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Introduction: Pyrazinamide (PZA) susceptibility testing plays a critical role in determining the appropriate treatment regimens for multidrug-resistant tuberculosis. We conducted a systematic revie...

Currently, there are numerous under development or developed assays with various sensitivities and specificities for diagnosis of the Coronavirus Disease 2019 (COVID-19) caused by the SARS-CoV-2 virus. The World Health Organization (WHO) has approved several detection protocols based on real-time reverse transcription PCR (RT-qPCR) and the reliability of tests to detect the N, S, or RdRp/Hel genes of the SARS-Cov-2 virus has also investigated. Among these targets, COVID-19-RdRp/Hel targets represented the highest sensitivity. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has also been developed to rapidly and efficiently amplify RNA under isothermal conditions. Other isothermal amplification approaches such as nucleic acid sequence-based amplification (NASBA), recombinase polymerase amplification (RPA), and rolling circle amplification (RCA) have also been reported for detecting coronaviruses but like LAMP assay. Different serological tests, including neutralization tests, immunofluorescent (IFA), enzyme-linked immunosorbent (ELISA), and western blotting assays, are available. Point-of-care tests (POCT) are emerging to detect the virus genome, IgG, or IgM antibodies against SARS-CoV-2. The advent of more sensitive, cheaper, and easier-to-perform diagnostic tests seems to be a fundamental prerequisite to improve the diagnosis of COVID-19 infection. Herein, we reviewed several commercially available diagnostic methods used in many clinical laboratories to detect COVID-19.

Background: Fast and precise detection of SARS-CoV-2 RNA in clinical samples and subsequent quarantine are two critical factors in preventing virus transmission and distribution through the community. The false-negative result is a major problem in the SARS-CoV-2 detection because of the kind of sample (swab sample), sampling error, and sensitivity of PCR test, which can be reduced by a much more sensitive test such as nested PCR. Objectives: This study aimed to evaluate the false-negative rate among samples that were negative by a real-time PCR test using RT-nested PCR. Methods: One hundred eighty-four negative samples were included in the study, and nucleic acid was extracted using a commercial kit based on a silica filter column and then subjected to RT-nested PCR using three sets of primers targeting Orf1ab, N, and RdRp regions. Results: Among 184 negative swab samples for SARS-CoV-2, 27 (14.6%) cases were positive for the Orf1ab gene using RT-nested PCR. The samples were tested using N and RdRp primer sets. Also, seven (3.8%) cases were positive for the N gene, and four (2.1%) cases were positive for the RdRp gene. Conclusions: The results indicated that RT-nested PCR could be more sensitive than real-time PCR and reduce the false-negative rate.

After about 2 years since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first infections were detected in Wuhan city of China in December 2019, which was followed by a worldwide pandemic with a record of 5.41 million deaths. Due to urgent need for the development of a safe and effective vaccine for coronavirus disease 2019 (COVID-19), attempts for producing efficient vaccines are inexhaustibly continuing. According to a report by the World Health Organization (WHO) on COVID-19 vaccine tracker and landscape, there are 149 vaccine candidates all over the world. Inactivated SARS-CoV-2 vaccines as a conventional vaccine platform consist of whole virus particles grown in cell culture and inactivated by chemicals. Because of benefits such as antigenic similarity to real virion inducing humoral and cellular immune responses and ease for transport and storage, these vaccines, including the vaccines produced by Bharat Biotech, Sinopharm, and Sinovac, are in use at large scales. In this study, we have a review on inactivated SARS-CoV-2 vaccines that are passing their phase 3 and 4 clinical trials, population which was included in the trials, vaccine producers, the efficiency, adverse effects, and components of vaccines, and other vaccine features.

