Order Enterobacteriales Research Articles

Description of three novel species of Scandinavium: Scandinavium hiltneri sp. nov., Scandinavium manionii sp. nov. and Scandinavium tedordense sp. nov., isolated from the oak rhizosphere and bleeding cankers of broadleaf hosts.

While investigating the bacterial populations of environmental samples taken from a mix of healthy and Acute Oak Decline afflicted Quercus robur (pedunculate or English oak) rhizosphere soil samples and swabs of bleeding lesions on Tilia spp. (lime) and Quercus rubra (red oak) trees, several strains belonging to the order Enterobacterales were isolated using selective media and enrichment broth. Seven strains from the Q. robur rhizosphere, three strains from Tilia spp. and one from Q. rubra were investigated, with their taxonomic status determined via a polyphasic taxonomic approach. Initially stains were identified as potential members of the recently described genus Scandinavium, based on the partial sequencing of three housekeeping genes. Further analysis of phenotypic traits, including fatty acid profiles, coupled with 16S rRNA gene and phylogenomic analysis of whole genome sequences were applied to a subset of the strains. Phylogenetic and phylogenomic analysis repeatedly placed the isolates in a monophyletic clade within Scandinavium, with four distinct clusters observed, one of which corresponded to Scandinavium goeteborgense, the type species of the genus. The remaining three clusters could be phenotypically and genotypically differentiated from each other and S. goeteborgense. As such, we describe three novel species of the genus, for which we propose the names Scandinavium hiltneri sp. nov. (type strain H11S7T = LMG 32612T = CCUG 76179T), Scandinavium manionii sp. nov. (type strain H17S15T = LMG 32613T = CCUG 76183T) and Scandinavium tedordense sp. nov. (type strain TWS1aT = LMG 32614T = CCUG 76188T). Additionally, the descriptions of the genus Scandinavium and the type species, S. goeteborgense, are emended.

Colonization dynamics of extended-spectrum beta-lactamase-producing Enterobacterales in the gut of Malawian adults

Drug-resistant bacteria of the order Enterobacterales which produce extended-spectrum beta-lactamase enzymes (ESBL-Enterobacterales, ESBL-E) are global priority pathogens. Antimicrobial stewardship interventions proposed to curb their spread include shorter courses of antimicrobials to reduce selection pressure but individual-level acquisition and selection dynamics are poorly understood. We sampled stool of 425 adults (aged 16–76 years) in Blantyre, Malawi, over 6 months and used multistate modelling and whole-genome sequencing to understand colonization dynamics of ESBL-E. Models suggest a prolonged effect of antimicrobials such that truncating an antimicrobial course at 2 days has a limited effect in reducing colonization. Genomic analysis shows largely indistinguishable diversity of healthcare-associated and community-acquired isolates, hence some apparent acquisition of ESBL-E during hospitalization may instead represent selection from a patient’s microbiota by antimicrobial exposure. Our approach could help guide stewardship protocols; interventions that aim to review and truncate courses of unneeded antimicrobials may be of limited use in preventing ESBL-E colonization.

Evaluation of canine raw food products for the presence of extended-spectrum beta-lactamase- and carbapenemase-producing bacteria of the order Enterobacterales.

To assess the potential contamination of commercial raw dog food products with bacteria of the Enterobacterales order that produce extended spectrum beta-lactamase (ESBL) and carbapenemase enzymes, determine risk factors for contamination, and understand isolate genetic diversity. A total of 200 canine raw food products. Products were cultured on selective chromogenic agar following enrichment steps. Whole-genome sequencing was performed for isolates that were confirmed to produce an ESBL. Isolates were characterized by antimicrobial resistance genes, and multilocus sequences typing, and compared to other isolates in the NCBI database for clonality. Preservation method and protein sources were assessed as potential risk factors for contamination with ESBL and carbapenemase-producing bacteria of the Enterobacterales order. No carbapenemase-producing Enterobacterales (CPE) were identified, but ESBL-producing Enterobacterales bacteria were isolated from 20/200 products (10.0%; 95% CI, 7.3 to 16.5%), all of which were frozen. Pork-derived protein source products were 8.1 times (P = .001; 95% CI, 2.53 to 26.2) more likely to carry ESBL-producing Enterobacterales bacteria than other protein sources. WGS analysis confirmed the presence of ESBL genes in a total of 25 distinct isolates (19 Escherichia coli, 5 Klebsiella pneumoniae, and 1 Citrobacter braakii). Genes encoding CTX-M type ESBL enzymes were the most common (24/25 isolates, 96.0%) with blaCTX-M-27 being the most common allele (8/25, 32.0%). Frozen, raw food products may serve as a route of transmission of ESBL-producing Enterobacterales bacteria to companion animals. Veterinarians should advise owners about the risks of raw food diets, including potential exposure to antimicrobial-resistant bacteria.

