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Introduction This study aimed to determine the prevalence of multidrug-resistant Gram-negative bacteria (GNB) from blood cultures in a tertiary-care hospital and the multiplex PCR assay's ability to detect resistance genes. Methods A total of 388 GNB isolates obtained from hospitalized patients between November 2019 and November 2021 were included in the study. Antimicrobial susceptibility testing was done by VITEK 2 system and broth microdilution method. Beta-lactamase-encoding genes were detected by multiplex PCR assays, BioFire-Blood Culture Identification 2 (BCID2) panel (bioMerieux, France). Extended-spectrum beta-lactamases (ESBLs) were detected phenotypically with VITEK AST-GN71 card (bioMerieux, France). The isolates of GNB were classified into multidrug-resistant, extensively-drug-resistant, and pandrug-resistant categories, and their prevalence and distribution in different wards, including coronavirus diseases 2019 (COVID-19) intensive care units (ICU), were calculated. Results Results revealed that all isolates of Acinetobacter baumannii and Pseudomonas aeruginosa were multidrug-resistant as well as 91.6% of Enterobacter cloacae, 80.6% of Proteus mirabilis, and 76.1% of Klebsiella pneumoniae, respectively. In fermentative bacteria, blaOXA-48-like (58.1%), blaNDM (16.1%), blaKPC (9.7%) and blaVIM (6.5%) genes were detected. More than half of Enterobacter cloacae (58.3%) and Klebsiella pneumoniae (53.7%) produced ESBLs. Among non-fermenters, the blaNDM gene was carried by 55% of Pseudomonas aeruginosa and 19.5% of Acinetobacter baumannii. In the COVID-19 ICU, Acinetobacter baumannii was the most common isolate (86.1%). Conclusions This study revealed high proportions of multidrug-resistant blood isolates and various underlying resistance genes in Gram-negative strains. The BCID2 panel seems to be helpful for the detection of the most prevalent resistance genes of fermentative bacteria.Copyright © GERMS 2022.
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OBJECTIVE: To analyze the role of nosocomial infection informatics surveillance system in the prevention and control of multidrug-resistant organisms(MDROs) infections. METHODS: The First Affiliated Hospital of Guangdong Pharmaceutical University was selected as the study subjects, which had adopted the nosocomial infection informatics surveillance system since Jan.2020. The period of Jan.to Dec.2020 were regarded as the study period, and Jan.to Dec.2019 were regarded as the control period. The situation of nosocomial infection and MDROs infections in the two periods were retrospectively analyzed. RESULTS: The incidence of nosocomial infections and underreporting of nosocomial infection cases in this hospital during the study period were 2.52%(1 325/52 624) and 1.74%(23/1 325), respectively, and the incidences of ventilator associated pneumonia(VAP), catheter related bloodstream infection(CRBSI), catheter related urinary tract infection(CAUTI)were 4.10(31/7 568), 2.11(14/6 634), and 2.50(25/9 993) respectively, which were lower than those during the control period(P< 0.05). The positive rate of pathogenic examination in the hospital during the study period was 77.95%(1 269/1 628), which was higher than that during the control period(P<0.05), the overall detection rate of MDROs was 15.77%(206/1 306), the detection rates of MDROs in Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, Staphylococcus epidermidis, Pseudomonas aeruginosa and Staphylococcus aureus were lower than those during the control period(P<0.05). CONCLUSION: The development and application of the informatics technology-based surveillance system of nosocomial infection could effectively reduce the incidence of nosocomial infections and device related infections, decrease the under-reporting of infection cases, and also reduce the detection rate of MDROs as well as the proportion of MDROs detected in common pathogenic species.
