics for Bacterial Identification

Bacterial infections continue to pose serious public health challenges. Though anti-bacterial therapeutics are effective remedies for treating these infections, the emergence of antibiotic resistance has imposed new challenges to treatment. Often, there is a delay in prescribing antibiotics at initial symptom presentation as it can be challenging to clinically differentiate bacterial infections from other organisms (e.g., viruses) causing infection. Moreover, bacterial infections can arise from food, water, or other sources. These challenges have demonstrated the need for rapid identification of bacteria in liquids, food, clinical spaces, and other environments. Conventional methods of bacterial identification rely on culture-based approaches which require long processing times and higher pathogen concentration thresholds. In the past few years, microfluidic devices paired with various bacterial identification methods have garnered attention for addressing the limitations of conventional methods and demonstrating feasibility for rapid bacterial identification with lower biomass thresholds. However, such culture-free methods often require integration of multiple steps from sample preparation to measurement. Research interest in using microfluidic methods for bacterial identification is growing; therefore, this review article is a summary of current advancements in this field with a focus on comparing the efficacy of polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and emerging spectroscopic methods.

Cost-effectiveness of screening with polymerase chain reaction for Helicobacter pylori to prevent gastric cancer and peptic ulcers

Background

Helicobacter pylori (H. pylori) is a major risk factor for gastric cancer. Screening and treatment of H. pylori may reduce the risk of gastric cancer and peptic ulcer disease (PUD). Polymerase chain reaction (PCR) of gastric biopsies provides superior sensitivity and specificity for the detection of H. pylori. This study explores whether population-based H. pylori screening with PCR is cost-effective in the US.

Methods

A Markov cohort state-transition model was developed to compare three strategies: no screening with opportunistic eradication, ¹³C-UBT population screening and treating of H. pylori, and PCR population screening and treating of H. pylori. Estimates of risks and costs were obtained from published literature. Since the efficacy of H. pylori therapy in gastric cancer prevention is not certain, we broadly varied the benefit 30-100% in sensitivity analysis.

Results

PCR screening was cost-effective and had an incremental-cost effectiveness ratio per quality adjusted life-year (QALY) of $38,591.89 when compared to ¹³C-UBT strategy with an ICER of $2,373.43 per QALY. When compared to no screening, PCR population screening reduced cumulative gastric cancer incidence from 0.84% to 0.74% and reduced PUD risk from 14.8% to 6.0%. The cost-effectiveness of PCR screening was robust to most parameters in the model.

Conclusions

Our modeling study finds PCR screening and treating of H. pylori to be cost-effective in the prevention of gastric cancer and PUD. However, the potential negative consequences of H. pylori eradication such as antibiotic resistance could change the balance of benefits of population screening.

Epstein-Barr Virus Detection in the Central Nervous System of HIV-Infected Patients

Simply detecting Epstein-Barr virus deoxyribonucleic acid (EBV-DNA) is insufficient to diagnose EBV-associated diseases. The current literature around EBV-DNA detection from cerebrospinal fluid (CSF) in human immunodeficiency virus (HIV)-positive non-lymphoma patients was systematically reviewed and a meta-analysis reporting the estimated pooled prevalence in this population when PCR methods are employed, targeting different sequence segments within the EBV genome, was conducted. Using a combination of three key concepts-Epstein-Barr virus detection, central nervous system disease, and human cerebrospinal fluid-and their MeSH terms, the PubMed database was searched. A total of 273 papers reporting the detection of EBV in CNS were screened, of which 13 met the inclusion criteria. The meta-analysis revealed a pooled prevalence of EBV-DNA in CSF of 20% (CI: 12-31%). The highest pooled prevalence was from studies conducted on the African population at 39% (CI: 27-51%). The investigation of the presence of EBV-DNA in the CSF was also very varied, with several gene targets used. While most patients from the articles included in this review and meta-analysis were symptomatic of CNS disorders, the pathogenicity of EBV in non-lymphoma HIV patients when detected in CSF has still not been determined. The presence of EBV-DNA in the CNS remains a concern, and further research is warranted to understand its significance in causing CNS disorders.

The Influence of DNA Extraction Methods on Species Identification Results of Seafood Products

In terms of species identification, the ultimate aim of extracting DNA is the subsequent amplification of the selected marker; therefore, the quality and quantity of the extracted DNA must be sufficient for PCR-based methods. The purpose of this study is to compare five DNA extraction methods according to the parameters of quantity, quality and simplicity, among others, in order to determine the most suitable method for identification for Cephalopoda, Gadiformes and Pleuronectiformes. The Wizard DNA clean-up system kit (Promega), MPure-12^TM automated nucleic acid purification system (MP Biomedicals), Chelex 100 resin (Biorad), DNeasy blood and tissue kit (Qiagen) and a swab method were examined. The obtained DNA quantity was determined by fluorescence, and quality was evaluated with ratios of absorbance of A260/A280 and A260/A230 by agarose gel visualization of the extracts and by analyzing the success of PCR amplifications of 720 bp fragments of cytochrome c oxidase I (COI) for Cephalopods and 465 bp fragments of cytochrome b for Gadiformes and Pleuronectiformes. Statistical results confirmed significant differences between the tested methods according to yield, efficiency and purity and no significant differences with respect to the species employed. The best yields were obtained with the Wizard kit, whereas other methods stand out in terms of their affordability (Chelex) and automation (Mpure).

Detection of Five Types of HPV Genotypes Causing Anogenital Warts (Condyloma Acuminatum) Using PCR-Tm Analysis Technology

Objectives

Condyloma acuminatum (CA) is a common sexually transmitted disease caused by human papillomavirus (HPV) infection. We established a high-throughput, simple, low-cost, and accurate HPV-typing assay (polymerase chain reaction-melting temperature [PCR-Tm] analysis) to detect HPV in CA.

Materials and Methods

We detected 280 cervical scraping samples, including positive samples of HPV-6 (26), HPV-11 (12), HPV-16 (22), HPV-42 (18), HPV-43 (25), HPV-multiple (19), HPV- other type (58), and HPV-negative samples (100). All samples were compared by PCR-Tm analysis and a flow fluorescence hybridization assay. Sequencing was used to confirm the results of the PCR-Tm analysis.