Etiological spectrum and antimicrobial resistance of the most frequently isolated pathogens, associated with urinary tract infections in ambulatory patients

Introduction: Urinary tract infections (UTIs) are among the most common infections both in the community and in the hospital setting. Aim: The aim of this study is to investigate the etiological spectrum and antimicrobial resistance of most frequently isolated pathogens, associated with UTIs in ambulatory patients in Varna city, Bulgaria during a seven-month period (October 2020–April 2021). Materials and Methods: A total of 1600 urine samples, collected from patients with suspected UTIs were tested. Screening for bacterial growth was done by HM&L Uroquattro instrument (ALIFAX, Italy). Species identification and antimicrobial susceptibility testing were performed by VITEK 2 Compact System (bioMerieux) and Kirby-Bauer disk diffusion method. Results: E. coli was the most commonly isolated uropathogen regardless of the age group (48%, n = 61), followed by Enterococcus faecalis (33%, n = 42) and other representatives of order Enterobacterales (13.3%, n = 18). The resistance rates in the group of Gram-negative isolates (n = 79) in decreasing order were as follows: ampicillin, 64.5% > trimethoprim/sulfamethoxazole, 36% > ciprofloxacin, 29.1% > amoxicillin-clavulanic acid, 27.8% > cefuroxime, levofloxacin, 21.5% > fosfomycin, 13.1% > ceftriaxone, 12.6% > ceftazidime, 10.1% > gentamicin, nitrofurantoin, 6.5% > nitroxoline, 4.9%. The resistance rates among the isolates of E. faecalis (n = 42) were as follows: ciprofloxacin, 28.6% > gentamicin, 23.8% > levofloxacin, 19% > nitrofurantoin, 4.7% > amoxicillin, 2.4%. No resistance to meropenem, amikacin, vancomycin, and teicoplanin was found in the studied collection of isolates (n = 127). Conclusion: The etiological spectrum of UTIs in ambulatory patients was dominated by E. coli , followed by E. faecalis. In the group of Gram-negative uropathogens, high resistance rates to ampicillin, trimethoprim/sulfamethoxazole and quinolones were detected. Third-generation cephalosporins, fosfomycin, nitrofurantoin and nitroxoline retained very good activity. Among Enterococcus faecalis isolates, the second most commonly isolated bacterial species, a decreased activity of quinolones was found too, but the aminopenicillins and nitrofurantoin remain highly active.

Peculiarities of Microbiota in Patients with Inflammatory Intestinal Diseases

Background. The intestinal microbiota, on the one hand, protects a person from pathogens, on the other hand, it itself may be one of the triggers and/or mediators of progression in inflammatory bowel diseases. Inflammatory bowel disease (IBD) predominantly affects young people of working age. It noted a steady increase in the incidence of IBD in recent decades throughout the world and in Russia. Inflammatory bowel diseases significantly affect quality of life and lead to complications of having to perform surgery, which significantly reduces the quality of life. Aims of the study was to investigate the composition of the microbiota of the colon, the search features of the microbial spectrum of patients with inflammatory bowel disease patients compared with control patients. Materials and methods. A prospective study was carried out between patients with inflammatory bowel disease and patients without inflammatory bowel disease for the period 20182019. The study included 157 IBD patients and 150 patients without IBD. All patients studied stool, which have been subjected to microbiological and metagenomic study. Results. Most often, facultative anaerobic microorganisms were present in the stool of patients with IBD (in 60%, 103109 CFU/g) and in patients without IBD (69%, 103109 CFU/g), the share of gram-negative bacteria accounted for 52%, in mostly represented by bacilli belonging to the order Enterobacteriales, only 7% of isolated gram-negative facultative aerobic microorganisms were gram-negative non-fermenting bacteria represented by 5 genera: Acinetobacter, Burkholderia, Pseudomonas, Stenotrophomonas, Ralstonia. Gram-positive facultative anaerobic microorganisms in 89% were represented by cocci of the genus Enterococcus, Streptococcus, Staphylococcus, Micrococcus, Gemella, Globicatella, Granulicatella. Conclusions. According to the results of our study, special attention should be paid to the presence of rare microaerophilic and obligate anaerobic microorganisms in the fecal microbiota of patients with IBD (Arcobacter butzleri, Gardnerella vaginalis, Aromatoleum aromaticum, Terrisporobacter glycolicus (Clostridium glycolicum), Solobacterium moorei, Alloscardovia omnicolens, Fusobacterium nucleatum, Fusobacterium ulcerans, Dialister micraerophilus), that have not been isolated from patients without IBD. A timely adequate assessment of the composition and functional characteristics of the microbiota in terms of key biomarkers will make it possible to carry out targeted diagnostics and prevention of the immediate and long-term consequences of inflammatory bowel diseases.