Conventional culture-based drug susceptibility testing (DST) of Mycobacterium tuberculosis to pyrazinamide (PZA) is time-consuming and difficult to perform. The current systematic review and meta-analysis was aimed to evaluate the diagnostic accuracy of Wayne assay against culture-based DSTs as the reference standard. We searched the MEDLINE/Pubmed, Embase, and Web of Science databases for the relevant records. The QUADAS-2 tool was used to assess the quality of the studies. Diagnostic accuracy measures (i.e., sensitivity and specificity) were pooled with a random-effects model. Statistical analyses were performed with STATA (version 14, Stata Corporation, College Station, TX, USA), RevMan (version 5.3; The Nordic Cochrane Centre, the Cochrane Collaboration, Copenhagen, Denmark), and Meta-DiSc (version 1.4, Cochrane Colloquium, Barcelona, Spain). A total of 31 articles comprising data for 2457 isolates of M. tuberculosis were included in the final analysis. The pooled sensitivity and specificity of the Wayne assay against all reference tests (the combination of BACTEC MGIT 960, BACTEC 460, and proportion method) were 86.6% (95% CI: 84.3-88.7) and 96.0% (95% CI: 94.8-97). The positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and the area under the curve (AUC) estimates were found to be 17.6 (95% CI: 10.5-29.3), 0.11 (95% CI: 0.06-0.20), 164 (95% CI: 83-320) and 97%, respectively. Deek's test result indicated no evidence for publication bias (P > 0.05). Although the current study shows that the Wayne test is sensitive and specific for detecting PZA resistance, it may be used in combination with conventional DSTs to diagnose PZA resistance accurately.

Background: Early-onset neonatal sepsis (ENOS) is one of the most common causes of mortality in neonates. The bacteria causing ENOS are generally transferred from the mother to the infant before or during labor. Objectives: This study aimed to determine the prevalence rate of nasopharyngeal colonization with common bacterial agents causing ENOS and their relationship with blood culture outcomes in neonates. Methods: All neonates transferred to the neonatal intensive care unit were included in the study. Posterior pharynx secretions were swabbed and cultured in blood agar and MacConkey agar. Also, a blood specimen from each neonate was inoculated into a blood culture bottle. The grown bacteria were identified by biochemical standard tests. The antibiotic sensitivity test was performed by the disk diffusion method using Mueller-Hinton agar, and the results were evaluated according to the CLSI guidelines. Results: The pharyngeal specimens collected from 114 newborns were positive in 83 (72.8%) cases. Staphylococcus epidermidis was the most common bacterium in all weight groups. However, the isolates of Klebsiella, Escherichia coli, S. aureus, and Streptococcus agalactiae were also high. Thirteen newborns died. Neonates’ pharyngeal specimens were positive among 11 (84.6%) cases who died and 101 (71.2%) neonates who survived. Twelve neonates had positive blood cultures. Simultaneous positive blood and pharyngeal cultures were reported in eight (7%) cases, in which the bacterial isolates from blood and pharyngeal samples were similar in three cases (37.5%). Among pharyngeal isolates, E. coli was resistant to ampicillin in 100% and gentamicin, cefotaxime, and ceftazidime in 50% of the cases. Also, S. epidermidis and Acinetobacter isolates from blood samples were resistant to ampicillin in 100% of the cases. Conclusions: Staphylococcus epidermidis accounted for 38.6% of bacteria cultured from pharyngeal swabs and 66.7% of bacteria cultured from blood samples, 37.5% of which were resistant to ampicillin and 100% were sensitive to vancomycin. One-hundred percent of E. coli cultures from neonatal pharynges were resistant to ampicillin and about 50% of them were resistant to gentamicin, cefotaxime, and ceftriaxone.

The emergence of a highly pathogenic virus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) accounts for severe pneumonia throughout the world. More than 7 million world population have been infected with SARS-CoV-2, and the number of deaths is increasing every day. This study aimed to evaluate the frequency of SARS-CoV-2 in hospitalized patients with acute respiratory infection (ARI). During an outbreak of the SARS-CoV-2, the nasopharyngeal and oropharyngeal swabs were collected from 909 hospitalized patients with severe pneumonia, including 517 (56.9%) males and 392 (43.1%) females. All the collected samples were from different cities of Khuzestan province from 19 February to- 27 March 2020. The RNA was extracted from samples and subjected to real-time polymerase chain reaction (PCR) tests for the detection of the SARS-CoV-2. Simultaneously, the computerized tomography (CT) scan was tested for the presence of ground-glass opacity in the lung among the patients. Of the total number of 909 specimens, 328 (36.08%) cases, including 185 (20.35%) females and 143 (15.73%) males, were positive for the SARS-CoV-2 while, 581 (63.9%) cases, including 374 (41.14%) males and 207 (22.77%) were negative for the SARS-CoV-2 by real-time PCR (p=0.001).Four hundred sixteen (45.76%) cases were positive for ground-glass opacity in the lung by CT scan, while 328/909 (36.08%) trials proved positive for SARS-CoV-2 by the real-time PCR (p=0.003). In this study, 36.08% of patients were positive for SARS-CoV-2. Although the results of positive cases by CT scan showed higher than real-time PCR, screening the SARS-CoV-2 with a real-time PCR method is the first line of choice.