Results

PCR-Tm analysis was specific for each genotype (HPV-6, HPV-11, HPV-16, HPV-42, and HPV-43). The sensitivity of the PCR-Tm analysis assay for each genotype was 10³, 10³, 10³, 10³, and 10² copies/reaction, respectively. Most of the 158 samples, including 58 HPV-other type positive and 100 HPV-negative samples tested by the flow fluorescence hybridization assay, were tested negative by PCR-Tm analysis. For the 122 remaining samples, 26 HPV-6, 12 HPV-11, 22 HPV-16, 18 HPV-42, 25 HPV-43, and 19 multiple HPV infections were detected through PCR-Tm analysis. In total, 25 HPV-6, 12 HPV-11, 21 HPV-16, 18 HPV-42, 25 HPV-43, and only 10 multiple HPV infections were detected by the flow fluorescence hybridization assay. The kappa coefficient for the analysis of PCR-Tm analysis and flow fluorescence hybridization assay was 0.940 (P < 0.0001), and the 95% confidence interval of the kappa coefficient was 90.3–97.7%.

Conclusion

PCR-Tm analysis enabled the detection of HPV-6, HPV-11, HPV-16, HPV-42, and HPV-43, including single and multiple infections.

Low-Cost, Real-Time Polymerase Chain Reaction System for Point-of-Care Medical Diagnosis

Global health crises due to the prevailing Coronavirus Disease 2019 (COVID-19) pandemic have placed significant strain on health care facilities such as hospitals and clinics around the world. Further, foodborne and waterborne diseases are not only spreading faster, but also appear to be emerging more rapidly than ever before and are able to circumvent conventional control measures. The Polymerase Chain Reaction (PCR) system is a well-known diagnostic tool for many applications in medical diagnostics, environmental monitoring, and food and water quality assessment. Here, we describe the design, development, and testing of a portable, low-cost, and real-time PCR system that can be used in emergency health crises and resource-poor situations. The described PCR system incorporates real-time reaction monitoring using fluorescence as an alternative to gel electrophoresis for reaction analysis, further decreasing the need of multiple reagents, reducing sample testing cost, and reducing sample analysis time. The bill of materials cost of the described system is approximately $340. The described PCR system utilizes a novel progressive selective proportional–integral–derivative controller that helps in reducing sample analysis time. In addition, the system employs a novel primer-based approach to quantify the initial target amplicon concentration, making it well-suited for food and water quality assessment. The developed PCR system performed DNA amplification at a level and speed comparable to larger and more expensive commercial table-top systems. The fluorescence detection sensitivity was also tested to be at the same level as commercially available multi-mode optical readers, thus making the PCR system an attractive solution for medical point-of-care and food and water quality assessment.

Development and Validation of a Novel and Fast Detection Method for Cannabis sativa: A 19-Plex Short Tandem Repeat Typing System

In recent years, influenced by the legalization of Cannabis sativa in some countries and regions, the number of people who smoke or abuse C. sativa has continuously grown, cases of transnational C. sativa trafficking have also been increasing. Therefore, fast and accurate identification and source tracking of C. sativa have become urgent social needs. In this study, we developed a new 19-plex short tandem repeats (STRs) typing system for C. sativa, which includes 15 autosomal STRs (D02-CANN1, C11-CANN1, 4910, B01-CANN1, E07-CANN1, 9269, B05-CANN1, H06-CANN2, 5159, nH09, CS1, ANUCS 305, 3735, and ANUCS 302 and 9043), two X-chromosome STRs (ANUCS 501 and 1528), one sex-determining marker (DM016, on Y-chromosome), and a quality control marker (DM029, on autosome). The whole polymerase chain reaction (PCR) process could finish within 1 h, making the system suitable for fast detection. The PCR products were detected and separated with an Applied Biosystems 3500XL Genetic Analyser. Developmental validation studies indicated that the 19-plex typing system was accurate, reliable and sensitive, which could also deconvolute mixed C. sativa samples. Specifically, the sensitivity study showed that a full genotyping profile was obtainable with as low as 125 pg of C. sativa DNA. The species specificity study demonstrated that this multiplex has no cross-reactivity with common non C. sativa DNA. In the population study, a total of 162 alleles at 15 autosomal STRs and 14 alleles at two X-chromosome STRs were detected among 85 samples. The efficiency parameters, including the total discrimination power (TDP) and the combined power of exclusion (CPE) of the system, were calculated to exceed 0.999 999 999 999 988 and 0.998 455 889 684 078, respectively, further proving that the system could meet the needs of individual identification. To the extent of the known studies, this is the first study that included the C. sativa sex-determining marker. In conclusion, the developed new 19-plex STR typing system can successfully achieve the purposes of species identification, gender determination, and individual identification, which could be a powerful tool in tracing trade routes of particular drug syndicates or dealers or in linking certain C. sativa to a crime scene.

Molecular Changes in the Glucokinase Gene (GCK) Associated with the Diagnosis of Maturity Onset Diabetes of the Young (MODY) in Pregnant Women and Newborns

BACKGROUND

Diabetes mellitus is the most common metabolic alteration in gestation. Monogenic diabetes or Maturity-Onset Diabetes of the Young (MODY) is a subtype caused by a primary defect in insulin secretion determined by autosomal dominant inheritance.

OBJECTIVES

This study aimed to analyze molecular changes of the Glucokinase gene (GCK) in pregnant women with hyperglycemia during gestation and in their neonates. Case Study and Methods: We collected 201 blood samples, 128 from pregnant patients diagnosed with hyperglycemia and 73 from umbilical cord blood from neonates of the respective patients. DNA extraction and polymerase chain reaction (PCR) were performed to identify molecular changes in the GCK gene.

RESULTS

In a total of 201 samples (128 from mothers and 73 from neonates), we found changes in 21 (10.6%), among which 12 were maternal samples (6.0%) and 9 were neonatal samples (4.5%). DNA sequencing identified two polymorphisms and one deleterious MODY GCK-diagnostic mutation.