Taxonomic structure of bacterial communities in sourdoughs of spontaneous fermentation.

The article is devoted to the study of the microbiome of spontaneously fermented sourdoughs. The aim of the work was to study the inf luence of the technological parameters of sourdough propagations on the taxonomic structure of the microbiome of spontaneously fermented sourdoughs. Two spontaneously fermented sourdoughs were studied: dense rye sourdough and liquid rye sourdough, both prepared using the same batch of peeled rye f lour. To study the taxonomic structure of the sourdough microbiome in dynamics, the method of high-throughput sequencing of 16S rRNA gene fragments of microorganisms was used. It was shown that the technological parameters of sourdough (humidity, temperature) do not affect the taxonomic composition of the microbiome of dense rye or liquid rye sourdough at the phylum/class/genus level. It was found that during the f irst three days of propagations, bacteria from the phyla Proteobacteria and Firmicutes dominated in the microbial community. In the phylum Proteobacteria, microorganisms from the order Enterobacterales took a large share, which persisted for three days of backslopping. The phylum Firmicutes was represented by lactic acid bacteria of the genera Weissella, Lactobacillus, Leuconostoc, Pediococcus, Lactococcus. It was established by classical microbiological methods that after a day of fermentation, the number of lactic acid bacteria cells was signif icantly higher in liquid rye sourdough compared to dense one. However, with further propagation of sourdoughs, the number of cells was comparable, while signif icant changes occurred at the level of genera and species. It was shown that as the relative number of lactic acid bacteria of the genus Lactobacillus increased, a gradual displacement of the coccal forms of Lactococcus, Leuconostoc, Weissella, Pediococcus happened. With further propagation of sourdough after 10 days, the position of the dominant groups of bacteria was occupied by representatives of the phylum Firmicutes, lactic acid bacteria of the genus Lactobacillus. The inf luence of the mode and parameters of the sourdough on the species composition of lactobacilli, which demonstrated a low bacterial diversity, is shown. In the f irst three days of propagations, lactobacilli L. curvatus, L. brevis, and Lactiplantibacil- lus sp. dominated in both sourdoughs. After a month of backslopping, Fructilactobacillus sanfranciscensis and Companilactobacillus sp. dominated in dense rye sourdough, and L. pontis dominated in liquid rye sourdough

Changes and Trends of Drug Resistance of Pathogenic Bacteria in Blood Samples of a Tertiary-Level Teaching Hospital from 2016 to 2020

To investigate the distribution of pathogenic bacteria in blood samples and changes in their drug resistance in our hospital from 2016 to 2020, and to provide evidence for the diagnosis and treatment of clinical bloodstream infections. Bruker Corporation's matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used for bacterial identification, VITEK 2 Compact was used for antimicrobial susceptibility test, some of which was done with the Kirby-Bauer method, and the data was statistically analyzed with WHONET 5.6 software. A total of 8931 bacterial strains, including 4502 (50.4%) Gram-positive bacteria and 4429 (49.6%) Gram-negative bacteria, were isolated from the blood samples between 2016 and 2020. Among the isolated bacteria of the order Enterobacterales, Escherichia coli (1773, 19.9%) ranked first, followed by Klebsiella pneumoniae (1067, 11.9%). The non-fermenting bacteria identified were predominantly Acinetobacter baumannii (293, 3.3%) and Pseudomonas aeruginosa (238, 2.7%). The top three Staphylococcus species were Staphylococcus epidermidis (970 strains, 10.9%), Staphylococcus hominis (713, 8.0%) and Staphylococcus aureus (541, 6.1%). Escherichia coli showed high in vitro susceptibility to cefoperazone/sulbactam, amikacin, polymyxin B, tigecycline, and carbapenems, and the sensitivity rate was consistently over 90%. The resistance rate to imipenem showed a trend of slow growth, and the resistance rate of meropenem was 2.2% to 3.4%. Klebsiella pneumoniae showed higher in vitro resistance rate to common antibiotics than that of Escherichia coli, with only the sensitivity rates to tigecycline and polymyxin B being higher than 90%, and the resistance rate to imipenem and meropenem increasing year by year. The resistance rate of Pseudomonas aeruginosa to imipenem decreased since 2017 (from 25.6% to18.6%), and the resistance rate of Acinetobacter baumanniito imipenem and meropenem were 73.7%-91.3% and 73.0%-91.3%. Staphylococcus resistant to vancomycin or linezolid was not found. Enterococci showed rather low resistance to vancomycin and linezolid. The distribution of common species of pathogenic bacteria in clinical blood samples in our hospital did not show significant changes, but the problem of multi-drug resistant bacteria is becoming increasingly more serious, especially so for carbapenem-resistant Klebsiella pneumoniae.

Microflora of sputum and autopsy material of patients with COVID-19.

