Jundishapur Journal of Microbiology
Volume:13 Issue: 12, Dec 2020

Context:

 First cases of Coronavirus disease 2019 (COVID-19) were reported in December 2019. With more than 100 million confirmed cases 14 months later, the disease has become the worst public-health dilemma of the century. The rapid global spread of COVID-19 has resulted in an international health emergency, threatening to overwhelm health care systems in many parts of the world, especially poor resource countries.

Evidence Acquisition: 

Influenza and COVID-19 have similar clinical symptoms, and both cause a respiratory illness that may vary from mild to severe. Both diseases have the same mode of transmission and require similar public health guidelines to prevent their spread, but their treatment strategies are different. In this study, an algorithmic method is proposed for managing patients according to their symptoms for each of these infections.

 In fall and winter, infections with seasonal influenza and other respiratory viruses become common. As influenza also causes significant morbidity and mortality, especially at the two extremes of age and in those with compromised immunity, it is of major importance to know the similarities and dissimilarities between COVID-19 and seasonal influenza and plan appropriate public health measures to deal with each of these illnesses.

 Will there be a devastating combined epidemic of COVID-19 and influenza (COV-Flu) during the 2020 - 2021 season? Does co-infection increase the risk of severe illness or amplify virus shedding? Actually, we do not yet know the answers to these questions; so, in this article, first, we attempt to define the similarities and differences between COV-Flu. Then, we will have a brief discussion on how to manage patients presenting with symptoms suggestive of both diseases. However, as COVID-19 has been recognized as a pandemic since December 2019, the management of this emerging disease is rapidly evolving as new information is collected from different parts of the world.

 Ciprofloxacin induces SOS response and mutagenesis by activation of UmuD’2C (DNA polymerase V) and DinB (DNA polymerase IV) in Escherichia coli, leading to antibiotic resistance during therapy. Inactivation of DNA polymerase V can result in the inhibition of mutagenesis in E. coli.

 The aim of this research was to investigate the effect of UmuC inactivation on resistance to ciprofloxacin and SOS mutagenesis in E. coli mutants.

 Ciprofloxacin-resistant mutants were produced in a umuC- genetic background in the presence of increasing concentrations of ciprofloxacin. The minimum inhibitory concentration of umuC-mutants was measured by broth dilution method. Alterations in the rifampin resistance-determing region of rpoB gene were assessed by PCR amplification and DNA sequencing. The expression of SOS genes was measured by quantitative real-time PCR assay.

 Results showed that despite the induction of SOS response (overexpression of recA, dinB, and umuD genes) following exposure to ciprofloxacin in E. coli umuC mutants, resistance to ciprofloxacin and SOS mutagenesis significantly decreased. However, rifampicin-resistant clones emerged in this genetic background. One of these clones showed mutations in the rifampicin resistance-determining region of rpoB (cluster II). The low mutation frequency of E. coli might be associated with the presence and overexpression of umuD gene, which could somehow limit the activity of DinB, the location and type of mutations in the β subunit of RNA polymerase.

 In conclusion, for increasing the efficiency of ciprofloxacin against Gram-negative bacteria, use of an inhibitor of umuC, along with ciprofloxacin, would be helpful.
 

 Bacteria are the most common causes of clinical infectious diseases. The distribution and antimicrobial resistance (AMR) rates of bacteria provide important guidelines for clinical antibacterial treatment; however, the information in this region is still missing.

 This study aimed to evaluate the changes in the distribution and AMR rates of clinical isolates from inpatients.

 We conducted a retrospective cross-sectional analysis of the distribution and antimicrobial susceptibility of all non-duplicate Gram-negative bacterial (GNB) and Gram-positive bacterial (GPB) isolates collected from January 1, 2013, to December 31, 2018, in our hospital.

