Iranian Journal of Microbiology
Volume:12 Issue: 5, Oct 2020

The novel Coronavirus COVID-19 is wrecking a havoc across the globe and has been declared as a pandemic by WHO. Apart from transmission and shedding of the virus through respiratory secretions in the form of droplets (mainly), several studies have shown the presence of the virus in various samples such as stool, urine and occasionally in blood, semen, tears and breastmilk. Whereas government authority guidelines consider a person as cured from COVID-19 when along with clinical improvement no more virus can be detected primarily on respiratory samples along with clinical improvement; the persistence of the virus in these body fluids even after clinical recovery and negative RT-PCR test results on respiratory samples, has raised many questions about the elusive nature of this novel virus along with the possibility of other routes of transmission of this virus in the community. Although studies performed till now across the globe on persistence of SARS-COV-2 in various body fluids are sparse, in this review we would like to present and analyse the results of those studies performed globally on the aforesaid topic to get a better insight of this side of the COVID-19 story.

Researchers all around the world are working hard to find an effective treatment for the new coronavirus 2019. We performed a comprehensive systematic review to investigate the latest clinical evidence on the efficacy and safety of treatment with Remdesivir in hospitalized patients with COVID-19.

We performed a systematic search in Pubmed, Embase, Web of Science, Google scholar and MedRxiv for relevant observational and interventional studies. The outcomes measures were mortality rates, improvement rates, time to clinical improvement, all adverse event rates and severe adverse event rates.

Three randomized controlled trials and 2 cohort studies were included in our study. In the 2 cohort studies, patients received Remdesivir for 10 days. 2 RCTs evaluated 10-day efficacy of treatment with Remdesivir versus placebo group and the other RCT compared its 5-day regimen versus 10-day regimen. Visual inspection of the forest plots revealed that the efficacy of Remdesivir was not much different in reducing 28-day mortality versus 14-day mortality rates. Besides, 10-day treatment regimen overpowered 5-day treatment and placebo in decreasing time to clinical improvement. All adverse event rates did not have a significant difference; however, severe adverse event rate was lower in the 5-day Remdesivir group compared to the 10-day and placebo groups.

5-day course of Remdesivir therapy in COVID-19 patients is probably efficacious and safe, and patients without invasive mechanical ventilation benefit the most. Treatment can be extended to 10 days if satisfactory improvement is not seen by day 5. Most benefits from Remdesivir therapy take place in the first 14 days of the start of the treatment.

Escherichia coli is the most common causative agent of urinary tract infections (UTIs) in 90-80% of patients in all age groups. Phylogenetic groups of these bacteria are variable and the most known groups are A, B1, B2 and D. The present study aimed to evaluate the phylogenetic groups of E. coli samples obtained from UTIs and their relation with antibiotic resistance patterns of isolates.

In this study 113 E. coli isolates were isolated from distinct patients with UTIs referred to Hamadan hospitals. After biochemical and molecular identification of the isolates, typing and phylogenetic grouping of E. coli strains were performed using multiplex PCR targeting chu, yjaA and TSPE4.C2 genes. The anti-microbial susceptibility of the isolates to amikacin, ampicillin, trimethoprim-sulfamethoxazole, amoxicillin/clavulanic acid, ciprofloxacin, cefotaxime, imipenem, aztreonam, gentamicin, meropenem, nitrofurantoin, nalidixic acid and cefazolin was determined using disk diffusion method.

Of 113 isolates, 50 (44.2%), 35 (31%), 23 (20.4%) and 5 (4.4%) of samples belonged to group B2, group D, group A and group B1 phylogenetic groups respectively. All isolates were susceptible to meropenem, imipenem (100%), followed by amikacin (99.1%). The highest resistance rates were observed against ampicillin (74.3%) and nalidixic acid (70.8%). Correlation between phylogenetic groups and antibiotic susceptibilities was significant only with co-amoxiclav (P = 0.006), which had the highest resistance in phylogenetic group A.

Prevalence of different phylogroup and resistance associated with them in E. coli samples could be variable in each region. Therefore, investigating of these items in E. coli infections, could be more helpful in selecting the appropriate antibiotic treatment and epidemiological studies.

Urinary tract infection (UTI) is a common infection affects people of different ages. It is important to explore the antibiotics susceptibility of the bacterial agents to improve the empirical antibacterial prescription because of emerging of multi-drug resistant (MDR) bacteria.

