Gut-Lung Microbiota Characterization in Patients with Non-Small Cell Lung Carcinoma and COVID-19 Coinfection.

BACKGROUND: Non-small cell lung cancer (NSCLC) patients with COVID-19 have an excessive chance of morbidity and mortality. The fecal-nasopharyngeal microbiota compositions of NSCLC patients were assessed in this study. METHODS: In total, 234 samples were collected from 17 NSCLC patients infected with COVID-19, 20 NSCLC patients without confirmed COVID-19, 40 non NSCLC patients with COVID-19, and 40 healthy individuals. RESULTS: In lung microbiota, the abundance of Streptococcus spp. in NSCLC patients with confirmed COVID-19 was significantly higher than the two control groups. Pseudomonas aeruginosa and Staphylococcus aureus were listed as the most frequent pulmonary bacterial groups that colonized COVID-19 patients. In fecal specimens, the numbers of Bacteroidetes, Firmicutes, and Actinobacteria phyla were significantly higher amongst NSCLC patients with COVID-19. NSCLC patients infected with COVID-19 showed lower levels of Lactobacillus spp., Akkermansia muciniphila, and Bifidobacterium spp. The counts of Streptococcus spp., in NSCLC patients with COVID-19 were significantly higher than those of healthy individuals (8.49±0.70 log CFU/g wet feces vs 8.49±0.70 log CFU/g wet feces). Prevotella spp. were enriched in the gut and respiratory tracts of COVID-19 patient groups. The unbiased analysis showed an increment in Enterococcus spp., Streptococcus spp., and Prevotella spp. CONCLUSION: Eventually, it was found that compared to control groups, COVID-19 patients with NSCLC showed diminished gut bacteria diversity and increase in Lactobacillus spp., A. muciniphila, and Bifidobacterium spp. The overgrowth of Enterococcus spp., Streptococcus spp., and Prevotella spp. could be potential predictive biomarkers in the gut-lung axis of NSCLC patients with COVID-19.

Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations.

BACKGROUND: Global real-time monitoring of SARS-CoV-2 variants is crucial to controlling the COVID-19 outbreak. The purpose of this study was to set up a Sanger-based platform for massive SARS-CoV-2 variant tracking in laboratories in low-resource settings. METHODS: We used nested RT-PCR assay, Sanger sequencing and lineage assignment for 930-bp of the SARS-CoV-2 spike gene, which harbors specific variants of concern (VOCs) mutations. We set up our platform by comparing its results with whole genome sequencing (WGS) data on 137 SARS-CoV-2 positive samples. Then, we applied it on 1028 samples from March-September 2021. RESULTS: In total, 125 out of 137 samples showed 91.24% concordance in mutation detection. In lineage assignment, 123 out of 137 samples demonstrated 89.78% concordance, 65 of which were assigned as VOCs and showed 100% concordance. Of 1028 samples screened by our in-house method, 78 distinct mutations were detected. The most common mutations were: S:D614G (21.91%), S:P681R (12.19%), S:L452R (12.15%), S:T478K (12.15%), S:N501Y (8.91%), S:A570D (8.89%), S:P681H (8.89%), S:T716I (8.74%), S:L699I (3.50%) and S:S477N (0.28%). Of 1028 samples, 980 were attributed as VOCs, which include the Delta (B.1.617.2) and Alpha (B.1.1.7) variants. CONCLUSION: Our proposed in-house Sanger-based assay for SARS-CoV-2 lineage assignment is an accessible strategy in countries with poor infrastructure facilities. It can be applied in the rapid tracking of SARS-CoV-2 VOCs in the SARS-CoV-2 pandemic.

Epidemiology of Bloodstream Infections and Antimicrobial Susceptibility Pattern in ICU and Non-ICU Wards: A Four-Year Retrospective Study in Isfahan, Iran.