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Objectives: In COVID-19 associated acute respiratory distress syndrome (ARDS) requiring VV-ECMO, ventilator-associated-pneumonia (VAP), pulmonary aspergillosis and viral reactivations are observed frequently, but there is only little knowledge on incidence, onset and causative pathogens. This study analyzes frequency of VAP, pulmonary aspergillus infections, and viral reactivations in a large cohort of patients with ARDS treated with VV-ECMO due to either COVID-19 or Influenza. Method(s): Retrospective analysis of all consecutively patients at the University Hospital Regensburg requiring VVECMO due to COVID-19 (March 2020 and May 2022) or Influenza (May 2012 and December 2022). VAP was diagnosed according to current guidelines. Pulmonary Aspergillosis met criteria of probable COVID-associated Aspergillosis according to current guidelines. Result(s): 147 patients (age (median [IQR]) 55.3 [48.7 - 61.7], SOFA at VV-ECMO initiation 9 [8 - 12], 23 [14 - 38] days on VV-ECMO) suffering from COVID-19 and 72 influenza patients (age 55.3 [46 - 61.3], SOFA at VV-ECMO initiation 13 [10 - 15], 16 [10 - 23] days on VV-ECMO) were included in the analysis. Pulmonary superinfections were more frequent in COVID-19 than in influenza (VAP: 61% vs. 39%, pulmonary Aspergillosis: 33% vs. 22%, CMV reactivation: 19% vs. 4%, HSV reactivation: 49% vs. 26%.) The first episode of VAP in COVID-19 and Influenza was detected 2 days [1 - 15] after and 1 day (-3 - 22) before ECMO initiation, respectively. First VAP-episode in COVID-19 were mainly caused by Klebsiella spp. (29%,), Staphylococcus aureus (27%) and E. coli (11%). Further VAP-episodes (30% in COVID-19) and relapses of VAP were mainly caused by Klebsiella spp. (53%, 64%, respectively). In Influenza, VAP was mainly caused by Staphylococcus aureus (28%) and Streptococcus pneumoniae(28%), further VAP episodes were not observed. Conclusion(s): Superinfections were common in patients treated with VV-ECMO and occur more frequently in COVID-19 ARDS compared to Influenza. VAP occurs early and may significantly contribute to the need of VV-ECMO. Therefore, a meticulous routine microbiologic workup is advisable. The observed differences in the spectrum of secondary infectious agents in COVID19 compared to Influenza are not understood yet.
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Is there an increased incidence of bacteraemia among COVID-19 patients requiring critical care admission who have received IL-6 inhibitors? Introduction: Interleukin-6 (IL-6) inhibitors have been shown to reduce mortality in hospitalised COVID-19 patients. There is, however, concern that induced immunosuppression may increase the risk of secondary nosocomial infection. Objective(s): Our primary aim was to determine if there was increased incidence of bacteraemia in COVID-19 patients requiring critical care admission who had received IL-6 inhibitors compared to those who had not. Method(s): A retrospective review of all COVID-19 admissions to two critical care units in Liverpool from 4th March 2020 to 31st October 2021. Patients were divided into those who received an IL-6 inhibitor (sarilumab or tociluzimab) and those who did not. Hospital antimicrobial policy was to administer a five day prophylactic course of co-amoxiclav and clarithromycin for patients with severe COVID-19 during the study period. Blood culture results from 14 days before admission to critical care and 90 days after admission were included. The blood culture results comprised cultures taken in both critical care and on the wards. Data were linked and analysed using Stata V15.1 (StataCorp, Stata Statistical Software: Release 15, College Station, Texas, USA). Result(s): 894 patients were included in the study. 134 patients had at least one positive blood culture result. The most commonly identified pathogens were Coliforms (23/134, 17.2%), Enterobacter (22/134, 16.4%) and Escherichia coli (16/134, 11.9%). Of patients administered an IL-6 antagonist, 16.8% (114/565) developed a positive blood culture compared to 11.6% (20/172) who did not, p=0.096. We did not observe an increased frequency of antimicrobial resistant culture in the IL-6 administered group 22.8% (26/114) vs. 20.0% (4/20) in this cohort, p=0.781. Data have not been adjusted for demographic and clinical factors in this preliminary analysis. Conclusion(s): We observed a trend toward increased frequency of blood culture positivity in patients administered an IL-6 antagonist within this COVID-19 positive cohort but this was not statistically significant. Further analysis is required to adjust for relevant demographic and clinical factors.
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Amid the COVID-19 pandemic, mask-wearing has become a common practice in the foodservice industry to prevent the spread of respiratory diseases. Like kitchen utensils, a mask may serve as a vehicle for cross-contamination of pathogens during food handling. The objective of this study was to quantify cross-contamination between tasks of handling contaminated chicken and chopping lettuce. Chicken breasts were inoculated with a high or a low level of nonpathogenic Escherichia coli surrogates (ca. 6 or 4 log CFU/ml) and sliced for 1, 5, or 10 min. During slicing, duplicate, single-use medical masks were touched each minute. One mask was immediately sampled, but the second mask was used to contaminate lettuce by touching the mask each minute while chopping the lettuce for 5 min. E. coli were enumerated from the second mask and lettuce. Masks touched while slicing both high- and low-inoculated chicken showed significant contamination (0.8-4.9 log CFU/cm2) after each slicing scenario of 1, 5, or 10 min (P > 0.05). Lettuce was significantly contaminated regardless of inoculation level (1.0-3.2 log CFU/g). Slicing time was a significant factor in some cases (P < 0.05), whereas inoculation level was not (P > 0.05). Data indicate masks can be a source of cross-contamination if not replaced appropriately.