The rapid spread of a new coronavirus infection in the country actualizes the conduct of bacteriological studies of clinical material obtained from the respiratory tract of patients with COVID-19. During the experiments, 230 sputum samples and 260 autopsy lung samples from patients with COVID-19 were analyzed. 946 high-risk strains were isolated and identified by MALDI-ToF mass spectrometry on a Microflex LT instrument (Bruker®). According to the results of bacteriological cultures of sputum, a predominance of gram-positive ones was revealed, amounting to 50.5% (222 strains) of the total number of isolated pathogens. However, falling into this group is manifested by natural representatives of the microflora of the human mucous membranes from the genera Streptococcus, Rothia and Lactobacillus (109 strains in total), which can be manifested by the detection of improper sputum collection, causing contamination by the substance of intense salivation and nasopharyngeal discharge. In turn, the "classic" gram-positive causative agents of pneumonia were detected much less frequently: S. aureus in 5 cases, S. pneumoniae in 6 patients. The causative agents in the order Enterobacterales are represented by 42 strains, among which the most likely species are K.pneumoniae (27 strains). In the group of non-fermenting gram-negative bacteria, A. baumanii (29 strains) prevailed, and P. aeruginosa was also identified in 2 cases. When analyzing the results of a microbiological study of autopsy material (lungs) of patients with COVID-19, significant differences in the qualitative and quantitative composition of the microflora were revealed, compared with sputum. In the group of gram-positive bacteria, 15 strains of the natural microflora of the mucous membranes were identified, while sensitive species dominated among gram-negative pathogens: K. pneumoniae (102 strains), A. baumanii (75 strains), P. aeruginosa (11 strains). Regular microbiological monitoring is essential for antibiotic therapy and prevention of secondary bacterial infection. In the event of a fatal outcome, the results of microbiological analysis of autopsy material can determine the cause of death of the patient.

The small genome, virulent, non-contractile tailed bacteriophages that infect Enterobacteriales hosts

Tailed bacteriophages are abundant and extremely diverse. Understanding this diversity is a challenge, and here we examine a small slice of that diversity in some detail. We contrast and compare the small genome, virulent, non-contractile tailed phages that infect the bacterial order Enterobacteriales. These phages, with genomes in the 35–60 kbp range, have very similar virions that are often difficult to distinguish by negative stain electron microscopy. There are currently 651 genome sequences of such phages in the public database. We show that these can be robustly parsed into fifteen well-defined clusters that have very different nucleotide sequences. We examine the similarities and differences among these clusters, as well as genetic exchange among clusters and the relationships between host species and phage clusters.

Network Pharmacology and Absolute Bacterial Quantification-Combined Approach to Explore the Mechanism of Tianqi Pingchan Granule Against 6-OHDA-Induced Parkinson's Disease in Rats.

Parkinson’s disease (PD) is the second most common neurodegenerative disease. Tianqi Pingchan Granule (TPG) is a clinically effective formula of traditional Chinese medicine to treat PD. However, the therapeutic effect and underlying mechanisms of TPG in PD remain unclear. Based on network pharmacology, the corresponding targets of TPG were identified using the Traditional Chinese Medicine Database and Analysis Platform Database. Differentially expressed genes in PD were obtained from the Therapeutic Target Database, Online Mendelian Inheritance in Man, GeneCards, and DrugBank databases. The protein-protein interaction (PPI) networks of intersected targets were constructed using the STRING database and visualized using Cytoscape. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed, and the pathways directly related to the pathogenesis of PD were integrated manually. Furthermore, in vivo studies were carried out based on network pharmacology. The gut microbiota, peripheral inflammatory cytokines, and glia-mediated neuroinflammation in substantia nigra were evaluated. A total of 99 target genes were intersected between targets of TPG and deferentially expressed genes in PD. The PPI network analysis indicated the proinflammatory cytokine as essential targets. GO and KEGG analyses indicated that inflammatory response and its related signaling pathways were closely associated with TPG-mediated PD treatment. In vivo studies revealed that class Negativicutes and order Selenomonadales decreased, whereas class Mollicutes, order Enterobacteriales, and Mycoplasmatales increased in fecal samples of PD rats via 16S rRNA sequence analysis. Furthermore, the function prediction methods purposely revealed that TPG therapy may be involved in flavonoid biosynthesis, which have anti-inflammatory properties. In addition, in vivo studies revealed that TPG exposure was found to not only attenuate the production of peripheral inflammatory cytokines but also inhibit the activation of microglia and astrocytes in substantia nigra of PD rats. Through network pharmacology and in vivo experiment-combined approach, the mechanisms of TPG in the treatment of PD were revealed, and the role of TPG in the regulation of gut microbiota and inflammatory response was confirmed.

A Comparison of Methods for Identifying Enterobacterales Isolates from Fish and Prawns.

