Rapid Detection of Uropathogens and Antibiotic-resistant Genes Using Open Array Multiplex PCR Technology

Introduction/Objective

Introduction: Standard diagnostic practices for Urinary Tract Infection (UTI) take 2–3 days for pathogen identification and antibiotic susceptibility testing leading to delayed diagnosis and an increase in healthcare expenditures. The rapid diagnostics tool is highly desirable to identify the pathogen and its antibiotic-resistant genes directly from the samples. Our objective is to validate and evaluate the performance of Open array multiplex PCR for pathogen identification and antibiotic resistance genes.

Methods/Case Report

Method: Open array multiplex PCR method for 20 UTI pathogens was validated using ATCC organisms and inter-laboratory correlation using 50 urine samples. Briefly, samples were homogenized using Omni bead ruptor 96, and DNA was extracted using Hamilton Vantage. Customized open array and UTI chips with 20 most common urinary tract pathogen target and 13 resistant genes target specifically for UTI treatment were filled with Taqman open array PCR master mix and extracted DNA in a 1:1 ratio. UTI chips were prepared on Accufill and real-time PCR was performed on Quantstudio 12K flex. A total of 116 de-identified patient samples were analyzed.

Results (if a Case Study enter NA)

Result: The sensitivity, specificity, and accuracy of this method were more than 90% considering the reference method as the standard method. A total of 14 different types of organisms were detected. Escherichia coli (n=49) was the highest among all. Multiple pathogens were identified in 27 urine samples. Organisms such as Ureaplasma and Megasphaera 1 were detected in nine and four samples, respectively. All positive samples were resistant to at least one or two resistant genes. tetM and tetS were resistant among 72 samples, erm A, B, and C in 60 samples, ESBL in 30 and fosfo A in 21 samples.

Conclusion

Conclusion: The open array multiplex PCR technology may help in the early diagnosis and treatment that can improve patient care, shorten hospitalization, and reduces the economic burden.

Performance Evaluation of TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR Multiplex Assay for the Detection of Respiratory Viruses

Purpose

To detect and differentiate co-infection with influenza and respiratory syncytial virus during the COVID pandemic, a rapid method that can detect multiple pathogens in a single test is a significant diagnostic advance to analyze the outcomes and clinical implications of co-infection. Therefore, we validated and evaluated the performance characteristics of TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR multiplex assay for the detection of SARS-CoV-2, Flu A/B, and RSV using nasopharyngeal and saliva samples.

Materials and Methods

The method validation was performed by using culture fluids of Influenza A virus (H3N2) (A/Wisconsin/67/2005), Influenza B virus (B/Virginia/ATCC4/2009), RSV A2 cpts-248, SARS-CoV-2 (USA-WA1/2020) and quantitative RNA controls of Influenza A virus (H1N1) strain A/PR/8/34 (VR-95DQ), RSV A2 (VR-1540DQ) and SARS-CoV-2 (MN908947.3 Wuhan-Hu-1) from ATCC and Zeptometrix, NY, USA. A total of 110 nasopharyngeal specimens and 70 saliva samples were used for the SARS-CoV-2 detection, and a total of 70 nasopharyngeal specimens were used for Influenza and RSV detection. Total RNA was extracted from all the samples and multiplex PCR was performed using TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR multiplex assay. The assay was used for SARS-CoV-2 variant (B.1.1.7_601443, B.1.617.1_1662307, P.1_792683, B.1.351_678597, B.1.1.529/BA.1).

Results

Validation controls showed accurate and precise results. The correlation study found the accuracy of 96.38 to 100% (95% CI) in nasopharyngeal and 94.87 to 100% (95% CI) in saliva for SARS-CoV-2 and 91.1 to 100% (95% CI) for both Influenza A/B and RSV. The diagnostic efficiency of this assay was not affected by SARS-CoV-2 variant, including Omicron.