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Background: Neutrophil extracellular traps (NETs) are composed of processed chromatin bound to granular and selected cytoplasmic proteins and released by neutrophils. NETs consist of smooth filaments composed of stacked nucleosomes. Fully hydrated NETs have a cloud-like appearance and occupy a space 10-15-fold larger than the volume of the cells they originate from. DNases are the enzymes that cleave extracellular DNA including NETs. Together with their protective role in microbial infections, NETs are involved in multiple pathological processes and represent key events in a variety of pathologies including cancer, autoimmunity, and cardiovascular disease. Sites of NETs concentration are dangerous for the host if the process of NETs formation becomes chronic or the mechanism of NETs removal does not work. NETosis has been linked to the development of periodontitis, cystic fibrosis, type 2 diabetes, COVID-19 or rheumatoid arthritis as well as cancer progression. Purpose(s): Thus, the destruction of NETs is of primary significance in many pathologies. In our approach, we are focusing on mimicking one of the natural mechanisms of destroying excessive NETs by delivering deoxyribonuclease I to the specific site of pathological NETs accumulation by modifying the nanoparticles using an anti-nucleosome monoclonal antibody (2C5). The antibody is specific to nucleosomes and can recognize histones in NETs. DNase I is U.S. Food and Drug Administration (FDA)-approved active component and is commonly used in therapeutic methods of modern medicine for cystic fibrosis to clear extracellular DNA fibers in the lungs and systemic lupus erythematosus. Recent findings have also shown the effectiveness of DNase I in the digestion of NETs. However, the low serum stability and fast deactivation by environmental stimuli have been considered as the limiting factors for clinical applications of DNase I, which can be overcome by its targeted specific delivery in pharmaceutical nanocarriers. Method(s): In this study, we generate NETs in vitro using human neutrophils and HL-60 cells differentiated into granulocyte-like cells. We used interleukin-8, lipopolysaccharide from E.Coli (LPS), phorbol myristate acetate (PMA), and calcium ionophore A23187 (CI) to generate the NETs. We confirmed the specificity of 2C5 toward NETs by ELISA, which showed that it binds to NETs with the specificity like that for purified nucleohistone substrate. We further utilized that feature to create two delivery systems (liposomes and micelles) for DNAse I enzyme to destroy NETs, which was confirmed by staining NETs with SYTOX Green dye and followed by flow cytometric measurements and microscopic images. Conclusion(s): Our results suggest that 2C5 could be used to identify and visualize NETs and serve as a ligand for NET-targeted diagnostics and therapies. Also, we proved that our carrier can successfully deliver DNase to NETs to provide their degradation.
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Background: Improving basic infection control (IC) practices, diagnostics and anti-microbial stewardship (AMS) are key tools to handle antimicrobial resistance (AMR). Material(s) and Method(s): This is a retrospective study done over 6 years (2016-2021) in an oncology centre in North India with many on-going interventions to improve IC practices, diagnostics and AMS. This study looked into AMR patterns from clinical isolates, rates of hospital acquired infections (HAI) and clinical outcomes. Result(s): Over all, 98,915 samples were sent for culture from 158,191 admitted patients. Most commonly isolated organism was E. coli (n = 6951;30.1%) followed by Klebsiella pneumoniae (n = 5801;25.1%) and Pseudomonas aeroginosa (n = 3041;13.1%). VRE (Vancomycin resistant Enterococcus) rates fell down from 43.5% in Jan-June 2016 to 12.2% in July-Dec 2021, same was seen in CR (carbapenem resistant) Pseudomonas (23.0%-20.6%, CR Acinetobacter (66.6%-17.02%) and CR E. coli (21.6%-19.4%) over the same study period. Rate of isolation of Candida spp. from non-sterile sites also showed reduction (1.68 per 100 patients to 0.65 per 100 patients). Incidence of health care associated infections also fell from 2.3 to 1.19 per 1000 line days for CLABSI, 2.28 to 1.88 per 1000 catheter days for CAUTI. There was no change in overall mortality rates across the study period. Conclusion(s): This study emphasizes the point that improving compliance to standard IC recommendations and improving diagnostics can help in reducing the burden of antimicrobial resistance.Copyright © 2023 Indian Association of Medical Microbiologists
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Introduction: Covid-19 epidemic results from an infection caused by SARS-CoV2. Evolution-based analyses on the nucleotide sequences show that SARS-CoV2 is a member of the genus Beta-coronaviruses and its genome consists of a single-stranded RNA, encoding 16 proteins. Among the structural proteins, the nucleocapsid is the most abundant protein in virus structure, highly immunogenic, with sequence conservatory. Due to a large number of mutations in the spike protein, the aim of this study was to investigate bioinformatics, expression of nucleocapsid protein and evaluate its immunogenicity as an immunogenic candidate. Materials and Methods: B and T cell epitopes of nucleocapsid protein were examined in the IEDB database. The PET28a-N plasmid was transferred to E. coli BL21(DE3) expression host, and IPTG induced recombinant protein expression. The protein was purified using Ni-NTA column affinity chromatography, and the Western blotting method was utilized to confirm it. Finally, mice were immunized with three routes of purified protein. Statistical analysis of the control group injection and test results was carried out by t-test from SPSS software. Results: The optimized gene had a Codon adaptation index (CAI) of 0/97 Percentage of codons having high- frequency distribution was improved to 85%. Expression of recombinant protein in E. coli led to the production of BoNT/B-HCC with a molecular weight of 45 kDa. The total yield of purified protein was 43 mg/L. Immunization of mice induced serum antibody response. Statistical analysis showed that the antibody titer ratio was significantly different compared to the control sample and the antibody titer was acceptable up to a dilution of 1.256000. Conclusion: According to the present study results, the protein can be used as an immunogenic candidate for developing vaccines against SARS-CoV2 in future research.