 In total, 56,535 and 3,518 non-repetitive isolates were detected in the whole hospital and intensive care units (ICUs), respectively. The isolates included GPB (26.3% and 18.4%, respectively) and GNB (73.7% and 81.6%, respectively). The five dominant bacteria were the same in the whole hospital and ICUs, but Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumannii percentages were different. The detection rates of all isolates and five dominant bacteria were significantly different between the ICUs and the whole hospital (P < 0.05). The detection rate of extended-spectrum β-lactamase (ESBL)-E. coli (54.1%) was significantly higher than that of K. pneumoniae (26.1%). The detection rates of carbapenem-resistant (CR) and extensively drug-resistant (XDR)-A. baumannii were the highest in both the ICUs (87.1% and 21.8%, respectively) and the whole hospital (65.5% and 12.9%, respectively). The methicillin-resistant S. aureus (MRSA) detection rate was high (26.5%) but showed a significant decreasing trend (P < 0.05). The detection rates of ESBL and XDR-E. coli, CRAB, and XDR-S. aureus were significantly different between the ICUs and the whole hospital (P < 0.05). Gram-negative bacteria were highly susceptible to amikacin (> 90%) and tigecycline (> 98%). Staphylococcus aureus showed 100% susceptibility to vancomycin and linezolid. Acinetobacter baumannii had the highest resistance to imipenem (62.8%) and meropenem (64.0%). Except for A. baumannii and E. coli (P < 0.05), the AMR levels and the trends of the other isolates were similar between the ICUs and the whole hospital (P > 0.05).

 Currently, the appropriate antimicrobial agents in our hospital include amikacin and tigecycline for the treatment of GNB infections and vancomycin and linezolid for the treatment of GPB infections. Moreover, it is still necessary to monitor AMR in the ICUs and the whole hospital simultaneously.

 The DNA oncoviruses, including human papillomavirus (HPV) and Epstein-Barr virus (EBV) are among the most important infectious agents involved in breast carcinogenesis. These oncoviruses have a broad disrupting effect on cellular miRNAs and their functions, by which they contribute to carcinogenesis.

 In this investigation, we evaluated the correlation between HPV and EBV and the expression level of tumor suppressor miRNAs (miR-143 and 145), clinical outcomes, and their association with stimulating inflammatory cytokines in patients with breast carcinoma.

 In our case-control study, 35 cancerous tissues and 35 adjacent non-cancerous tissues were collected from 35 patients. Nested-PCR was set up for the detection of HPV and EBV genomes, and RT-qPCR was used for miRNA expression in the case and control groups. In addition, serum specimens were obtained from all patients (n = 35) and healthy controls (n = 35) to determine the IL-8 serum concentration.

 We found HPV and EBV in 14.2% (10/70) and 7% (5/70) of all samples, respectively. The distributions of positive samples in the case and control groups were 25.7% (9/35) and 2.9% (1/35) (P = 0.006) for HPV and 11.4% (4/35) and 2.9% (1/35) (P = 0.164) for EBV, respectively. Besides, RT-qPCR showed that miR-143 and miR-145 were significantly downregulated in HPV and EBV-infected cases compared to non-infected ones (P < 0.05). Data also indicated that the promotion of metastasis status was related to miR-143/145 downregulation and HPV infection (P = 0.003). No significant difference was found in serum IL-8 concentration concerning viral infections.

 Our results suggested the possible involvement of viral infections in breast carcinogenesis and adverse clinical outcomes by downregulating miR-143/145.

 Currently, it appears that new molecular-based methods could substitute microscopic and culture assessment for the first-line detection of microorganisms isolated from clinical specimens. However, it will remain the "continual strategy" until this technology is attuned to identifying all fungi that can be isolated from biological specimens.

 The present study aimed to validate a high-resolution melting (HRM) technique to identify clinical filamentous fungi. Moreover, it was attempted to compare the results with those of the target gene’s polymerase chain reaction (PCR) sequencing.

 A total of 54 specimens of bronchoalveolar lavage (BAL), nail, ear discharge, blood culture, and cornea were collected from patients suspected of fungal infection. All Fusarium spp. and Aspergillus spp. were recognized based on Tef-α and beta-tubulin region sequencing, as well as PCR-HRM analysis.

 The Tef-α sequence analysis revealed the most frequent spp. to be Fusarium solani followed by F. oxysporum (n = 3), F. caucasicum (n = 3), F. coeruleum (n = 3), F. falciforme (n = 1), F. proliferatum (n = 1), F. brevicatenulatum (n = 1), F. globosom (n = 1), and F. verticillioides (n = 1). Based on the beta-tubulin sequences, Aspergillus flavus (n = 10), A. fumigatus (n = 7), A. niger (n = 2), A. terreus (n = 1), and A. orezea (n = 1) were identified in this study. Furthermore, the dataset analysis of PCR-HRM revealed that 33 isolates belonging to Fusarium spp. were F. solani (n = 24), F. oxysporum (n = 3), F. proliferatum (n = 3), F. falciforme (n = 1), F. verticillioides (n = 1), and F. brevicatenulatum (n = 1). Moreover, isolates (n = 21) belonging to Aspergillus spp. included A. flavus (n = 11), A. fumigatus (n = 7), A. niger (n = 2), and A. terreus (n = 1).