This is a retrospective observational study including 322 patients with UTI at the largest hospital at the center of Al-Basrah Governorate in the far south of Iraq from August 2018 to November 2019. Bacterial isolates from urine samples with significant bacteria were investigated by automated VITEK® 2 compact system to determine the causative bacteria and their antibiotics susceptibility.

Escherichia coli and Klebsiella pneumoniae were the first and second most frequent Gram-negative isolates, whereas Staphylococcus haemolyticus and Enterococcus faecalis were the first and second most frequent Gram-positive isolates. Fosfomycin, tigecycline, colistin, meropenem, imipenem, amikacin and nitrofurantoin had high susceptibility rates against Gram-negative isolates. Nitrofurantoin, tigecycline, daptomycin, teicoplanin, vancomycin and linezolid had a high effect against Gram-positive isolates.

The leading causative isolates especially the most predominant Gram-negative isolates E. coli and K. pneumoniae show high resistance rates against important antibiotics including penicillin/β-lactamase inhibitors piperacillin/tazobactam, third-generation cephalosporins as ceftazidime, and cefepime quinolones as ciprofloxacin and levofloxacin and trimethoprim/sulfamethoxazole which call for reconsidering them for treatment of UTI.

The aim of this study was to determine the prevalence of Salmonella at broiler breeder farms of Iran and investigate the factors underlying salmonellosis in these farms. This is a cross-sectional investigation conducted in 23 provinces of Iran.

Fecal samples were collected from 139 broiler breeder farms in the country and standard bacteriological tests were carried out on the samples for the isolation of Salmonella. The serological tests were then applied for the samples that were positive in the bacteriological test. The information on the sampled farms extracted from the Iran GIS-VET Monitoring and Surveillance System was used for the analysis of the risk factors.

A total of 11 farms out of the 139 sampled farms were infected with Salmonella with the largest number of infected cases related to Tehran and Fars Provinces.

The statistical analysis results showed that flocks with older ages and farms with larger number of houses are at greater risk of Salmonella infection.

Due to important role of Streptococcus agalactiae, Group B streptococci (GBS), in production of invasive disease in neonates, investigation regarding the pathogenicity and antibiotic resistance factors is necessary in selecting the appropriate therapeutic agents. Beside capsule, the pilus has been currently recognized as an important factor in enhancing the pathogenicity of GBS. Resistance of GBS to selected antibiotics is noticeably increasing which is mainly due to the anomalous use of these drugs for treatment. The aim of this study was to determine the prevalence of pili genes followed by antibiotic susceptibility of GBS, previously serotyped, isolated from pregnant women in the city of Yazd, Iran.

Fifty seven GBS from pregnant women were subjected to multiplex PCR for determination of PI-1, PI-2a and PI-2b pilus-islands and simultaneously, the phenotype of antibiotic resistance to penicillin, tetracycline, erythromycin, clindamycin, gentamycin and levofloxacin was determined. Antibiotic resistance genes (ermA, ermB, mefA, tetM, int-Tn) were further diagnosed using PCR and multiplex PCR.

PI-1+PI-2a with 71.9%; followed by PI-2a (21.1%) and PI-2b (7%) were observed. PI-1+PI-2a in serotype III was (73.2%), serotype II, Ia, Ib and V were 12.2%, 9.8%, 2.4% and 2.4% respectively. GBS penicillin sensitive was 89.5% and 96.5% resistance to Tetracycline. The frequency of resistance genes were as follows: tetM (93%), ermA (33.3%), ermB (8.8%), int-Tn (80.7%) and mefA (0).

Majority of GBS contained PI-1+PI-2a. Hence presence of this pilus stabilizes the colonization, therefore designing a program for diagnosing and treatment of infected pregnant women seems to be necessary.

Nontypeable Haemophilus influenzae (NTHi) are major causes of non-invasive infections, including otitis media and sinusitis and it can also contribute to respiratory infections of all ages. Currently, there is no licensed vaccine against NTHi commercially available. Many studies have been conducted on the use of OMV as a vaccine against NTHi. The purpose of this study is to achieve an immunogenic vaccine against NTHi.

In this study, standard OMV Haemophilus (ATCC49766) with adjuncts CpG and MPLA was used and after infusion into BALB/c mice, the levels of antibodies and cytokines were measured on serum of immunized mice.

The results showed that total IgG antibody and IgG1 and IgG2a isotypes in OMV immunized mice with mixture of CpG-MPLA adjuvant had a significant increase. Also, the results of cytokines (IL-10, IL-4 and IFN-γ) showed that IL-4 had the highest rate.

These findings indicate that OMVs derived from NTHi strains have a high potential to act as a vaccine against NTHi infections.

