Iranian Journal of Microbiology
Volume:13 Issue: 5, Oct 2021

In this study, the performance of three different commercial antibody assays for COVID-19 was examined and parameters affecting the antibody response were investigated. The correlation of patients’ chest CT results, procalcitonin, CRP, and D-dimer levels with the antibody response were retrospectively evaluated.

COVID-19 antibodies were detected by three commercially available assays in each patient. Two of the assays were rapid immunochromatographic tests and - one was an ELISA-based IgG assay. SARS-CoV-2 RNA was tested by “COVID-19 RT-qPCR Detection Kit” using nasopharyngeal swab samples. The results of antibody tests were compared with each other, RT-qPCR, Biochemical parameters and chest CT findings.

RT-qPCR was positive in 46.6% (41/88) of the evaluated patients among which 77.3% (68/88) were healthcare workers. Seventeen (41.4%) of viral RNA positive patients had a positive antibody result with at least two assays. Both of the rapid immunochromatographic tests had identical sensitivity of 36.6% and specificity of 100%, compared to RT-qPCR assay; while the sensitivity of the ELISA based Euroimmune test was 43.9%, and the specificity was 95.7%. The sensitivity and specificity of the immunochromatographic tests were 75% and 100% respectively, compared to ELISA test result. There was a correlation between antibody positivity and old age and male gender. The presence of typical chest CT findings increased the antibody positivity 13.62 times. Antibody positivity was also increased with the decrease in Ct value of the PCR assay. There was no significant relationship between the biochemical parameters (CRP, D-dimer and procalcitonin values) and the antibody or RT-qPCR results.

There was a correlation between antibody response and male gender, older age, presence of symptoms, typical chest CT findings and low PCR-Ct value.

Glanders is a serious zoonotic disease caused by Burkholderia mallei. Prevention, control, and treatment strategies of glanders are prerequisites for microbial source tracking. The present study was aimed to analyze the genomic pattern of B. mallei Iranian field isolates by pulsed-field gel electrophoresis (PFGE) typing.

B. mallei isolates were aerobically cultured in nutrient broth/agar supplemented with glycerol 4% for 48 h at 37°C. API 20NE identification system was used for the biochemical characterization. Genomic DNA of bacterial isolates was extracted using OIE-recommended protocol. Molecular identification of bacterial isolates was done based on amplification of BimA and IS407-flip genes. PFGE was applied to prepare the genomic pattern of B. mallei isolates. The guinea pig was used as a suitable model for studying the histopathological characterization of B. mallei.

In both enzymatic digestion patterns by using Af1II and VspI, we found three different clonal types; І) PFGE type of B. mallei Razi 325 strain, ІІ) PFGE type of Tiger, Kordan, and Oshnavieh strains, and ІІІ) PFGE type of Semirom strain. B. mallei Razi 325 was categorized as unrelated strain which was belonged to the different cluster differing more than four bands.

PFGE showed more discriminatory power and considerable reproducibility for molecular typing of B. mallei strains in our study. It is standardized the approaches for outbreak detection, pathogen phylogeny, molecular epidemiology, and population studies.

Information on the genetic epidemiology of cholera in Assam, a northeastern state of India is lacking despite cholera being a major public health problem. The study aimed to determine the virulence genes and genes encoding antibiotic resistance in Vibrio cholerae isolates and to determine the prevalent genotypes based on the presence or absence of the virulence genes and ctxB genotype.

Twenty-five V. cholerae strains were subjected to conventional biotyping and serotyping followed by multiplex PCR to detect ctxA, ctxB, zot, ace, O1rfb, tcpA, ompU, ompW, rtxC, hly and toxR and antibiotic resistance genes. Cholera toxin B (ctxB) gene was amplified followed by sequencing.

All the V. cholerae O1 isolates were El Tor Ogawa and showed the presence of the core toxin region representing the genome of the filamentous bacteriophage CTXø. The complete cassette of virulence genes was seen in 48% of the isolates which was the predominant genotype. All the isolates possessed amino acid sequences identical to the El Tor ctxB subunit of genotype 3. sulII gene was detected in 68% of the isolates, dfrA1 in 88%, strB in 48% and SXT gene was detected in 36% of the isolates.

