Impact of FilmArray respiratory panel test for hospitalized pediatric respiratory tract infection in Taiwan: A 3-year single-center cohort study

Respiratory tract infections are prevalent and clinically significant in pediatric populations globally. However, pathogen testing often involves time-consuming processes, resulting in delays in diagnosis. To date, commercial testing machines, such as the FilmArray respiratory panel, have been proposed for hospitals. Therefore, this study aimed to investigate the impact of the FilmArray respiratory panel at a single center. This study utilized the medical records of our hospital to select pediatric inpatients with respiratory tract infections who underwent the FilmArray respiratory panel between September 2020 and April 2021 and those who did not undergo nucleic acid detection (a rapid test group) between September 2019 and April 2020. FilmArray is a polymerase chain reaction-based diagnostic tool. The FilmArray respiratory panel group was scheduled to recruit 150 patients (final 137 patients), whereas the rapid test group was scheduled to recruit 300 patients (final 267 patients). Differences in continuous variables between the 2 groups were analyzed using independent Student t tests. The FilmArray respiratory panel group had a longer length of inpatient days, longer duration of antibiotic use, and higher proportion of pathogens that tested positive, with significant differences than those in the rapid test group. Fever duration showed no significant difference between the 2 groups. For the polymerase chain reaction method, respiratory syncytial virus was the most commonly detected pathogen causing pneumonia, followed by human rhinovirus/enterovirus and parainfluenza virus. Mycoplasma was detected using the rapid test but not with the FilmArray respiratory panel. The FilmArray respiratory panel provides clinicians with a rapid and useful diagnostic tool. The effect was quite good for virus detection, but not for bacteria. Given its limited adoption, the tool may not aid clinicians in the diagnosis of mild cases.

Detection of Toxoplasma gondii in artisanal salted meat products sold in street markets of the Ilhéus-Itabuna microregion

This study aimed to detect Toxoplasma gondii in artisanal salted meat products sold in street markets in the Ilhéus-Itabuna microregion and to assess the salt concentration used in their preparation and its influence on the parasite's viability. A total of 125 samples of various artisanal meat products sold in street markets located in the Ilhéus-Itabuna microregion were collected during 2021. Serological analysis using indirect hemagglutination (HAI) and molecular analysis (PCR) were performed on these samples to detect the presence of the parasite. Möhr's method was utilized to determine the sodium chloride concentration in the samples. Of all samples, 21 were subjected to a bioassay in albino mice to verify the viability of possible tissue cysts. Among the 125 meat products, 10 (8%) tested positive in the serological analysis including four cured pork sausages, five beef sun-dried meats, and one mixed fresh sausage (pork and chicken). None of 125 samples tested positive in the molecular analysis. On bioassay, all mice tested negative for the presence of the parasite. The NaCl concentration in the positive samples ranged from 2.9% to 8%. The results demonstrated that the salt concentration in the collected samples was sufficient to inactivate the parasite T. gondii.

Evaluation of Oral Squamous Cell Carcinoma Patients Using Polymerase Chain Reaction Regarding the Prevalence of Human Papillomavirus Types 16 and 18

BACKGROUND

Epstein-Barr virus, human papillomavirus (HPV), and herpes simplex virus type 1 (HSV-1) are examples of viruses that have been associated with the development of oral squamous cell carcinoma (OSCC). These viruses can infect various epithelial tissues in the human body. The use of incredibly accurate cellular biology techniques, such as the polymerase chain reaction (PCR), which permits the rapid identification of viruses following infection, has increased. The parameters of human head and neck oncology have been widened.

AIM

In this study, using the PCR, the presence of HPV variants such as HPV 18 and HPV 16 in patients with OSCC was assessed.

MATERIALS AND METHODS

Tissue specimens were obtained from clinically presumed OSCC individuals taken as cases, and tissues from the retromolar region were obtained from people who experienced an operation for partially and completely impacted tooth and taken as controls. The study included 80 samples divided into two separate categories: case category (n = 40) = OSCC-diagnosed individuals; control category (n = 40) = controls with a comparable age. For verification of the diagnosis, a specimen of the tissue has been processed and sections have been stained and inspected for standard hematoxylin and eosin stain. Deoxyribonucleic acid (DNA) was extracted from the leftover histopathologically verified tissue specimens and then exposed to PCR for the assessment of HPV infiltration.

RESULTS

It was observed in this research that 22 cases out of 40 cases of OSCC were found positive for HPV-DNA. While 12 out of 40 age-matched healthy controls were found positive for HPV-DNA. Out of 40 cases of OSCC, 12 cases were found positive for HPV 16. While six out of 40 age-matched healthy controls were found positive for HPV 16. Six cases out of 40 cases of OSCC were found positive for HPV 16. While two out of 40 age-matched healthy controls were found positive for HPV 18. Four cases out of 40 cases of OSCC were found positive for HPV 16. While four out of 40 age-matched healthy controls were found positive for HPV 16 and HPV 18. On carrying out statistical analysis, the variation between the two categories was non-meaningful statistically (p = 0.662). However, the prevalence was greater in the case (OSCC) subgroup.

CONCLUSION

When evaluated against controls in the current investigation, OSCC cases had a greater level of HPV expression and a greater proportion of HPV 16 positives. However, there was no statistically noteworthy change.

Growth Factor Independence-1 (GFI-1) Gene Expression in Hematopoietic Stem Cell Lineage Differentiation in Low Birth Weight Newborns Compared With Normal Birth Weight Newborns at Term Pregnancy

Introduction Low birth weight (LBW), which is a risk factor for noncommunicable diseases throughout life, is a significant public health concern. In addition to regulating myeloid cell differentiation and proliferation, a transcriptional repressor identified as growth factor independence-1 (GFI-1) is essential for hematopoietic stem cell maintenance and self-renewal. The current study was designed to compare the expression of the GFI-1 gene in the differentiation of hematopoietic stem cells in newborns with LBW and those with normal birth weight (NBW). Methods A prospective comparative analytical study was carried out from September 2019 to September 2021 after obtaining Institute Ethical Committee approval at a tertiary care center in north India. The GFI-1 gene expression levels in 50 cord blood samples from women with term gestation and LBW newborns (<2500 grams) were measured using quantitative real-time polymerase chain reaction (RT-PCR) and compared to gene expression levels in 50 cord blood samples from women with term gestation and NBW newborns (≥2500 grams). The data were analyzed using IBM SPSS statistics software version 24.0 (IBM Corp., Armonk, NY). Results The median GFI-1 expression in LBW newborns is 3.1, whereas among NBW newborns it is 9.39. The difference is significant (P <0.001). The level of GFI-1 gene expression in LBW newborns was correlated with their birth weight. The coefficient of correlation was found to be weakly positive (r = 0.223). The birth weight of NBW newborns was correlated to the level of expression of the GFI-1 gene, which was found to be positively correlated (r = 0.332). Conclusion The levels of the GFI-1 gene and newborn birth weight were compared in LBW infants, which were weakly positively correlated. The level of GFI-1 gene expression at birth was compared to the birth weight of NBW newborns, which was positively correlated.

Sensitivity of PCR in conjunctival swab samples for the diagnosis of canine visceral leishmaniasis: a systematic review and meta-analysis

To compare the sensitivity of conjunctival swab (CS) and conventional samples (blood, spleen, liver, lymphoid and cutaneous tissue) in the diagnosis of canine visceral leishmaniasis (CVL) by polymerase chain reaction (PCR), a systematic review and meta-analysis was carried out using PubMed, Science Direct, Scopus, Web of Science, VHL/BVS (Virtual Health Library), CAPES, and Scielo databases. Articles published from 2002 to 2022 were considered and the review was updated in Jul 2023. From the total of 371 identified studies, 8 met all the eligibility criteria and were included in this review. Data from 658 CVL-positive dogs and 2541 PCR results were considered. Using a random effect model, data on the sensitivity of the test was compared between intervention (CS samples) and comparison (all the other samples) groups. Overall, the use of CS in the PCR diagnosis of CVL produced 12% higher sensitivity (p=0.013) in the test than all the other samples in combination. The animals' clinical condition did not influence (p>0.142) this overall result. However, when CS was individually compared to each of the conventional samples, the consistent result was observed (p=0.012) only in the CS versus bone marrow comparison. Given their rapid acquisition, minimal invasiveness, and lower cost relative to conventional samples, CS samples present a promising alternative for the molecular diagnosis of CVL.

The evaluation of superoxide dismutase 1 gene insertion/deletion variant in athletes

OBJECTIVE

Regular exercise benefits health by increasing the body's antioxidant defenses. However, excessive exercise can produce excessive reactive oxygen species, which can lead to oxidative stress. Superoxide dismutase is the primary enzyme involved in the elimination of reactive oxygen species. This study aimed to determine the relationship between the SOD1 gene insertion/deletion variant and elite athletes.