Enterobacterales is a prevalent order, which inhabits a variety of environments including food. Due to the high similarities between pathogenic and non-pathogenic species, their identification might be difficult and laborious, and therefore there is a need for rapid and precise identification. The aim of this study was to compare the effectiveness of the available methods of identifying order Enterobacterales strains isolated from fresh fish and shrimps (n = 62). The following methods were used in this study: biochemical, sequencing and identification using the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). For this purpose, biochemical identification was performed with the use of the EnteroTest 24N set, while the identification using the MALDI-TOF MS technology was operated on VITEK® MS. Results were compared with identification made by 16S rRNA sequencing. The results of the study showed that conventional identification methods might provide a false result. Identification by VITEK® MS to the species level was correct at 70.97%, and the accuracy of EnteroTest 24N identification did not exceed 50.0%. The genus identification reached 90.32% for the MALDI-TOF technique, while for EnteroTest 24N it was nearly 70.0%. Due to errors in identification, especially of pathogenic organisms, the use of each of these methods should be confirmed by another method, preferably sequencing.

Impact of Empirical Antibiotic Therapy on Outcomes of Outpatient Urinary Tract Infection Due to Nonsusceptible Enterobacterales.

ABSTRACTResistance to oral antibiotics commonly used to treat outpatient urinary tract infections (UTIs) is increasing, but the implications of empirical treatment of resistant pathogens are not well described. Using an electronic records database, we reviewed the outcomes of patients >18 years of age who developed an outpatient UTI and had an outpatient urine culture result showing a member of the order Enterobacterales along with prescription data for an oral antibiotic filled on the day before, day of, or day after the culture was collected. Linear probability models were used to estimate partial effects of select clinical and demographic variables on the composite outcome. In all, 4,792 patients had 5,587 oral antibiotic prescriptions. Of 5,395 evaluable episodes, 22% of patients received an antibiotic to which the pathogen was resistant in vitro, and those patients were almost twice as likely to require a second prescription (34% versus 19%) or be hospitalized (15% versus 8%) within 28 days of the initial prescription fill compared to patients who received an antibiotic to which the pathogen was susceptible. Approximately 1% of Enterobacterales isolates were resistant to all commonly available classes of oral antibiotics. A greater risk of treatment failure was seen in patients over 60 years of age, patients with diabetes mellitus, men, and those treated with an antibiotic when prior culture identified an organism resistant to that class. The increasing resistance among members of Enterobacterales responsible for outpatient UTIs is limiting the effectiveness of empirical treatment with existing antibiotics, and consequently, outpatients with UTI are more likely to require additional courses of therapy or be hospitalized.IMPORTANCE Resistance rates for bacteria that cause urinary tract infections (UTIs) have increased dramatically. Regional rates of resistance to commonly prescribed antibiotics now exceed 20%, which is the threshold at which the Infectious Diseases Society of America recommends therapy be guided by culture. Our goals were to describe outcomes for outpatients with UTIs caused by bacteria resistant to empirically chosen antibiotics and to create a simple stratification schema for clinicians to identify UTI patients at increased risk of treatment failure due to antibiotic mismatch. These data are relevant to clinicians, given how common uncomplicated UTIs are, and highlight the need for clinicians to understand local resistance rates and the importance of culture-guided treatment, especially in vulnerable patients. These findings also showed that 1% of bacteria were resistant to all major classes of oral antibiotics, underscoring the need for new antibiotics to treat patients with UTIs due to resistant bacteria.

Carbapenem-resistant IMP-1-producing Pseudocitrobacter vendiensis emerging in a hemodialysis unit.

Hemodialysis patients are at high risk for bloodstream infections associated with highest morbidity and mortality rates. Bacterial species not commonly related to such infections has been hardly identified by traditional methods. Pseudocitrobacter is a novel genus of the order Enterobacterales that is associated with carbapenemase genes and nosocomial infection. In this context, we have investigated nine cases of bloodstream infections by carbapenem-resistant Gram-negative bacilli in patients assisted at a hemodialysis unit in Brazil. The infections were caused by a metallo-β-lactamase (IMP-1)-producing clone (> 90% XbaI-PFGE similarity) of Pseudocitrobacter vendiensis, displaying a multidrug-resistant profile to broad-spectrum cephalosporins, carbapenems, chloramphenicol, and trimethoprim-sulfamethoxazole. S1-PFGE and Southern blot hybridization revealed that blaIMP-1 was carried by a 200-kb IncC/ST3 plasmid. Patients were successfully treated with amikacin, and strict disinfection procedures and hand washing protocols were reinforced. We report the emergence of P. vendiensis, a recently described species of the genus, in bloodstream infections of patients undergoing hemodialysis. Considering the epidemic potential of carbapenemase-producing Enterobacterales in hospital settings, surveillance of this emerging pathogen is of utmost importance.