Conclusion

The TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR multiplex assay is a rapid method to detect and differentiate SAR-CoV-2, Flu A and B, and RSV in nasopharyngeal and saliva samples. It has a significant role in the diagnosis and management of respiratory illnesses and the clinical implications of co-infection.

SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays

PURPOSE

For rapid detection and tracking of SARS-CoV-2, a simple screening method alternative to laborious and expensive sequencing is highly desirable. Here, we evaluated performance characteristics of TaqMan SARS-CoV-2 mutation panel genotyping molecular assay for detection of most common reported SARS-CoV-2 variants using specific RT-PCR assays targeting single nucleotide polymorphisms (SNP).

PATIENTS AND METHODS

A total of 150 SARS-CoV-2 positive samples from March to July were included for this study. In addition, five controls comprised of synthetic RNA B.1.1.7_601443, B.1.351_678597, P.1_792683, B.1.617.1_1662307 and MN908947.3-Wuhan-hu-1 from Twist bioscience and B.1.1.7 (England/204820464/2020) and B.1.351 (South Africa/KRISP-K005325/2020) from Zeptometrix, NY, USA were used for validation. Total RNA from specimens was extracted using Omega Bio-Tek Mag-Bind Viral RNA Xpress Extraction Kit and tested for known SARS-CoV2 variants using ThermoFisher TaqMan SARS-CoV-2 mutation panel molecular assay on the QuantStudio 12K Flex. Nine representative samples have been compared with sequencing. Data were analyzed by genotype calling using QuantStudio™ design and analysis software v 2.5 with the genotyping analysis module.

RESULTS

All validation controls were tested in triplicate and repeated in singlet on three different days and all reported variants were matched as expected. Out of 150 SARS-CoV-2 positive specimens, 69 (46%) were B.1.617.2, 49 (32.7%) were B.1.1.7, P.1 and P.2 were 4 (2.7%) each and B.1.351 and B.1.427/B.1429 were 2 (1.3%) each. Three (2%) were B.1.526, and 17 (11.3%) have a mutation in D614G. Genotyping results from the present study showing B.1.617.2, B.1.1.7, and B.1.526 variants and their mutation genes were concordant with sequencing results.

CONCLUSION

Our study indicates that TaqMan SARS-CoV-2 mutation panel molecular genotyping assays detect and differentiate all published common variants B.1.617.2 (Delta), B.1.1.7 (Alpha), B.1.526 (Iota), B.1.351 (Beta), P.1 (Gamma), P.2 (Zeta), B.1.617.1 (Kappa) and B.1.427/B.1.429 (Epsilon) that can be used for surveillance and epidemic control and prevention.

Direct reprogramming of epithelial cell rests of malassez into mesenchymal-like cells by epigenetic agents

The DNA demethylating agent, 5-Azacytidine (5Aza), and histone deacetylase inhibitor, valproic acid (Vpa), can improve the reprogramming efficiencies of pluripotent cells. This study aimed to examine the roles of 5Aza and Vpa in the dedifferentiation of epithelial cell rests of Malassez (ERM) into stem-like cells. Additionally, the ability of stem-like cells to differentiate into mesenchymal cells was evaluated. ERM was cultured in embryonic stem cell medium (ESCM) with 1 µM of 5Aza, or 2 mM of Vpa, or a combination of 5Aza and Vpa. The cells stimulated with both 5Aza and Vpa were named as progenitor-dedifferentiated into stem-like cells (Pro-DSLCs). The Pro-DSLCs cultured in ESCM alone for another week were named as DSLCs. The stem cell markers were significantly higher in the DSLCs than the controls (no additions). The mRNA and protein levels of the endothelial, mesenchymal stem, and osteogenic cell markers were significantly higher in the Pro-DSLCs and DSLCs than the controls. The combination of a demethylating agent and a deacetylated inhibitor induced the dedifferentiation of ERM into DSLCs. The Pro-DSLCs derived from ERM can be directly reprogrammed into mesenchymal-like cells without dedifferentiation into stem-like cells. Isolated ERM treated with epigenetic agents may be used for periodontal regeneration.