METHODS

A total of 305 subjects, including 165 elite athletes from different branches and 140 sedentary individuals, participated in this study. The SOD1 insertion/deletion variant was genotyped using polymerase chain reaction. The results were evaluated statistically.

RESULTS

There was no statistical significance between the athletes and control groups in terms of SOD1 insertion/deletion genotype distribution and allele frequency. Then, we evaluated the groups as females and males. There were no female athletes carrying the D/D genotype. The SOD1 I/I genotype and the I allele were more prevalent in female athletes than in the control group. There was a significant difference in terms of SOD1 I/I: I/D+D/D in females (p=0.028). SOD1 genotype and allele distribution did not differ between male athletes and male controls.

CONCLUSION

As far as we know, this is the first study to evaluate the SOD1 insertion/deletion variant in athletes in Turkey. Our results showed that the SOD1 I allele was more common in female athletes, but not in male athletes.

Evaluating the Usefulness of a Large Language Model as a Wholesome Tool for De Novo Polymerase Chain Reaction (PCR) Primer Design

This study aimed to assess the ability of language learning models (LLMs), specifically GPT-3.5 (Chat Generative Pre-trained Transformer 3.5) and GPT-4 (Chat Generative Pre-trained Transformer 3.5), in designing primers for diagnostic polymerase chain reaction (PCR) of the monkeypox virus (MPXV). Five primer pairs were generated by each LLM, and their thermodynamic properties and specificity were analysed post-hoc using commonly used software. The LLMs demonstrated ability in sequence generation and predicting melting temperatures (Tm), but their accuracy in predicting GC content was suboptimal, necessitating further investigation. Results indicated that, of the total primer pairs, only three designed by GPT-4 and two by GPT-3.5 could theoretically form a PCR product, but only one pair demonstrated suitable parameters for experimental validation. This preliminary exploration suggests that while LLMs have a potential in aiding primer design, their accuracy needs improvement to match current deterministic, rule-based tools used in the field. Consequently, manual intervention remains a crucial step in PCR primer design.

Pneumocystis jirovecii Pneumonia (PCP) in a Non-HIV Lung Cancer Patient in the Absence of Common Risk Factors

Pneumocystis jirovecii pneumonia (PCP) has been described mainly in AIDs and in immunocompromised patients with hematological malignancies, organ transplant recipients, collagen vascular disease, and primary immune deficiencies or those under treatment with steroids or chemotherapy. The incidence of PCP pneumonia is increasing in solid organ tumors and hematological malignancies receiving chemotherapy. Pneumocystis pneumonia has been rarely reported in patients with non-small cell lung cancer (NSCLC). We describe a 68-year-old woman with a recent diagnosis of squamous cell lung cancer, who received radiotherapy two weeks prior to the current hospital admission with shortness of breath and dry cough. The initial investigations, including chest X-ray and CT images, were suggestive of atypical pneumonia, with PCP pneumonia as the top differential. Treatment was started with high-dose trimethoprim-sulfamethoxazole (cotrimoxazole) and oxygen support. Serum beta-glucan was found to be more than 500 pg/ml in favor of PCP infection. Oral steroids were added to the treatment in view of hypoxia (arterial oxygen pressure (PaO2) < 70 mmHg) requiring high-flow nasal cannula support. Subsequently, bronchoscopy was done and the bronchoalveolar lavage (BAL) sample came positive for PCP polymerase chain reaction (PCR). The patient made a significant recovery after four weeks of treatment with cotrimoxazole and was discharged home in stable condition with cotrimoxazole prophylaxis. The reported cases of PCP pneumonia in lung cancers were following chemotherapy, chemoradiation, or steroid treatment. The incidence of PCP pneumonia in lung cancer patients receiving radiotherapy is relatively rare. Our patient could not tolerate chemotherapy for the cancer due to an anaphylactic reaction and hence was treated with radiotherapy alone for the lung cancer prior to getting PCP pneumonia. Therefore, it is important to carry a high index of suspicion for PCP infection in a lung cancer patient presenting with features of atypical pneumonia following cancer treatments, including radiotherapy alone.

A multicenter, single-arm, open study of neoadjuvant or conversion atezolizumab in combination with chemotherapy in resectable small cell lung cancer (Cohort Study)

BACKGROUND

This study aimed to investigate the prospects of using chemotherapy in combination with atezolizumab in the neoadjuvant or conversion treatment of small cell lung cancer (SCLC).

METHODS

Prior to surgery, untreated patients with limited-stage SCLC received three cycles of neoadjuvant or conversion atezolizumab combined with chemotherapy of etoposide and platinum. The primary endpoint of the trial was pathological complete response (pCR) in the per-protocol (PP) cohort. In addition, safety was assessed based on treatment-related adverse events (AEs) and postoperative complications.

RESULTS

Overall, 13 of 17 patients (including 14 males and 3 females) underwent surgery. In the PP cohort, pCR and major pathological response were observed in 8 (8/13, 61.5%) and 12 (12/13, 92.3%) patients, respectively. According to the intention-to-treat (ITT) analysis, the pCR and major pathological response in the ITT cohort were 47.1% (8/17) and 70.6% (12/17), respectively. In addition, an overall response rate of 100% was recorded in the PP cohort. Moreover, 15 (15/17, 88.2%) patients and 1 (1/17, 5.9%) in the ITT cohort attained partial remission (PR), and complete remission, respectively, with an overall response rate of 94.1%. The median overall survival of the patients of pCR and the median event-free survival of the patients on surgery had not achieved. However, the median overall survival of the patients of non-pCR was 18.2 months and the median event-free survival of the nonsurgical patients was 9.5 months. During the neoadjuvant treatment, the incidence of grade 3 or higher AEs was 58.8% (10/17). Additionally, three patients (17.6%) developed immune-related adverse event (grades 1-2).

CONCLUSION

In patients with SCLC, neoadjuvant or conversion atezolizumab combined with chemotherapy significantly improved pCR with manageable AEs. Therefore, this regimen may be considered a safe and effective treatment for SCLC.

Neoadjuvant chemoradiotherapy with capecitabine based regimen in locally advanced rectal cancer: A retrospective study

Capecitabine-based neoadjuvant chemoradiotherapy (nCRT) is the standard treatment for locally advanced rectal cancer. The objective of this study is to analyze overall survival (OS), disease-free survival (DFS) and prognostic factors of patients with stage II to III rectal cancer treated with nCRT in our institution. Between March 2014 to June 2020, 121 locally advanced rectal cancer patients were retrospectively reviewed and analyzed. All of the enrolled patients were treated with capecitabine-based nCRT (pelvic radiotherapy: 45-50.4 Gy, 1.8 Gy/d plus concomitant capecitabine-based chemotherapy), total mesorectal excision surgery (surgery was carried out 8-12 weeks after the end of CRT), and capecitabine-based adjuvant chemotherapy. We examined the pathological complete response rate, 3-year OS, 3-year DFS and the other prognostic factors. Kaplan-Meier method and Log-rank test were used to estimate and compare survival rate. With a median follow-up of 36 months, 3-year DFS and 3-year OS was 74.4% and 83.2%, respectively. Among the 121 patients, 24 achieved pathological complete remission (19.8%). After multivariate analysis, ypTNM stage (TNM stage after neoadjuvant therapy) was significantly associated with DFS. Positive mesorectal fasciae (MRF) status on magnetic resonance imaging and ypTNM stage were significantly related to OS. CRT with capecitabine based regimen provides high rates of survival and sphincter preservation with acceptable toxicity. YpTNM stage was significantly associated with DFS; magnetic resonance imaging MRF status and ypTNM stage were significant factors for OS after multivariate analysis. Distant metastasis is the dominant mode of treatment failure, and it is crucial to optimize systemic treatment for newly diagnosed patients.

Plasmid-Mediated AmpC (pAmpC) Genotypes Among Uropathogenic Escherichia coli: A Hospital-Based Study From Western Uttar Pradesh

Introduction Resistance due to AmpC and extended-spectrum beta (β)-lactamases (ESBLs) in Escherichia coli is an emerging problem worldwide. AmpC enzymes are a subclass of β-lactamases that have a capacity to hydrolyze and deactivate a large range of β-lactam antibiotics, particularly cephalosporins, penicillins, and monobactams, although frequently being susceptible to carbapenems and fourth-generation cephalosporins. The prevalence of plasmid-mediated AmpC (pAmpC) genotypes in uropathogenic E. coli isolates were looked at a tertiary care teaching hospital of Western Uttar Pradesh. Materials and methods A total of 312 non-repeat clinical E. coli isolates among patients presented with urinary tract infections (UTIs) were investigated by standard microbiological methods. Isolates were screened for the presence of ampC using a cefoxitin (30 µg) disc and confirmed using an inhibitor-based assay. Using multiplex polymerase chain reaction (PCR), six AmpC genotypes, namely, CIT, DHA, EBC, ACC, FOX, and MOX, were genotypically identified. Results A total of 152 (48.72%) uropathogenic E. coli isolates tested positive on the cefoxitin screening. Out of which, AmpC production was confirmed in 118/152 (77.63%) using a phenotypic method. In particular, the pAmpC gene was found in 56/152 (36.84%) isolates. CIT was the most common gene detected in this geographical area (57.14 %). Multiple genes, i.e., CIT and FOX, were also detected in 14.29% of the isolates.  Conclusion Identifying AmpC producers is important in routine microbiology laboratory as they are a nosocomial threat requiring strict adherence to infection control protocols. A confirmatory phenotypic test followed by genotypic tests will help in the correct and accurate identification of this resistance.