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The increasing prevalence of antibiotic-resistant bacteria is an emerging threat to global health. The analysis of antibiotic-resistant enterobacteria in wastewater can indicate the prevalence and spread of certain clonal groups of multiresistant bacteria. In a previous study of Escherichia coli that were isolated from a pump station in Norway over 15 months, we found a recurring E. coli clone that was resistant to trimethoprim, ampicillin, and tetracycline in 201 of 3,123 analyzed isolates (6.1%). 11 representative isolates were subjected to whole-genome sequencing and were found to belong to the MLST ST2797 E. coli clone with plasmids carrying resistance genes, including blaTEM-1B, sul2, dfrA7, and tetB. A phenotypic comparison of the ST2797 isolates with the uropathogenic ST131 and ST648 that were repeatedly identified in the same wastewater samples revealed that the ST2797 isolates exhibited a comparable capacity for temporal survival in wastewater, greater biofilm formation, and similar potential for the colonization of mammalian epithelial cells. ST2797 has been isolated from humans and has been found to carry extended spectrum ß-lactamase (ESBL) genes in other studies, suggesting that this clonal type is an emerging ESBL E. coli. Collectively, these findings show that ST2797 was more ubiquitous in the studied wastewater than were the infamous ST131 and ST648 and that ST2797 may have similar abilities to survive in the environment and cause infections in humans. IMPORTANCE The incidence of drug-resistant bacteria found in the environment is increasing together with the levels of antibiotic-resistant bacteria that cause infections. The COVID-19 pandemic has shed new light on the importance of monitoring emerging threats and finding early warning systems. Therefore, to mitigate the antimicrobial resistance burden, the monitoring and early identification of antibiotic-resistant bacteria in hot spots, such as wastewater treatment plants, are required to combat the occurrence and spread of antibiotic-resistant bacteria. Here, we applied a PhenePlate system as a phenotypic screening method for genomic surveillance and discovered a dominant and persistent E. coli clone ST2797 with a multidrug resistance pattern and equivalent phenotypic characteristics to those of the major pandemic lineages, namely, ST131 and ST648, which frequently carry ESBL genes. This study highlights the continuous surveillance and report of multidrug resistant bacteria with the potential to spread in One Health settings.
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Introduction: Liver abscesses are caused by direct spread from peritonitis, biliary tract infection or via hematogenous seeding from a distant source. Most are polymicrobial, however Escherichia coli and Klebsiella pneumoniae are the most common offending pathogens. Patients usually present with pain, fever, and clinical signs of infection. We describe a case of spontaneous liver abscess in a non-toxic patient that recurred 10 years after a previous abscess. Case Description/Methods: A 73-year-old-man with a history of type 2 diabetes mellitus, hypertension, CAD status post CABG and PCI 3 years ago, and abdominal aortic aneurysm status post endovascular aneurysm repair presented with 2 weeks of dark urine. After receiving his COVID-19 booster and influenza vaccinations, he developed flu-like symptoms with a self-resolving fever of 101.8degreeF. He had dark amber urine without dysuria or hematuria. Later, he experienced generalized weakness and decreased oral intake. Outpatient labs showed elevated liver function tests, and he was told to present to the ED. On arrival, he was afebrile with stable vitals. Physical exam was unremarkable. Laboratory evaluation showed a hemoglobin of 11.7 g/dL, sodium of 133 mEq/L, creatinine of 1.4 mg/dL, aspartate aminotransferase of 117 U/L, alanine aminotransferase of 212 U/L, alkaline phosphatase of 825 U/L, total bilirubin of 4.1 mg/dL, and direct bilirubin of 2.1 mg/dL. Triple-phase CT showed a 2.8 cm mass in the right liver lobe with linear enhancement. Ultrasound showed mixed echogenicity measuring 3.6 x 2.9 x 3.3 cm in segment 8 of the liver. On further evaluation, patient had an E. coli abscess diagnosed 10 years prior, managed with antibiotics and drainage. At that time, the abscess was within the right inferior liver lobe, similar to his current abscess. LFTs downtrended. Abscess was aspirated, with culture growing oxidase negative, gramnegative rods, likely E. coli. Patient started on ceftriaxone and metronidazole, to undergo colonoscopy as an outpatient and rule out colonic bacterial translocation. Discussion(s): Pyogenic liver abscess can result in significant morbidity and mortality because of worsening infection and sepsis. Abscesses occur because of spread from adjacent infection or after recent surgeries. Recurrence is very rare. Here, we describe a very unusual case of a pyogenic liver abscess growing E. coli in a non-toxic patient, with the same location and causative organism as an abscess managed 10 years prior. (Figure Presented).
