Iranian Journal of Microbiology
Volume:16 Issue: 1, Feb 2024

The majority of all kidney stone cases are oxalate urolithiasis with a high risk of recurrence. Beside its widespread occurrence, kidney stones are characterized by severe complications and high treatment costs. Pro- biotics and herbal medications could be forthcoming therapeutic interventions in the management of oxalate kidney stones.

The PubMed/MEDLINE database was searched for keywords “Oxalobacter formigenes” AND “Oxalate” OR “oxalate degradation” AND “Lactobacillus” OR “Bifidobacterium” OR “recombinant Lactobacillus” OR “Bacillus subtilis”, and “urolithiasis” AND “herbal extract”. The search returned 253 results, 38 of which were included in the review.

Most of the oxalate-degrading probiotics belong to the Oxalobacter formigenes, Lactobacillus, Bifidobacterium, and Bacillus genus with a minimum dosage of 107 CFU in the form of capsules, sachets, and lyophilized powder. Oxalate concentration in media was 5-50mM with an incubation time ranging from 24h to 14 days. The majority of the studies suggested that probiotic supplementation might be useful for reducing urinary excretion of oxalate and urea and alleviation of stone formation. Different herbal extracts were used on murine models of nephrolithiasis (induced by 0.5-3% ethylene glycol) with reduction of renal inflammation and urinary parameters, and calcium oxalate crystals.

Several strains of probiotics and herbal extracts confer protective effects against kidney stone/nephrolithiasis, indicating their promising nature for being considered as elements of preventive / adjuvant therapeutic strategies.

Newborns as a vulnerable population are exposed to congenital and acquired infections during and after birth. There are several reports of the isolation and reporting of infectious agents (IAs) in early life of newborns with respiratory manifestations, and the present comprehensive study provides a snapshot of the current global situation of the prevalence of IAs in newborns with respiratory symptoms.

A systematic search was conducted in main databases, including PubMed, Scopus, Web of science, and Google scholar. The pooled prevalence of infectious agents (IAs) in newborns was estimated using comprehensive me- ta-analysis software based on random effects model.

Out of 44 inclusive studies (50 datasets) for IAs in newborns, the pooled prevalence was estimated to be 12.2% (95% CI: 6.40-22.0%) and the highest and lowest prevalence of IAs was related to the Brazil (78.2%, 95% CI: 31.0-96.6%), and UK (0.01%, 95% CI 0.01-0.01%) respectively.

The high prevalence of IAs in newborns emphasizes considers the necessary measures to prevent respiratory infections.

Salmonella species (spp) are the most prevalent zoonotic pathogens that cause outbreaks of gastroenteritis worldwide. Therefore evaluation of the profile of antibiotic resistance, virulence factors, and plasmid replicon types in these bacteria is necessary to control and prevent the spread of potentially pathogenic and drug-resistant strains.

This study was performed on 39 Salmonella spp. The antibacterial susceptibility of isolates to various antibiotic agents was determined using disk diffusion test. β-lactamases (bla) including ESBLs, AmpC, MBLs, and virulence genes were detected by PCR methods. Plasmid incompatibility groups among the isolates were identified using PCR-based replicon typing (PBRT).

The most prevalent virulent gene was phoP/Q (84.6%). slyA, sopB, and stn were identified in 79.4% (n=31), 69.2% (n=27), and 2.5% (n=1) of the isolates, respectively. The antibiotic susceptibility testing showed that 30.7% of the isolates were ESBL-producing. bla TEM (41%; n=16) was the most frequent β-lactamase gene among the isolates followed by bla NDM-1 (15.4%; n=6), bla DHA (7.7%; n=3), and bla CTX-M (1.5%; n=1). Six different plasmid replicon types, including IncP (n=9; 23%), IncFIC (n=3; 7.70%), IncY (n=3; 7.70%), IncI1-Iγ (n=2; 5.12%), IncFIIAs (n=1; 2.56%), and IncN (n=1; 2.56%) were ob- served among the isolates.

Our study showed the emergence of carbapenem-resistant and bla NDM-1 among Salmonella spp. for the first time in Kerman, Iran. Since Salmonella spp. plays an important role in the transmission of resistance genes in livestock and humans in the food chains, so more stringent control policies are recommended to prevent the circulation of drug-resistant and potentially pathogenic strains from animals to humans.