Prevalence of Human Papillomavirus (HPV)-16 in Different Dental Infections in the Lebanese Population

BACKGROUND

Dental infections, which are the main cause of tooth loss, are known to be caused by bacteria. However, recent research suggests that other organisms, such as viruses, may also play a role. In this study, we aim to detect the presence of human papillomavirus (HPV)-16 and assess its prevalence in tissues infected with various dental infections, including aggressive and chronic periodontitis, pericoronitis, and periapical infection, as well as healthy gingival tissues, saliva, and gingival crevicular fluid, for comparison.

METHODS

A cross-sectional study including 124 adult healthy patients presenting with dental infections requiring dental extractions were conducted to assess the prevalence of HPV-16 in saliva, infected, and healthy tissues using quantitative polymerase chain reaction (PCR) tests. Samples were collected and a categorical scale was used for the prevalence. Statistical analyses were performed using Chi-square for the prevalence of HPV-16.

RESULTS

Among the HPV-16-positive PCR cases, the prevalence of HPV-16 was highest in periapical infection tissues as compared to chronic periodontitis, aggressive periodontitis, pericoronitis, and control tissues.

CONCLUSION

The prevalence of HPV-16 in periapical infection samples was the highest among the studied dental infection samples. Thus, a primary conclusion can be drawn about the presence of an association between HPV-16 and the occurrence of periapical infection.

Periodontal disease severity is associated to pathogenic consortia comprising putative and candidate periodontal pathogens

BACKGROUND

Based on a holistic concept of polymicrobial etiology, we have hypothesized that putative and candidate periodontal pathogens are more frequently detected in consortia than alone in advanced forms of periodontal diseases (PD).

OBJECTIVE

To correlate specific consortia of periodontal pathogens with clinical periodontal status and severity of periodontitis.

METHODOLOGY

Subgingival biofilm was obtained from individuals with periodontal health (113, PH), gingivitis (91, G), and periodontitis (209, P). Genomic DNA was purified and the species Aggregatibacter actinomycetemcomitans (Aa), Aa JP2-like strain, Porphyromonas gingivalis (Pg), Dialister pneumosintes (Dp), and Filifactor alocis (Fa) were detected by PCR. Configural frequency and logistic regression analyses were performed to correlate microbial consortia and PD.

RESULTS

Aa + Pg in the presence of Dp (phi=0.240; χ2=11.9, p<0.01), as well as Aa JP2 + Dp + Fa (phi=0.186, χ2=4.6, p<0.05) were significantly more associated in advanced stages of P. The consortium Aa + Fa + Dp was strongly associated with deep pocketing and inflammation (p<0.001). The best predictors of disease severity (80% accuracy) included older age (OR 1.11 [95% CI 1.07 - 1.15], p<0.001), Black/African-American ancestry (OR 1.89 [95% CI 1.19 - 2.99], p=0.007), and high frequency of Aa + Pg + Dp (OR 3.04 [95% CI 1.49 - 6.22], p=0.002).

CONCLUSION

Specific microbial consortia of putative and novel periodontal pathogens, associated with demographic parameters, correlate with severe periodontitis, supporting the multifactorial nature of PD.

The relationship between cardiological parameters and PCR in patients with coronavirus infection: A cross-sectional study

Cardiovascular injuries induced by SARS CoV-2 have been reported repeatedly in various studies. Therefore, it is necessary to understand cardiac complications at a low cost, quickly. This study aimed to determine the relationship between cardiological parameters and polymerase chain reaction (PCR) in patients with coronavirus infection. : Patients who were admitted to the emergency department due to the ongoing pandemic, all patients with similar symptoms to coronavirus disease 2019 infection were initially admitted to the respiratory emergency room and underwent subsequent evaluations to confirm or rule out SARS-COV2 infection symptoms were assessed for eligibility. Patient were categorized into 2 groups 1. Positive PCR and negative PCR groups. Binary logistic regression was performed to assess the effect of several factors on the likelihood of developing positive troponin, reduced ejection fraction (EF), and Positive brain natriuretic peptide (BNP). Among 195 patients included, 115 (58.9%) had positive PCR. Patient in the positive PCR and negative PCR were 58.04 ± 18.03 and 59.19 ± 15.38 years of age, respectively. Patients in the "positive PCR" were significantly less likely to have chronic kidney disease (6.69% vs 17.5%, P value: .022), consume calcium channel blockers (6.69% vs 18.75%, P value:0.012). At the univariable level, positive PCR was significantly associated with fewer odds for positive BNP (OR:0.46, P = .019); nevertheless, the association was no longer significant after adjusting for confounders (adjusted OR:0.56, P = .158). Unadjusted positive PCR results were not found to have a significant association with positive troponin or reduced EF. Likewise, multivariable regression revealed no association between positive PCR and positive troponin (aOR:1.28, P = .529) and reduced EF (aOR:0.65, P = .369). PCR positivity did not result in positive troponin and BNP and did not appear to decrease EF. In other words, serial troponin and BNP checks and initial echocardiography in coronavirus disease 2019 respiratory emergencies do not make significant differences in diagnostic and therapeutic management and inpatient outcomes of patients with positive or negative PCR and are not specific findings. Evidence suggests some coronavirus-induced cardiac complications will be manifested in the long term.

Two Leishmania species separation targeting the ITS-rDNA and Cyt b genes by developing and evaluating HRM- qPCR

BACKGROUND

Incidence of Cutaneous Leishmaniasis as an infectious and neglected disease is increasing, for the diagnosis of which several traditional methods and conventional PCR techniques have been developed, employing different genes for species identification.

METHODS

Leishmania parasites were sampled, DNA was extracted, and new specific and sensitive primers were designed. Two ITS-rDNA and Cyt b genes were targeted by qPCR using the High- Resolution Melting method to identify Leishmania parasites. The standard curves were drawn, compared, and identified by high-resolution melting curve analysis.

RESULTS

Melting temperature and Cycle of Threshold of ITS-rDNA was higher than Cyt b but Cyt b was more sensitive than ITS-rDNA when Leishmania major and Leishmania tropica were analyzed and evaluated. By aligning melt curves, normalizing fluorescence curves, and difference plotting melt curves, each Leishmania species was distinguished easily. L. major and L. tropica were separated at 83.6 °C and 84.7 °C, respectively, with less than 0.9 °C of temperature difference. Developing sensitivity and specificity of real-time PCR based on EvaGreen could detect DNA concentration to less than one pmol.

CONCLUSIONS

Precise identification of Leishmania parasites is crucial for strategies of disease control. Real-time PCR using EvaGreen provides rapid, highly sensitive, and specific detection of parasite's DNA. The modified High-Resolution Melting could determine unique curves and was able to detect single nucleotide polymorphisms according to small differences in the nucleotide content of Leishmania parasites.

Diagnostic value of EBV-DNA in CSF for PCNSL in AIDS patients with focal brain lesions: A meta-analysis of diagnostic test

BACKGROUND

Epstein-Barr virus (EBV) infection plays a crucial role in the progression of acquired immunodeficiency syndrome related primary central nervous system lymphoma (AR-PCNSL). This study aimed at evaluating the diagnostic value of cerebrospinal spinal fluid (CSF) EBV-deoxyribonucleic acid (DNA) for PCNSL in patients with infection of human immunodeficiency (HIV) virus through a meta-analysis of diagnostic test.

METHODS

A systematic search in PubMed, Embase, Web of Science, Wanfang, Chinese Biomedical Database and Chinese National Knowledge Infrastructure was conducted before May 10, 2022. Heterogeneity among the studies was assessed using Q test and I2 statistics. Publication bias was assessed using the Deek's funnel plot asymmetry test. Statistical analyses were performed using Stata 16.0 software. The pooled sensitivity, specificity, positive and negative likelihood ratios (PLR and NLR), diagnostic odds ratios (DOR) and 95% confidence intervals (CI) were caculated to evaluate the diagnostic value. A symmetric receiver operating characteristic (SROC) curve and the area under the SROC curve (AUC) were constructed to evaluate the test-performance.