Toxigenic V. cholerae O1 El Tor Ogawa strains of ctxB genotype 3 carrying a large pool of virulence genes are prevailing in Assam. Presence of a transmissible genetic element SXT in 36% of the strains is of major concern as it indicates the emergence of multiple drug resistance among the V. cholerae isolates.

Urinary tract infections (UTI) are the most common bacterial infections in both outpatient and inpatient department received for routine bacterial culture and sensitivity. We looked for significant bacteriuria in requested repeat urine sample after primary urine culture yielded significant growth (>105 CFU/ml) of ≥3 types of colonies. Also studied, different isolates grown with their sensitivity pattern and contamination rates of urine samples from different departments.

In routine, primary urine cultures yielding ≥3 types of colonies on Cystine Lactose Electrolyte Deficient (C.L.E.D) were requested for repeat samples, collected with aseptic precautions after proper instructions. Data was analyzed for the Microbiological profile and its clinical correlation.

Among 617 received requested urine samples, 292 (47.3%) yielded significant bacteriuria. Clinical details were available for 252 cases out of which 100 (39.7%) showed asymptomatic bacteriuria, 87 (34.5%) complicated UTI and 65 (25.7%) uncomplicated UTI. Null hypothesis was rejected as 292 (47.3%) of the received repeat samples showed significant bacteriuria and 325 (53%) showed normal flora/no growth i.e. there is a 50% chance of getting either a positive culture or normal flora/no growth in repeat urine samples after the primary urine culture showed ≥3 types of colonies. It indicates the importance of requesting repeat urine samples for an accurate urine culture report. Male patients were significantly associated with significant bacteriuria and complicated UTI (p= 0.001). Escherichia coli (n=112, 28%) was the most common followed by Klebsiella species (n=66, 16.4%) and Enterococcus species (n=69, 17.2%). 183 (45.6%) isolates were Multi-Drug Resistant (MDR) Gram Negative Bacilli (GNBs), Escherichia coli (50.3%) being most common. Vancomycin Resistant Enterococcus (VRE) (n=8, 2.0%) was also isolated.

Our study justifies the rationale for asking a repeat urine samples which helps in providing an appropriate microbiological report with antibiotic sensitivity pattern, hence preventing unwanted reporting of commensals/contaminants facilitating evidence based therapy.

Sexually transmitted infections (STIs) can remain undetected and untreated; therefore, rapid diagnosis and treatment of STIs are important. Mycoplasma genitalium (MG), Mycoplasma hominis (MH), and Ureaplasma urealyticum are sexually transmitted pathogens that cause asymptomatic, organ-specific, and chronic infections, thereby posing a threat to community health. Therefore, we investigated the epidemiological trends of MG and MH infections in South Korea for rapid diagnosis and treatment.

From September 2018 to December 2020, samples (catheter, pus, tissue, swab, and urine) were collected from outpatients of hospitals in South Korea for molecular biological venereal disease testing. DNA was extracted and analyzed using real-time polymerase chain reaction.

Of the 59,381 samples analyzed, 8.78% (n=5,215) were positive for MG and MH. The MH positivity rate (5.51%, n=3,273) was higher than the MG positivity rate (3.27%, n=1,942). MG and MH positivity rates were the highest in patients aged <19 years. Men had higher MG positivity rate, whereas women had higher MH positivity rates. Furthermore, the MGpositivity rate was the highest in the swab samples of both men and women, whereas that of MH was the highest in the urine samples of men and swab samples of women.

We identified the differences between MG and MH positivity rates based on sex, specimen, and age. Our findings can provide information for strategies that protect public health and reduce STI incidence and transmission.

Dermatophytosis induced by Trichophyton mentagrophytes is a major human and animal fungal contamination. Antifungals like terbinafine and fluconazole are widely used to treat dermatophytosis; nevertheless, the prevalence of drug resistance has increased. Hence, novel curative strategies are needed. In the present study, we compared the efficacies of conventional and nanoform of antifungals agents in guinea pig model of dermatophytosis.

Guinea pigs (n=36) were injected (the posterior dorsal portion) with Trichophyton mentagrophytes conidia. The guinea pigs were divided into 6 groups (positive control, negative control, fluconazole 0.5% treated group, nano-fluconazole treated group, terbinafine 1% treated group, and nano-terbinafine treated group), then were scored both clinically (redness and lesion intensity) and mycologically (microscopy and culture) until day 40 of inoculation. The treatment started 5 days after the inoculation and continued until day 40 of inoculation.