Colorectal cancer is one of the most types of cancer. Researchers have shown that lactic acid bacteria have antitumor activity. The cell wall of Lactococcus lactis, as the bacterial cytoplasmic extract and nisin can affect the proliferation of cancer cells. Since cyclin D1 plays an important role in the progression of the cell cycle, its regulation can also be a therapeutic approach. We investigated the antiproliferative effect of cell wall, cytoplasmic extract and nisin on SW480 cancer cell line and the expression level of cyclin D1 gene in treated cancer cells.

SW480 cell lines were treated with different concentrations of bacterial cell wall, cytoplasmic extract and nisin. MTT test was also performed. The expression level of cyclin D1 gene was determined using Real time PCR. Data were analyzed using Graph Pad Prism software.

The growth rate of cancer cells treated with nisin has significantly decreased compared to the cancer cells treated by other two substances (p< 0.05). Survival rates of the cancer cells treated by nisin at a concentration of 2000 μg, cytoplasmic extract, and cell wall were 34%, 47% and 49%, respectively. Real-time PCR results showed that cyclin D1 mRNA expression has significantly decreased in nisin treated sw480 cells (P<0.05).

The results of this study show that nisin, bacterial cytoplasmic extract, and bacterial cell wall have antiproliferative effects, which are associated with the decreased expression of cyclin D1 in SW480 cell line.

Lactobacillus casei, an acid-resistant bacterium, has a protective role against the pathogens. So we aimed to determine the proteome of Lactobacillus casei ATCC39392 strain in response to different pHs of 5 and 7 using proteomic analysis.

Supernatant and bacterial extraction of Lactobacillus casei ATCC39392 adapts at pHs 5 and 7 were isolated using sodium dodecyl sulfate–polyacrylamide gel and two-dimensional gel electrophoresis. The comparison of results showed that 7 protein spots were seen in pH 5 but not in pH 7. Afterward, they were excised and sent for Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to be identified.

Seven different proteins (four secretory and three structural) with different roles in human body health were identified. Prescribed proteins include putative cell wall associated Hydrolase, Glycoside Hydrolase, beta-N-Acetyl hexosaminidase, Histidine Kinase, Chaperonin, metal dependent Hydrolase and Lysozyme.

Seven isolated proteins with anti-cancer and digestive impresses are proper subjects in therapy or drug delivery approaches especially oral drug usage for protection against stomach acidic area.

Lontar (Borassus flabellifer L.) is widely grown in Indonesia and one of its products is palm sap. Palm sap contains a high level of sugar, making it suitable as a medium to increase the lactic acid bacteria (LAB) production of exopolysaccharides (EPS). This study aimed to isolate the EPS-producing LAB from palm sap and evaluate its EPS production. LAB isolation was carried out on MRS agar containing 0.5% CaCO3.

The screening and production of EPS were carried out on MRS media supplemented with 10% sucrose. The molecular identification of the selected EPS-producing LAB was based on 16S rDNA. A quantitative analysis of EPS polymer dry mass and total sugar was conducted using one-way ANOVA.

In this study, five EPS-producing LABs were found: Fructobacillus fructosus N4, Leuconostoc mesenteroides N5, Leuconostoc mesenteroides N7, Leuconostoc mesenteroides N9, and Fructobacillus fructosus N10. The highest EPS yield in liquid media was 10.997 ± 1.591 g/L by Leuconostoc mesenteroides N7, whereas the lowest was 4.505 ± 0.459 g/L by Fructobacillus fructosus N10.

This study found Fructobacillus fructosus strains as EPS producers that have never been reported before.

Probiotics have been widely used for host immune system enhancement but with limited knowledge regarding the immunomodulation mechanisms by which they assist the mucosal innate immune response. We investigated the effects of probiotics on the modulation of the innate mucosal immune response particularly in association with Toll-like receptor (TLR)-2, TLR-4 and nuclear factor-kappa B (NF-κB) p65 and p105.

We randomized 24 male BALB/c mice into four groups. Two groups were administered probiotics for 21 consecutive days; one of these groups was challenged with Lipopolysaccharide (LPS) on day 15. The third group was challenged with only LPS. The fourth group remained untreated. All mice were sacrificed after 21 days. An immunohistochemistry procedure on the ileum was performed and monoclonal antibodies specific for TLR-2, TLR-4 and NF-κB p65 and p105 were used for the analysis of innate lymphoid cells.

