Iranian Journal of Microbiology
Volume:12 Issue: 3, Jun 2020

Fluoroquinolones (FQs) are widely used in the treatment of infections caused by Escherichia coli. FQs are broad spectrum antibiotics with high tissue penetration, and ease of use. Therefore, given the concerns existing about drug resistance, we aim to review the latest findings about resistance patterns to levofloxacin (LVX) along with other FQs in E. coli infections in different parts of Iran. Evidence shows that quinolones have been used in Iran for nearly 50 years, and that 0-65% of E. coli isolates show resistance to FQs. In the western parts of Iran, the highest rate of resistance to LVX (66.7%) has been reported among patients having urinary tract infections with E. coli isolates. Few studies and information exist on the antimicrobial resistance of E. coli to LVX in different geographical locations of Iran. However, the findings of various studies on this subject show that E. coli resistance to LVX is more in the western part of Iran than in central and southern regions, but it is similar among inpatients and outpatients. Therefore, it is reasonable advisable to limit the overuse, inappropriate prescription, and self-medication of LVX to prevent the induction of FQ-resistant strains. Accordingly, in order to obtain a clearer image of resistance to FQs, especially LVX in E. coli in Iran, more extensive investigations in different geographical locations and periods of time are required. In addition, antimicrobial stewardship would be helpful in this regard.

The new beta-coronavirus, which caused Severe Acute Respiratory Coronavirus-2 Syndrome (SARS-CoV-2), a major respiratory outbreak in Wuhan, China in December 2019, is now prevalent in many countries around the world. Identifying PCR-based viruses is a well-known and relatively stable protocol. Unfortunately, the high mutation rates may lead to widespread changes in viral nucleic acid sequences, and so using specific primers for PCR can be recommended. In this study, we evaluated the power of a conventional RT-PCR to detect SARS-CoV-2 RNA among the five set primer sets.

The five genomic regions of the Coronavirus SARS-2 virus including Nucleocapsids (N), Envelope (E), RNA depended RNA Polymerase (RdRp), ORF1ab and Spike (S) were selected for primer designing. A conventional RT-PCR was performed to compare sensitivity, specificity and other analytical characteristics of primers designed against two Real Time PCR commercial kits.

The result of the comparative analysis showed that the ORF1ab, N and RdRp primers had a sensitivity, specificity and positive predictive value higher than other primers. A significant difference in the analytical sensitivity between the studied primer sets in RT-PCR kits was observed.

In this study, the ORF1ab, Nucleocapsid and RdRp regions have the best primers for identifying the SARS-CoV-2 RNA between different genes that have been suggested.

With this study, for the first time among patients diagnosed with COVID-19, the neutrophil-lymphocyte-ratios of men and women were compared.

The study was conducted with 80 patients and the data was gained retrospectively on the electronic documents of the hospital.

The neutrophil-lymphocyte-ratio was statistically significant and higher in the male than the women for all ages and geriatric patients (p<0.05).

The higher neutrophil-lymphocyte-ratio in older males diagnosed with COVID-19 could be a causative reason for the higher mortality rates in men. We hope that these findings would be helpful for further studies.

Cytomegalovirus (CMV) constitutes the most common viral cause of congenital infections in newborns worldwide. There are a significant number of asymptomatic newborns with congenital CMV infection in Iran, which may develop long-term sequelae of infection. Unfortunately, limited data exsists from Iran on the rate of congenital CMV infection among neonates. The current study was aimed to investigate the prevalence of congenital CMV infection among Iranian neonates by testing Guthrie cards.

Guthrie cards were collected from infants within 2 weeks of life, and total DNA was extracted from samples by thermal shock and evaluated for CMV DNA using nested-PCR assay. CMV infection in newborns was confirmed through a commercial CMV PCR kit. Infected infants underwent further evaluation at the hospital.

CMV infection was identified in four of 1174 infants (0.34%) which is approximately 3 cases per 1000 live births. Infected infants were asymptomatic at birth and had a normal hearing status similar to other children. There were no factors in relation with CMV infection among newborns.