Klebsiella pneumoniae is an opportunistic pathogen responsible for causing nosocomial and community-acquired infections. Its pathogenicity is associated with a variety of virulence factors and antibiotic resistance. The aim of the present study was to compare virulence attributes between ESBL and non-ESBL producing isolates.

A total of 113 K. pneumoniae including 56 ESBL and 57 non ESBL-producers were collected in Bushehr province, Iran, from November 2017 to February 2019. Enzymatic profile, hypermucoviscosity and biofilm forma- tion were investigated phenotypically. In addition, the presence of rmpA, aerobactin, kfu, allS, mrkD, ybtS, entB, iutA, fimH, wabG, wcaG, K1 and K2 genes were detected by PCR and sequencing.

There was no statistically significant difference in enzymatic profile between ESBL and non-ESBL producers. The prevalence of the hypermocoviscosity was lower among ESBL compared to non-ESBL producers but the intensity of biofilm was higher in the ESBL producers. Among the virulence genes, K1, rmpA, iutA, and aero were observed only in non-ESBLs. Moreover, the carriage of allS, K, K2, rmpA, iutA and aero genes was higher in hypermucoviscous in comparison with non hypermucoviscous isolates.

The identification of potentially pathogenic isolates plays an important role in preventing their spread as well as the success of their treatment.

Periodontal diseases are resulted from gum infections and dental plaques, which are mainly caused by the bacterial agents. Since dental monitoring includes important prognostic roles, the aim of this study was to detect the most common periodontal pathogenic bacteria in children.

A total of 200 clinical samples were collected from dental plaques and gingival grooves. Tar- get-specific primers were designed for hbpA in Aggregatibacter actinomycetemcomitans, fimA in Porphyromonas gingivalis and 16S rRNA in Prevotella intermedia, Tannerella forsythia and Treponema denticola. Then, a multiplex polymerase chain reaction method was optimized for the highlighted bacterial agents.

In general, the highest and the lowest bacterial prevalence rates belonged to Tannerella forsythia (88%) and Por- phyromonas gingivalis (13%), respectively. Furthermore, prevalence rates of Aggregatibacter actinomycetemcomitans, Prevotella intermedia and Treponema denticola were 25, 21 and 45% in samples, respectively.

There were significant associations between dental/oral health and microbial community. Metabolism of the oral bacteria, including biofilm formation, can affect gums and develop dental plaques and hence dental caries, especially in children. Early diagnosis of dental caries in children via rapid, accurate molecular methods can increase the diagnostic capacity in clinical cases and therefore prevent periodontal infections in adulthood.

Antimicrobial resistance has emerged as a significant global health threat. Infections caused by Multi Drug-Resistant (MDR) bacteria pose formidable challenges in terms of treatment options and patient outcomes. Pus cultures serve as crucial diagnostic tools in identifying the agents responsible for various infections, and their antimicrobial susceptibility patterns which help in establishment of empirical therapy guidelines. This study was conducted to determine the pathogen and its susceptibility pattern from pus cultures and to generate antibiogram in our tertiary care setting.

It was a cross-sectional study, conducted for a period of six months, from July 2022 to December 2022, in the Pathology Department of Pakistan Institute of Medical Sciences (PIMS).

Out of total 2507 samples received, 1242 (49.5%) showed positive culture. Among the 1242 positive samples, 364 were Gram positive cocci (GPCs) and 878 were Gram negative rods (GNRs). Methicillin resistant Staphylococcus aureus (MRSA) was the most common isolate (23%) followed by Klebsiella pneumoniae (22.6%), Pseudomonas aeruginosa (16.9%), Enterobacter spp. (15.5%) and Escherichia coli (14.2%). Vancomycin was found to be highly effective (100%) against MRSA. GPCs were highly susceptible to linezolid (98%) while GNRs showed high level of sensitivity to colistin (96%) and tigecycline (92%).

The generation of a local antibiogram specific to the hospital setting is essential to effectively manage infections empirically and preserve the efficacy of existing antibiotics. By implementing antimicrobial stewardship practices based on a better understanding of antibiotic susceptibility patterns, we can contribute to the mitigation of antibiotic resistance and improve patient outcomes.