Involvement of RNase 7 in the malignant potential of oral squamous cell carcinoma cells

RNase 7 is involved in the innate immunity of the oral epithelium. Variations in the expression levels of RNase 7 have been reported in cutaneous squamous cell carcinoma, but not in oral squamous cell carcinoma (OSCC). The present study investigated the expression levels of RNase 7 in OSCC and its role in the malignant potential of these cells. The localization of RNase 7 in OSCC tissue sections was determined via immunohistochemistry. Positive staining for RNase 7 was observed around the epithelial pearls and spinous cells of the OSCC tissues. Four different types of OSCC cell lines (OSC‑19, BSC‑OF, SAS, and HSC‑2) and a normal keratinocyte (HaCaT) were used. The mRNA and protein expression levels of RNase 7 were significantly higher in the OSCC cells compared to the HaCaT cells. Based on our hypothesis that high levels of RNase 7 expression may be involved in the malignant potential of OSCC cells, the effect of RNase 7 knockdown on both proliferation and invasion were evaluated by transfecting the cells with siRNA. Cell numbers, cell invasion, and MMP 9 expression levels were significantly higher in the siRNA‑BSC‑OF, ‑SAS, and ‑HSC‑2 cells compared to the BSC‑OF, SAS, and HSC‑2 cells. The extent of differentiation of the siRNA‑OSCC cells was examined using the differentiation and undifferentiation markers involucrin (INV) and K14, respectively. The expression level of K14 was significantly higher in the siRNA‑OSCC cells compared to the OSCC cells. Alternatively, HSC‑2 and SAS cells demonstrated higher expression levels of INV compared to the siRNA‑HSC‑2 and ‑SAS cells. These findings indicate that RNase 7 may contribute to the suppression of the malignant potential of OSCC.

Chronic stress-induced elevation of IL-1β in the saliva and submandibular glands of mice

Psychological stress is involved in the development of various oral diseases. Alterations in the levels of cytokines in the saliva of patients with stress-related oral diseases have been reported. However, the inconsistencies in the results of these studies might be attributed to differences in the local and systemic factors in the oral cavities of the patients. We examined the effect of chronic stress on three major inflammatory cytokines Interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF)-α in the saliva and salivary glands of chronically stressed mice. Six-week-old C57BL/6 J mice were randomly divided into a control and a stress group. The mice in stress group were exposed to 4 h of stress daily for 10 days and subsequently saliva, as well as the submandibular glands, were collected from both groups. The expression levels of cytokines in the saliva were examined by enzyme-linked immunosorbent assay. The submandibular glands were subjected to histopathological and mRNA expression analyses. IL-1β was significantly elevated in saliva of the chronic stressed mice. Furthermore, the mRNA expression levels of both IL-1β and IL-6 were significantly elevated in the submandibular gland of chronic stressed mice. IL-1β may be a potential salivary biomarker in response to chronic stress in mice.

Curcumin inhibits the expression of proinflammatory mediators and MMP-9 in gingival epithelial cells stimulated for a prolonged period with lipopolysaccharides derived from Porphyromonas gingivalis

Curcumin, a yellow phytochemical found in the rhizomes of Curcuma longa, has various biological effects, including anti-oxidant and anti-inflammatory activities. In the present study, we examined the effect of curcumin on the expression of inflammatory cytokines in human gingival epithelial progenitor cells (HGEPs) stimulated for a prolonged period with lipopolysaccharide (LPS) derived from Porphyromonas gingivalis. The cells were alternately cultured with LPS and/or curcumin every 3 days for 18 days. The expression levels of TNF-α, IL-1β, IL-6, TIMP-1, and MMP-9 in the HGEPs were evaluated by quantitative real-time polymerase chain reaction. Enzyme-linked immunosorbent assay was used to measure the concentrations of these five proteins in the supernatant and nuclear factor (NF)-κB in the nuclear extracts. Curcumin inhibited the mRNA expression levels of TNF-α, IL-1β, IL-6, and MMP-9 in HGEPs treated with curcumin over a prolonged period. Similarly, the expression levels of IL-1β, IL-6, and MMP-9 were decreased in the culture supernatants. NF-κB activity was also inhibited in the cells cultured with curcumin. In conclusion, these findings indicate that curcumin inhibits the expression of inflammatory cytokines and MMP-9 in primary gingival epithelial cells stimulated with P. gingivalis-derived LPS via NF-κB activation.