Assessment of the mean score of clinical lesions in groups treated with nano-drug forms of fluconazole and terbinafine on the first day of treatment showed a score of 3 (significant redness with large scaling) and for the conventional form of terbinafine and fluconazole had a score of 4 (ulcer and scar). The decrease in lesion score in nano-drug treated groups was observed between days 15 and 20 and continued until day 40. On day 40, all groups had zero scores except the positive control group.

This study indicated that nano-drugs are more suitable for the treatment of dermatophytosis and could be considered as future alternatives for the treatment of dermatophytosis.

Sphingomonas paucimobilis is an opportunistic pathogen and was rarely encountered in clinical specimens previously. This study aimed to investigate the clinical features, associated co-morbidities, and antimicrobial susceptibility patterns of S. paucimobilis infection in a tertiary hospital in Uttarakhand.

S. paucimobilis isolates cultured from various sections of hospital and OPDs were identified and analyzed for their antibiograms in the microbiology laboratory for a duration of one year from January 2020 to December 2020.

S. paucimobilis was isolated from 49 samples (0.01%) out of 3792 samples processed in VITEK 2 Compact automated ID/AST instrument. The maximum number of isolates were obtained from urine samples (31%), followed by blood (24%). Septicemia (41%), meningitis (17%), lower respiratory tract infections and ventilator associated pneumonia (14%) constituted a major portion of infections caused by this organism. Diabetes mellitus (22%) and steroid usage (16%) were major associated co-morbid conditions. Third and Fourth generation cephalosporins like ceftriaxone (81%) and cefepime (86%) were found to be the most susceptible drugs whereas 61% of isolates were resistant to colistin.

This organism is an up-and-coming pathogen and should not be simply labeled as a contaminant. Although the organism is not grossly virulent and still might not be associated with serious life-threatening infections; however their evolving resistance patterns and increased spectrum of infections should be seriously taken into account.

Public health protection requires timely evaluation of pathogens in potable water to minimize outbreaks caused by microbial contaminations. The present study was aimed at assessing the microbiological quality of water obtained from Shantinagar (a rural area in the South Goa region of Goa, India) using 5-Bromo-4-Chloro-3-Indoxyl β-D-glucuronide-Sorbitol MacConkey agar (BCIG-SMAC) medium and, propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) assay for differential detection and quantification of viable Escherichia coli cells in water samples.

Membrane filtration method was used for both BCIG-SMAC medium and PMA-qPCR methods. To determine the efficiency of detection of viable cells, we first evaluated the PMA treatment protocol and established the standard calibration curves using previously reported primers.

PMA-qPCR detected as low as 7 femtograms of DNA of E. coli per qPCR reaction whereas the limit of detection (LOD) of BCIG-SMAC medium was 1.8 CFU/100mL. A total of 71 water samples spanning 2017-2018 have been analyzed using BCIG-SMAC medium and PMA-qPCR, of which 95.77% (68/71) and 7.04% (5/71) were found to be total E. coli and E. coli O157:H7, respectively. PMA-qPCR study showed the viable counts of total viable E. coli cells ranging from 3 CFU/100mL to 8.2×102 CFU/100mL. The total E. coli CFU/100mL quantified by PMA-qPCR significantly exceeded (paired t-test; P<0.05) the number on BCIG-SMAC medium.

The present study indicates that the microbiological quality of environmental water samples analyzed do not comply with the regulatory standard. Therefore, special attention is warranted to improve the overall portable quality of water in the perspective of public health.

Gut microbiota is assumed to play an essential role in the pathogenesis of multiple sclerosis (MS). This study aimed to investigate the abundance of some gut microbiota among Egyptian patients with relapsing remitting multiple sclerosis (RR-MS).

Forty cases of RR-MS diagnosed according to McDonald diagnostic criteria (2017) were recruited consecutively from the Department of Neurology, Assiut University Hospitals. The results were compared with 22 healthy age and sex matched control subjects. DNA was extracted from stool and measures made of concentration and copy number of bacterial organisms by real-time PCR using group specific primers for 16S rRNA targeting predominant genera of gut microbiota previously hypothesized to participate in MS pathogenesis.