CONCLUSION

The prevalence of molecular changes in the Glucokinase gene (GCK) and the deleterious MODY GCK-diagnostic mutation were 9.3% and 0.7%, respectively, in women with hyperglycemia during gestation and 12.5% and 1.3%, respectively, in their neonates. The deleterious MODY GCK mutation identified is associated with a reduction in GCK activity and hyperglycemia. In the other molecular changes identified, it was impossible to exclude phenotypic change despite not having clinical significance. Therefore, these changes may interfere with the management and clinical outcome of the patients.

Profiling the Quality and Quantity of Naturally Induced Antibody Responses Against Pfs230 and Pfs48/45 Among Non-Febrile Children Living in Southern Ghana: A Longitudinal Study

A clear understanding of the properties of naturally induced antibody responses against transmission-blocking vaccine candidates can accelerate the understanding of the development of transmission-blocking immunity. This study characterized the naturally induced IgG responses against two leading transmission-blocking vaccine antigens, Pfs230 and Pfs48/45, in non-febrile children living in Simiw, Ghana. Consecutive sampling was used to recruit 84 non-febrile children aged from 6 to 12 years old into the 6-month (November 2017 until May 2018) longitudinal study. Venous blood (1 ml) was collected once every 2 months and used to determine hemoglobin levels, P. falciparum prevalence using microscopy and polymerase chain reaction, and the levels and relative avidity of IgG responses against Pfs230 and Pfs48/45 using indirect ELISA. IgG levels against Pfs230 and Pfs48/45 decreased from the start (November) to the middle (January) and end (March) of the dry season respectively, then they began to increase. Participants, especially older children (10-12 years old) with active infections generally had lower antibody levels against both antigens. The relative avidities of IgG against both antigens followed the trend of IgG levels until the middle of the dry season, after which the relative avidities of both antigens correlated inversely with the antibody levels. In conclusion, although IgG antibody levels against both Pfs48/45 and Pfs230 began to increase by the early rainy season, they were inversely correlated to their respective relative avidities.

Disseminated Fungal Infection and Fungemia Caused by Trichosporon asahii in a Captive Plumed Basilisk (Basiliscus plumifrons)

Trichosporon spp. are heavily arthroconidiating fungi and widely distributed in nature. Due to the similar fungal morphology, confusion among Trichosporon spp., Geotrichum spp., and Nannizziopsis spp. in reptiles is apparent and cannot be overlooked. Although few reptile Trichosporon isolates have been examined using the newer speciation criteria, the information on Trichosporon asahii in reptiles is still scarce. In the present study, we report the case of disseminated fungal infection and fungemia caused by T. asahii in a captive plumed basilisk (Basiliscus plumifrons). Multiple 0.2-0.5 cm, irregularly shaped, ulcerative nodules on the left hind foot were observed. The animal died due to the non-responsiveness to treatment. A microscopic evaluation revealed the fungal infection that primarily affected the left hind foot and right lung lobe with fungal embolisms in the lung and liver. The molecular identification of the fungal species by the DNA sequences of the ITS regions and D1/D2 gene from the fungal culture and ITS regions, from formalin-fixed paraffin-embedded (FFPE) lung tissues, were completely matched to those of T. asahii. The current report describes the first confirmed case of disseminated fungal infection and fungemia caused by T. asahii in a captive plumed basilisk.

Detection of VAR2CSA-Captured Colorectal Cancer Cells from Blood Samples by Real-Time Reverse Transcription PCR

Simple Summary

Circulating tumor cells are cancer cells that have entered blood or lymphatic vessels wherefrom they might get access to distant body parts and form metastases. The presence of cancer cells in a blood sample can be exploited for non-invasive diagnostic purposes. However, as blood consists of a vast number of healthy red and white blood cells the task of identifying the few potential cancer cells in a sample is a technical challenge. In this study we explore strategies for detecting circulating tumor cells after a pre-enrichment through binding to VAR2CSA protein coupled to magnetic beads. We evaluate the performance of a novel workflow that recognizes and detects the cancer cells based on their gene expression and compare this with the more traditional detection strategy using antibodies for cell staining. The highly sensitive assay presented here could potentially provide a novel strategy for early cancer detection.

Abstract

Analysis of circulating tumor cells (CTCs) from blood samples provides a non-invasive approach for early cancer detection. However, the rarity of CTCs makes it challenging to establish assays with the required sensitivity and specificity. We combine a highly sensitive CTC capture assay exploiting the cancer cell binding recombinant malaria VAR2CSA protein (rVAR2) with the detection of colon-related mRNA transcripts (USH1C and CKMT1A). Cancer cell transcripts are detected by RT-qPCR using proprietary Target Enrichment Long-probe Quantitative Amplified Signal (TELQAS) technology. We validate each step of the workflow using colorectal cancer (CRC) cell lines spiked into blood and compare this with antibody-based cell detection. USH1C and CKMT1A are expressed in healthy colon tissue and CRC cell lines, while only low-level expression can be detected in healthy white blood cells (WBCs). The qPCR reaction shows a near-perfect amplification efficiency for all primer targets with minimal interference of WBC cDNA. Spike-in of 10 cancer cells in 3 mL blood can be detected and statistically separated from control blood using the RT-qPCR assay after rVAR2 capture (p < 0.01 for both primer targets, Mann-Whitney test). Our results provide a validated workflow for highly sensitive detection of magnetically enriched cancer cells.

Sensitivity and Specificity of CD19.CAR-T Cell Detection by Flow Cytometry and PCR

Chimeric-antigen-receptor-T (CAR-T) cells are currently revolutionizing the field of cancer immunotherapy. Therefore, there is an urgent need for CAR-T cell monitoring by clinicians to assess cell expansion and persistence in patients. CAR-T cell manufacturers and researchers need to evaluate transduction efficiency and vector copy number for quality control. Here, CAR expression was analyzed in peripheral blood samples from patients and healthy donors by flow cytometry with four commercially available detection reagents and on the gene level by quantitative polymerase chain reaction (qPCR). Flow cytometric analysis of CAR expression showed higher mean CAR expression values for CD19 CAR detection reagent and the F(ab')2 antibody than Protein L and CD19 Protein. In addition, the CD19 CAR detection reagent showed a significantly lower median background staining of 0.02% (range 0.007-0.06%) when compared to the F(ab')2 antibody, CD19 protein and Protein L with 0.80% (range 0.47-1.58%), 0.65% (range 0.25-1.35%) and 0.73% (range 0.44-1.23%). Furthermore, flow cytometry-based CAR-T cell frequencies by CD19 CAR detection reagent showed a good correlation with qPCR results. In conclusion, quality control of CAR-T cell products can be performed by FACS and qPCR. For the monitoring of CAR-T cell frequencies by FACS in patients, CAR detection reagents with a low background staining are preferable.