Potatoes (Solanum tuberosum), as starchy plants, have been highly esteemed for their rich supply of nutrients. Numerous studies have investigated the potential health benefits of potatoes and explored potential solutions. Among these considerations, the discussion regarding microbial contaminants has remained an important topic.

The present study used cold atmospheric plasma (CAP) to evaluate the microbial quality (includ- ing mesophilic and psychrotrophic bacteria and mold and yeasts) of raw potato slices during a 14-day storage period. To achieve this goal, the duration of CAP exposure was set at 5, 10, and 15 min, utilizing an electric voltage of 60 kV and a specific frequency of 20 kHz.

The findings revealed the effectiveness of CAP pre-treatment in inhibiting microbial growth over the 14 days when compared to the control sample (untreated sample), with a statistically significant difference (P < 0.05). Moreover, with an extension of the CAP exposure duration to 15 min, there was a significant reduction in the logarithmic count of mesophilic, psychrotrophic microorganisms, molds, and yeasts (4.95, 2.85, and 2.22CFU/g, respectively) in comparison to the control groups (7.5, 5.62, and 5.5CFU/g) on days 0, 7, and 14 of the storage periods (P < 0.05).

The results of this study highlight the potential of CAP pre-treatment on reducing the microbial load in raw potato slices prior to frying, which could potentially influence the overall quality of potato-based products.

Colorectal cancer (CRC) is a prevalent form of cancer worldwide. Recent studies suggest that postbiotics derived from probiotic bacteria have the potential as an adjunct therapy for CRC. This study investigates the anti-cancer effects of Bifidobacterium breve (B. breve) and Lactobacillus rhamnosus (L. rhamnosus) postbiotics on the HT-29 cell line.

Through MTT and scratch assay, we investigated the anti-proliferation and anti-migration effects of B. breve and L. rhamnosus postbiotics on HT-29 cells. Furthermore, postbiotic-mediated apoptosis was assessed by ana- lyzing the expression of Bax, Bcl-2, and caspase-3. We also investigated the effects of B. breve postbiotics on the expression of three important genes involved in metastasis, including RSPO2, NGF, and MMP7. Consequently, we validated the expres- sion of selected genes in twelve adenocarcinoma tissues.

The results demonstrated the significant impact of postbiotics on HT-29 cells, highlighting their ability to induce anti-proliferation, anti-migration, and apoptosis-related effects. Notably, these effects were more pronounced using B. breve postbiotics than L. rhamnosus. Additionally, B. breve postbiotics could inhibit metastasis through upregulation of RSPO2 while downregulating NGF and MMP7 expression in HT-29 cells.

Our research suggests that postbiotic metabolites may be effective biological products for the prevention and treatment of cancer.

Mesenchymal Stem Cells (MSCs) can repair gastrointestinal tract damage. The Secretome of MSCs has a high capacity to inhibit bacterial colonization and the subsequent inflammatory responses of Vibrio cholerae.

The Caco-2 cells were treated with adipose-derived MSCs (AD-MSCs) secretome and then in- fected with V. cholerae. Subsequently, the bacterial attachment and invasion, cholera toxin gene expression, PGE2 and IL-6 secretion, TNF-α, IL-1β, and IL-8 expression, and apoptosis of Caco-2 cells were evaluated.

The secretome of AD-MSCs significantly reduced the V. cholerae attachment and internalization on Caco-2 epithe- lial cells (P<0.0001). The cholera toxin (Ctx-B) gene expression (FR=4.56 ± 0.66) and PGE2 production (P=0.0007) were also significantly reduced. The production of NO and TNF-α, IL-1β, and IL-8 pro-inflammatory cytokines were significantly (P<0.05) reduced in exposure to the secretome of AD-MSCs. Secretome also improved a significant 81.33% increase in IL-6 production (128.1 ± 37.6 pg/mL) and showed a 12.36% significant decrease in epithelial cell apoptosis (P< 0.0001) after exposure to V. cholerae.

The secretome of AD-MSCs can play a critical role in inhibiting bacterial colonization, and subsequent inflam- matory responses, and maintaining the integrity of the epithelial barrier. The secretome may be effective in the prevention of hypovolemic shock.