 The sequencing method has a time-consuming and costly nature, and there exists conformity between the sequence results of the Tef-α/beta-tubulin regions and PCR-HRM. The PCR-HRM method is a reliable approach in the clinical laboratory to identify Aspergillus and Fusarium spp. However, some closely related spp. show no curve algorithm differences in PCR-HRM.

 Protozoa have the ability to replace the human lung. Over recent years, the incidence of pulmonary infections caused by these microorganisms has increased, particularly in individuals with an immunodeficiency. The use of appropriate diagnostic methods is particularly important in the identification of parasites in pulmonary secretions.

 The present study aimed to evaluate and compare PCR-based diagnostic methods with the gold standard method to detect three pathogenic protozoa, including Toxoplasma, Cryptosporidium, and Microsporidia in bronchoalveolar lavage (BAL) samples obtained from immunocompromised patients with chronic obstructive pulmonary disease.

 A BAL sample of immunodeficient patients suffering from chronic obstructive pulmonary disease (COPD) was examined by direct microscopy and PCR methods.

 In this study, we examined 64 patients with immunodeficiency accompanied by COPD. Microsporidia were not identified in the samples. Direct methods identified three and nine cases of Toxoplasma and Cryptosporidium, respectively. However, the molecular method identified two and two cases of pulmonary infection with these parasites.

 Determining the standard diagnostic method for parasites is dependent on factors, such as the type of specimen and the type of parasite. Based on the results of the present study, the direct microscopic method is the optimal diagnostic method for Toxoplasma and Cryptosporidium in BAL samples.
 

 Ventilator-associated pneumonia (VAP), a subset of hospital infections, occurs in patients who have been mechanically ventilated for at least 48 hours.

 Our study aimed at determining the frequency and antibiotic susceptibility patterns of bacteria causing VAP in teaching hospitals of Shiraz.

 This was a descriptive cross-sectional study conducted in Shiraz for eight months (November 2017 to June 2018). Samples were detected according to diagnostic bacteriologic tests, and antibiotic susceptibility tests were performed by the disk diffusion (Kirby-Bauer) method based on the Clinical and Laboratory Standards Institute (CLSI).

 A total of 51 patients with VAP were examined, of whom 10 and eight patients had a chronic obstructive pulmonary disease and acute respiratory distress syndrome, respectively. The late-onset VAP rate (61.7%) was higher than the early-onset VAP rate (38.3%). In our study, 45.2% of patients with VAP received antibiotics before the incidence of pneumonia, of whom 31.6% died. Of the remaining 54.8%, only 8.7% died. In other words, patients who received antibiotics before the incidence of pneumonia had higher mortality. The most frequently used antibiotics were meropenem (76.6%) and vancomycin (78.7%). Among 59 bacteria isolated, Acinetobacter and Pseudomonas were the most prevalent organisms.

 Our results showed that most of the isolates (40%) belonged to multi-drug resistant (MDR) pathogens. Probably, antimicrobial treatment before the onset of VAP led to the selection of these MDR pathogens.

 The resistance rate of carbapenem-resistant Enterobacteriaceae (CRE) is increasing yearly but rarely reported in children.

 This retrospective study analyzed the characteristics of isolated CRE strains in pediatric patients, intending to explore reasonable antimicrobial treatment options.

 Some CRE isolates were collected from infected pediatric patients in Liaocheng People’s Hospital from January 2014 to December 2019. The strain identification and antimicrobial susceptibility testing were conducted using Vitek mass spectrometry and the Vitek 2 system, respectively. The carbapenemase genotypes of blaKPC, blaIMP, blaVIM, blaNDM-1, and blaOXA-48 were each detected by polymerase chain reaction and sequencing. The molecular homology analysis of strains was conducted via Pulse-field Gel Electrophoresis (PFGE). The clinical data of CRE-infected pediatric patients were collected from the hospital’s medical data information system.

 Twenty CRE strains were isolated from 1945 infected pediatric patients with Enterobacteriaceae. All CRE strains showed multiple resistance to commonly used antimicrobials. Twelve strains of imipenemase (IMP)-4 and seven strains of IMP-8 carbapenemase were confirmed. Besides, PFGE revealed that two strains of Escherichia coli and three of Klebsiella pneumoniae had indistinguishable patterns. Sixteen patients were cured, including 10 patients using piperacillin/tazobactam.

 This study found the major sources of resistance were IMP carbapenemases. Piperacillin/tazobactam is potentially effective for the treatment of CRE infection, despite insensitivity in vitro.