Background: Bloodstream infections (BSIs) are one of the causes of morbidity and mortality in hospitalised patients. This study evaluated BSI's incidence, trend, antimicrobial susceptibility patterns and mortality in AL Zahra Hospital in Isfahan, Iran. Materials and Methods: This retrospective study was conducted in AL Zahra Hospital from March 2017 to March 2021. The Iranian nosocomial infection surveillance system was used for data gathering. The data included demographic and hospital data, type of bacteria, and antibiotic susceptibility findings and were analysed in SPSS-18 software. Results: The incidence of BSIs was 1.67% and 0.47%, and the mortality was 30% and 15.2% in the intensive care unit (ICU) and non-ICU wards, respectively. In the ICU, the mortality was correlated with the use of the catheter, type of organism and year of study, but in non-ICU, correlated with age, gender, use of the catheter, ward, year of study and duration between the incidence of BSIs and discharging/death. Staphylococcus epidermidis, Acinetobacter spp. and Klebsiella spp. were the most frequent germs isolated in all wards. Vancomycin (63.6%) and Gentamycin (37.7%) for ICU and Vancomycin (55.6%) and Meropenem (53.3) for other wards were the most sensitive antibiotics. Conclusion: Despite the few rate of BSI in the last four years in AL Zahra Hospital, our data showed that its incidence and mortality in the ICU ward are significantly more than in other hospital wards. We recommend prospective multicentre studies to know the total incidence of BSI, local risk factors and patterns of pathogens causing BSI.

Efficacy of plasmapheresis in neutropenic patients suffering from cytokine storm because of severe COVID-19 infection.

Background: With the emergence of the coronavirus disease 2019 (COVID-19) and inability of healthcare systems to control the disease, various therapeutic theories with controversial responses have been proposed. Plasmapheresis was administered as a medication. However, the knowledge of its efficacy and indications is inadequate. This study evaluated the use of plasmapheresis in critically ill patients with cancer. Methods: This randomized clinical trial was conducted on 86 patients with malignancies, including a control group (N=41) and an intervention group (N=45) with severe COVID-19 during 2020-21. Both groups were treated with routine medications for COVID-19 management according to national guidelines, and plasmapheresis was applied to the intervention group. C-reactive protein (CRP), D-dimer, ferritin, lactate dehydrogenase, hemoglobin, and white blood cell, polymorphonuclear, lymphocyte, and platelet levels were measured at admission and at the end of plasmapheresis. Other variables included neutrophil recovery, intensive care unit admission, intubation requirements, length of hospital stay, and hospitalization outcomes. Results: CRP(P<0.001), D-dimer (P<0.001), ferritin (P=0.039), and hemoglobin (P=0.006) levels were significantly different between the groups after the intervention. Neutrophil recovery was remarkably higher in the case than in the control group (P<0.001). However, plasmapheresis did not affect the length of hospital stay (P=0.076), which could have significantly increased survival rates (P<0.001). Conclusion: Based on the study findings, plasmapheresis led to a significant improvement in laboratory markers and survival rate in patients with severe COVID-19. These findings reinforce the value of plasmapheresis in cancer patients as a critical population suffering from neutropenia and insufficient immune responses.

SARS-CoV-2 Seroprevalence among Health-Care Workers in Isfahan, Iran.

Background: Health-care workers (HCWs) are in the frontline for fighting the coronavirus disease 2019 (COVID-19) pandemic and are at higher risk of acquiring the infection. Therefore, the defining immunity status among HCWs helps mitigate the exposure risk. In this study, we investigated the anti-SARS-CoV-2 immunoglobulin G (IgG) and immunoglobulin M (IgM) and also the associated risk factors in the HCWs working in Isfahan University of Medical Sciences COVID-19 referral hospitals. Materials and Methods: In a cross-sectional study, demographics, COVID-19 symptoms during the past 2 weeks, and health-care details were collected from 200 consenting health workers of COVID-center-hospitals of Isfahan University of Medical Sciences from 23 October to 21 December 2020. The recombinant SARS-CoV2 nucleocapsid protein enzyme-linked immunosorbent assay-based IgM, and IgG antibody tests were evaluated. Data were analyzed using Chi-square and independent-t-student tests, and P < 0.05 was considered significant. Results: One hundred and forty-one women and 59 men with a mean age of 36.4 ± 7.77 years participated in the study. IgG Ab and IgM Ab were positive in 77 (38.5%) and 12 (6%) of samples, respectively, and both antibodies were detected in 9 (4.5%). Higher ages, direct contact with the patients with COVID-19, muscle pain, loss of taste and smell, fever, and cough were the factors associated with antibody seropositivity against SARS-CoV2. Conclusion: This study demonstrated that the prevalence of HCWs with antibodies against SARS-CoV-2 is relatively high in Isfahan University referral hospitals. The development of safety protocols and screening and vaccination strategies in the frontline HCWs must be implemented to reduce the burden of infection.