RESULTS

Twelve studies were included in the final analyses, with a total of 141 patients with AR-PCNSL and 590 controls. The pooled diagnostic values were sensitivity of 0.83 (95% CI: 0.73-0.90), specificity of 0.95 (95%CI: 0.89-0.98), PLR of 17.8 (95%CI: 6.8-46.1), NLR of 0.17 (95%CI: 0.10-0.30), DOR of 102 (95%CI: 28-379), and AUC of 0.94 (95%CI: 0.91-0.96).

CONCLUSION

In summary the overall diagnostic value of CSF EBV-DNA is very high and it can be a reliable diagnostic biomarker for AR-PCNSL.

Detection of Escherichia coli in Food Samples Using Culture and Polymerase Chain Reaction Methods

Methods for the rapid detection of Escherichia coli and its related toxins are key to minimizing the risk of exposure to foodborne pathogens. The present study aimed to detect E. coli in food specimens using culture and polymerase chain reaction (PCR) techniques. One hundred and fifty samples from different types of food, comprising beef (n=60), chicken (n=72), and fish (n=18), were analyzed for the identification of E. coli by conventional and PCR methods. The results showed that out of 150 food samples, 44 (29.3%) were positive by culture, and 50 (33.3%) were positive by PCR. Significant differences were detected between sample types with culture (p-value < 0.005). When culture was considered the gold standard, the sensitivity of PCR was 100%, while the specificity was 94.34%. The six-hour pre-enrichment and PCR analysis are reliable in fast detection of E. coli in food samples. Hence, the identification of food pathogens using molecular-based methods would become more useful in routine diagnostic laboratories.

Diagnostic test accuracy of PCR by saliva specimen for cytomegalovirus infection in newborn: A protocol for systematic review and meta-analysis

BACKGROUND

This study aimed to assess the diagnostic accuracy of polymerase-chain-reaction by saliva.

METHOD

We searched Pubmed, EMBASE, Cochrane Library and Web of Science. A case-control or cohort study designed to explore the saliva specimens for diagnosing the cytomegalovirus infection was eligible for this study. Sensitivity (SEN), specificity (SPE), diagnostic odds ratio (DOR), and summary receiver operating characteristic curves were calculated.

RESULTS

Nine articles were selected for the meta-analysis. For assessing saliva PCR with urine culture, the SEN, SPE, and DOR were 0.97 [95% confidential interval (CI):0.61,1.00] 1.00 [95%CI:0.99, 1.00] 15672 [95%CI:558, 440325], respectively; for assessing saliva PCR with urine PCR, the SEN, SPE, and DOR were 0.87 [95%CI:0.79, 0.92] 1.00 [95%CI:1.00, 1.00] 15637 [95%CI:5946, 41126], respectively; for total assessment, the SEN, SPE, and DOR were0.91 [95%CI:0.70, 0.98] 1.00 [95%CI:1.00, 1.00] 8493 [95%CI:1429, 50487], respectively.

CONCLUSION

We reported that saliva PCR performed well in the diagnosis of cytomegalovirus infection.

Microbial toxins in fermented foods: health implications and analytical techniques for detection

Recently, demand for fermented foods has increased due to their improved nutritional value, taste, and health-promoting properties. Worldwide consumption of these products is increasing. Fermented foods are generally safe for human consumption. However, some toxins, primarily biogenic amines (putrescine, phenylethylamine, histamine, tyramine, and cadaverine), mycotoxins (fumonisins, aflatoxins, ochratoxin A, zearalenone, and trichothecenes), and bacterial toxins (endotoxins, enterotoxins, and emetic toxins) can be produced as a result of using an inappropriate starter culture, processing conditions, and improper storage. These toxins can cause a multitude of foodborne illnesses and can lead to cardiovascular aberration and adverse gastrointestinal symptoms. Analytical techniques are in use for the detection of toxins in fermented foods for monitoring and control purposes. These include culture, chromatographic, immunoassays, and nano sensor-based techniques. These detection techniques can be used during the production process and along the food chain. On an industrial scale, HPLC is widely used for sensitive quantification of toxins in fermented foods. Recently, biosensor and nano sensor-based techniques have gained popularity due to accuracy, time efficiency, and simultaneous detection of multiple toxins. Other strategic methods being investigated for the removal of toxins from fermented foods include the use of specific starter cultures for bio-preservation, aflatoxin-binding, and biogenic amine-degradation agents that may help to appropriately manage the food safety concerns associated with fermented foods.

Viral meningitis in Sudanese children: Differentiation, etiology and review of literature

Diagnosis of viral meningitis (VM) is uncommon practice in Sudan and there is no local viral etiological map. We therefore intended to differentiate VM using standardized clinical codes and determine the involvement of herpes simplex virus types-1 and 2 (HSV-1/2), varicella zoster virus, non-polio human enteroviruses (HEVs), and human parechoviruses in meningeal infections in children in Sudan. This is a cross-sectional hospital-based study. Viral meningitis was differentiated in 503 suspected febrile attendee of Omdurman Hospital for Children following the criteria listed in the Clinical Case Definition for Aseptic/Viral Meningitis. Patients were children age 0 to 15 years. Viral nucleic acids (DNA/RNA) were extracted from cerebrospinal fluid (CSF) specimens using QIAamp® UltraSens Virus Technology. Complementary DNA was prepared from viral RNA using GoScriptTM Reverse Transcription System. Viral nucleic acids were amplified and detected using quantitative TaqMan® Real-Time and conventional polymerase chain reactions (PCRs). Hospital diagnosis of VM was assigned to 0%, when clinical codes were applied; we considered 3.2% as having VM among the total study population and as 40% among those with proven infectious meningitis. Two (0.4%) out of total 503 CSF specimens were positive for HSV-1; Ct values were 37.05 and 39.10 and virus copies were 652/PCR run (261 × 103/mL CSF) and 123/PCR run (49.3 × 103/mL CSF), respectively. Other 2 (0.4%) CSF specimens were positive for non-polio HEVs; Ct values were 37.70 and 38.30, and the approximate virus copies were 5E2/PCR run (~2E5/mL CSF) and 2E2/PCR run (~8E4/mL CSF), respectively. No genetic materials were detected for HSV-2, varicella zoster virus, and human parechoviruses. The diagnosis of VM was never assigned by the hospital despite fulfilling the clinical case definition. Virus detection rate was 10% among cases with proven infectious meningitis. Detected viruses were HSV-1 and non-polio HEVs. Positive virus PCRs in CSFs with normal cellular counts were seen.

Healthcare workers' SARS-CoV-2 infection rates during the second wave of the pandemic: follow-up study

OBJECTIVES

This study aimed to assess if, during the second wave of the COVID-19 pandemic, healthcare workers had increased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection rates, following close contact with patients, co-workers and persons outside work with COVID-19.

METHODS

A follow-up study of 5985 healthcare workers from Denmark was conducted between November 2020 and April 2021 and provided day-to-day information on COVID-19 contacts. SARS-CoV-2 infection was defined by the first positive polymerase chain reaction (PCR) test ever. Data was analyzed in multivariable Poisson regression models.

RESULTS

The SARS-CoV-2 infection rates following close contact 3-7 days earlier with patients, co-workers and persons outside work with COVID-19 were 153.7, 240.8, and 728.1 per 100 000 person-days, respectively. This corresponded with age, sex, month, number of PCR tests and mutually adjusted incidence rate ratios of 3.17 [40 cases, 95% confidence interval (CI) 2.15-4.66], 2.54 (10 cases, 95% CI 1.30-4.96) and 17.79 (35 cases, 95% CI 12.05-26.28). The risk of SARS-CoV-2 infection was thus lower, but the absolute numbers affected was higher following COVID-19 contact at work than COVID-19 contact off work.

CONCLUSIONS

Despite strong focus on preventive measures during the second wave of the pandemic, healthcare workers were still at increased risk of SARS-CoV-2 infection when in close contact with patients or co-workers with COVID-19. There is a need for increased focus on infection control measures in order to secure healthcare workers' health and reduce transmission into the community during ongoing and future waves of SARS-CoV-2 and other infections.

Contribution of COVID Antigenic RDT to the Management Strategy of COVID-19 Pandemic in a Senegalese Company

OBJECTIVE

To describe the contribution of the rapid antigen diagnostic testing (RDT) to the management strategy of the COVID-19 pandemic.

METHODOLOGIES

The protein chain reaction (PCR) and the RDT have been performed on each COVID-19 suspected workers from December 2020 to September 2021.

RESULTS

A total of 286 people tested. A positivity rate of 38.1% was recorded. The average time to obtain PCR results was 8.3 days. 54.8% (n = 142) of the RDT were followed by a PCR for confirmation or invalidation and 100% of positive cases with Ag-RDT were confirmed by the PCR. We have noticed a 58.3% reduction of lost work days due to COVID-19, since the use of the Ag-RDT.