Immunohistochemical Localization of RNase 7 in Normal and Inflamed Oral Epithelia and Salivary Glands

RNase 7 is a skin-derived antimicrobial peptide expressed in various epithelial tissues. It is upregulated by stimulation with microbes and pro-inflammatory cytokines. Herein, we examined the expression levels of RNase 7 in tissues from normal and inflamed oral epithelia and salivary glands via immunohistochemistry. RNase 7 was expressed mainly in the surface layers of the parakeratinized and orthokeratinized oral epithelium. In addition, it was strongly and weakly expressed in oral lichen planus and radicular cysts, respectively. RNase 7 was constitutively expressed in salivary glands, particularly in the serous and duct cells. In the case of Sjogren’s syndrome, RNase 7 was strongly expressed in serous, ductal, and mucous cells in areas with lymphocytic infiltration. The localization patterns of RNase 7 were similar to those of other epithelial antimicrobial peptides, including beta-defensins. Thus, epithelial antimicrobial peptides may act against microbial infections in a coordinated manner in oral epithelia and salivary glands.

Adenomatous ductal proliferation/hyperplasia in the parotid gland associated without any other pathological lesions; a report and survey of the literatures

Adenomatous ductal proliferation/hyperplasia (ADP/H) is a rare hyperplastic condition of the salivary gland. It is mostly associated with other salivary gland pathologies such as tumors and inflammations, and is incidentally found in tissue sections during histopathological examinations of those diseases. Herein, we report a case of ADP/H in the parotid gland not associated with any other pathological lesions, and present a review of the literature on this condition. A 60-year-old Japanese female complained of swelling on the left side of parotid region. Clinical examination revealed a swelling on the lower lobe of the left parotid gland. The lesion was firm but non-tender and was not attached to adjacent structures. A clinical diagnosis of benign salivary gland tumor was reached, and surgical excision was performed under general anesthesia. Histopathological examination revealed an intact parotid gland capsule with isomorphic and basaloid cells within scanty cytoplasm. In addition, an admixture of hyperplasia and proliferation of the intercalated ducts, the presence of zymogen granules, the absence of solid nests, and a peripheral palisaded arrangement of the cells were observed. Based on these findings, a diagnosis of ADP/H was confirmed. ADP/H is a non-tumorous lesion; therefore, tumor involvement should be ruled out before the diagnosis is reached.

In vitro biofilm formation by Staphylococcus aureus isolated from wounds of hospital-admitted patients and their association with antimicrobial resistance

Introduction

Staphylococcus aureus including methicillin-resistant S. aureus (MRSA) has the propensity to form biofilms, and causes significant mortality and morbidity in the patients with wounds. Our aim was to study the in vitro biofilm-forming ability of S. aureus isolated from wounds of hospitalized patients and their association with antimicrobial resistance.

Materials and methods

Forty-three clinical isolates of S. aureus were obtained from 150 pus samples using standard microbiological techniques. Biofilm formation in these isolates was detected by tissue culture plate (TCP) method and tube adherence method (TM). Antimicrobial susceptibility test was performed using the modified Kirby–Bauer disk diffusion method as per Clinical and Laboratory Standards Institute guidelines. MRSA was detected using the cefoxitin disk test.