Efficacy of Hydroxychloroquine in Pre-exposure Severe Acute Respiratory Syndrome Coronavirus 2 Prophylaxis among High-Risk HealthCare Workers: A Multicenter Study.

Background: Prophylaxis could be an established strategy to potentially prevent and control infectious diseases and should be considered in the coronavirus disease 2019 (COVID-19) pandemic. The present study aimed to assess the effectiveness of hydroxychloroquine as a prophylaxis treatment strategy in the reduction of the risk of COVID-19 among health professionals. Materials and Methods: The health professionals were randomly assigned (1:1) to the control group without receiving any hydroxychloroquine as prophylaxis and the hydroxychloroquine group receiving a weekly hydroxychloroquine dose of 400 mg up to 12 weeks. Results: A total of 146 health professionals were randomly enrolled in this study between August 11 and November 11 in 2020. Among the screened health professionals, 21 (14.6%) were infected with COVID-19 during the 12 weeks, and 14 (66.6%) out of the 21 health professionals were in the control group. Most participants with COVID-19 had mild symptoms (62%). In addition, 9.5% (n = 2) of the participants suffered from moderate disease and 28.5% were diagnosed with severe symptoms. In the hydroxychloroquine group, 5 (7.1%) and 2 (2.8%) participants were reported with mild and moderate symptoms of COVID-19, respectively, and 2 participants had moderate, 8 (10.9%) participants had mild symptoms, and 6 (8.2%) participants had severe symptoms in the control group, within 3 months. Severe symptoms of COVID-19 were not observed in the hydroxychloroquine group. Conclusion: This study addressed the effect and benefit of hydroxychloroquine administration for the prevention of COVID-19 among health professionals. The improved perception of prophylaxis might highlight its important role in future COVID-19 outbreaks to prevent hospital transmission, which is a major route of spread.

A Process Evaluation of the Isfahan Antibiotic Awareness Campaign: Developing Engagement on Antimicrobial Resistance.

Background: One of the most prominent global health threats is antibiotic resistance, leading to infection treatment failure. The first Iranian antibiotic awareness week campaign was initiated to improve the prudent use and wise prescription of antibiotics. Materials and Methods: The Isfahan antibiotic awareness campaign was held from November 30 to December 6, 2019, among two targeted populations; the general population and health-care workers by Isfahan University of Medical Sciences. In this campaign held in the main squares, streets, and a city's referral hospital, various educational methods were used to aware and sensitize the general population and medical staff about antibiotics and microbial resistance. These methods include face-to-face training, brochures, advertisement posters and billboards around the city, educational videos, social media messages, retraining for medical doctors and medical specialists, and interviewing in the Islamic Republic of Iran Broadcast. Results: Two hundred and twenty general practitioners, medical specialists, and residents participated in two retraining educational conferences in Al-Zahra Hospital, Isfahan, Iran. The mean score satisfaction of the two conferences was three from four. Nearly 2000 of the general population were under face-to-face educational programs whom after that, 83.6% had the correct answer to the questions around antimicrobial awareness. Conclusions: This campaign was an excellent experience as a pilot study with appealing issues. Further, activities are required to improve engagement with the target population and determine the impact of this campaign on antibiotic consumption and prescription behavior among the public and health-care professionals.

Quality of Professional Life and Its Association with Emotional Well-Being among COVID-19 Physicians and Nurses.