Molecular Detection of Borrelia Bacteria in Cerebrospinal Fluid-Optimisation of Pre-Analytical Sample Handling for Increased Analytical Sensitivity

The main tools for clinical diagnostics of Lyme neuroborreliosis (LNB) are based on serology, i.e., detection of antibodies in cerebrospinal fluid (CSF). In some cases, PCR may be used as a supplement, e.g., on CSF from patients with early LNB. Standardisation of the molecular methods and systematic evaluation of the pre-analytical handling is lacking. To increase the analytical sensitivity for detection of Borrelia bacteria in CSF by PCR targeting the 16S rRNA gene, parameters were systematically evaluated on CSF samples spiked with a known amount of cultured Borrelia bacteria. The results showed that the parameters such as centrifugation time and speed, the use of complementary DNA as a template (in combination with primers and a probe aiming at target gene 16S rRNA), and the absence of inhibitors (e.g., erythrocytes) had the highest impact on the analytical sensitivity. Based on these results, a protocol for optimised handling of CSF samples before molecular analysis was proposed. However, no clinical evaluation of the proposed protocol has been done so far, and further investigations of the diagnostic sensitivity need to be performed on well-characterised clinical samples from patients with LNB.

The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients

Rapid and reliable detection of severe acute respiratory syndrome coronavirus 2 mutations are significant to control the contagion and spread rate of the virus. We aimed to evaluate the N501Y mutation rate in randomly chosen positive patients with the polymerase chain reaction (PCR). The evaluation and analysis of the data with a retrospective approach in cases with mutations, in terms of public health, will contribute to the literature on the global pandemic that affects our society. Public health authorities will take the necessary precautions and evaluate the current situation. The N501Y mutation was detected in patients with positive Covid‐19 PCR test results. The positive samples were examined based on the 6‐carboxy‐fluorescein (FAM) channel in reverse transcription PCR (RT‐PCR) quantitation cycle (Cq) values as low Cq (<25), medium Cq (25–32), and high Cq (32–38) groups. In the study, 2757 (19.7%) of 13 972 cases were detected as mutation suspects and 159 (5.8%) of them were found to have mutations. The ages of the cases with mutations ranged from 1 to 88 years (mean age of 40.99 ± 17.55). 49.7% (n = 79) of the cases with mutations were male, and 50.3% (n = 80) were female. When the RT‐PCR‐Cq results were examined, it was seen that it varied between 11.3 and 35.03, with an average of 20.75 ± 3.32.

Is point-of-care testing feasible and safe in care homes in England? An exploratory usability and accuracy evaluation of a point-of-care polymerase chain reaction test for SARS-CoV-2

Introduction

Reliable rapid testing for COVID-19 is needed in care homes to reduce the risk of outbreaks and enable timely care. This study aimed to examine the usability and test performance of a point of care polymerase chain reaction (PCR) test for detection of SARS-CoV-2 (POCKIT^TM Central) in care homes.

Methods

POCKIT^TM Central was evaluated in a purposeful sample of four UK care homes. Test agreement with laboratory real-time PCR and usability and used errors were assessed.

Results

No significant usability-related hazards emerged, and the sources of error identified were found to be amendable with minor changes in training or test workflow. POCKIT^TM Central has acceptable sensitivity and specificity based on RT-PCR as the reference standard, especially for symptomatic cases.

Asymptomatic specimens showed 83.3% (95% confidence interval (CI): 35.9–99.6%) positive agreement and 98.7% negative agreement (95% CI: 96.2–99.7%), with overall prevalence and bias-adjusted kappa (PABAK) of 0.965 (95% CI: 0.932– 0.999). Symptomatic specimens showed 100% (95% CI: 2.5–100%) positive agreement and 100% negative agreement (95% CI: 85.8–100%), with overall PABAK of 1.

Recommendations are provided to mitigate the frequency of occurrence of the residual use errors observed. Integration pathways were discussed to identify opportunities and limitations of adopting POCKIT™ Central for screening and diagnostic testing purposes.

Conclusions

Point-of-care PCR testing in care homes can be considered with appropriate preparatory steps and safeguards. Further diagnostic accuracy evaluations and in-service evaluation studies should be conducted, if the test is to be implemented more widely, to build greater certainty on this initial exploratory analysis.

Improving the diagnosis and management of acute schistosomiasis with antibody, antigen and molecular techniques: lessons from a cluster of six travellers

Different diagnostic tests were evaluated in a cluster of six European travellers with acute schistosomiasis (AS) acquired in Mozambique. Adult worm and soluble egg antibodies, circulating anodic antigen (CAA) and DNA detection allowed early confirmation of AS. CAA permitted monitoring treatment response and Sm1-7 polymerase chain reaction allowed identification of Schistosoma mansoni complex.

Development of Loop-Mediated Isothermal Amplification Assay for Detection of Clinically Significant Members of Acinetobacter calcoaceticus-baumannii Complex and Associated Carbapenem Resistance

Background:Acinetobacter calcoaceticus–baumannii (ACB) complex has emerged as an important nosocomial pathogen and is associated with life-threatening infections, especially among ICU patients, including neonates. Carbapenem resistance in Acinetobacter baumannii has emerged globally and is commonly mediated by bla_OXA-23. Clinically significant infections with carbapenem-resistant Acinetobacter baumannii (CRAB) are a major concern since therapeutic options are limited and associated mortality is high. Early diagnosis of both the pathogen and resistance is important to initiate the optimal therapy and prevent selection of resistance. In the current study, a loop-mediated isothermal amplification (LAMP) assay was developed for rapid detection of the ACB complex and carbapenem resistance mediated by bla_OXA-23.