According to the results of this study, infected infants with congenital CMV infection could identify at early stage by testing Guthrie cards (within 21 days of life). Furthermore, since there is a lack of CMV knowledge in our population, educating and effective counseling by obstetricians/ gynecologists to the pregnant women are recommended.

Scrub typhus is re-emerging as an important cause of acute undifferentiated fever in the last decade from various parts of India. Complexity in performing the “gold standard” immunofluorescent assay and the unreliable nature of Weil Felix test often results in delayed or misdiagnosis in a majority of cases. The present study seeks to integrate the results of rapid diagnostic tests, clinical and laboratory features to aid the diagnosis and management of scrub typhus patients.

A total of 645 serum samples with suspected scrub typhus sent to the Department of Microbiology were included in the study. Scrub typhus was tested by rapid immunochromatographic test (SD Diagnostics) and IgM ELISA (Inbios International, USA). Clinical features, laboratory parameters and final outcome were analysed from the clinical records of positive patients.

Scrub typhus was diagnosed in 13.7% of patients and majority of them were observed in the month of August. 58.6% of scrub typhus patients presented with fever of one to two weeks duration. Eschar was documented in 13.7% of patients and 24% of patients gave a history of working outdoors or exposure to vegetation. All the patients responded to Doxycycline treatment and there was no mortality.

High index of suspicion for scrub typhus is necessary in febrile patients not responding to conventional antibiotics especially during outbreak situations. Rapid immunochromatographic tests with excellent specificity and acceptable sensitivity can be used as potential point of care tests for quick diagnosis of scrub typhus especially in delayed presentation.

The Beijing family of Mycobacterium tuberculosis has been identified as a severe pathogen among this species and found in many clinical isolates during the last decade. Early identification of such genotype is important for better prevention and treatment of tuberculosis. The present study performed to compare the efficiency of Real-Time PCR and IS6110-Based Inverse PCR methods to identify the Beijing family.

This study was carried out on 173 clinical isolates of Mycobacterium tuberculosis complex in Golestan Province, northern Iran. DNA extraction performed by boiling and determining the Beijing and non-Beijing strains carried out using Real-Time PCR and IS6110-Based Inverse PCR.

In both Real-Time PCR and IS6110-Based Inverse PCR method, 24 specimens (13.9%) of the Beijing family were identified and the result of the IS6110-Based Inverse PCR method showed that all the Beijing strains in this region belonged to the Ancient Beijing sub-lineage.

Although the efficacy of the two methods in the diagnosis of the Beijing family is similar, the IS6110-Based Inverse PCR is more applicable to the ability to detect new and old Beijing family.

Antimicrobial resistance of Neisseria gonorrhoeae is globally spread and threatening. Culturing of N. gonorrhoeae is the only method to collect live isolates for investigation antimicrobial resistance profile. Therefore, quality assessment of N. gonorrhoeae culture is essential for successful isolation of gonococci. This study was conducted to evaluate deferred and bedside culture of N. gonorrhoeae depending on the year season and temperature condition of transport media temporary storage.

Urogenital swabs from 46 symptomatic heterosexual patients with gonorrhoea and subculture of N. gonorrhoeae in 46 suspensions in concentrations 1.5 × 108 CFU/ml were subjected to the study. Non-nutritive transporting medium Amies Agar Gel Medium with charcoal (Copan Diagnostics Inc., Brescia, Italy) was used for deferred culture and selective Chocolate agar TM+PolyViteX VCAT3 (BioMérieux, Marcy-l'Étoile, France) for both tested methods of culture.

The specificity of both bedside and deferred methods of culture was 100%. The sensitivity of deferred culture was higher than of bedside culture (82.6% vs 47.8%, p<0.0005). Deferred culture showed significantly higher sensitivity comparing to bedside culture in summer (100% vs 50%, p=0.003), and comparably the same as for bedside culture in autumn, winter and spring.