In the LPS-only treated group, there was a significant decrease in p105, indicating an alternative transcription pathway for the process of pro-inflammatory cytokine production. In the probiotics-only treated group there was significant enhancement of TLR-2 and TLR-4 and NF-κB p65 and p105. When mice treated with probiotics were exposed to LPS, there was a significant decrease in NF-κB p65 and p105, indicating employment of the classical pathway for pro-inflammatory cytokine production.

Probiotics can enhance the innate mucosal immune response in healthy mice and can maintain the homeostasis of the gut mucosal immune response against LPS through the activation of the classical NF-κB pathway.

Serratia marcescens has emerged as a nosocomial pathogen responsible for human infections, where antibiotic resistance further complicates the treatments. In S. marcescens, biofilm formation and virulence factor production are controlled via quorum sensing (QS) system. QS is a signaling system that enables gene regulation to control diverse physiological functions in bacteria. Essential oils have shown to be potential in diminishing the pathogenicity and virulence of drug-resistant bacteria. This study was performed to determine whether eugenol would affect QS system, biofilm formation and virulence factor production of S. marcescens.

Biofilm formation, extracellular virulence factor production (hemolysin and protease), swarming motility and pigment formation of S. marcescens ATCC 13880 and S. marcescens Sm2 were assessed after eugenol exposure at 1.25 and 2.5 µg/ml concentrations. The expression of genes involved in motility (flhD), attachment (fimC), biofilm formation (bsmB, bsmA), and QS regulatory (swrR) were also evaluated.

Eugenol treatment at 1.25 and 2.5 µg/ml concentrations caused a significant reduction in biofilm formation. The pigment, hemolysin and protease production of two studied S. marcescens strains, also reduced significantly by eugenol treatments (p<0.05). The bsmA, bsmB, flhD and fimC genes were down-regulated after eugenol treatment. The swrR gene expression was also reduced significantly by eugenol in both S. marcescens strains (p<0.05).

Eugenol inhibited quorum sensing-regulated functions of two studied S. marcescens strains.

Catharanthus roseus is generally used to treat many diseases in folklore remedies. The present study is aimed at determining phytochemical constituents, cytotoxicity and antiviral activities for crude extract of the plant.

The whole plant of C. roseus was extracted using methanol extraction method. Phytochemical qualitative screening was carried out for C. roseus extract according to standard procedures used to test for the presence of alkaloid, saponin, terpenoid and steroid. Cytotoxicity was assessed using 3-(4,5-dimethylthiazol-2,5-diphenyltetrazolium bromide (MTT) assay. Plaque reduction assays were carried out to evaluate the antiviral activity of C. roseus extract against herpes simplex virus type 1 (HSV-1). These include post-treatment, pre-treatment and virucidal assays.

C. roseus extract contain secondary metabolites such as alkaloid, saponin and terpenoid but does not contain steroid. Cytotoxicity screening against Vero cells using MTT assay showed that the CC50 values for crude extract of C. roseus was 0.5 mg/mL. The extract prepared from C. roseus possesses phytochemical compound that was non-cytotoxic to the cell with potential antiviral activity. Plaque reduction assays against herpes simplex virus type 1 (HSV-1) showed that the selective indices (SI = CC50 / EC50) of C. roseus extract in post-treatment, pre-treatment and virucidal assays were 36, 20 and 4.7 respectively. The results revealed that the extract prepared from C. roseus possesses phytochemical compound that was non-cytotoxic to the cell with potential antiviral activity.

This study showed that C. roseus extract has promising potential to be explored as anti-HSV-1 agent regardless of the mode of treatment.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was first described during a pneumonia outbreak in Wuhan, has attracted tremendous attention in a short period of time as the death toll and the number of confirmed cases is growing unceasingly. Although molecular testing is the gold standard method of SARS-CoV-2 detection, the existence of the false-negative results presents a major limitation to this method.

This retrospective Double-Centre study was conducted on 1320 COVID-19 patients recruited at Taleghani and Shohadae Tajrish Hospitals in Tehran, Iran. We analyzed the leukocyte, lymphocyte and neutrophil counts of hospitalized cases both on admission and at discharge. We also evaluated the alteration of these parameters within a seven-day follow-up.

Of the whole, 1077 (81.6%) neither were admitted to intensive care unit (ICU) nor experienced death, and were defined as the mild-moderate group. Of 243 severe cases, while 59 (24.3%) were admitted to ICU and cured with the intensive care services, 184 (75.7%) patients died of the disease, either with or without ICU admission. Calculation of neutrophil-to-lymphocyte ratio (NLR) revealed that the mild-moderate cases had a lower ratio at discharge. On the other hand, the ratio was significantly higher in the death group as compared to the ICU group; highlighting the fact that patients with a higher degree of neutrophilia and a greater level of lymphopenia have a poor prognosis.