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Antimicrobial resistance is a major threat to human health that is predicted to impact most heavily on sub-Saharan Africa, however there is a lack of clinical outcome data from drug-resistant infections in this setting. There are reasons to expect the COVID-19 pandemic to have both positive and negative impacts on AMR in Africa. We have recruited a series of prospective longitudinal cohorts from Queen Elizabeth Central Hospital (QECH), Blantyre, Malawi and the surrounding communities in the Southern Region of Malawi. The data from these cohorts has been used to describe the aetiology of febrile illness, the burden of antimicrobial resistance in this setting and the distribution of extended spectrum beta-lactamase producing bacteria in humans, animals and the environment. Amongst a cohort of patients presenting to QECH unwell with febrile illness, 67% were living with human immunodeficiency virus (HIV). We identified a diagnosis in 145 of 225 (64%) participants, most commonly tuberculosis (TB;34%) followed by invasive bacterial infections (17%), arboviral infections (13%), and malaria (9%). In a second cohort with drug resistant infection, resistance to third-generation cephalosporins was associated with an increased probability of in-hospital mortality (hazard ratio [HR] 1.44, 95% CI 1.02-2.04), longer hospital stays (1.5 days, 1.0-2.0) and decreased probability of discharge alive (HR 0.31, 0.22-0.45). In the community cohorts, a paucity of environmental health infrastructure and materials for safe sanitation was identified across all sites and ESBL-Enterobacterales were isolated from 41.8% of human stool, 29.8% of animal stool and 66.2% of river water samples and was associated with the wet season, living in urban areas, advanced age and in household-animal interactions. Life threatening febrile illness is common in Blantyre however, diagnostics are few, however the COVID-19 pandemic has led to rapid expansion of diagnostic capacity. We are, however frequently treating the wrong bugs with ceftriaxone, further there was significant expansion of azithromycin demand and usage during the pandemic. Current management of sepsis has not been optimised and ceftriaxone use is promoting carriage of ESBL bacteria out of the hospital and ESBL E. coli and K. pneumoniae are ubiquitous in the community, where environmental hygiene infrastructure and community antimicrobial stewardship are critically lacking.Copyright © 2023
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Bovine rhinitis virus (BRV) is an important pathogen responsible for the bovine respiratory disease complex (BRDC) and can be divided into two genotypes (BRAV and BRBV). To establish a duplex quantitative real-time RT-PCR assay for simultaneous detection of BRAV and BRBV, specific primers and TaqMan probes targeting the 5'NTR of BRAV and 3'NTR of BRBV were designed. A duplex quantitative real- time RT- PCR assay for simultaneous detecting BRAV and BRBV was preliminarily established by optimizing reaction conditions for each step. The assay specifically detects BRAV and BRBV, and no crossreaction with other common bovine respiratory pathogens, including IDV, BCoV, BVDV-1, BRSV, BPIV-3, BAdV-3, mycoplasma bovis, Pasteurella multocida, Mannheimia haemolytica, Escherichia coli, and Salmonella, was observed. In addition, the sensitivity test showed that the detection limits of this assay were 3.2x101 copies/L for both BRAV and BRBV plasmid standards. Besides, the repeatability test showed that the variation coefficients of this assay were less than 0.05 from both lot-to-lot and intra-lot. These results showed that the assay has high specificity, extreme sensitivity, and good repeatability. Moreover, a total of 43 nasal swabs of BRDC cattle were tested by our assay and four other quantitative real-time RT-PCR assays, including 3 BRAV assays and 4 BRBV assays. The results showed that the detection rates of our assay were 32.56%(14/43) for BRAV and 30.23%(13/43) for BRBV, and the detection rates of other quantitative real-time RT-PCR assays were 0(0/43), 2.33%(1/43), 23.26%(10/43) for BRAV and 27.91% (12/43), 27.91%(12/43), 27.91%(12/43), 27.91%(12/43) for BRBV, indicating that our assay has a more substantial detection capability than other assays. This study firstly established a duplex quantitative real-time RT-PCR assay for simultaneous detection of BRAV and BRBV, and the assay exhibited high specificity, sensitivity, and stability. Moreover, the study firstly confirmed the existence of BRAV in China, contributing to the prevention and control of BRDC.