Introduction: Vancomycin-resistant Enterococcus faecium (VREfm) is a common cause of nosocomial infections. Biofilm formation is an important factor in recurrence of infections, facilitating transfer of genetic elements, leading to treatment failures. The aim of this study was to investigate the virulence genes in biofilm producing isolates and to determine possible association between biofilm formation and the presence of these genes; also to determine association between antibiotic susceptibility patterns of VREfm isolates and their biofilm formation ability. Methodology: A total of 57 isolates of VREfm were recovered from different sources of hospitals under Ahvaz University, Iran. The isolates were examined by conventional microbiological methods and molecular test using PCR. The antibiotic susceptibility patterns of the isolates were determined by disk-diffusion and E-test. The biofilm formation ability of the isolates was investigated by Modified Congo red agar and microtiter plate techniques. The presence of virulence genes was examined using Multiplex-PCR method. Results: Out of 57 VREfm isolates, 63.15% of isolates were biofilm producers. The frequency of biofilm producing isolates from clinical specimens, colonized patients and environmental sources were 78.26%, 60%, and 42.85%, respectively. The prevalence of acm, esp and hyl genes among biofilm producing isolates was 86.10%, 55.56% and 52.77%, respectively. There was statistically significant association between esp gene and biofilm formation among isolates from the clinical specimens. Conclusion: Clinical isolates producing biofilms showed a positive association with the presence of the esp. Our study further suggests that the link between virulence genes and biofilms is affected by the environmental context.

This study aimed at determining the prevalence, antibiotic resistance patterns, and genetic linkage of Vancomycin Resistant Enterococcus faecium (VREfm) from different sources in the southwest of Iran. A total of 51 VREfm isolates were obtained and subjected to antibiotic susceptibility testing, carriage of virulence genes, and pulsed-field gel electrophoresis (PFGE) method. All the VRE isolates exhibited a high level of resistance to teicoplanin, ampicillin, erythromycin, ciprofloxacin, and gentamicin, also carried the vanA gene. A total of 59% and 34% of the VREfm strains harbored esp and hyl genes, respectively. The results from PFGE showed 31 PFGE patterns including 10 common types (CT) and 21 single types (ST) among the VRE isolates. Furthermore, isolates from different sources in each common type revealed cross transmission between clinical and environmental sources. Overall, the study showed a high prevalence of diverse VRE faecium strains with threatening resistance phenotypes in the environment and clinical sections among different ICU wards of Ahvaz hospitals.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the major causes of hospital- and community-acquired infections worldwide. Although S. aureus rarely accounts for urinary tract infections (UTI), untreated UTI can lead to several complications. For decades vancomycin has been used for the treatment of MRSA infections. This study was performed to assess the in vitro activity of vancomycin, tigecycline, linezolid and quinupristin/dalfopristin against MRSA isolates from UTI patients. Thirty MRSA strains from 54 S. aureus isolates were isolated from patients with UTI. The antimicrobial susceptibility patterns of the strains were determined by the Kirby-Bauer disk diffusion and broth microdilution methods. PCR assays were used to detect the vanA gene. The MRSA isolates resistant to vancomycin were confirmed using the broth microdilution method. The results revealed that the MRSA isolates were 100% susceptible to linezolid and quinupristin/dalfopristin but 93.3% susceptible to vancomycin and tigecycline respectively. The broth microdilution method confirmed two MRSA strains (6.6%) to be resistant to vancomycin and tigecycline. The study identified vancomycin resistance among the MRSA isolates from UTI patients. This vancomycin resistance in MRSA isolates poses a challenge in managing S. aureus infections. Our study's results highlight the need to correctly identify patients in whom last-resort therapy such as linezolid and quinupristin/dalfopristin should be administered.