High-resolution Microbiome Analyses of Nine Psyllid Species of the Family Triozidae Identified Previously Unrecognized but Major Bacterial Populations, including <i>Liberibacter</i> and <i>Wolbachia</i> of Supergroup O

Psyllids (Hemiptera: Sternorrhyncha: Psylloidea) are plant sap-sucking insects that include important agricultural pests. To obtain insights into the ecological and evolutionary behaviors of microbes, including plant pathogens, in Psylloidea, high-resolution ana-lyses of the microbiomes of nine psyllid species belonging to the family Triozidae were performed using high-throughput amplicon sequencing of the 16S rRNA gene. Analyses identified various bacterial populations, showing that all nine psyllids have at least one secondary symbiont, along with the primary symbiont "Candidatus Carsonella ruddii" (Gammaproteobacteria: Oceanospirillales: Halomonadaceae). The majority of the secondary symbionts were gammaproteobacteria, particularly those of the order Enterobacterales, which included Arsenophonus and Serratia symbiotica, a bacterium formerly recognized only as a secondary symbiont of aphids (Hemiptera: Sternorrhyncha: Aphidoidea). The non-Enterobacterales gammaproteobacteria identified in the present study were Diplorickettsia (Diplorickettsiales: Diplorickettsiaceae), a potential human pathogen, and Carnimonas (Oceanospirillales: Halomonadaceae), a lineage detected for the first time in Psylloidea. Regarding alphaproteobacteria, the potential plant pathogen "Ca. Liberibacter europaeus" (Rhizobiales: Rhizobiaceae) was detected for the first time in Epitrioza yasumatsui, which feeds on the Japanese silverberry Elaeagnus umbellata (Elaeagnaceae), an aggressive invasive plant in the United States and Europe. Besides the detection of Wolbachia (Rickettsiales: Anaplasmataceae) of supergroup B in three psyllid species, a lineage belonging to supergroup O was identified for the first time in Psylloidea. These results suggest the rampant transfer of bacterial symbionts among animals and plants, thereby providing deeper insights into the evolution of interkingdom interactions among multicellular organisms and bacteria, which will facilitate the control of pest psyllids.

Detection of mcr-1-mediated resistance to polymyxins in Enterobacterales using colistin disk chelator application

Objective. To evaluate the possibility of using the colistin disk chelator application (CDCA) method as simple and available screening tool for detection of mcr-1-mediated resistance to polymyxins in Enterobacterales. Materials and Methods. A total of 47 colistin-resistant Enterobacterales isolates obtained in 2014–2020 within multicenter MARATHON study were included in the experiment. Colistin susceptibility testing was performed using Mueller–Hinton broth microdilution method according to ISO 20776-1:2006. Interpretation of the results was performed according to EUCAST v.12.0 clinical breakpoints. MCR-genes were detected by multiplex real-time PCR. Phenotypic screening for mcr-expression was performed on Mueller–Hinton agar by application of dipicolinic acid in concentration of 1,000 mcg/disk in 10 µL volume per disk and 0.5 M solution of EDTA in 5 µL volume per disk. Chelating effect was registered by differences in zone of growth inhibition around colistin disks with and without chelator. Measurements were performed with the help of caliper in millimeters. Statistical data processing was carried out in accordance with guidelines for statistical analysis in medical researches using MS-Excel tool. Results. In 25 of 47 included in the experiment enterobacteria isolates mcr-genes were detected by molecular method. MCR-detection by CDCA method identified the average difference value of the zones of growth inhibition for colistin and its combination with EDTA and DPA as 4.1 mm and 3.7 mm respectively for mcr-positive isolates and 1.7 mm and 1.2 mm respectively for mcr-negative isolates. Statistical analysis estimated that a difference of ≥ 3 mm in zone of growth inhibition for combination of colistin with one of the chelating agents when compared to colistin only allows us to conclude that a studied isolated carries mcr-1-mediated resistance to polymyxins. In addition, sensitivity of the test was 96% and specificity was 91% if DPA is used, while EDTA showed only 88% sensitivity and 77% specificity. Conclusions. Proposed method appears as available technique for phenotypic screening of the Enterobacterales order for mcr-1-mediated resistance to polymyxins for practical laboratories in present conditions. The use of DPA is preferred because of better specificity and sensitivity rates.

Carbapenem-resistant Escherichia coli from shrimp and salmon available for purchase by consumers in Canada: a risk profile using the Codex framework.