Background: The present study was to compare the professional quality of life (ProQOL) and its association with the emotional well-being among the physicians and nurses in contact with COVID-19 patients in Iran and France. Materials and Methods: The study was performed on 903 nurses and physicians in contact with COVID-19 patients in Iran and France.he subjects completed their demographics online and then answered questions addressing their job stress and emotion associated with their contact with COVID-19 patients and ProQOL. Finally, the collected data were analyzed using the SPSS software (ver. 25). Results: According to the results of the present study, the degree of contact with COVID-19 patients had a significant role in compassion satisfaction, burnout, and compassion fatigue, with the coefficient effects of 0.459, 0.688, and 0.433, respectively (P < 0.05). The emotional well-being had a significant role in increasing compassion satisfaction (B = 0.505, P < 0.05). Conclusion: According to the results of the present study, factors such as contact with a COVID-19 patient, emotional well-being, gender, and marital status had a significant effect on dimensions of ProQOL in both Iran and France. Considering that the entire focus of the physicians and nurses is on the health of COVID-19 patients and they have no concentration on improving their emotional state, it seems that supporting them in terms of psychological self-care and considering its indirect impact on the quality of professional performance are of particular significance.

Comparing inhaled colistin with inhaled fosfomycin/tobramycin as an adjunctive treatment for ventilator-associated pneumonia: An open-label randomized controlled trial.

PURPOSE: Although investigations are limited, adjunctive aerosolized antibiotics have been advised in the setting of gram-negative ventilator-associated pneumonia (VAP). This study aimed to compare the efficiency of inhaled colistin with inhaled fosfomycin/tobramycin in treating VAP due to extensively drug-resistant (XDR) Acinetobacter baumannii. METHODS: This single center open-label randomized controlled trial included 60 patients who developed XDR A. bumannii VAP. Eligible participants were randomly assigned to two groups (no. 30). Regardless of the assignment, all participants received meropenem (2 g as a 3-h extended infusion every 8 h) plus intravenous colistin (a loading dose of 9 million IU and then 4.5 million IU every 12 h). The control group was given inhaled colistin (1 million IU every 8 h), and the case group received inhaled tobramycin/fosfomycin (300 mg every 12 h/80 mg every 12 h) as adjunctive therapy. The primary outcome was treatment duration, and the secondary outcomes were Clinical Pulmonary Infection Score (CPIS) trend and mortality rate in the groups. The decision to stop treatment was made by the treating physician. RESULTS: The mean treatment duration was 13.73 ± 3.22 days in the colistin group and 10.85 ± 2.84 days in the tobramycin/fosfomycin group; the mean treatment duration in the latter group was lower significantly (P = 0.001). CPIS was decreased in the groups significantly (P < 0.001), but the mean changes of CPIS were significantly different between the groups, and in the inhaled tobramycin/fosfomycin group, a greater reduction (P = 0.005) was observed. Two (6.67%) patients in the control group and three (10%) patients in the case group died. CONCLUSION: The use of inhaled tobramycin/fosfomycin in cases with XDR A. bumannii VAP was associated with a shorter treatment duration in this open-label trial.

Species distribution and susceptibility profiles of oral candidiasis in hematological malignancy and solid tumor patients.

Oral colonization and infection by Candida species are common in cancer patients receiving chemoradiotherapy, which has significantly increased in recent years. This study aimed to evaluate the frequency, distribution, and antifungal susceptibility profiles of Candida species isolates in patients with hematological malignancy and solid tumors. This study was conducted on a total of 45 cancer patients undergoing treatment with concurrent chemoradiotherapy within 2019-2020. The identification of Candida species was accomplished based on conventional examination and molecular assays. The minimum inhibitory concentrations were determined based on the guidelines of Clinical and Laboratory Standards Institute. The highest prevalence rates of oral candidiasis were observed in patients with chronic lymphoid leukemia (24.4%) and lymphoma (20%). The majority of the patients had oral candidiasis caused by non-albicans Candida species (64.4%). The results of the multiplex PCR for the identification of Candida glabrata, Candida nivariensis, Candida bracarensis, and species-specific Candida parapsilosis complex showed that all isolate amplification products at 397 bp and 171 bp were related to C. glabrata and C. parapsilosis, respectively. There was a significant difference in the Candida species distribution between the hematological malignancies and solid tumors patients. The results of MIC showed that clotrimazole, voriconazole, and caspofungin were the most effective antifungal drugs against oral non-Candida albicans isolates. An understanding of the epidemiology of oral candidiasis among hematological malignancies and solid tumors patients is currently imperative to guide optimal empirical treatment strategies for affected patients.