CONCLUSION

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapid diagnostic tests are efficient. They have enabled early treatment of COVID-19 patients, helped hold back the spread of the disease in a high-risk professional environment, and reduced the impact of the pandemic on a vital sector in developing countries.

Clinical evaluation of the Diagnostic Analyzer for Selective Hybridization (DASH): a point-of-care PCR test for rapid detection of SARS-CoV-2 infection

BACKGROUND

Rapid and accurate testing for SARS-CoV-2 is an essential tool in the medical and public health response to the COVID-19 pandemic. An ideal test for COVID-19 would combine the sensitivity of laboratory-based PCR combined with the speed and ease of use of point-of-care (POC) or home-based rapid antigen testing.

METHODS

To evaluate the performance of the Diagnostic Analyzer for Selective Hybridization (DASH) SARS-CoV-2 POC PCR (sample insertion to result time of 16 minutes), we conducted a cross-sectional study of adults with and without symptoms of COVID-19 at four clinical sites. We collected two bilateral anterior nasal swabs from each participant and information on COVID-19 symptoms, vaccination, and exposure. One swab was tested with the DASH SARS-CoV-2 POC PCR and the second in a central laboratory using Cepheid Xpert Xpress SARS-CoV-2 PCR. We assessed test concordance and calculated sensitivity, specificity, negative and positive predictive values using Xpert as the "gold standard."

RESULTS

We enrolled 315 and analyzed 313 participants with median age 42 years; 65% were female, 62% symptomatic, 75% had received ≥2 doses of mRNA COVID-19 vaccine, and 16% currently COVID-19 positive. There were concordant results for 307 tests indicating an overall agreement for DASH of 0.98 [95% CI 0.96, 0.99] compared to Xpert. DASH performed at 0.96 [95% CI 0.86, 1.00] sensitivity and 0.98 [95% CI 0.96, 1.00] specificity, with a positive predictive value of 0.85 [95% CI 0.73, 0.96] and negative predictive value of 0.996 [95% CI 0.99, 1.00]. The six discordant tests between DASH and Xpert all had high Ct values (>30) on the respective positive assay. DASH and Xpert Ct values were highly correlated (R=0.89 [95% CI 0.81, 0.94]).

CONCLUSIONS

DASH POC SARS-CoV-2 PCR was accurate, easy to use, and provided fast results in real-life clinical settings with an overall performance similar to an EUA-approved laboratory-based PCR. Its compact design and ease of use are optimal for a variety of healthcare, and potentially community settings, including areas with lack of access to central laboratory-based PCR testing.

SUMMARY

DASH is an accurate, easy to use, and fast point-of-care test with applications for diagnosis and screening of SARS-CoV-2 infection.

Evaluation of the Potential Impact of a Multiplex Rapid Diagnostic Panel in Critically Ill Patients With Hospital-Acquired Pneumonia

Background Rapid diagnostic tools have emerged as valuable assets assisting clinicians in decision-making regarding patient management in the hospital setting. Our study sought to identify the potential impact of the BioFire® FilmArray® Pneumonia Panel (FP Panel) (BioFire Diagnostics, Salt Lake City, UT, USA) in patients with hospital-acquired pneumonia (HAP). Methods Respiratory samples obtained by bronchoalveolar lavage (BAL) or tracheal aspiration (TA) from ICU patients with a diagnosis of HAP were tested by the FP panel in addition to routine bacterial cultures. In addition, the electronic health records of these patients were reviewed to determine what potential changes in antimicrobial therapy could have been implemented if the panel results were known to the treatment team in real-time. A cost analysis was also performed incorporating the cost of the pneumonia panel and the savings associated with the potential decrease of antibiotic use and avoidance of the rapid viral diagnostic panel.  Results Fifty-six patients met the study criteria. The FP panel results could have prompted a change in therapy in 36 (64.3%) patients, with an anticipated mean reduction in time to optimized therapy of approximately 51 hours. In addition, the panel identified three cases where antimicrobials should have been altered because patients were not receiving empiric therapy with activity against the causative pathogen and 34 opportunities for antibiotic de-escalation. The cost analysis calculated an additional cost of $10 per patient associated with using the FP panel.  Conclusions The FP panel could have prompted a change in therapy in about two-thirds of patients studied. Its potential benefits include a more rapid time to optimized therapy, reduced exposure to and cost of broad-spectrum antimicrobials, and reduced cost of other rapid diagnostic tests.

Mediterranean visceral leishmaniasis : update on biological diagnosis

Visceral leishmaniasis (VL) is a severe life threatening parasitosis requiring early management of cases. It is an emerging disease in the Mediterranean region with a spread of endemic areas and an increase in case incidence. The patient profile has also evolved with more affected adults, presenting generally non-specific symptoms. Hence the interest of a systematic biological confirmation. The microscopic detection of Leishmania amastigotes in bone marrow aspirates (BMA) smears is the gold standard diagnostic technique. However, it requires invasive sampling. Serological tests searching for specific antibodies remain highly contributory, but their interpretation must always take into account the epidemiological context and the patient's clinical and biological features. Currently, the Western-Blot represents the most specific serological technique for diagnostic confirmation. VL diagnosis has greatly improved by the introduction of both rapid diagnostic tests (RDTs) and molecular biological techniques. RDTs using recombinant rk39 antigen are easy to perform and deliver results in less than 30 minutes. Real-time PCR (Polymerase Chain Reaction) is currently retained as the best technique for VL diagnosis. It is efficient on simple blood samples, allowing to avoid invasive BMA needed for microscopy. In addition, real time PCR estimates parasite load which is helpful for the post-treatment follow-up. In any case, the choice of techniques to be used should be strategic and adapted to the local epidemiology as well as to the means available.

Association of Serotonergic Pathway Gene Polymorphisms With Behavioral Parameters in Patients With Opioid Dependence

Background and aims Opioid dependence is a chronic, relapsing substance use disorder with a multifactorial etiology, including a genetic component. Serotonin pathway gene polymorphisms have been an important focus of research for psychiatric disorders, including substance use disorders. This study aimed to identify the association of serotonin pathway gene polymorphisms with self-harm, depressive symptoms, impulsiveness, and aggression in patients with opioid dependence. Method The study group comprised 366 subjects with opioid dependence and 200 healthy volunteers. Patients were assessed for a history of self-harm, depressive symptoms, impulsiveness, and aggression using standard tools. Genomic DNA was used for genotyping of four polymorphisms - 5-HTTLPR, STin2 VNTR, TPH1 A218C, and TPH2 G703T. Results The short allele of 5-HTTLPR polymorphism showed a significant difference between cases (59.8%) and controls (40.1%) (p=0.001) and revealed an association with age at opioid dependence (p=0.033). There was a borderline significance of the short allele of 5-HTTLPR with the duration of opioid use (p=0.061) and non-plan impulsivity (p=0.076), suggesting a role of 5-HTTLPR in the susceptibility of opioid dependence. The other markers did not differ between cases and controls. However, the STin2A polymorphism revealed a significant association with anger scores, which may indicate its role in aggressive behavior. Conclusions The present study, the first of its kind, suggests an association of 5-HTTLPR polymorphism with opioid dependence and STin2A polymorphism with aggressive behavior among opioid-dependence patients, signifying the role of these markers in our patient population.

Human Herpesvirus 6 (HHV-6) Encephalitis in a Non-Transplant Patient With Polymyositis

Human herpesvirus 6 (HHV-6) was initially labeled as a human B lymphotropic virus because it was isolated in patients diagnosed with lymphoproliferative disorders. There are two variants of HHV-6: HHV-6A and HHV-6B. A considerable majority of recorded primary infections and reactivation events are primarily due to HHV-6B. We report a case of HHV-6 encephalitis reactivation in a 75-year-old Caucasian diabetic female with a past medical history of polymyositis treated with prednisone for a long time who presented with generalized weakness and drowsiness. She developed her symptoms after contact with her grandchildren, who recently had viral-like symptoms treated with antibiotics. Magnetic resonance imaging (MRI) of the brain without contrast showed 14 mm high transverse relaxation time (T2)/fluid-attenuated inversion recovery (FLAIR) signal intensity focus on the left temporal lobe, suspicious for primary versus metastatic neoplasm. Cerebrospinal fluid analysis found that protein concentration was 75 mg/dl, glucose concentration 55 mg/dl, white blood cell count was 22/mm3, with a lymphocytic predominance. Meningitis/encephalitis polymerase chain reaction (PCR) panel detected HHV-6. She was discharged after treatment with ganciclovir for 14 days. It is crucial to recognize HHV-6 infections in immunocompromised patients who present with a T2/FLAIR signal intensity focus in the left temporal lobe. In a hospital setting, rapid HHV-6 encephalitis testing is important to make a correct diagnosis to avoid any delay to prevent further morbidity and mortality.