The mean age was 31.4 ± 8.8 yrs; 75% of the patients were women. The mean and SD of EDSS score was 3.43 ± 1.35. Seven cases had cervical cord plaques (17%). There were significantly increased copy numbers of Desulfovibrio, Actinobacteria, Firmcutes, and Lactic acid bacteria in patients compared with the control group. In contrast there was a significantly lower level of Clostridium cluster IV in the patients. Patients who had EDSS < 3.5 had a significantly higher copy number of Actinobacteria, Bacteroidetes, and Bifidobacterium, compared with patients who had EDSS > 3.5. There was a significant negative correlation between duration of illness and copy number of Firmcutes, Akkermansia, and Lactic acid bacteria (P = 0.01, 0.04, and 0.004 respectively).

The changes in gut microbiota are associated with exacerbation of MS disease. Disruption of the intestinal microbiota results in the depletion or enrichment of certain bacteria that may affect the immune balance leading to predisposition to MS.

Immunization is a promising strategy to combat against the life-threatening infections by Multi Drug Resistance Acinetobacter baumannii. In this study, we directed to design and evaluate the efficacy of a recombinant multi-epitope protein against this pathogen.

Epitopes prediction was performed for candidate proteins OmpA and BAM complex (BamA, BamB, BamC, BamD, BamE) from A. baumannii, using immune-informatics tools with high affinity for the human HLA alleles. After expression and purification of the recombinant protein, its functional activity was confirmed by interaction with positive sera.

Cloning and expression of the desired multi-epitopes protein were verified. Circular Dichroism study showed the secondary structure and proper refolding of the recombinant protein was achieved and matched with computational prediction. There was a significant interaction between designed protein with antibodies presented in ICU patients' and staff's sera.

The interaction of the recombinant protein with patients' sera antibodies suggests that it may be a promising determinant protein for immunization against of MDR A. baumannii.

This study aimed to investigate the accessible regions of the fimH mRNA using computational prediction and dot-blot hybridization to increase the effectiveness of antisense anti-virulence therapeutics against Uropathogenic Escherichia coli.

We predicted the secondary structure of the E. coli fimH mRNA using the Sfold and Mfold Web servers and RNA structure 5.5 program. Considering the predicted secondary structure, accessible regions in mRNA of fimH were determined and oligonucleotides complementary to these regions were synthesized and hybridization activity of those oligonucleotides to the fimH Digoxigenin (DIG) labeled mRNA was assessed with dot-blot hybridization.

When searching the fimH gene in the GenBank database, two lengths for this gene was discovered in different strains of E. coli. The difference was related to the nine bases in the first part of the gene utilizing either of two translation initiation sites. Based on the bioinformatics analyses, five regions lacking obvious stable secondary structures were selected in mRNA of fimH. The result of dot-blot hybridization exhibited strongest hybridization signal between the antisense oligonucleotide number one and fimH labeled mRNA, whereas hybridization signals were not seen for the negative control.

The results obtained here demonstrate that the region contains start codon of fimH mRNA could act as the potential mRNA target site for anti-fimH antisense therapeutics. It is recommended in the future both of utilizing translation initiation sites be targeted with antisense oligomers compounds.

Phytase has a hydrolysis function of phytic acid, which yields inorganic phosphate. Bacillus species can produce thermostable alkaline phytase. The aim of this study was to isolate and clone a Phytase gene (Phy) from Bacillus subtilis in Escherichia coli.

In this study, the extracellular PhyC gene was isolated from Bacillus subtilis Phytase C. After purification of the bands, DNA fragment of Phy gene was cloned by T/A cloning technique, and the clone was transformed into Escherichia coli. Afterward, the pGEM-Phy was transferred into E. coli Top-10 strain and the recombinants were plated on LB agar containing 100 µg/ml ampicillin. The colonization of 1171 bp of gene Phytase C was confirmed by PCR. The presence of gene-targeting in vector was confirmed with enzymatic digestion by XhoI and XbaI restriction enzymes.

The Phytase gene was successfully cloned in E. coli. The result of cloning of 1171 bp Phytase gene was confirmed by PCR assay.

Our impression of this article is that several methods, such as using along with microbial, plant phytase reproduction, or low-phytic acid corn may be the better way from a single phytase.