Overuse of Antibiotics: Who is to Blame? A Qualitative Study.

Background: The irrational use of antibiotics seriously threatens global health. Clinicians undoubtedly play an essential role in consuming antibiotics in hospitals and communities, and their attitudes may help the health system's optimal treatment of antibiotics. In this study, we reported clinicians' experiences with antibiotics used in Isfahan, Iran. Methods: In a qualitative study conducted from October 2020 to March 2021, the experiences of 13 clinicians with different clinical specialties were collected through one-to-one interviews. Participants were selected through purposive sampling until data saturation; data collection was conducted through semi-structured interviews. Conventional content analysis was used to analyze the transcribed interviews. The main category was recognized and subcategorized and coded by three researchers. Results: Eight women and five men with a mean work experience of 12.54 ± 10.047 years participated in the study. All of them worried about the overuse of antibiotics and antibiotic resistance. Clinicians believe that the antimicrobial stewardship committee is not active in our country. Laboratory challenges, healthcare providers, the poor performance of the health system, and marketing and business were the main categories of the study. Subcategrories of main categories included inefficiency in the function of laboratories, harmful profit, challenges in medical education, ups and downs of disease treatment, the unacceptable performance of hospitals, failure to upgrade the health system, threats and opportunities, and jobbery. Conclusions: The participants of this study believed that excessive use of antibiotics is a serious challenge in our country. Physicians were concerned about antibiotic resistance and believed that the pattern of antibiotic resistance was not routinely reported. Therefore, in our region, we should make more efforts to collect data in this field and provide this information to physicians. Also, this study confirmed many obstacles to implementing the antimicrobial stewardship program, and the infrastructure needs strengthening. There is also a need for cultural changes and the views of physicians.

Evaluation of Synbiotics in the Prevention of Ventilator-Associated Pneumonia: A Randomized, Triple-Blind, Placebo-Controlled Clinical Trial.

Background: Ventilator-associated pneumonia (VAP) is one of the most common nosocomial infections. The role of probiotics in preventing VAP is still questionable. This study aimed at evaluating the effect of synbiotic FamiLact 2plus on the prevention of VAP in patients admitted to the intensive care unit (ICU). Methods: A total of 80 mechanically ventilated patients were included and divided into two groups of 40. Group 1 received FamiLact 2plus, and group 2 received placebo. The outcome variables were compared, including the incidence of VAP, the time interval between the onset of ventilation and VAP, the duration of mechanical ventilation, and the length of stay in the ICU. Results: VAP is documented in four patients (10%) in group 1 and 11 patients (27.5%) in group 2 (P = 0.045). The length of stay in the ICU in group 1 was significantly shorter than in group 2, and the time interval between the start of intubation and the onset of VAP in group 1 was longer than in the placebo group. During the intervention, 15 patients in group 1 (37.5%) and 26 patients in group 2 (65%) developed diarrhea, which was a significant difference (P = 0.02). Conclusions: Synbiotic is associated with a reduction in the incidence of VAP as well as a reduction in ICU stay and delayed VAP.

Association of Clinical Features with Spike Glycoprotein Mutations in Iranian COVID-19 Patients.

BACKGROUND: Mutations in spike glycoprotein, a critical protein of SARS-CoV-2, could directly impact pathogenicity and virulence. The D614G mutation, a non-synonymous mutation at position 614 of the spike glycoprotein, is a predominant variant circulating worldwide. This study investigated the occurrence of mutations in the crucial zone of the spike gene and the association of clinical symptoms with spike mutations in isolated viruses from Iranian patients infected with SARS-CoV-2 during the second and third waves of the COVID-19 epidemic in Isfahan, the third-largest city in Iran. METHODS: The extracted RNA from 60 nasopharyngeal samples of COVID-19 patients were subjected to cDNA synthesis and RT-PCR (in three overlapping fragments). Each patient's reverse transcriptase polymerase chain reaction (RT-PCR) products were assembled and sequenced. Information and clinical features of all sixty patients were collected, summarized, and analyzed using the GENMOD procedure of SAS 9.4. RESULTS: Analysis of 60 assembled sequences identified nine nonsynonymous mutations. The D614G mutation has the highest frequency among the amino acid changes. In our study, in 31 patients (51.66%), D614G mutation was determined. For all the studied symptoms, no significant relationship was observed with the incidence of D614G mutation. CONCLUSIONS: D614G, a common mutation among several of the variants of SARS-CoV-2, had the highest frequency among the studied sequences and its frequency increased significantly in the samples of the third wave compared to the samples of the second wave of the disease.