Results

Biofilm formation was observed in 30 (69.8%) and 28 (65.1%) isolates of S. aureus via TCP method and TM, respectively. Biofilm-producing S. aureus exhibited a higher incidence of antimicrobial resistance when compared with the biofilm nonproducers (P<0.05). Importantly, 86.7% of biofilm-producing S. aureus were multidrug resistant (MDR), whereas all the biofilm nonproducers were non-MDR (P<0.05). Large proportions (43.3%) of biofilm producers were identified as MRSA; however, none of the biofilm nonproducers were found to be MRSA (P<0.05).

Conclusion

Both the in vitro methods showed that S. aureus isolated from wound infection of hospitalized patients have high degree of biofilm-forming ability. Biofilm-producing strains have very high tendency to exhibit antimicrobial resistance, multidrug resistance and methicillin resistance. Regular surveillance of biofilm formation by S. aureus and their antimicrobial resistance profile may lead to the early treatment of the wound infection.

Burden of bacterial upper respiratory tract pathogens in school children of Nepal

INTRODUCTION

Respiratory tract infections are one of the most common human infections in all age group and important cause of mortality and morbidity worldwide. Most bacterial upper respiratory tract infections are vaccine preventable. This study aimed to determine the prevalence of carrier state of bacterial upper respiratory tract pathogens among school children. It also aimed to study their antibiograms.

METHODS

The specimen from posterior pharyngeal wall and tonsils were collected from 204 participants on calcium alginate coated swabs (HiMedia). Isolates were identified by standard microbiological methods and tested for in vitro antibiotic susceptibility testing by modified Kirby-Bauer disc diffusion method.

RESULTS

In this study, Streptococcus pneumoniae (16.6%) was the most common bacterial pathogen recovered, followed by Staphylococcus aureus (14.7%), β-haemolytic streptococci (non-Group A) (8.8%), Streptococcus pyogenes (5.3%) and Corynebacterium diphtheriae (3.4%). The Gram negative bacteria were Klebsiella pneumoniae (4.9%), Haemophilus influenzae (3.4%) and Neisseria meningitidis (1.4%). Important findings in antibiogram include high resistance of Streptococcus pneumoniae to penicillin (91.17%) and resistance of S. aureus to oxacillin (23.3%).

CONCLUSION

Pharyngeal colonisation by S. pneumoniae was found high among school children and this calls for an urgent need to include pneumococcal vaccine in routine national immunisation schedule of Nepal given the high burden of invasive pneumococcal disease. Despite expected universal vaccination, pharyngeal colonisation by C. diphtheriae is possible and there is possibility of transmission of these respiratory pathogens to other healthy children.

Community acquired multi-drug resistant clinical isolates of Escherichia coli in a tertiary care center of Nepal

Background

Multi-drug resistance (MDR) in Gram-negative organisms is an alarming problem in the world. MDR and extensively-drug resistance (XDR) is in increasing trend due to the production of different types of beta (β)-lactamases. Thus the aim of this study was to document the incidence of MDR and XDR in clinical isolates of Escherichia coli and also to find out the enzymatic mechanisms of β-lactam antibiotics resistance.

Methods

Two hundred clinical isolates of Escherichia coli (E. coli) identified by standard laboratory methods were studied. Antibiotic susceptibility profile was performed for all the isolates and the suspected isolates were phenotypically tested for the production of extended spectrum β-lactamase (ESBL), metallo β-lactamase (MBL) and AmpC β-lactamase (AmpC) by recommended methods.

Results

Around three-fourth (78%) of the total isolates were multi-drug resistant. ESBL, MBL and AmpC production was found in 24%, 15% and 9% of isolates respectively. Amikacin, chloramphenicol and colistin were found to be the most effective antibiotics.

Conclusions

High percentage of MDR was observed. β-lactamase mediated resistance was also high. Thus, regular surveillance of drug resistance due to β-lactamases production and infection control policy are of utmost importance to minimize the spread of resistant strains.