Resistance to carbapenems in human pathogens is a growing clinical and public health concern. The carbapenems are in an antimicrobial class considered last-resort, they are used to treat human infections caused by multidrug-resistant Enterobacterales, and they are classified by the World Health Organization as 'High Priority Critically Important Antimicrobials'. The presence of carbapenem-resistant Enterobacterales (CREs) of animal-origin is of concern because targeted studies of Canadian retail seafood revealed the presence of carbapenem resistance in a small number of Enterobacterales isolates. To further investigate this issue, a risk profile was developed examining shrimp and salmon, the two most important seafood commodities consumed by Canadians and Escherichia coli, a member of the Enterobacterales order. Carbapenem-resistant E. coli (CREc) isolates have been identified in shrimp and other seafood products. Although carbapenem use in aquaculture has not been reported, several classes of antimicrobials are utilised globally and co-selection of antimicrobial-resistant microorganisms in an aquaculture setting is also of concern. CREs have been identified in retail seafood purchased in Canada and are currently thought to be uncommon. However, data concerning CRE or CREc occurrence and distribution in seafood are limited, and argue for implementation of ongoing or periodic surveillance.

1288. Evaluation of Predictors for Clinical Success in Patients Treated with Eravacycline for Various Infections

Abstract Background Eravacycline (ERV) is approved in the United States (US) for the treatment of complicated intra-abdominal infections in adults. We aimed to evaluate the independent predictors of clinical success in patients treated with ERV for various infections. Methods Multicenter, retrospective, observational study conducted from September, 2018 to April, 2021. We included adults treated with ERV for ≥ 72hours. Clinical success was defined as 30-day survival, lack of 30-day infection-recurrence, and resolution of infection signs/symptoms. All outcomes were measured from ERV initiation. Multivariable logistic regression (MLR) was performed to identify independent predictors of clinical success. Clinically relevant variables were selected for model entry based on bivariate comparisons (P< 0.2) in a backward fashion. Results We included 223 patients from 16 medical centers in 13 geographically unique states. The median (IQR) age was 61 (50-69) years, 57% were male and 62% were Caucasian. Median (IQR) APACHE II, and Charlson Comorbidity scores were 15 (10-21), and 3 (1-5), respectively. Sources of infection were primarily intra-abdominal (27%) and respiratory (27%). Common pathogens included Acinetobacter baumannii (21%) and those of the Enterobacterales order (36%). Infectious diseases consultation and surgical interventions were obtained in 93.7% and 52% respectively. Clinical success occurred in 64%, specifically 30-day survival in 78%, absence of 30-day infection-recurrence in 93%, and 74% experienced resolution of infection signs/symptoms. Since characteristics and outcomes were similar among various pathogens, MLR was conducted using the overall cohort. Skin as a source and combination therapy with ERV were independently associated with higher clinical success: odds ratio 3.3 [CI 1.1-10.2] and 2.9 [1.4-5.9], respectively. Whereas, ICU admission at culture time and undergoing surgery within 30 days of culture were independently associated with reduced odds of clinical success: 0.4 [0.17-0.80] and 0.3 [0.11-0.63] respectively. Conclusion Although most ERV treated patients experienced clinical success, factors independently associated with higher clinical success are crucial to consider for optimum antibiotic selection. Disclosures Kimberly C. Claeys, PharmD, GenMark (Speaker’s Bureau) Madeline King, PharmD, tetraphase (Speaker’s Bureau) Michael P. Veve, Pharm.D., Cumberland (Grant/Research Support)Paratek Pharmaceuticals (Research Grant or Support) Bruce M. Jones, PharmD, BCPS, Abbvie (Consultant, Advisor or Review Panel member, Speaker’s Bureau)La Jolla (Speaker’s Bureau)Melinta (Consultant)Merck (Consultant)Paratek (Consultant, Speaker’s Bureau) Susan L. Davis, PharmD, Nothing to disclose Michael J. Rybak, PharmD, MPH, PhD, Paratek Pharmaceuticals (Research Grant or Support)

Clinical Efficacy of Ceftazidime-Avibactam in the Treatment of Infections Caused by Carbapenem–Resistant Gram-Negative Bacteria

The wide spread of carbapenemases among gram-negative bacteria of the Enterobacterales order in hospitals around the world, including Russia, creates great difficulties in the effective use of antibiotics for these infections in the ICU. Ceftazidime-avibactam is the first antibiotic developed and studied for the treatment of infections caused by carbapenem-resistant enterobacteria. Ceftazidime-avibactam shows high activity against producers of class A and D serine carbapenemases (KPC and OXA-48). In combination with aztreonam it is effective in infections caused by producers of class B metallo-beta-lactamases (NDM and VIM). The review analyzes the results of 19 non-comparative and 10 comparative studies of ceftazidime-avibactam in infections caused by carbapenem-resistant Enterobacterales, as well as case reports. According to the data of non- comparative studies, the clinical efficacy of ceftazidime-avibactam ranged from 45.0 to 87.2%, on average 71.7±11.3%, and the eradication rate of KPC or OXA-48 carbapenemase producers ranged from 40.0 to 100%, on average 65.5±18.6%. The effectiveness of ceftazidime-avibactam in comparative studies was 67.9±17.3%, which was significantly higher compared to other antibiotics (44.3±14.4%,P=0.012). Treatment with ceftazidime-avibactam was accompanied by a significantly lower 30-day mortality in contrast to other antibiotics – 23.8±13.5% and 41.0±13.6%, respectively,P=0.001. The development of resistance in Enterobacterales species to ceftazidime-avibactam during therapy is rarely observed, on average 5.4±4.4%, which characterizes a rather low potential of the antibiotic in resistance selection. Early administration of ceftazidime-avibactam is accompanied by better treatment results as opposed to delayed therapy. Treatment of infections caused by carbapenem-resistant enterobacteria with ceftazidime-avibactam is associated with a significantly higher recovery rate and a lower mortality compared to other regimens of antibacterial therapy.