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Objective: To analyze the distribution and drug resistance of pathogenic bacteria in blood culture specimens of patients with bloodstream infections before and after COVID-19 (2018-2019 and 2020-2021), and to provide scientific basis and reference for rational treatment and effective control of bloodstream infections in the post-epidemic period. Methods: Blood culture specimens were collected from patients in Zhongnan Hospital of Wuhan University in the two years before and after the COVID-19 outbreak (2018-2021). The Automated Blood Culture Systems were used to perform blood culture on blood specimens sent for clinical inspection, and the Vitek MS automatic bacterial identification mass spectrometer was used for strain identification and the Vitek 2 automatic bacterial drug susceptibility analyzer was used for drug susceptibility testing and drug resistance analysis. Results: Blood culture specimens were performed on 28 736 patients with suspected bloodstream infection submitted for inspection from January 2018 to December 2019, and a total of 2 181 strains of pathogenic bacteria were detected after removing duplicate strains, with a positive rate of 7.69%, including 1 046 strains of Gram-negative bacteria, accounting for 47.96%. From January 2020 to December 2021, blood culture specimens from 26 083 patients with suspected bloodstream infection were submitted for inspection, and a total of 2 111 strains of pathogenic bacteria were detected after excluding duplicate strains, with a positive rate of 8.09%, including 1 000 strains of Gram-negative bacteria accounted for 47.37%. The drug resistance of Klebsiella pneumoniae was relatively serious, and the sensitivity rate to ertapenem, polymyxin B and tigecycline was more than 90%. The main non-fermentative bacteria Acinetobacter baumannii was more than 50% sensitive to piperacillin/tazobactam, amikacin and polymyxin B. The sensitivity rates of Pseudomonas aeruginosa to piperacillin/tazobactam, ceftazidime, cefepime, amikacin, gentamicin, tobramycin, ciprofloxacin, levofloxacin, piperacillin and meropenem were more than 50%. Conclusions: In the two years before and after COVID-19, there are many types of pathogenic bacteria in bloodstream infection, but the distribution do not differ significantly. The pathogens of bloodstream infection are mainly distributed in ICU, hepatobiliary research institute, and nephrology department. Among them, Gram-negative bacteria such as Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii are the main ones, and different pathogens showed great differences in drug resistance.
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Intro: The COVID-19 pandemic is caused by the SARS-CoV-2 virus, an enveloped RNA of the coronavirus family. The advancement in molecular technology and biochemistry has accelerated the development of diagnostic reagents and assays. Much attention has been focused on the S protein, but the high mutation rate in this region could lead to false negative results. Thus, a better target protein for diagnostic application is needed for accurate detection. Method(s): Nucleotide sequences encoded for membrane (M) glycoprotein gene region of SARS-CoV-2 from Malaysian isolates were extracted from GISAID, aligned, and selected accordingly. The DNA plasmid was commercially synthesized with codon optimization for Escherichia coli (E. coli), and the presence of the M gene was confirmed by PCR. The plasmid was then transformed into E. coli. Later, the expression of M glycoprotein was induced, separated on an SDS-PAGE gel, and transferred onto a nitrocellulose membrane, followed by immunostaining. Finding(s): The analysis of the M glycoprotein against the Omicron strains demonstrated that the amino acid is conserved (99.5%). The M glycoprotein was successfully expressed and detected with antibodies from SARS-CoV-2 infected patients at ~26 kDa. The protein is currently upscale for the generation of monoclonal Ab (Mab). Discussion(s): The M protein of SARS-CoV-2 is more conserved among the virus and also has been reported to confer antigenic properties. Selection of M protein perhaps a better option compared to current detection assays that use spike (S) protein, which could lead to false negative results, as this gene region particularly the ribosome-binding domain (RBD) rapidly undergoes mutations. The utilization of M protein potentially improves negative predictive value (NPV) of the diagnostic test. Conclusion(s): Further development of diagnostic reagents is needed to improve the assay's specificity. The newly developed M protein and the MAb can be used to generate a more accurate viral detection assay.Copyright © 2023
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Introduction: Biliary fistulas are a rare complication of gallstones. Fistula formation can occur in a number of adjacent sites;even more rare complication is the formation of a cholecystocolonic fistula. Case Description/Methods: A 74-year-old man who had recently undergone an extensive hospitalization secondary to inflammatory demyelinating polyneuropathy (IDP) and COVID-19 infection. During his hospitalization, he required ICU admission and mechanical ventilation with subsequent PEG tube placement. He was discharged to an inpatient rehabilitation facility when he developed worsening respiratory distress. Laboratory examinations were pertinent for ALT of 252, AST of 140 and ALP of 401 without hyperbilirubinemia. Blood cultures revealed Escherichia coli bacteremia. Given transaminitis and bacteremia, an MRCP was performed which demonstrated evidence absent space between gallbladder and hepatic flexure of the colon suggesting a CCF (Figure A). An ERCP with sphincterotomy was performed which showed extravasation of contrast from the gallbladder into the colon at the hepatic flexure (Figure B). He underwent cholecystectomy and fistula repair without any complications and gradual improvement in liver function test. He was discharged to a rehabilitation facility. Discussion(s): Complications of gallstones are well established, which include the common bile duct obstruction, but also include the rare occurrences of acute cholangitis, malignancy, and fistula formation. CCF is a rare complication of gallstones which can occur in the stomach, duodenum, or colon with a variable clinical presentation. Complications from an undiagnosed fistula can be life threatening including colon perforation and fecal peritonitis. This case highlights the diagnostic challenge and the high degree of clinical suspicion involved in establishing the diagnosis of CCF in patient without abdominal symptoms suggestive of gallbladder disease. We hypothesize that stone formation resulting in the development of the fistula may be secondary to the underlying history of IDP and subsequent immobility. Although rare, CCF should be considered in patients presenting with unexplained pneumobilia and bacteremia. A timely diagnosis should be made to proceed with immediate treatment including cholecystectomy and fistula closure to prevent fatal complications.