Methodology: Universal LAMP primers were designed for the detection of significant members of the ACB complex and carbapenem resistance targeting the ITS 16S–23S rRNA and bla_OXA-23 gene respectively. The optimal conditions for the LAMP assay were standardized for each primer set using standard ATCC strains. The sensitivity of the LAMP assay was assessed based on the limit of detection (LOD) using different DNA concentrations and colony counts. The specificity of LAMP was determined using the non-ACB complex and non-Acinetobacter species. The results of the LAMP assay were compared with those of polymerase chain reaction (PCR).

Results: The optimal temperature for the LAMP assay was 65°C, and the detection time varied with various primers designed. Using the ITS Ab1 primer, LODs of LAMP and PCR assays were 100 pg/μl and 1 ng/μl of DNA concentration and 10⁴ cfu/ml and 10⁸ cfu/ml of colony count, respectively. The LAMP assay was 10- and 10⁴-fold more sensitive than PCR using DNA concentration and colony count, respectively. The LAMP assay was found to be specific for clinically important ACB complex species.

Significance of the study: The LAMP assay can be applied for early detection of significant species of the ACB complex from clinical samples and their carbapenem-resistant variants. Depending on the emerging pathogen and locally prevalent resistance genes, the LAMP assay can be modified for detection of colonization or infection by various resistant bugs.

Optimum DNA Extraction Methods for Edible Bird's Nest Identification Using Simple Additive Weighting Technique

A simple additive weighting (SAW) technique was used to determine and compare the overall performance of five DNA extraction methods from conventional (SDS method) to commercial kits (Qiagen, Wizard, and NucleoSpin) for identifying origins of edible bird’s nest (EBN) using end-point polymerase chain reaction (PCR). A hybrid method (SDS/Qiagen) which has been developed by combining the conventional SDS method with commercialised Qiagen was determined as the most suitable in terms of speed and cost-effectiveness. The determination of optimum extraction method was by the performances on efficiency and feasibility, extracted DNA concentration, purity, PCR amplifiability, handling time and safety of reagents used. The hybrid SDS/Qiagen method is less costly compared to the commercial kits and offered a more rapid alternative to the conventional SDS method with significant improvement in the yield, purity and PCR amplifiability. The developed hybrid SDS/Qiagen method provides a more practical alternative over the lengthy process using conventional method and expensive process using commercial kits. Using the simple additive weighting (SAW) technique and analysis, the Qiagen method is considered the most efficient and feasible method without consideration of cost as it yielded the purest extracted DNA and achieved the highest PCR amplifiability with the shortest turnaround time.

Molecular Identification of Trypanosoma evansi Isolated from Arabian Camels (Camelus dromedarius) in Riyadh and Al-Qassim, Saudi Arabia

We analyzed the blood from 400 one-humped camels, Camelus dromedarius (C. dromedarius), in Riyadh and Al-Qassim, Saudi Arabia to determine if they were infected with the parasite Trypanosoma spp. Polymerase chain reaction (PCR) targeting the internal transcribed spacer 1 (ITS1) gene was used to detect the prevalence of Trypanosoma spp. in the camels. Trypanosoma evansi (T. evansi) was detected in 79 of 200 camels in Riyadh, an infection rate of 39.5%, and in 92 of 200 camels in Al-Qassim, an infection rate of 46%. Sequence and phylogenetic analyses revealed that the isolated T. evansi was closely related to the T. evansi that was detected in C. dromedarius in Egypt and the T. evansi strain B15.1 18S ribosomal RNA gene identified from buffalo in Thailand. A BLAST search revealed that the sequences are also similar to those of T. evansi from beef cattle in Thailand and to T. brucei B8/18 18S ribosomal RNA from pigs in Nigeria.

Cervicovaginal Immune Activation in Zambian Women With Female Genital Schistosomiasis

HIV-1 infection disproportionately affects women in sub-Saharan Africa, where areas of high HIV-1 prevalence and Schistosoma haematobium endemicity largely overlap. Female genital schistosomiasis (FGS), an inflammatory disease caused by S. haematobium egg deposition in the genital tract, has been associated with prevalent HIV-1 infection. Elevated levels of the chemokines MIP-1α (CCL-3), MIP-1β (CCL-4), IP-10 (CXCL-10), and IL-8 (CXCL-8) in cervicovaginal lavage (CVL) have been associated with HIV-1 acquisition. We hypothesize that levels of cervicovaginal cytokines may be raised in FGS and could provide a causal mechanism for the association between FGS and HIV-1. In the cross-sectional BILHIV study, specimens were collected from 603 female participants who were aged 18–31 years, sexually active, not pregnant and participated in the HPTN 071 (PopART) HIV-1 prevention trial in Zambia. Participants self-collected urine, and vaginal and cervical swabs, while CVLs were clinically obtained. Microscopy and Schistosoma circulating anodic antigen (CAA) were performed on urine. Genital samples were examined for parasite-specific DNA by PCR. Women with FGS (n=28), defined as a positive Schistosoma PCR from any genital sample were frequency age-matched with 159 FGS negative (defined as negative Schistosoma PCR, urine CAA, urine microscopy, and colposcopy imaging) women. Participants with probable FGS (n=25) (defined as the presence of either urine CAA or microscopy in combination with one of four clinical findings suggestive of FGS on colposcope-obtained photographs) were also included, for a total sample size of 212. The concentrations of 17 soluble cytokines and chemokines were quantified by a multiplex bead-based immunoassay. There was no difference in the concentrations of cytokines or chemokines between participants with and without FGS. An exploratory analysis of those women with a higher FGS burden, defined by ≥2 genital specimens with detectable Schistosoma DNA (n=15) showed, after adjusting for potential confounders, a higher Th2 (IL-4, IL-5, and IL-13) and pro-inflammatory (IL-15) expression pattern in comparison to FGS negative women, with differences unlikely to be due to chance (p=0.037 for IL-4 and p<0.001 for IL-5 after adjusting for multiple testing). FGS may alter the female genital tract immune environment, but larger studies in areas of varying endemicity are needed to evaluate the association with HIV-1 vulnerability.