Molecular sequencing technologies in the diagnosis and management of prosthetic joint infections

INTRODUCTION

Prosthetic joint infections (PJIs) can be challenging to eradicate and have high morbidity and mortality. Current microbiology culture methods can be associated with a high false-negative rate of up to 50%. Early and accurate diagnosis is crucial for effective treatment, and negative results have been linked to a greater rate of reoperation.

AREAS COVERED

There has been increasing investigation of the use of next-generation sequencing (NGS) technology such as metagenomic shotgun sequencing to help identify causative organisms and decrease the uncertainty around culture-negative infections. The clinical importance of the organisms detected and their management, however, requires further study. The polymerase chain reaction (PCR) has shown promise, but in recent years multiple studies have reported similar or lower sensitivity for bacteria detection in PJIs when compared to traditional culture. Furthermore, issues such as high cost and complexity of sample preparation and data analysis are to be addressed before it can move further toward routine clinical practice.

EXPERT OPINION

Metagenomic NGS has shown results that inspire cautious optimism - both in culture-positive and culture-negative cases of joint infection. Refinement of technique could revolutionize the way PJIs are diagnosed, managed, and drastically improve outcomes from this currently devastating complication.

Recent advances in rapid antimicrobial susceptibility testing systems

INTRODUCTION

Until recently antimicrobial susceptibility testing (AST) methods based on the demonstration of phenotypic susceptibility in 16-24 h remained largely unchanged.

AREAS COVERED

Advances in rapid phenotypic and molecular-based AST systems.

EXPERT OPINION

AST has changed over the past decade, with many rapid phenotypic and molecular methods developed to demonstrate phenotypic or genotypic resistance, or biochemical markers of resistance such as β-lactamases associated with carbapenem resistance. Most methods still require isolation of bacteria from specimens before both legacy and newer methods can be used. Bacterial identification by MALDI-TOF mass spectroscopy is now widely used and is often key to the interpretation of rapid AST results. Several PCR arrays are available to detect the most frequent pathogens associated with bloodstream infections and their major antimicrobial resistance genes. Many advances in whole-genome sequencing of bacteria and fungi isolated by culture as well as directly from clinical specimens have been made but are not yet widely available. High cost and limited throughput are the major obstacles to uptake of rapid methods, but targeted use, continued development and decreasing costs are expected to result in more extensive use of these increasingly useful methods.

Pathological Complete Response to Neoadjuvant Chemotherapy in Patients With Breast Cancer: The Relationship Between Inflammatory Biomarkers and Molecular Subtypes

Purpose

Among patients with breast cancer, pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) is an important prognostic predictor of survival. This study aimed to investigate the relationship between platelet-lymphocyte ratio (PLR) and neutrophil-lymphocyte ratio (NLR) along with overall pCR.

Method

A total of 150 patients with breast cancer who were first administered NAC and then operated on were retrospectively evaluated. Neutrophil-lymphocyte ratio and PLR obtained from the complete blood count analysis performed immediately before NAC treatment were analyzed. The cut-off value was calculated as 150 for PLR and 2.24 for NLR. We studied the predictive value of NLR and PLR levels for the pathologic response of breast cancer to NAC.

Results

Pathological complete response was observed in 34.7% (n = 52) of the patients, pCR in the breast in 42.7% (n = 64), and that in the axilla in 44% (n = 66). There was a statistically significant difference between the pCR rates according to the PLR levels (p = 0.013). In addition, a statistically significant difference was found in the pCR rates in the breast and axilla according to PLR levels (p = 0.018, p = 0.009). Patients with low PLR in the human epidermal growth factor receptor 2 (HER-2) group had significantly higher axillary pCR rates than in those with high PLR (p = 0.019).

Conclusions

A low PLR level showed high chemotherapy sensitivity independent of molecular subtypes in the treatment of breast cancer with NAC. The PLR level can serve as a predictive marker of the therapeutic effect of NAC on the breast and axilla. Low PLR levels in HER-2 enriched groups can predict pCR in the axilla.

Changes in Diffuse Optical Tomography Images During Early Stages of Neoadjuvant Chemotherapy Correlate with Tumor Response in Different Breast Cancer Subtypes

PURPOSE

This study's primary objective was to evaluate the changes in optically derived parameters acquired with a diffuse optical tomography breast imaging system (DOTBIS) in the tumor volume of patients with breast carcinoma receiving neoadjuvant chemotherapy (NAC).

EXPERIMENTAL DESIGN

In this analysis of 105 patients with stage II-III breast cancer, normalized mean values of total hemoglobin ([Formula: see text]), oxyhemoglobin ([Formula: see text]), deoxy-hemoglobin concentration ([Formula: see text]), water, and oxygen saturation ([Formula: see text]) percentages were collected at different timepoints during NAC and compared with baseline measurements. This report compared changes in these optical biomarkers measured in patients who did not achieve a pathologic complete response (non-pCR) and those with a pCR. Differences regarding molecular subtypes were included for hormone receptor-positive and HER2-negative, HER2-positive, and triple-negative breast cancer.

RESULTS

At baseline, [Formula: see text] was higher for pCR tumors (3.97 ± 2.29) compared with non-pCR tumors (3.00 ± 1.72; P = 0.031). At the earliest imaging point after starting therapy, the mean change of [Formula: see text] compared with baseline ([Formula: see text]) was statistically significantly higher in non-pCR (1.23 ± 0.67) than in those with a pCR (0.87 ± 0.61; P < 0.0005), and significantly correlated to residual cancer burden classification (r = 0.448; P < 0.0005). [Formula: see text] combined with HER2 status was proposed as a two-predictor logistic model, with AUC = 0.891; P < 0.0005; and 95% confidence interval, 0.812-0.969.

CONCLUSIONS

This study demonstrates that DOTBIS measured features change over time according to tumor pCR status and may predict early in the NAC treatment course whether a patient is responding to NAC.

Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs

PURPOSE

This study was designed to detect CoV-RNA in the tears of polymerase chain reaction (PCR)-confirmed SARS-CoV-2 positive patients.

METHODS

We performed a prospective case series study of hospitalized patients who have been confirmed SARS-CoV-2 positive by oropharyngeal swab within the previous 5 days. Tear samples obtained with a laboratory capillary and oropharyngeal swabs were analyzed by real-time PCR using the Altona SARS-CoV-2 Assay or the Roche SARS-CoV-2 LightMix PCR, depending on the availability. Patient history was documented, and ophthalmoscopy was used to assess for ocular surface disease.

RESULTS

Of all 18 patients recruited in April 2020, 5 suffered from respiratory failure and were submitted to an intensive care unit. None of our patients had signs of viral conjunctivitis although all patients in intensive care showed chemosis and conjunctival hyperemia because of third-spacing or fluid overload. The presence of coronavirus RNA was confirmed by PCR in 5 of 18 patients (28%) in tears and 72% for oropharyngeal swabs.

CONCLUSIONS

Using a tear fluid sampling technique similar to oropharyngeal lavage presents a higher percentage of SARS-CoV-2 positive tears in contrast to earlier reports that used a conjunctival swab. This does not automatically indicate viral shedding in ocular tissue or contagiousness of tear fluid.

Lessons and Considerations for the Creation of Universal Primers Targeting Non-Conserved, Horizontally Mobile Genes

Effective and accurate primer design is an increasingly important skill as the use of PCR-based diagnostics in clinical and environmental settings is on the rise. While universal primer sets have been successfully designed for highly conserved core genes such as 16S rRNA and characteristic genes such as dsrAB and dnaJ, primer sets for mobile, accessory genes such as multidrug resistance efflux pumps (MDREP) have not been explored. Here, we describe an approach to create universal primer sets for select MDREP genes chosen from five superfamilies (SMR, MFS, MATE, ABC and RND) identified in a model community of six members (Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica). Using sequence alignments and in silico PCR analyses, a new approach for creating universal primers sets targeting mobile, non-conserved genes has been developed and compared to more traditional approaches used for highly conserved genes. A discussion of the potential shortfalls of the primer sets designed this way are described. The approach described here can be adapted to any unique gene set and aid in creating a wider, more robust library of primer sets to detect less conserved genes and improve the field of PCR-based screening research.IMPORTANCE Increasing use of molecular detection methods, specifically PCR and qPCR, requires utmost confidence in the results while minimizing false positives and negatives due to poor primer designs. Frequently, these detection methods are focused on conserved, core genes which limits their applications. These screening methods are being used in various industries for specific genetic targets or key organisms such as viral or infectious strains, or characteristic genes indicating the presence of key metabolic processes. The significance of this work is to improve primer design approaches to broaden the scope of detectable genes. The use of the techniques explored here will improve detection of non-conserved genes through unique primer design approaches. Additionally, the approaches here highlight additional, important information which can be gleaned during the in silico phase of primer design which will improve our gene annotations based on percent identities.