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Immobilized metal affinity chromatography (IMAC) is a popular and valuable method for the affinity purification of polyhistidine-tagged recombinant proteins. However, it often shows practical limitations, which might require cumbersome optimizations, additional polishing, and enrichment steps. Here, we present functionalized corundum particles for the efficient, economical, and fast purification of recombinant proteins in a column-free format. The corundum surface is first derivatized with the amino silane APTES, then EDTA dianhydride, and subsequently loaded with nickel ions. The Kaiser test, well known in solid-phase peptide synthesis, was used to monitor amino silanization and the reaction with EDTA dianhydride. In addition, ICP-MS was performed to quantify the metal-binding capacity. His-tagged protein A/G (PAG), mixed with bovine serum albumin (BSA), was used as a test system. The PAG binding capacity was around 3 mg protein per gram of corundum or 2.4 mg per 1 mL of corundum suspension. Cytoplasm obtained from different E. coli strains was examined as examples of a complex matrix. The imidazole concentration was varied in the loading and washing buffers. As expected, higher imidazole concentrations during loading are usually beneficial when higher purities are desired. Even when higher sample volumes, such as one liter, were used, recombinant protein down to a concentration of 1 µg/mL could be isolated selectively. Comparing the corundum material with standard Ni-NTA agarose beads indicated higher purities of proteins isolated using corundum. His6-MBP-mSA2, a fusion protein consisting of monomeric streptavidin and maltose-binding protein in the cytoplasm of E. coli, was purified successfully. To show that this method is also suitable for mammalian cell culture supernatants, purification of the SARS-CoV-2-S-RBD-His8 expressed in human Expi293F cells was performed. The material cost of the nickel-loaded corundum material (without regeneration) is estimated to be less than 30 cents for 1 g of functionalized support or 10 cents per milligram of isolated protein. Another advantage of the novel system is the corundum particles' extremely high physical and chemical stability. The new material should be applicable in small laboratories and large-scale industrial applications. In summary, we could show that this new material is an efficient, robust, and cost-effective purification platform for the purification of His-tagged proteins, even in challenging, complex matrices and large sample volumes of low product concentration.
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Objective: To explore the distribution and correlation of pathogens in the elderly patients with AECOPD, so as to guide the rational use of antibiotics and hormones in clinic. Methods: A total of 111 patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD) admitted to Nanjing First Hospital from January 2019 to January 2020 were retrospectively analyzed. The basic data such as eosinophil, neutrophil and lymphocyte count, the levels of C-reactive protein(CRP) and erythrocyte sedimentation rate (ESR)in blood routine examination were collected. Further, the pathogens were qualified by sputum fluorescence quantitative polymerase chain reaction, and the pathogens distribution was analyzed. Results: The level of ESR and the ratio of cardiovascular diseases showed significant differences between the pathogen-positive group and pathogen-negative group. In this study, the top five pathogens in AECOPD patients were EB virus (21.6%), Haemophilus influenzae (19.8%), Streptococcus pneumoniae (17.1%), herpes simplex virus(14.4%), influenza A virus(14.4%). The detection rate of influenza A virus was correlated with influenza B virus and Aspergillus (P < 0.05);The detection rate of respiratory syncytial virus was correlated with Candida, Moraxella catarrholis, Streptococcus pneumoniae and Haemophilus influenzae (P < 0.05);The detection rate of Escherichia coli was correlated with rhinovirus, adenovirus, Klebsiella pneumoniae and Acinetobacter baumannii (P < 0.05);The detection rate of Candida was correlated with that of Moraxella catarrholis and Pseudomonas aeruginosa(P<0.05);The detection rate of human coronavirus was correlated with Haemophilus influenzae, herpes simplex virus and Streptococcus pneumoniae(P < 0.05). Conclusions: AECOPD are mostly induced by different pathogens, especially mixed infection of bacteria and virus. It is helpful to guide the rational use of antibiotics by analyzing the etiological characteristics in the elderly patients with AECOPD.