Human herpes virus type 1 (HSV-1) is a neurotropic pathogen that is infected more than 70% of the world population. The increasing of viral resistance to antiviral drugs and the emergence of side effects has motivated researchers to study the use of probiotics as new antiviral agents. The aim of the present study was to study for the first time the potential antiviral activity of Lactobacillus reuteri (L. reuteri) supernatant against HSV-1.

After measuring the cytotoxicity of L. reuteri supernatant by MTT assay, 1:16 dilution of it was added to HeLa cells before and after HSV-1 infection, after 1.5 hours incubation with HSV-1, and simultaneously with HSV- 1 infection. After 48 hours of incubation at 37°C, the viral titer and expression levels of UL54, UL52 and UL27 genes were measured by tissue culture infectious dose 50 (TCID ) and Real-Time PCR methods, respectively.

HSV-1 titer in the treatment conditions before infection, incubation with HSV-1, simultaneously with infection and after infection was reduced by 0.42, 3.42, 1.83, and 0.83 log 10 TCID /ml, respectively. When the bacterial supernatant was first incubated with the virus and then added to the cell, or when it was added simultaneously with the virus, the expression of the UL27, UL52, and UL54 genes decreased significantly (p<0.05). When the bacterial supernatant is added to the cell before or after virus infection, the expression of UL52 and UL54 genes does not change significantly (P>0.05).

The study findings indicated that the supernatant of L. reuteri has a potent anti-HSV-1 effect especially if it is incubated with the virus before inoculation into the cell. Its possible antiviral mechanism is to inhibit the virus by binding to it or changing the surface structure of the virus. Metabolites of L. reuteri can be considered as a novel inhibitor of HSV-1in- fection.

Colorectal cancer (CRC) is a common type of cancer that has a high death rate and is be- coming more common in developed countries. Currently, there are several treatment options available for CRC patients, and clinical trials are being conducted to improve conventional therapies. This study investigates the combined impact of Bacillus coagulans (B.C) and Newcastle disease virus (NDV) on the growth of human colorectal adenocarcinoma cells (HT29 cell line).

The HT29 cell line was cultured under controlled laboratory conditions. They were treated with Fluorouracil (5-FU), NDV, and B.C., after which various assessments were conducted to determine the effects of these treat- ments. These assessments included MTT assay for cytotoxicity, evaluation of cell viability, and measurement of caspase 8 and 9 activity levels. The significance of the data was determined at a threshold of P<0.05 following analysis.

The usage of NDV and B.C significantly increased cell death and reduced cell growth in the HT29 cell line, when compared to the control group. Moreover, the combined application of NDV and B.C along with 5-FU exhibited a synergistic effect in decreasing the proliferation of HT29 cells. Additionally, the results indicated that intrinsic apoptosis pathway was activated by B.C and NDV.

It appears that utilizing oncolytic viruses (OV) and bacteria in conjunction with chemotherapy drugs could potentially aid in reducing the growth of colorectal cancer cells. However, further research is necessary, including animal studies, to confirm the efficacy of this treatment method.

Multiple outbreaks over two decades and a high mortality rate have emphasized the Nipah virus (NiV) as a priority research area. The study focuses on identifying the mutational landscape in sequences from NiV human isolates from different geographical regions.

Thirty-seven NiV genomes of human samples from Malaysia, Bangladesh, and India were subject- ed to phylogeny and metagenomic analysis to decipher the genome variability using MEGA11 software and the meta-CATS web server. Using the Single-Likelihood Ancestor Counting method, the synonymous and nonsynonymous mutations among NiV genes were identified. Further, the nonsynonymous variations were used to identify mutations in all the NiV proteins.

The NiV isolates were categorized into NiV-M, NiV-B, and NiV-I clades based on phylogenetic analysis. Metag- enomic analysis revealed 1636 variations in the noncoding and coding regions of the genomes of the three clades of NiV. Further analysis of nonsynonymous mutations showed the phosphoprotein to be highly mutating, whereas the matrix protein was stable.

Deciphering the mutation pattern using a comparative genomics approach for human isolates provided valuable insight into the stability of NiV proteins which can be further used for understanding variations in host-pathogen interaction and developing effective therapeutic measures.