Rapid detection of Mycobacterium tuberculosis in children using blood and urine specimens

INTRODUCTION

Laboratory and clinical features of childhood tuberculosis (TB) are non-specific and establishing an accurate diagnosis remains a challenge. This study evaluated a Single tube nested-PCR (STNPCR) to detect genomic DNA of Mycobacterium tuberculosis complex in blood and urine.

METHODS

Biological samples were obtained from children (<15 years old) with clinical suspicion of pulmonary and extrapulmonary TB at public hospitals in Recife-Pernambuco, Brazil. Cultures yielded negative results in a majority of childhood TB cases, which are generally paucibacillary. A set of clinical, epidemiological, radiological, and laboratory criteria with evident clinical improvement after anti-TB treatment were frequently used to define childhood TB cases.

RESULTS

Ninety children with clinical suspicion were enrolled in this study (44 with TB and 46 without TB). The pulmonary TB group had 20 confirmed cases and 46 negative controls, while the extrapulmonary TB group had 24 confirmed cases. The STNPCR showed sensitivities to pulmonary and extrapulmonary TB of 47.4% and 52.2% (blood) and 38.8% and 20% (urine), respectively. Considering the low performance of STNPCR on separate samples, we decided to perform a combined analysis (parallel sensitivity analysis) of the results from blood and urine samples. The parallel sensitivity increased to 65% in blood and 62.5% in urine. The specificity in both samples ranged from 93.5-97.8%.

CONCLUSIONS

Although STNPCR showed moderate sensitivity, the specificity is high; therefore, the test can be used as an auxiliary tool to diagnose TB in children. It is a rapid test that demonstrated better performance than other diagnostic tests in paucibacillary samples as it does in childhood tuberculosis.

Varicella-Zoster Meningitis With Hypoglycorrhachia in an Immunocompetent Patient Presenting With Disseminated Varicella-Zoster Infection

Varicella-zoster virus (VZV) infection is rarely reported in immunocompetent hosts. We report the case of a 40-year-old male who presented with altered mental status. One week prior, he was seen at his outpatient physician's office for a rash along the lateral right thigh. Erythema of the right gluteal region was noted, but no vesicles were present. He was treated for shingles rash with acyclovir with improvement. After a period of initial improvement in the rash, the patient developed a persistent headache. Given his migraine history, he overlooked the headache. He then developed fever, followed by confusion and was brought to the ED for further evaluation. CT head was unremarkable. Lumbar puncture revealed aseptic meningitis. This case highlights the unusual presentation of disseminated VZV infection in an immunocompetent host. It stresses the importance of maintaining high suspicion for disseminated VZV infection despite the patient being immunocompetent.

Pediatric Crohn Disease and Multisystem Inflammatory Syndrome in Children (MIS-C) and COVID-19 Treated With Infliximab

Coronavirus disease 2019 (COVID-19) may lead to a severe inflammatory response referred to as a cytokine storm. We describe a case of severe COVID-19 infection in a recently diagnosed pediatric Crohn disease patient successfully treated with tumor necrosis factor-alpha (TNF-α) blockade. The patient presented with 5 days of fever, an erythematous maculopapular facial rash, and abdominal pain without respiratory symptoms. SARS-CoV-2 polymerase chain reaction was positive. Despite inpatient treatment for COVID-19 and a perianal abscess, the patient acutely decompensated, with worsening fever, tachycardia, fluid-refractory hypotension, elevation of liver enzymes, and transformation of the rash into purpura extending from the face to the trunk, upper and lower extremities, including the palmar and plantar surfaces of the hands and feet. Cytokine profile revealed rising levels of interleukin (IL)-6, IL-8, and TNF-α, higher than those described in either inflammatory bowel disease or severe COVID-19 alone. The patient was treated with infliximab for TNF-α blockade to address both moderately to severely active Crohn disease and multisystem inflammatory syndrome in children temporally related to COVID-19. Within hours of infliximab treatment, fever, tachycardia, and hypotension resolved. Cytokine profile improved with normalization of TNF-α, a decrease in IL-6, and IL-8 concentrations. This case supports a role for blockade of TNF-α in the treatment of COVID-19 inflammatory cascade. The role of anti-TNF agents in patients with multisystem inflammatory syndrome in children temporally related to COVID-19 requires further investigation.

The Carotenoid Compound of Saffron Crocetin Alleviates Effects of Ischemia Reperfusion Injury via a Mechanism Possibly Involving MiR-127

Renal impairment is associated with high mortality rates in severely ill patients. The need to prevent and treat renal damage underlines the importance of understanding the pathophysiological mechanisms that characterize it. This could also enable early diagnosis and the design of alternative therapeutic approaches. The aim of this study is to investigate the effect of crocetin, a known antioxidant, on the prevention of renal damage due to ischemia-reperfusion injury and the investigation of the mechanisms involved. The present study was performed on C57BL/6 mice aged 10-12 weeks. The animals had access to water and food ad libitum. The experiment, as described in materials and methods, was completed at 24 h, in which case the kidneys were removed for further study, both at tissue morphology (with immunohistochemistry) and changes in the level of miRs’ expression by qRT-PCR. Accordingly, using the automatic precision analyzer, the serum levels of the basic parameters currently used clinically for the monitoring of renal function were determined. The administration of crocetin, despite the short presence of the substance in the body, affects all the biochemical parameters analyzed (urea, creatinine, uric acid, and ions of Na, K, Cl, P, Mg and Ca), ​​causing significant decrease of their measured values. Crocetin also resulted in a significant limitation of the inflammation elements and the degree of epithelial damage. Furthermore, the administration of crocetin appears to restore levels of expression of miR21, miR127 and miR132.

Chest CT in COVID-19 pneumonia: a correlation of lung abnormalities with duration and severity of symptoms

Background

After the spread of COVID-19 pneumonia, chest CT examination was used as a substantial non-invasive complement to RT-PCR for diagnosing and as a rapid screening tool when RT-PCR results are unavailable. Our study aimed at the analysis of the lung abnormalities detected by chest CT in COVID-19 pneumonia according to the severity and duration of symptoms.

Results

In the early phase (n = 60), 32 patients had negative CT findings and 28 patients had positive findings with a mean total lung severity score of 2.13. In the intermediate phase (n = 116), 4 patients had negative CT findings and 112 patients had positive findings with a mean total lung severity score of 16.08. In the late phase (n = 36), all patients had positive findings with a mean total lung severity score of 17.83. CT lung abnormalities were progressed on follow-up CT studies. We found a high total lung severity score in many patients with mild symptoms with a mean of 14.77 and a low total lung severity score in many patients with moderate to severe symptoms with a mean of 9.14.

Conclusion

Chest CT should be used as a routine examination for diagnosing COVID-19 pneumonia and follow-up of disease advance. The progression of lung abnormalities was related to the duration more than the severity of symptoms.

Design of genomic signatures for pathogen identification and characterization

Once the genome of a microbial organism has been sequenced, it becomes possible to utilize portions of the genome, known as “signatures” to identify when that organism is present in a complex clinical or environmental sample. Genomic signatures can be at multiple levels of resolution depending on the questions being asked. (“Is this white powder anthrax?”; “Does this white powder match any of the anthrax samples taken from every laboratory in the United States that possesses anthrax?”) Multiple technologies exist to turn abstract genomic signatures into assays that can interrogate complex samples with varying degrees of speed, sensitivity, specificity, and cost. The recent flood of microbial genomic data has complicated the task of designing genomic signatures.

First report of root-knot nematode, Meloidogyne arenaria, on lavender in Turkey

Lavender is a medicinal and aromatic plant that is widely grown in Turkey. Gall symptoms were observed on roots of lavender (Lavandula angustifolia Mill.) collected from Kırklareli and Edirne provinces. Egg masses were collected from galled roots. DNA isolated from all samples was screened by species-specific primers belonging to the most common species of root-knot nematodes and M. arenaria was the only species that was identified in all of the samples analyzed. This is the first report of M. arenaria infecting lavender in Turkey.

Lavender is a medicinal and aromatic plant that is widely grown in Turkey. Gall symptoms were observed on roots of lavender (Lavandula angustifolia Mill.) collected from Kırklareli and Edirne provinces. Egg masses were collected from galled roots. DNA isolated from all samples was screened by species-specific primers belonging to the most common species of root-knot nematodes and M. arenaria was the only species that was identified in all of the samples analyzed. This is the first report of M. arenaria infecting lavender in Turkey.