Vitamin D Level in Laboratory Confirmed COVID-19 and Disease Progression.

OBJECTIVE: There is no conclusive evidence to suggest vitamin D level can prevent or treat infection with the new coronavirus disease 2019. This study aimed to investigate the effects of serum level of vitamin D in patients with coronavirus disease 2019 on death, severity, and hospitalization duration. MATERIALS AND METHODS: Baseline characteristic of patients was extracted from the Isfahan coronavirus disease 2019 registry database (I-CORE). Blood samples were taken from all patients to measure the level of vitamin D (25-hydroxyvitamin D) and categorized. The effect of 25(OH) D on death, severity, and hospitalization duration was analyzed by logistic regression. RESULTS: Among our study patients, 5.5% had a severe deficiency of vitamin D, 23.7% deficiency, and 24.8% insufficiency. Of the 107 patients who died, 7.5% were severely deficient in vitamin D. We found that vitamin D deficiency had no significant effect on death, disease severity, and hospitalization (P > .05). However, having at least one comorbidity increased the odds of death five times after adjusting age > 60 years and gender (P < .0001). The results showed that among all comorbidities, diabetes has the greatest impact on the outcomes as it raised the odds of death, disease severity, and length of hospital stay by 2.23,1.72, and 1.48, respectively, after controlling the age > 60 and gender (P = .0002, P=.08, P=.012). CONCLUSIONS: The mortality, disease severity, and hospitalization of coronavirus disease 2019 patients seem to be not affected by the low levels of 25(OH)D. However, the synergy between vitamin D levels and comorbidities, age, and gender could affect the outcome of coronavirus disease 2019 patients.

The correlation between viral shedding duration and blood biomarkers in COVID-19-infected patients.

Background: Since December 2019, the world is struggling with an outbreak of coronavirus disease-2019 (COVID-19) infection mostly represented as an acute respiratory distress syndrome and has turned into the most critical health issue worldwide. Limited information is available about the association between dynamic changes in the naso/oropharyngeal viral shedding in infected patients and biomarkers, aiming to be assessed in the current study. Materials and Methods: This quasi-cohort study was conducted on 31 patients with moderate severity of COVID-19 manifestations, whose real-time polymerase chain reaction (RT-PCR) test was positive for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) RNA at baseline. RT-PCR was rechecked for patients every 3-4 days until achieving two negative ones. In parallel, biomarkers, including lymphocyte count, lactate dehydrogenase (LDH), and C-reactive protein (CRP), were assessed every other day, as well. Viral shedding also was assessed. Results: Spearman's correlation test revealed a significant direct correlation between the viral shedding from the symptom onset and the time, in which CRP (P = 0.0015, r = 0.54) and LDH (P = 0.001, r = 0.6207) return to normal levels after symptom onset, but not for lymphocyte count (P = 0.068, r = 0.34). Conclusion: Based on the current study's findings, the duration of SARS-CoV-2 RNA shedding was directly correlated with the required time for LDH and CRP return to normal levels. Therefore, these factors can be considered the determinants for patients' discharge, isolation, and return to social activities; however, further investigations are required to generalize the outcomes.

A Nationwide Study on the Seroprevalence of Measles, Mumps, and Rubella in Iranian Children and Adolescents.