The viability of N. gonorrhoeae subcultures was significantly higher in refrigerated samples from transport media than from ambient one after exposition from 48 to 96 hours. Optimal viability of N. gonorrhoeae was observed when transport swabs were kept refrigerated up to 48 h (73.9-93.5%) or ambiently – up to 24 h (87%). Updating laboratory guidelines regarding sampling and timely specimen processing might improve gonococcal culture performance.

Escherichia coli is known to be the pathogen commonly isolated from those infected with urinary tract infections (UTIs). The aim of this study was to investigate the presence of E. coli virulence genes and antibiotics’ resistance pattern among clinical isolates in the Northeast of Iran. Relationships between virulence genes and antimicrobial resistances were studied as well.

Three hundred isolates of E. coli were isolated from patients with UTIs that referred to Ghaem and Imam Reza hospitals (Mashhad, Iran) during August 2016 to February 2017. A multiplex PCR was employed to amplify the genes encoding pyelonephritis associated pili (pap), S-family adhesions (sfa), type1fimbriae (fimH) and aerobactin (aer). Disk diffusion test was performed to test the susceptibility of isolates to β-lactams, aminoglycosides, cephalosporins, quinolone, fluoroquinolones, carbapenems and trimethoprim-sulfamethoxazole.

The PCR results identified the fimH in 78.4%, aer in 70.5%, sfa in 13.6% and the pap in 8.2% of isolates. The rates of antibiotic resistance of the isolates were as follows: 64.7% resistant to cephalosporins, 34% to trimethoprim-sulfamethoxazole, 31% to fluoroquinolones, 15.3% to aminoglycosides, 13.3% to β-lactams, 7.8% to quinolones and 4.4% to carbapenems. Significant relationships existed between pap and aer, pap and sfa, aer and fluoroquinolones also pap and cephalosporins.

fimH and aer were found in > 50% of isolates suggesting the importance of both genes in UPEC. The majority of isolates had fimH as adhesion factor for colonization. Determining antibiotic resistance patterns in specific geographical areas is necessary for appropriate treatment of urinary tract infection. The high rate of resistance to cephalosporins is most likely due to incorrect drug administration.

Intestinal microbiota is involved in the development and maintenance of immune homeostasis. This study was conducted to investigate the levels of key immunoregulatory bacteria in the intestinal wall-associated microflora and its effect on the transcriptional activity of the Foxp3 and RORyt genes in the gut-associated lymphoid tissue (GALT) of rats with Salmonella-induced inflammation, both untreated and treated with vancomycin and Bacteroides fragilis.

To determine the levels of immunoregulatory bacteria in GALT of rats Q-PCR was used to identify them by species-specific 16S rDNA genes. Transcriptional activity of Foxp3 and RORyt genes was determined using Q-PCR with reverse transcription.

In animals treated with both vancomycin and Salmonella, the levels of segmented filamentous bacteria (SFB) increased while Akkermansia muciniphila and Faecalibacterium prausnitzii decreased. In rats that received pretreatment with vancomycin and then were infected with S. Enteritidis and S. Typhimurium, the levels of SFB increased, and the number of Bacteroides-Prevotela group, A. muciniphila, Clostridium spp. clusters XIV, IV, and F. prausnitzii significantly decreased, decreasing Foxp3 and increasing Rorγt mRNA expression. Administration of B. fragilis to animals treated with S. Enteritidis or S. Typhimurium and pre-treated with vancomycin caused a decrease in SFB and Rorγt mRNA levels and conversely, increased the numbers of the Bacteroides-Prevotela group, Clostridium spp. clusters XIV, IV, A. muciniphila, F. prausnitzii and Foxp3 gene expression in GALT.

Our results suggest that the commensal microorganism B. fragilis may provide a protective role against the development of experimental colitis, which has to be taken into consideration for further clarification of the effective therapeutic strategy of inflammatory bowel diseases, irritable bowel syndrome and necrotising colitis.