Host genetic changes like single nucleotide polymorphisms (SNPs) are one of the main fac- tors influencing susceptibility to viral infectious diseases. This study aimed to investigate the association between the host SNP of Toll-Like Receptor3 (TLR3) and Toll-Like Receptor7 (TLR7) genes involved in the immune system and susceptibil- ity to COVID-19 in a sample of the Iranian population.

This retrospective case-control study evaluated 244 hospitalized COVID-19 patients as the case group and 156 suspected COVID-19 patients with mild signs as the control group. The genomic DNA of patients was gen- otyped for TLR7 (rs179008 and rs179009) and TLR3 (rs3775291 and rs3775296) SNPs using the polymerase chain reac- tion-restriction fragment length polymorphism (PCR-RFLP) method.

A significant association between rs179008 SNP in the TLR7 gene and the susceptibility of COVID-19 was found between case and control groups. The AT genotype (Heterozygous) of TLR7 rs179008 A>T polymorphism showed a sig- nificant association with a 2.261-fold increased odds of COVID-19 (P=0.003; adjusted OR: 2.261; 99% CI: 1.117-4.575). In addition, a significant association between TC genotype of TLR7 rs179009 T>C polymorphism and increased odds of COVID-19 (P< 0.0001; adjusted OR: 6.818; 99% CI: 3.149-14.134) were determined. The polymorphism frequency of TLR3 rs3775291 and rs3775296 genotypes were not significantly different between the case and control groups (P> 0.004167).

SNPs in TLR7 rs179008 and rs179009 genotypes are considered host genetic factors that could be influenced individual susceptibility to COVID-19. The SNPs in TLR3 (rs3775296 and rs3775291) showed no significant association with COVID-19 in Iranian population.

This study aimed to compare the production of antibodies in three different groups of patients with COVID-19. These groups included patients with pulmonary and cerebral symptoms, as well as those with mild symp- toms.

Blood samples were collected from 80 patients admitted to COVID-19-specific hospitals. The pa- tients had various forms of SARS-CoV-2 disease, including those with pulmonary symptoms, brain involvement, and those with positive PCR test results but mild symptoms. The enzyme-linked immunosorbent assay (ELISA) technique was used to determine the levels of IgM and IgG antibody titers.

The levels of IgM and IgG antibody production differed significantly between groups of patients experiencing pul- monary symptoms and cerebral symptoms, with mild symptom patients also showing differences (P=0.0068), (P=0.0487), (P<0.0001), and (P=0.0120), respectively. Furthermore, there was no significant relationship between IgM antibody secre- tion and age or pulmonary involvement (P=0.1959). However, there was a direct and significant relationship between age and brain involvement (P=0.0317).

The findings of this study revealed that the risk of central nervous system involvement increases with age and that older people have lower antibody levels than younger people. Consequently, strengthening the immune systems of peo- ple over the age of 78 during this pandemic through vaccination and nutrition is very effective in reducing mortality in this age group.

In India, it is estimated that there are 40 million people suffering from Hepatitis B virus (HBV). Quantification of the viral burden is an important laboratory tool in the management. However, widespread use of different HBV-DNA assays is still affected by the high cost and variable diagnostic precision. The present study was conduct- ed to evaluate the diagnostic precision and co-relation of ALT levels with HBV-DNA by Truenat®-PCR.

In this prospective cross-sectional study a total of 567 serums were collected from patients by rapid HBsAg, and processed for liver function tests (LFT). The viral HBV-DNA amplification detection was carried out through by Truenat®-PCR test.

Out of 567 samples, 452 samples were found to be positive by both rapid and Truenat®-PCR and 106 were negative for HBV-DNA followed by 9 invalid. High ALT level found in 73% of positive patients who had HBV-DNA level (>100000 copies/ml) which is significantly higher in 447 patients as compared to those have below ≤100000 copies/ml.

Truenat®-PCR technique is a highly sensitive and can be performed with low resources for effective control of HBV infection. Evaluation of HBV-DNA levels and serum ALT levels showed a significant proportion of patient harbored ongoing viral replication and disease progression.

Infectious agents are considered one of the possible etiological factors of systemic lupus ery- thematosus (SLE). It has been suggested that human herpesvirus type 6 (HHV-6) may trigger autoimmune disorders, but few studies have been conducted on the relationship between this virus and autoimmune diseases, especially SLE. The present study aimed to compare the frequency of HHV-6 infection between SLE patients and healthy individuals.