A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage.

Enterobacterales from livestock are potentially important reservoirs for antimicrobial resistance (AMR) to pass through the food chain to humans, thereby increasing the AMR burden and affecting our ability to tackle infections. In this study 168 isolates from four genera of the order Enterobacterales , primarily Escherichia coli , were purified from livestock (cattle, pigs and sheep) faeces from 14 farms in the United Kingdom. Their genomes were resolved using long- and short-read sequencing to analyse AMR genes and their genetic context, as well as to explore the relationship between AMR burden and on-farm antimicrobial usage (AMU), in the three months prior to sampling. Although E. coli isolates were genomically diverse, phylogenetic analysis using a core-genome SNP tree indicated pig isolates to generally be distinct from sheep isolates, with cattle isolates being intermediates. Approximately 28 % of isolates harboured AMR genes, with the greatest proportion detected in pigs, followed by cattle then sheep; pig isolates also harboured the highest number of AMR genes per isolate. Although 90 % of sequenced isolates harboured diverse plasmids, only 11 % of plasmids (n=58 out of 522) identified contained AMR genes, with 91 % of AMR plasmids being from pig, 9 % from cattle and none from sheep isolates; these results indicated that pigs were a principle reservoir of AMR genes harboured by plasmids and likely to be involved in their horizontal transfer. Significant associations were observed between AMU (mg kg−1) and AMR. As both the total and the numbers of different antimicrobial classes used on-farm increased, the risk of multi-drug resistance (MDR) in isolates rose. However, even when AMU on pig farms was comparatively low, pig isolates had increased likelihood of being MDR; harbouring relatively more resistances than those from other livestock species. Therefore, our results indicate that AMR prevalence in livestock is not only influenced by recent AMU on-farm but also livestock-related factors, which can influence the AMR burden in these reservoirs and its plasmid mediated transmission.

Инфекции мочевых путей у новорожденных детей: микробный пейзаж и проблемы антибиотикорезистентности

Urinary tract infection is one of the most common bacterial infections in children, which in 30% of cases may be the first manifestation of the presence of congenital malformations of the urinary tract and urodynamic disorders in a child. Late diagnosis, initiation of therapy, and the choice of an inadequate antimicrobial drug increase the risks of disease progression, development of nephrosclerosis and patient disability. Purpose – to study the microbial landscape in urinary tract infections, its antibiotic resistance in newborns with anomalies in the development of the urinary system. Materials and methods. The results of microbiological examination of urine in newborns with urinary tract infections against the background of anomalies in the development of the urinary tract, which are being treated in intensive care units and neonatal pathology in the period 2016–2020, have been analyzed. Results. The main causative agents of urinary tract infections in newborns with anomalies of the urinary system are Enterobacterales (63.4%), 13.8% are producers of extended spectrum beta-lactamases. Cefoperazone/sulbactam, amikacin, meropenem and nitrofurantoin were most active against Escherichia coli. In relation to other representatives of the order Enterobacterales, only amikacin was highly active. The strains of Enterococcus spp., Detected in 20%, were resistant to reserve vancomycin in every fourth case. Representatives of non-fermenting gram-negative bacteria were found in 6.4% of cases, resistance to the main titrated antibiotics ranged from 44.4% to 100%. Conclusions. The main causative agents of urinary tract infections in newborns with anomalies of the urinary system are representatives of the order Enterobacterales, Enterococcus spp. and non-fermenting gram-negative bacteria, which were characterized by high resistance, including to reserve antibiotics. The high indices of resistance of the isolated microflora make it difficult to choose an effective antibacterial therapy in this category of patients and in most cases requires combined antibiotic therapy. The research was carried out in accordance with the principles of the Helsinki declaration. The study protocol was approved by the Local ethics committee of all participating institution. The informed consent of the patient was obtained for conducting the studies. No conflict of interest was declared by the authors. Key words: Urinary tract infection, newborn babies, urinary tract abnormalities, antibiotic resistance.