Influence of preformed bone defects on key pathogens and bone loss during experimental peri-implantitis formation in a canine model

PURPOSE

To determine the impact of experimentally preformed peri-implant crater-shaped bone defects on the evolution of in situ microbiota and development of bone defects compared to those induced over time by ligature placement only.

METHODS

Implants were installed in the mandibles of eight dogs. Standardized bone defects were preformed in four test animals but not in the other four control animals, prior to implant (3.3 mm × 8 mm) installation. After 2 months of healing, peri-implantitis was induced with silk ligatures in both groups for 2 months. Microbial samples were obtained from implants and teeth for analysis at three time points (qPCR), and the average depths of the bone defects were measured.

RESULTS

At the baseline, the total marker load of periodontal-pathogenic bacteria (TML) for teeth accounted for 5.2% (0-17.4%). After implant healing, TMLs for implants and teeth were comparable (7.1% [0.3-17.4%]). The TML of both groups was 3.5%, 2 months after ligature placement. Bone defects had a mean depth of 1.84 mm at preformed defects and 1.64 mm at control sites (P > 0.05).

CONCLUSION

Preformed defects in the test group showed comparable results to the control group in terms of TML, the incidence of periodontal-pathogenic bacteria, and bone defect depth.

Clinical influence of switching companion diagnostic tests for EGFR-TKs from Therascreen to Cobas v2

Background

Several companion diagnostic (CDx) tests for epidermal growth factor receptor tyrosine kinase inhibitors (EGFR‐TKIs) have been approved. In our institute, the CDx test for EGFR‐TKIs was changed from the Therascreen test (Therascreen) to the Cobas EGFR v2 test (Cobas) because only Cobas was approved for the use of osimertinib in patients with EGFR‐mutated non‐small cell lung cancer (NSCLC) with T790M mutations. The clinical influence of switching the CDx test has not yet been examined comprehensively.

Methods

All serial patients with lung cancer tested for EGFR mutations with CDx tests between February 2014 and February 2016 at the Cancer Institute Hospital of the Japanese Foundation for Cancer Research (JFCR) were enrolled in this analysis.

Results

Therascreen was used as a CDx test for EGFR‐TKI therapy in 607 patients between February 2014 and January 2015, and Cobas was used in 621 patients between February 2015 and February 2016. EGFR mutations were detected in 218 patients (35.9%) and 244 patients (39.3%) tested with Therascreen and Cobas, respectively. At the initial diagnosis, 400 and 459 patients were tested with Therascreen and Cobas, respectively. EGFR mutation subtypes, including del19, L858R, and others, were detected in 13.0%, 17.0%, and 2.5% of patients using Therascreen and 17.4%, 14.4%, and 1.5% of patients using Cobas, respectively.

Conclusions

No significant impact of switching from Therascreen to Cobas as the CDx test for EGFR mutations in clinical practice was observed. However, the detection pattern of the EGFR mutation subtypes between the two CDx tests was slightly different.

Key points

Significant findings of the study

We examined the influence of changing the EGFR test in 1228 patients in total. The detection rate of EGFR mutations was similar. However, the detection pattern for EGFR subtype mutations was slightly different between the two tests.

What this study adds

Switching CDx tests from target polymerase chain reaction (PCR)‐ to next‐generation sequencing (NGS)‐based methods may lead to obvious changes in clinical practice. When the CDx test is required to change, the investigation of this influence is warranted in future studies.

A Forensic Detection Method for Hallucinogenic Mushrooms via High-Resolution Melting (HRM) Analysis

In recent years, trafficking and abuse of hallucinogenic mushrooms have become a serious social problem. It is therefore imperative to identify hallucinogenic mushrooms of the genus Psilocybe for national drug control legislation. An internal transcribed spacer (ITS) is a DNA barcoding tool utilized for species identification. Many methods have been used to discriminate the ITS region, but they are often limited by having a low resolution. In this study, we sought to analyze the ITS and its fragments, ITS1 and ITS2, by using high-resolution melting (HRM) analysis, which is a rapid and sensitive method for evaluating sequence variation within PCR amplicons. The ITS HRM assay was tested for specificity, reproducibility, sensitivity, and the capacity to analyze mixture samples. It was shown that the melting temperatures of the ITS, ITS1, and ITS2 of Psilocybe cubensis were 83.72 ± 0.01, 80.98 ± 0.06, and 83.46 ± 0.08 °C, and for other species, we also obtained species-specific results. Finally, we performed ITS sequencing to validate the presumptive taxonomic identity of our samples, and the sequencing output significantly supported our HRM data. Taken together, these results indicate that the HRM method can quickly distinguish the DNA barcoding of Psilocybe cubensis and other fungi, which can be utilized for drug trafficking cases and forensic science.

A study of the association between angiotensinogen (AGT) gene polymorphism (M235T) and preeclampsia in Thai pregnant women

AGT M235T gene polymorphism may cause increased blood pressure in preeclampsia in pregnancy; however, the evidence remains controversial. This study investigated the association between AGT M235T and preeclampsia in Thai pregnant women. A case-control study was conducted to compare the distributions of AGT M235T genotypes and alleles between 142 normotensive pregnancies as controls and 61 preeclampsia pregnancies as cases in a tertiary-care university hospital in Chiang Mai, Thailand. The results show that the distribution of AGT M235T genotypes (MM, MT and TT) of both groups were not significantly different (preeclampsia: 0.0, 16.4, 83.6%; control: 2.1, 22.5, 75.4%, respectively; p = .30). Additionally, there was no statistical difference in the distribution of AGT M235T alleles (M and T alleles) (preeclampsia: 8.2 and 91.8% versus control: 13.4 and 86.6%, respectively; p = .14). In this study, the distributions of AGT M235T were not different in both groups. Therefore, AGT M235T polymorphism may not play a significant role in preeclampsia pathophysiology in Thai population.Impact statementWhat is already known on this subject? Preeclampsia is one of the major complications during pregnancy; it significantly affects maternal and perinatal morbidity and mortality. Effort has been made to find markers and predictors that are associated with the pathophysiology of preeclampsia. AGT M235T gene polymorphism may cause increased blood pressure in preeclampsia pregnancy; however, evidences are still controversial.What do the results of this study add? We conducted a case-control study to compare the distributions of AGT M235T genotypes and alleles between 142 normotensive pregnancies as controls and 61 preeclampsia pregnancies as cases. The results show that preeclamptic women are more likely to deliver at an earlier gestational age and have a smaller baby in comparison with the normotensive group. In addition, women with preeclampsia had a higher chance of having an operative delivery and caesarean section. However, the distribution of AGT M235T polymorphism of preeclampsia women and the control group were not significantly different.What are the implications of these findings for clinical practice and/or further research? AGT M235T polymorphism may not play a significant role in preeclampsia pathophysiology in Thai population.