In recent decades, enterococcal resistance to antimicrobials has greatly increased. Furthermore, these chemicals include several side effects on the patients. Since no reports are available of the bacteriophages' effects on eukaryotic cells, they can be good solutions for multidrug-resistant bacterial problems. Therefore, the major aim of this study was to isolate bacteriophages from wastewaters on clinical antibiotic-resistant enterococci.

Clinical bacteria were isolated, then enterococcal isolates were identified using different methods. The antibiotic resistance scheme of the enterococcal isolates was assessed. The bacterial isolates were exposed to wastewater samples containing potential bacteriophages. Technically, isolated bacteriophages were studied by electron microscopy.

Isolated bacteria were verified as Enterococcus faecium. Results showed that bacteriophages could easily be isolated from wastewater sources. The isolated bacteriophages were effective on E. faecium as well as Streptococcus dysgalactiae. Furthermore, these bacteriophages were challenged with five other bacteria (ATCC) with no visible effects. In general, the isolated bacteriophages belonged to the Myoviridae, Siphoviridae, and Inoviridae families.

Further studies on bacteriophages and their efficacy on enterococcal strains could increase the treatment possibility of enterococcal infections. Due to these bacteriophages' effects on Streptococcus strains, bacteriophages may be used to treat streptococcal infections as well.

Prevalence of extended spectrum β-lactamase (ESBL) leads to the development of antibiotic resistance and mortality in burn patients. One of the alternative strategies for controlling ESBL bacterial infections is clinical trials of bacteriophage therapy. The aim of this study was to isolate and characterize specific bacteriophages against ESBL-producing Klebsiella pneumoniae in patients with burn ulcers.

Clinical samples were isolated from the hospitalized patient in burn medical centers, Iran. Biochemical screenings and 16S rRNA gene sequencing were determined. The phages were isolated from municipal sewerage treatment plants, Isfahan, Iran. TEM and FESEM, adsorption velocity, growth curve, host range, and the viability of the phage particles as well as proteomics and enzyme digestion patterns were examined.

The results showed that Klebsiella pneumoniae Iaufa_lad2 (GenBank accession number: MW836954) was confirmed as an ESBL-producing strain using combined disk method. This bacterium showed significant sensitivity to three phages including PɸBw-Kp1, PɸBw-Kp2, and PɸBw-Kp3. Morphological characterization demonstrated that the phage PɸBw-Kp3 to the Siphoviridae family (lambda-like phages) and both phages PɸBw-Kp1 and ɸBw-Kp2 to the Podoviridae family (T1-like phages). The isolated bacteriophages had a large burst size, thermal and pH viability and efficient adsorption rate to the host cells.

In present study, the efficacy of bacteriophages against ESBL pathogenic bacterium promises a remarkable achievement for phage therapy. It seems that, these isolated bacteriophages, in the form of phage cocktails, had a strong antibacterial impacts and a broad-spectrum strategy against ESBL-producing Klebsiella pneumoniae isolated from burn ulcers.

An important leading cause of the emergence of vancomycin-resistant enterococci, especially Enterococcus faecium, is the inefficiency of antibiotics in the elimination of drug-resistant pathogens. Consequently, the need for alternative treatments is more necessary than ever.

A highly effective bacteriophage against vancomycin-resistant E. faecium called vB-EfmS-S2 was isolated from hospital sewage. The biological properties of phage S2 and its effect on biofilm structures were determined.

Phage S2 was specifically capable of lysing a wide range of clinical E. faecium isolates. According to Electron microscopy observations, the phage S2 belonged to the Siphoviridea family. Suitable pH spectra for phage survival was 5-11, at which the phage showed 100% activity. The optimal temperature for phage growth was 30-45°C, with the highest growth at 37°C. Based on one-step growth curve results, the latent period of phage S2 was 14 min with a burst size of 200 PFU/ml. The phage S2 was also able to tolerate bile at concentrations of 1 and 2% and required Mg2+ for an effective infection cycle. Biofilms were significantly inhibited and disrupted in the presence of the phage.

According to the results, phage S2 could potentially be an alternative for the elimination and control of vancomycin-resistant E. faecium biofilm.