We suggest that NLR greater than 6.5 may reflect the progression of the disease towards an unfavorable clinical outcome, with this notion that the ratios higher than 9 may strongly result in death.

The prevalence of Hepatitis B virus (HBV) infection among haemodialysis (HD) patients has been well documented. In addition to overt infection, occult Hepatitis B infection exists in which a patient who is diagnosed seronegative for Hepatitis B surface antigen (HBsAg) shows positive HBV-DNA on using more accurate molecular methods. This study aims to determine the prevalence of overt and occult HBV infection among the HD patients who had attended Al-Nasiriyah dialysis centre during a two-month period.

Serological qualitative detection of HBsAg by rapid test (strips), enzyme immunoassay (EIA, HBsAg) and molecular (real-time polymerase chain reaction (real-time PCR)) was conducted for quantitative detection of HBV in HD patients’ serum.

The prevalence of overt HBV infection among HD patients was 3.7%. The viral load of HBV positive patients was ranging from 5.85 × 101 to 2.16 × 106 copies/ml of serum with median (7.4 × 105 copies/ml). Occult Hepatitis B was not detected in any of the seronegative HD patients (0%). Overt infection was found more in males (80%) than females (20%) (P<0.05). Similarly, infection was found to be higher among patients who had blood transfusions (80%) than those who had not (20%) with statistical significant p<0.05. Although not statistically significant, the mean duration of HD was higher among HBV positive HD patients (17.6) than HBV negative HD patients (14.3). A dual infection of HBV and HCV was not detected in this study.

Nosocomial transmissions at HD centres and blood transfusion are important risk factors. Besides serological screening, real-time PCR offers a safeguard against the spread of overt and occult HBV infection and determines the viral load of the positive patients.

Influenza A/H1N1pdm09 causes respiratory illness and remains a concern for public health. Since its first emergence in 2009, the virus has been continuously circulating in the form of its genetic variants. Influenza A/H1N1pdm09 surveillance is essential for uncovering emerging variants of epidemiologic and vaccine efficacy. The present study attempts in silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India during 2009-2019.

We have investigated the antigenic drift analysis of 96 isolates’ hemagglutinin (HA) gene sequences (59 central Indian and 37 local Indian and 28 global reference HA gene sequences) of Influenza A/H1N1pdm09 viruses from 2009 to 2019. The study includes mutational (Multiple sequence Alignment), phylogenetic (Maximum Likelihood Method), and statistical analysis (Covariance and correlation) of HA sequences submitted in NCBI, IRD and GISAID from central India.

Phylogenetic analysis indicated maximum clustering of central Indian HA gene sequences in genogroup 6B. Analysis of amino acid sequence alignment revealed changes in receptor binding site (RBS). The frequency of S220T amino acid substitution was found to be high followed by S202T, K300E A273T, K180Q. The Karl Pearson correlation coefficient (r) and covariance between the number of mutations and the death toll was found +0.246 and +100.3 respectively.

The study identifies the continuous genetic variations in the HA gene sequences of circulating Influenza A/H1N1pdm09 in central India from the year 2009 to 2019. Further suggesting importance of monitoring the gradual evolution of the virus with regards to an increase in virulence, pathogenicity and vaccine efficacy timely.

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection in many populations, including military recruits receiving basic training. Therefore, this study was set out to determine the molecular epidemiology, genotype and phylogenetic features of RSVs in patients with respiratory infection as a case study.

In this study, military barracks of Tehran, Iran, between January to March 2017 exposed to respiratory diseases were used for sampling. Throat swabs were taken, a reverse transcriptase-polymerase chain reaction (RT-PCR) assay was performed to identify RSV and then the genotyping and phylogenetic analyses of RSVs in patients with a respiratory infection.

Among 400 Iranian military trainees with respiratory symptoms, RSV infection was identified in 2.75% (11/400) using RT-PCR. Sequencing showed the incidence of type A (2.5%, n=10) to be much higher than type B (0.25%, n=1); Sore throat was the most common symptom among RSV patients. Phylogenetic analysis revealed that the majority of strains from the studied samples were more consistent with those from the Philippines and the US strains.

This study is the first to document RSV as a major cause of acute respiratory illness among military trainees in Iran. The prevalence of RSV is substantial in the cold season and the prevalence of genotype A is dominant in the country, leading to take essential steps in preparing a preventive vaccine against this viral infection.