The association of CMTM6 expression with prognosis and PD-L1 expression in triple-negative breast cancer

Background

Immune checkpoint inhibitors play a vital role in triple-negative breast cancer (TNBC) immunotherapy. A recent study showed that chemokine-like factor (CKLF)-like MARVEL transmembrane domain containing 6 (CMTM6) has a crucial role in programmed death-ligand 1 (PD-L1) stability. The aim of this study was to investigate the relationship between CMTM6 and PD-L1 in TNBC and the association with clinical characteristics.

Methods

A total of 143 patients, including 75 with human epidermal growth factor receptor 2 (HER2)-driven breast cancer and 68 with TNBC, were included in this study. In 83 paired primary breast cancers (PBCs) and metastatic breast cancers (MBC) comprising 45 HER2-driven breast cancers and 38 TNBC, CMTM6 and PD-L1 were detected based on immunohistochemistry (IHC) with FFPE tissues. Another 60 PBCs comprising 30 HER2-driven breast cancers and 30 TNBC in order to detect CMTM6 and PD-L1 mRNA expressions based on real-time polymerase chain reaction (RT-PCR) using frozen tissues. Furthermore, 153 patients comprising 30 TNBC and 123 HER2-driven breast cancer based on The Cancer Genome Atlas (TCGA) database were used to confirm the difference mRNA expression.

Results

The expression of CMTM6 in patients with TNBC was significantly higher than in those with HER2-driven PBC (IHC, P=0.036, mRNA, P=0.036, TCGA dataset, P=0.039). CMTM6 was correlated with PD-L1 based on IHC in triple-negative MBC (P=0.004); the same result was found based on mRNA data in triple- negative PBC (P=0.021). Moreover, a high expression of CMTM6 in TNBC was associated with poor progression-free survival (PFS) (P=0.030, 95% CI: 1.08-4.57, HR =2.22). After multiple Cox regression analysis, CMTM6 in TNBC emerged as an independent risk factor for PFS (P=0.027, 95% CI: 1.11-5.20, HR =2.40). The expression of PD-L1 was negatively correlated with lymph node metastasis (P=0.026) and was not associated with PFS.

Conclusions

The expression of CMTM6 was higher in TNBC than in HER2-driven breast cancer. In TNBC, CMTM6 was correlated with PD-L1 expression, and potentially could be used as an independent risk factor for predicting PFS.

Development of a Novel Detection Method Targeting an Ultrashort 25 bp Sequence Found in Agrobacterium-Mediated Transformed GM Plants

Agrobacterium-mediated transformation is the most commonly used technique for plant genetic engineering. During the transformation, a T-DNA region, which is flanked by the right border (RB) and the left border, is transferred to plant nuclear chromosomes. Simultaneously, a sequence adjacent to the RB on T-DNA is frequently transferred to plant genomes together with the intentionally introduced recombinant DNA. We developed a novel polymerase chain reaction (PCR)-mediated detection method targeting this region. The conserved sequence of the region found in genetically modified (GM) crops is only 25 bp in length. To detect this ultrashort 25 bp sequence near the RB region, we designed a primer set consisting of a 12-base forward primer and a 13-base reverse primer. The predicted band was detected from GM crops by optimizing the PCR conditions. We used lateral flow DNA chromatography for rapid and inexpensive detection. The developed method would be applicable for screening the GM crops generated by Agrobacterium-mediated transformation.

Low-Bias Manipulation of DNA Oligo Pool for Robust Data Storage

In DNA data storage, the massive sequence complexity creates challenges in repeatable and efficient information readout. Here, our study clearly demonstrated that PCR created significant DNA amplification biases due to its inherent mechanism of inefficient priming, product-as-template, and error-spreading prone, which greatly hinder subsequent applications such as data retrieval in DNA-based storage. To mitigate the amplification bias, we recruited an isothermal DNA amplification by combining strand displacement amplification (SDA) with magnetic beads (MB) DNA immobilization for robust, repeated, and low-bias amplification of DNA oligo pool, comprising over 100 thousand oligos, in a primer-free and low-error-spreading fashion. Furthermore, we introduced oligo pool normalization (OPN), a cost-effective and scalable method for normalizing an oligo pool, by which oligo pools comprising from 256 to 1024 distinct oligos were simply modified with improved Gini-index. Therefore, we believe that the combination of SDA and OPN can provide an ideal amplification mechanism for a low-bias copy of a large oligo pool, which is of vital importance for successful data retrieval in DNA information storage.

Transplantation of Kidneys From Hepatitis C Virus-Infected Donors to Hepatitis C Virus-Negative Recipients: One-Year Kidney Allograft Outcomes

RATIONALE & OBJECTIVE

Transplant centers in the United States are increasingly willing to transplant kidneys from hepatitis C virus (HCV)-infected (HCV⁺) donors into HCV^- recipients. We studied the association between donor HCV infection status and kidney allograft function and posttransplantation allograft biopsy findings.

STUDY DESIGN

Retrospective cohort study.

SETTING & PARTICIPANTS

We examined 65 HCV^- recipients who received a kidney from a HCV⁺ donor and 59 HCV^- recipients who received a kidney from a HCV^- donor during 2018 at a single transplant center.

EXPOSURE

Predictor(s) of donor infection with HCV.

OUTCOMES

Kidney allograft function and allograft biopsy findings during the first year following transplantation.