Background: Assessing the prevalence of infections, which are preventable by vaccination, is crucial to monitor the vaccination program efficacy, and it can demonstrate the gaps in population immunity. The current study attempted to assess the specific Immunoglobulin (IgG) antibody against measles, mumps, and rubella (MMR) in Iranian children and adolescents, years after their vaccination. Methods: This cross-sectional study was conducted in Iran. Serum samples of 2100 students, aged 7-18 years, included in a national health survey, were tested for MMR antibodies by ELISA assay. Multistage random cluster sampling was used to select subjects from 30 provinces in Iran. Results: Overall, 1871, 1718, and 1678 serums were tested for measles, mumps, and rubella antibodies, respectively. The prevalence of positive test was 1231 (65.8%) for measles, 1327 (77.2%) for mumps and 1344 (80.1%) for rubella. Conclusion: Despite high vaccination coverage in Iran, IgG antibody against measles, mumps, and rubella was not detected in a considerable proportion of children and adolescents aged 7-18 years. In case of contacts with residents of other countries, where measles or rubella have not yet been eliminated, it may create problems for Iranian children.

Evaluation of Virulence Factors, Antibiotic Resistance, and Biofilm Formation of Escherichia coli Isolated from Milk and Dairy Products in Isfahan, Iran.

Diarrheagenic E. coli (DEC) strains are important causes of gastrointestinal diseases worldwide, especially in developing countries. This study aimed to investigate the presence, antibiotic resistance, and potential biofilm formation in dairy products in Isfahan, Iran. A total of 200 samples, including traditional and pasteurized dairy products, were analyzed. In 200 samples, 54 E. coli isolates, including (48/110) and (6/90) positive samples of traditional and pasteurized dairy products, were detected. Furthermore, pathogenic strains were isolated from 30% of traditional dairy products and 5.55% of pasteurized dairy products. Most isolates were classified as enteropathogenic E. coli (EPEC). Moreover, antibiotic resistance was evaluated using the disk diffusion method for pathogenic E. coli. Overall, 73.68% of contaminated samples by pathogenic strains were resistant to at least one antibiotic. The highest resistance was observed against streptomycin (57.9%), followed by tetracycline (50%). Additionally, all isolates were sensitive to amikacin. For evaluating biofilm formation, the violet crystal assay was applied on a polystyrene microplate well for pathogenic isolates. In total, 68.42% of isolates were able to form biofilms. The presence of E. coli in dairy products indicates potential health risks for Iranian consumers. Serious measures are needed to control and prevent the spread of this pathogen.

Disease Waves of SARS-CoV-2 in Iran Closely Mirror Global Pandemic Trends.

BACKGROUND: Complete SARS-CoV-2 genome sequencing in the early phase of the outbreak in Iran showed two independent viral entries. Subsequently, as part of a genome surveillance project, we aimed to characterize the genetic diversity of SARS-CoV-2 in Iran over one year after emerging. METHODS: We provided 319 SARS-CoV-2 whole-genome sequences used to monitor circulating lineages in March 2020-May 2021 time interval. RESULTS: The temporal dynamics of major SARS-CoV-2 clades/lineages circulating in Iran is comparable to the global perspective and represent the 19A clade (B.4) dominating the first disease wave, followed by 20A (B.1.36), 20B (B.1.1.413), 20I (B.1.1.7), leading the second, third and fourth waves, respectively. We observed a mixture of circulating B.1.36, B.1.1.413, B.1.1.7 lineages in winter 2021, paralleled in a fading manner for B.1.36/B.1.1.413 and a growing rise for B.1.1.7, prompting the fourth outbreak. Entry of the Delta variant, leading to the fifth disease wave in summer 2021, was detected in April 2021. This study highlights three lineages as hallmarks of the SARS-CoV-2 outbreak in Iran; B4, dominating early periods of the epidemic, B.1.1.413 (B.1.1 with the combination of [D138Y-S477N-D614G] spike mutations) as a characterizing lineage in Iran, and the co-occurrence of [I100T-L699I] spike mutations in half of B.1.1.7 sequences mediating the fourth peak. It also designates the renowned combination of G and GR clades' mutations as the top recurrent mutations. CONCLUSION: In brief, we provided a real-time and comprehensive picture of the SARS-CoV-2 genetic diversity in Iran and shed light on the SARS-CoV-2 transmission and circulation on the regional scale.