Nanoparticles are widely used in various fields such as electronics, cosmetics, water purification, biomedical and biotechnology. Biosynthesis of nanoparticles using biological agents have gained much attention in the area of nanotechnology in the last few decades because of cost effective, non-toxic, and eco-friendly. Algae have been used to reduce metal ions and subsequently for the biosynthesis of nanoparticles.

Silver nanoparticles (AgNPs) have been biosynthesized by Phormidium formosum isolated from Mediterranean Sea coast Egypt in an aqueous system. An aqueous solution of silver ions was treated with alive biomass of P. formousm for the formation of AgNPs. The physio-chemical properties of synthesized silver nanoparticles were studied using analytical techniques such as UV-Vis spectrophotometer, transmission electron microscopy (TEM), and Fourier Transform Infrared Spectroscopy (FTIR). The antimicrobial effect of synthesized silver nanoparticles was also tested on several microorganisms by measuring the inhibition zone.

These nanoparticles showed an absorption peak at λmax 437 nm in the UV-visible spectrum, corresponding to the Surface Plasmon Resonance of AgNPs. The transmission electron micrographs of nanoparticles in an aqueous solution showed production of silver nanoparticles synthesized by P. formosum. The obtained AgNPs are spherical in shape with a size ranging from 1.83 nm to 26.15nm. The Fourier transmittance infrared spectrum (FTIR) confirms the presence of bio component in alive biomass of P. formosum which was responsible for the nanoparticles synthesis. The antimicrobial test revealed that AgNPs synthesized by P. formosum is capable to inhibit the growth of microorganisms.

The results confirmed that AgNPs can act as a powerful antimicrobial agent against fish and human pathogens.

The outcome of Leishmania infection mainly depends upon the Leishmania species which causes the disease and the generation of the type of host immune response, the healing process and protection in leishmaniasis depends upon induction of Th1 response. In this study, the Th1/Th2 cytokine profile in cutaneous leishmaniasis (CL) is evaluated.

This study was carried out in leishmaniasis clinic of CRTSDL, TUMS, during March 2018 to March 2019. Peripheral blood mononuclear cells (PBMC) of volunteers with active healing and non-healing lesion (s) of cutaneous leishmaniasis (CL), volunteers with and without history of CL were cultured and stimulated with Soluble Leishmania antigen (SLA). The supernatants were collected and the levels of IFN-γ, IL-5 and IL-10 were titrated using ELISA method.

The results showed a significantly higher levels of IFN-γ in volunteers with active CL healing form (p<0.005), history of CL (p<0.005) than healthy volunteers. A significantly (p<0.005) higher level of IFN-γ was seen in volunteers with active healing form of lesion than non-healing form. There was a significantly (p<0.005) higher level of IL-10 in volunteers with a history of non-healing form and active non-healing form of CL. There was no significant difference in IL-5 production in PBMC of different groups.

IFN-γ production starts at early stage of cutaneous leishmaniasis and enhance during course of lesion healing, IFN-γ level is significantly higher in all patients compared to healthy volunteers, IFN-γ is significantly higher in patients with healing form than non-healing form of lesion.

In this study the clinical manifestations, laboratory findings, and management of five patients diagnosed with Mediterranean spotted fever (MSF) from southeast of Iran are presented. All patients but one had recent thick-bite histories which were noticeable as black eschars (tache noire). Patients’ samples were tested by real-time PCR and serology (IFA). The disease was confirmed by fourfold rising of IgG antibodies against Rickettsia conorii. This is the first report of MSF cases in Iran.

COVID-19 has literally ravaged the entire world. People from all walks of life are badly affected because of compulsory lockdown around the world. Timely diagnosis is a problem as there is no single test that can achieve the highest acceptable sensitivity. Some of the tests are indeed costly and footing the bill by the governments can cause a tremendous load on the Treasury. As it stands, the current tests are beyond patient means and, thus, the patient would never have it performed. Lastly, there is no consensus as to whether everyone should be tested for COVID-19 and not based on presence of clinical features.Unfortunately, since the disease has been declared a pandemic, all should be considered to be infected unless provenotherwise by the tests that are performed.