ANALYTICAL APPROACH

We compared estimated glomerular filtration rate (eGFR), findings on for-cause and surveillance protocol biopsies, development of de novo donor-specific antibodies (DSAs), and patient and allograft outcomes during the first year following transplantation between recipients of HCV⁺ and HCV^- kidneys. We used linear regression to estimate the independent association between allograft function and HCV viremic status of the kidney donor.

RESULTS

The mean age of recipients was 52 ± 11 (SD) years, 43% were female, 19% and 80% of recipients were White and Black, respectively. Baseline characteristics were similar between the HCV⁺ and HCV^- groups. There were no statistically significant differences between the HCV⁺ and HCV^- groups in delayed graft function rates (12% vs 8%, respectively); eGFRs at 3, 6, 9, and 12 months post-transplantation; proportions of patients with cellular rejection (6% vs 7%, respectively); and proportions with antibody-mediated rejection (7% vs 10%, respectively) or de novo DSAs (31% vs 20%, respectively). HCV viremic status was not associated with eGFR at 3, 6, 9, or 12 months.

LIMITATIONS

Generalizability from a single-center study and small sample size was limited.

CONCLUSIONS

Recipients of kidneys from donors infected with HCV had similar kidney allograft function and probability of rejection in the first year after transplantation compared to those who received kidneys from donors without HCV infection.

Chinese Expert Consensus on the Nucleic Acid Detection of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) has already become a pandemic wherein the infection's timely diagnosis has proven beneficial to patient treatment and disease control. Nucleic acid detection has been the primary laboratory diagnostic method for the detection of SARS-CoV-2. To ensure laboratory staff safety and quality nucleic acid testing, the Chinese Society of Laboratory Medicine formulated this consensus, based on the Chinese National Recommendations and previous literature for nucleic acid detection. A working group comprises 34 hospital professionals experience with real-time polymerase chain reactions (PCR) testing for SARS-CoV-2 drafted guidance statements during online discussions. A modified Delphi methodology was used in forming a consensus among a wider group of hospital professionals with SARS-CoV-2 detection experience. Guidance statements were developed for four categories: (I) specimen type, priority, collecting, transportation and receiving; (II) nucleic acid isolation and amplification; (III) quality control; (IV) biosafety management and decontamination. The modified Delphi voting process included a total of 29 guidance statements and final agreement. Consensus was reached after two rounds of voting. Recommendations were established for the detection of SARS-CoV-2 using real time PCR testing based on evidence and group consensus. The manuscript was evaluated against The Appraisal of Guidelines for Research & Evaluation Instrument (AGREE II) and was developed to aid medical laboratory staff in the detection of the ribonucleic acid (RNA) of SARS-CoV-2.

A blueprint for academic laboratories to produce SARS-CoV-2 quantitative RT-PCR test kits

Widespread testing for the presence of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise, and/or instrumentation necessary to detect the virus by quantitative RT-PCR (RT-qPCR), the most robust, sensitive, and specific assay currently available. Here we show that academic biochemistry and molecular biology laboratories equipped with appropriate expertise and infrastructure can replicate commercially available SARS-CoV-2 RT-qPCR test kits and backfill pipeline shortages. The Georgia Tech COVID-19 Test Kit Support Group, composed of faculty, staff, and trainees across the biotechnology quad at Georgia Institute of Technology, synthesized multiplexed primers and probes and formulated a master mix composed of enzymes and proteins produced in-house. Our in-house kit compares favorably with a commercial product used for diagnostic testing. We also developed an environmental testing protocol to readily monitor surfaces for the presence of SARS-CoV-2. Our blueprint should be readily reproducible by research teams at other institutions, and our protocols may be modified and adapted to enable SARS-CoV-2 detection in more resource-limited settings.

Tuberculosis: A Cunning Disease Presenting with Endopericarditis-Associated Bilateral Uveitis

Mycobacterium tuberculosis can spread through the entire body but rarely involves the eye. We report a patient with endophthalmitis in one eye and simultaneous retinal vasculitis in the fellow eye. Systemic work-up suggested infective endopericarditis. Polymerase chain reaction analyses of the vitreous and pericardial fluid were positive for M. tuberculosis. We initiated a four-drug antituberculous treatment regimen (isoniazid, ethambutol, pyrazinamide, and rifampin). After two weeks, we discontinued all the medications due to drug-induced hepatitis. We restarted isoniazid and rifampin, but hepatitis recurred. Finally, we chose isoniazid/ethambutol combination for 18 months, and also administered short-term systemic corticosteroid. His vision improved considerably with no recurrence of hepatitis or tuberculosis for 3 years after completion of treatment. Ocular tuberculosis can masquerade as other causes of intraocular inflammation, and a medical team consisting of an ophthalmologist and an infectious disease specialist might be needed for the diagnosis and management.

Development of pure red cell aplasia by transmission and persistent infection of parvovirus B19 through a kidney allograft

We report a case of pure red cell aplasia (PRCA) caused by parvovirus B19 (PVB19) infection, which was transmitted through a kidney allograft. The patient underwent a living-donor kidney transplant from his wife at the age of 60. Despite successful engraftment with a normal creatinine level, he developed severe anemia that required frequent blood transfusions 2 months after transplantation. Renal anemia was unlikely as his serum erythropoietin level was extremely high. A bone marrow aspiration test demonstrated the existence of large proerythroblasts. Although anti-PVB19 IgM antibody levels were not increased, polymerase chain reaction (PCR) detected PVB19 DNA in his serum. Thus, he was diagnosed as having PRCA induced by PVB19 infection. PCR analysis of total DNA isolated from 0-hour biopsy sections showed the existence of PVB19 DNA. Furthermore, PVB19 proteins was detected on renal tubules of 0-hour allograft by immunoperoxidase staining. Thus, transmission of PVB19 through the allograft was confirmed. A single course of intravenous immunoglobulin (IVIG) therapy resulted in substantial improvement; however, the effect was limited, and severe anemia relapsed after 5-6 months. Several courses of IVIG with adjustment of immunosuppressive drugs resulted in long-term remission. Our case demonstrates that donor-transmitted PVB19 infection should be suspected in kidney transplant recipients who develop refractory anemia during the early post-operative phase.