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IDWeek is the joint annual meeting of the Infectious Diseases Society of America (IDSA), Society for Healthcare Epidemiology of America (SHEA), the HIV Medicine Association (HIVMA), the Pediatric Infectious Diseases Society (PIDS) and the Society of Infectious Diseases Pharmacists (SIDP). For the first time since the COVID-19 public health emergency began, IDWeek 2022 returned to in-person attendance. It was held in Washington, D.C., and the meeting comprised 5 days of live sessions and on-demand content that included posters and oral presentations.Copyright © 2023 Clarivate.
ABSTRACT
Objectives: The COVID-19 pandemic has had a major impact on the healthcare system, which has been forced to manage large num-bers of patients, including those with respiratory insufficiency and in need of oxygen therapy. Due to concerns about bacterial co-in-fection, antibiotic therapy was administered to many patients. The aim of the present study was to compare antimicrobial resistance in intensive care patients in the pre-pandemic and pandemic periods. Material(s) and Method(s): Patients hospitalized at the Department of Anesthesiology, Resuscitation and Intensive Care Medicine of the University Hospital Olomouc in the pre-COVID-19 period (2018-2019) and during the pandemic (2020-2021) were enrolled in the stu-dy. Clinical samples from the lower respiratory tract were routinely collected twice a week, with one strain of a given species first isolated from each patient being included in the study. Result(s): While several bacterial species (Escherichia coli, Proteus mirabilis and Haemophilus influenzae) were found to occur less fre-quently, an increased occurrence was documented for Enterococcus faecium, Serratia marcescens and Klebsiella variicola. Overall, ho-wever, it can be concluded that there was no major change in the frequency of bacterial pathogens isolated from the lower respiratory tract during the COVID-19 period. Similarly, with only a few exceptions, antimicrobial resistance did not change significantly. More significant increases in resistance to piperacillin/tazobactam, cefotaxime, ciprofloxacin and gentamicin have been demonstrated for Serratia marcescens. However, a decrease in the resistance of Pseudomonas aeruginosa and Burkholderia cepacia complex to mero-penem was also observed. Conclusion(s): There was no significant change in the frequency of bacterial pathogens and their resistance to antibiotics during the COVID-19 pandemic. However, there was an increase or decrease in the percentage of some species and in their resistance.Copyright © 2022, Trios spol. s.r.o.. All rights reserved.
ABSTRACT
Objective To explore the application value of Biofire Filmarry pneumonia panel (PN) in detection of secondary and concomitant pathogen among critically ill patients with coronavirus disease 2019(COVID-19). Methods We consecutively included and analyzed the clinical data of critically ill patients with COVID-19 transferred to the ICU from February to April 2020 in the Sino-French Campus of Wuhan Tongji Hospital. Samples of Bronchoalveolar lavage fluid obtained by bedside bronchoscopy were sent for Biofire Filmarray PN and standard culture concomitantly. We compared the results of two methods and evaluated their concordance. Results In total, 21 critically ill patients with COVID-19 were included and 54 samples were tested, including 33 (61.1%) Biofire Filmarray PN tests (21 patients) and 21 (38.9%) standard cultures (14 patients), in which 19 pairs (38 samples) underwent both tests simultaneously. In Biofire Filmarray PN group, the turnaround time was about 1 hour. There were 74 positive results in 32 samples (97.0%) from 20 patients, including 29 cases(39.2%) of Acinetobacter baumannii complex, 21 cases (28.4%) of Pseudomonas aeruginosa, 16 cases (21.6%)of Klebsiella pneumoniae, 5 cases (6.8%) of Escherichia coli, 1 case (1.4%)each of Enterobacter cloacae, Haemophilus influenzae, and respiratory syncytial virus. In the standard culture group, the turnaround time was about 3 days. 19 positive results returned in 16 (76.2%) samples from 11 patients, including 8 cases (42.1%) of Pseudomonas aeruginosa, 6 cases (31.6%) of Acinetobacter baumannii, 4 cases (21.1%) of Stenotrophomonas malt and 1 case (5.3%) of Myxobacterium. Among the 19 pairs of "back-to-back" specimens, 15 pairs were concordant, and the agreement ratio was 78.9%. Conclusions Acinetobacter baumannii and Pseudomonas aeruginosa may be the common pathogens of secondary or concomitant infection in critically ill patients with COVID-19. Biofire Filmarray PN is a rapid diagnostic test and has application value in such patients;its sensitivity and accuracy require further investigation with larger sample sizes.Copyright © 2021, Peking Union Medical College Hospital. All rights reserved.