Diabetes is recognized as a great concern and a public health problem worldwide. Several factors including environmental and genetic factors have been involved. Recently, infectious agents such as hepatitis C virus (HCV) have been reported to be associated with diabetes. Thus, this study was conducted to determine the frequency of HCV infection among patients with diabetes type 2 in Ahvaz city, Iran.

A case-control study design was conducted at Ahvaz Jundishapur University of Medical Sciences. A total of 600 study subjects were included in this research. All the patient sera were tested for Anti- HCV antibody, HBsAg, and HIV antibody. The sera of positive Anti-HCV antibody, were assayed for 5'- UTR and core regions of the HCV genome by Nested RT-PCR. Finally, the HCV genotyping was determined by sequencing.

The prevalence of HCV in type 2 diabetes and nondiabetic controls was 2% and 0.33%, respectively. The distribution of HCV genotypes among the HCV-positive patients were 3a (1.66%) and 1a (0.33%).

To control and improve the treatment, the screening of HCV infection with anti-HCV antibody was followed by molecular techniques such as PCR and HCV genotyping which should be implemented for all patients with diabetes type 2.

Respiratory syncytial virus (RSV) is one of the most common viruses associated with acute lower respiratory tract infections in infants, young children, and the elderly. Due to a lack of effective anti-viral drugs or vaccines, using an immunomodulatory strategy is probably the best option to decrease the burden of RSV disease. Here, we studied carvacrol as a known immunomodulator on RSV infection outcome in a mice model.

Balb/c mice were infected by intranasal inoculation of RSV-A2, and treatment started daily 24 h after infection. Mice were sacrificed on day five after infection and experimental analyses were performed to study airway immune cell influx, CD4 and CD8 subtypes, cytokine/chemokine secretion, lung histopathology, and viral load.

Results showed that using carvacrol enhanced immune cell influx, cytokine/chemokine production, and virus titer, and aggravated lung pathology. Our result showed that carvacrol administration increased viral titer compared to the RSV-PBS group. Also, carvacrol significantly induced IFN-γ production and did not induce IL-10 production. Besides, carvacrol non-significantly increased lymphocytes and monocytes count but did not affect the neutrophil count.

Carvacrol at the concentration of 80 (mg/kg) did not show immunomodulatory activity to alleviate the RSV infection outcome. Further research is needed to uncover the effects of the carvacrol intervention on virus replication and immune responses following RSV infection. Many herbal remedies in use contain carvacrol. However, the use of herbal remedies to treat viral respiratory infections such as RSV has to be performed with caution.

Cutaneous leishmaniasis (CL) treatment is a challenging issue, although numerous modalities have been introduced as candidate treatment for CL yet only antimonial agents are commonly used to treat CL, a different form of amphotericin B is used to treat visceral form of leishmaniasis but the efficacy against CL is not high. There are a few reliable clinical trials on CL, the main reason is the nature of the disease which required a well design protocol to evaluate the efficacy of any candidate treatment against CL. In this study, a protocol was developed and used to evaluate a topical formulation of a nano-liposomal form of amphotericin B in addition to glucantime to treat CL caused by L. tropica.

This study is a phase 3, randomized, double-blind, placebo-controlled trial to evaluate the efficacy and safety of topical nano-liposomal amphotericin B (SinaAmpholeish 0.4%) in combination with intralesional injections of meglumine antimoniate in the treatment of ACL caused by L. tropica. Overall, 130 patients, aged 12-60 years, with a diagnosis of ACL caused by L. tropica are recruited and treated according to the protocol.

A total of 130 patients with CL lesion will be recruited and double- blind randomly treated with received intralesional injections of Glucantime weekly or Glucantime plus SinaAmpholeish for 4 weeks.

The results of this study showed that the protocol works well and the treatment was tolerated by both groups of patients.

Acinetobacter baumannii is an opportunistic bacterial pathogen predominantly associated with hospital-acquired infections. Here we present a case of infective endocarditis of native Mitral and Aorta valves caused by A. baumannii in a 73-year-old man. He underwent surgical excision and Pathologic specimen showed A. baumannii growth after 48 hours that was extensively drug-resistant (XDR). He was treated with colistin and tigecycline. Finally, he discharged with no important complication. To our best knowledge, it is the first case of Acinetobacter endocarditis has ever been reported in Iran. Although XDR A. baumannii is a life-threatening pathogen, proper and timely treatment can be life-saving.