Porcine reproductive and respiratory syndrome virus RNA detection in different matrices under typical storage conditions in the UK

In the UK, approximately 40 per cent of the pig breeding herds are outdoors. To monitor their porcine reproductive and respiratory syndrome virus (PRRSV) status, blood is collected commonly from piglets around weaning. Sample collection in British outdoor pigs often occurs during the early morning hours when the piglets tend to accumulate inside sheltered areas. For practical reasons, dry cotton swabs are occasionally used for blood collection and stored at room temperature until arrival in the laboratory. Detection of PRRSV RNA is a function of viral concentration, sample type and storage condition. To evaluate a possible impact of the sampling protocol on PRRSV1 detection, experimentally spiked blood samples using three dilutions of a representative PRRSV1 strain were prepared. In addition, blood samples from pigs naturally infected with PRRSV were obtained from a PRRSV-positive British herd. Spiked blood and blood from infected pigs were used to obtain sera, dry or wet (immersed in saline) polyester or cotton swabs and FTA cards. The different samples were stored for 24 hours, 48 hours or 7 days at 4°C or 20°C and tested by a real-time reverse transcriptase PRRSV PCR assay. Under the study conditions, the best matrix was serum (96.7 per cent), followed by wet swabs (78 per cent), dry swabs (61.3 per cent) and FTA cards (51 per cent). Polyester swabs (76 per cent) showed a better performance than cotton swabs (63.3 per cent). The reduction in sensitivity obtained for swabs and FTA cards was particularly high at low viral concentrations. The results indicate that wet polyester swabs should be used whenever possible.

Murine typhus in Mexico City: report of an imported case

Murine typhus is endemic in several countries. We herein report an imported case of murine typhus caused by Rickettsia typhi in Mexico City. This is the first report of a case after almost 20 years since the last report. The species was confirmed by DNA sequencing and phylogenetic reconstruction.

Norrie disease gene polymorphism in Indonesian infants with retinopathy of prematurity

OBJECTIVE

Retinopathy of prematurity (ROP) is a major cause of blindness in newborn infants, which also occurs in low-income and middle-income countries. Why ROP progresses in some infants while it regresses in others is still presently unknown. Studies suggest that genetic factors might be involved. Mutations in the Norrie disease (ND) gene are suspected to be related to advanced ROP development. Indonesia is a country with relatively high incidence of ROP, yet the role of these genetic factors in the pathogenesis of ROP cases is still unknown. The study aimed to investigate the presence of mutations in ND on the X chromosome in infants with both non-advanced and advanced ROP in Indonesia.

METHODS AND ANALYSIS

This is a case-control study of polymorphisms in six variants within the ND gene in exon 3, C597A, L108P, R121W, A105T, V60E and C110G, in preterm newborn infants in four major hospitals in Greater Jakarta, Indonesia.

RESULTS

We included 162 preterm newborn infants. ROP was diagnosed in 83 infants, and 79 infants served as controls. Among those with ROP, 57 infants had type 2, while others had type 1. We did not find any gene polymorphisms in any of the infants with ROP nor in the control group.

CONCLUSION

We conclude that it is very unlikely that the six polymorphisms in exon 3 of the ND gene studied in this paper are involved in the development or progression of ROP in preterm infants in our population sample in Indonesia.

Recurring and emerging questions related to management of HIV-related opportunistic infections

The incidence of HIV-related opportunistic infections (OIs) has dramatically declined with the ability to achieve viral suppression and immune reconstitution with potent antiretroviral therapy. However, a large number of patients remain at risk for OIs because they are diagnosed at late stages of HIV disease, fail to stay in treatment, or fail to maintain viral suppression. Clinicians should remain vigilant for OIs and for changes in recommended management strategies. Issues that often arise in this regard include how to interpret polymerase chain reaction diagnostic results in individuals with HIV infection; whether primary prophylaxis for Mycobacterium avium complex is still needed; whether clinicians should screen asymptomatic patients for cryptococcal antigen; and need for amphotericin B in treatment regimens for cryptococcal meningitis. This article summarizes a presentation by Henry Masur, MD, at the IAS-USA continuing education program held in Washington, DC, in April 2018.

Using Conventional PCR on Citrus Leaf Tissue Samples

Citrus greening, also known as huanglongbing, is a destructive citrus disease ravaging citrus farms globally. This disease causes asymmetrical yellow leaf mottling, vein yellowing, defoliation, root decay, and ultimately, the death of the citrus plant. When infected, the citrus plants have stunted growth and produce flowers out of season. These flowers rarely yield fruit, and those that do yield small, bitter, irregularly shaped citrus fruit that are not desirable. This disease is spread by the Asian citrus psyllid, Diaphorina citri, and by the grafting of infected citrus tissue. The pathogen has a long and variable incubation period within the citrus plant-sometimes years, before symptoms appear. Attempts to culture this pathogen in vitro have been unsuccessful, possibly due to the low and uneven concentration of the pathogen within infected citrus tissue, or because it is difficult to replicate the environmental conditions conducive to growth of the pathogen. It is very difficult to identify the disease before it has spread, due to its long incubation period and researchers' inability to culture the pathogen. As a result, the disease only becomes apparent after suddenly destroying a citrus farmer's entire yield. Presented here is a method for the accurate and specific detection of the citrus greening pathogen, Candidatus liberibacter spp. using a genomic DNA extraction kit and PCR. This method is simple, efficient, cost effective, and adaptable for quantitative analysis. This method can be adapted for use on any citrus tissue; however, it is potentially limited by the amount of pathogen present in the tissue. Nevertheless, this method will allow citrus farmers to identify infected citrus plants earlier, and curb the spread of this destructive disease before it can further spread.

[Prevalence and phylogenetic analysis of Chlamydia trachomatis in a population of women in Posadas, Misiones]

OBJECTIVE

Chlamydia trachomatis is the most prevalent bacteria causing sexually transmitted infections. In women, this infection can cause cervicitis and urethritis, although it's usually asymptomatic. The aim of this study was to investigate the prevalence of C. trachomatis in women attending the lab Instituto de Previsión Social and detect the genotypes.

METHODS

Endocervical samples from 505 symptomatic and asymptomatic women were assayed. It was determined the presence of C. trachomatis by PCR through amplification of a fragment of the cryptic plasmid. Positive samples were genotyped by the partial amplification of the ompA gene and analyzed phylogenetically.

RESULTS

Forty-three positive samples were detected to infection with C. trachomatis, obtaining a prevalence of 8.5% (IC 95%: 6.4-11.3%). The prevalence of C. trachomatis was higher in women with vaginal symptoms [11.3% (30/265) vs. 5.4% (13/240)] (p = 0.018), as well as in women under 26 year-old [11.5% (28/244) vs. 6.2% (15/246)] (p = 0.021). Based on phylogenetic analysis, it was observed that 62% of the samples were genotype E, 15% genotype J, 15% genotype D, and 8% genotype F.

CONCLUSIONS

This work is the first contribution on the molecular epidemiology of C. trachomatis in the Misiones province, Argentina, which shows the rate of prevalence of this bacterium and offers information on circulating genotypes.

Efficacy of a bovine colostrum and egg-based intervention in acute childhood diarrhoea in Guatemala: a randomised, double-blind, placebo-controlled trial

Background

Treatments for paediatric diarrhoeal disease are limited. We assessed the impact of a bovine colostrum and egg-based treatment designed to reduce diarrhoea duration through non-specific and pathogen-directed mechanisms in children.

Methods

Randomised, double-blind, placebo-controlled trial of PTM202, derived from bovine colostrum and hyperimmune hen’s egg on the duration of acute diarrhoeal disease in Guatemalan children. PTM202 contains specific immunoglobulins that target rotavirus, enterotoxigenic Escherichia coli, Shiga toxin-producing E. coli and Salmonella. Children aged 6–35 months presenting to three sites (one rural and two urban) with acute non-bloody diarrhoea were computer randomised to receive three daily doses of PTM202 or placebo. The primary outcome was the post-treatment duration of diarrhoea assessed in the per protocol population. Diarrhoeal pathogens were identified in stool by multiplex PCR (FilmArray Gastrointestinal-Panel, BioFire, Salt Lake City, Utah, USA). Key secondary outcomes included postdiarrhoeal weight gain and impact on diarrhoeal duration stratified by study site and presence of PTM202-targeted organisms in stool at enrolment. Safety was assessed in all participants.

Results

From 9 March 2015 to 25 January 2016, 325 children were enrolled, and 301 (154 intervention and 147 placebo) were analysed for the primary outcome. No difference in diarrhoea duration was observed between intervention and placebo in the total population, but a significant reduction was observed in the treatment group among children with at least one targeted pathogen in stool (HR=1.46, P=0.02), an effect most pronounced in urban subjects (HR 2.20, P=0.007) who had fewer stool pathogens and better nutritional status. No impact on 2-week or 4-week weight gain was noted. No adverse events attributed to PTM202 occurred.

Conclusion

Results demonstrate the potential to target specific pathogens occurring in children with acute non-bloody diarrhoea and shorten illness duration using a novel, safe, nutrition-based intervention. PTM202 may represent a new tool to ameliorate the effects of acute diarrhoeal disease in low/middle-income populations.

Trial registration number

NCT02385773; Results.