Serum samples were collected from 60 healthy people and 60 SLE patients referred to the rheu- matology clinic of Shahid-Beheshti Hospital, Kashan, Iran, from January 2020 to January 2021. The following data were collected from the medical records of patients: sex; age; duration of disease; SLE clinical manifestations; and disease activ- ity. After the extraction of viral DNA from samples, a nested polymerase chain reaction (PCR) test was performed to detect HHV-6.

HHV-6 was detected in 12 SLE patients (20%) and in 8 healthy individuals (13.3%). A significant correlation was not obtained between SLE and the presence of HHV-6 (P = 0.09). There was no correlation between musculoskeletal involvements, skin lesions, renal manifestations, and hematological manifestations with the presence of HHV-6 (P˃0.05). HHV-6 was detected more frequently in patients with active lupus than in patients with quiescent disease, but this difference was not significant (P=0.08).

Although patients with SLE had a higher prevalence of HHV-6 compared with healthy people, there is no strong link between HHV-6 infection and SLE. Future research is necessary because this data does not support the hypothesis that human herpesvirus 6 plays a role in the pathogenesis of SLE.

Fusarium spp. is an emerging pathogen that presents with varied clinical presentations but there are very few studies from India that elaborate on the spectrum of infection caused by the fungus. Hence, the present study was conducted in our institute to understand the clinical spectrum of fusariosis.

The present study was a retrospective study conducted at a tertiary care institute, in Hyderabad, Telangana, India for four years from January 2018 to December 2022. All the patients with clinically significant isolation of Fusarium spp. from various samples were included in the study.

There were 25 cases of fusariosis diagnosed during the study period. Fusarium was isolated predominantly from debrided tissue following road traffic accidents in 12/25 (84%) of the cases, nails in 3/25 (12%) and superficial leg ulcer in 1/25 (4%) of the cases. Speciation was done for four patients. Three were Fusarium incarnatum and one was Fusarium solani. The patients were treated surgically and with/without antifungal therapy and were discharged in a stable condition.

Traumatic injuries were the major cause of infections in the present study. As Fusarium is a virulent and highly resistant pathogen, an early suspicion and an appropriate diagnosis would lead to a better outcome in these patients.

Extra-intestinal salmonellosis is associated with higher case fatality and is underestimated in the developing countries like India. Here we present a case series of bacteriologically proven extra-intestinal salmonellosis managed at our institute over the past two years.

Retrospective analysis of bacteriologically proven extra-intestinal salmonellosis over two years between January 2020 to December 2021 was carried out. Medical records were reviewed for site of infection, evidence of any underlying or predisposing illnesses and antimicrobial susceptibility report.

Eight patients were diagnosed with extra-intestinal salmonellosis. Male to female ratio was 3:1. Mean age was 44 years. Four were typhoidal and four were nontyphoidal Salmonellae. The extra-intestinal sites involved were purulent aspi- rates from scrotum, caecum, perianal region, intraperitoneal collection, synovium, and urine. Predisposing factors include chronic myeloid leukemia, HIV and gastric malignancy. All deep seated abscess required surgical intervention. All typhoidal Salmonella (n=4) were sensitive to cotrimoxazole, ampicillin, ceftriaxone. Among nontyphoidal Salmonella, one was resis- tant to cotrimoxazole; two were resistant to ampicillin, ceftriaxone and three resistant to ciprofloxacin.

The diagnosis of extra-intestinal salmonellosis requires a high degree of clinical suspicion and should be in- cluded in the differential diagnosis in patients with deep-seated abscesses.

We present a case of a 43-year-old immunocompromised female patient diagnosed with disseminated histoplasmosis on bone marrow examination, at clinical laboratory of Kasturba Hospital, Manipal, Karnataka, India. The patient, presenting with symptoms like weight loss, appetite loss, and pancytopenia, underwent bone marrow aspiration and biopsy. The bone marrow studies revealed HIV-associated changes and the yeast form of Histoplasma capsulatum, confirming disseminated histoplasmosis. Bone marrow examination is highlighted as a diagnostic tool with significant sensitivity in such cases. The report stresses on the importance of awareness and early diagnosis of histoplasmosis in immunocompromised patients, given its potential lethality and the need for timely therapeutic intervention for better prognosis.