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Objective: To address the research gap in the epidemiology of pediatric respiratory tract infections (RTIs) in Luzhou, Southern Sichuan, China, by analyzing respiratory pathogens in a large pediatric cohort from 2018 to 2021, covering the pre- and during-COVID-19 periods. Methods: This study conducted a retrospective analysis of children with RTIs in Luzhou from July 2018 to January 2021. Strict exclusion criteria were applied to ensure an accurate representation of the pediatric population. Pathogen detection included viruses, bacteria, and atypical agents. Results: Pathogens were identified in 52.8% of 12,546 cases. Viruses accounted for 32.2% of infections, bacteria for 29.8%, and atypical agents for 29.7%, with significant findings of Staphylococcus aureus, Moraxella catarrhalis, and Mycoplasma pneumoniae. Age-related analysis indicated a higher incidence of bacterial infections in infants and viral infections in preschool-aged children, with atypical pathogens being most prevalent in 3-5-year-olds. Gender-based analysis, adjusted for age, revealed similar overall pathogen presence; however, females were more susceptible to viral infections, while males were more prone to Streptococcus pneumoniae. Notably, there was an unusual increase in pathogen cases during spring, potentially influenced by behavioral changes and public health measures related to COVID-19. Co-infections were identified as a significant risk factor for the development of pneumonia. Conclusion: The study provides essential insights into the epidemiology of respiratory pathogens in pediatric populations, emphasizing the need for healthcare strategies tailored to age, gender, and seasonality. The findings highlight the impact of environmental and public health factors, including COVID-19 measures, on respiratory pathogen prevalence, underscoring the importance of targeted diagnostic and treatment protocols in pediatric respiratory infections.
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Springtails (Collembola) stand as one of the most abundant, widespread, and ancient terrestrial arthropods on earth. However, their evolutionary history and deep phylogenetic relationships remain elusive. In this study, we employed phylogenomic approaches to elucidate the basal relationships among Collembola. We sampled whole-genome data representing all major collembolan lineages in proportion to their known diversity. To account for potential phylogenomic biases, we implemented various data extraction, locus sampling, and signal filtering strategies to generate matrices. Subsequently, we applied a diverse array of tree-searching and rate-modelling methods to reconstruct the phylogeny. Our analyses, utilizing different matrices and methods, converged on the same unrooted relationships among collembolan ingroups, supporting the current ordinal classification and challenging the monophyly of Arthropleona and Symphypleona s.l. However, discrepancies across analyses existed in the root of Collembola. Among various root positions, those based on more informative matrices and biologically realistic models, favoring a basal topology of Entomobryomorpha + (Symphypleona s.s. + (Neelipleona + Poduromorpha)), were supported by subsequent methodological assessment, topology tests, and rooting analyses. This optimal topology suggests multiple independent reduction of the pronotum in non-poduromorph orders and aligns with the plesiomorphic status of neuroendocrine organs and epicuticular structure of Entomobryomorpha. Fossil-calibrated dating analyses based on the optimal topology indicated late-Paleozoic to mid-Mesozoic origins of the crown Collembola and four orders. In addition, our results questioned the monophyly of Isotomidae and Neanuridae, underscoring the need for further attention to the systematics of these families. Overall, this study provides novel insights into the phylogenetic backbone of Collembola, which will inform future studies on the systematics, ecology, and evolution of this significant arthropod lineage.
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OBJECTIVES: The emergence of carbapenem-resistant Pseudomonas putida (CRPP) has raised public awareness. This study investigated two strains from the Pseudomonas putida group that were resistant to carbapenem, tigecycline, and aztreonam-avibactam (ATM-AVI), with a focus on their microbial and genomic characteristics. METHODS: We assessed the antibiotic resistance profile using broth dilution, disk diffusion, and E-test methods. Efflux pump phenotype testing and real-time quantitative PCR were employed to evaluate efflux pump activity in tigecycline resistance, while polymerase chain reaction was utilized to detect common carbapenem genes. Additionally, whole-genome sequencing was performed to analyze genomic characteristics. The transferability of blaIMP-1 and blaAFM-4 was assessed through a conjugation experiment. Furthermore, growth kinetics and biofilm formation were examined using growth curves and crystal violet staining. RESULTS: Both strains demonstrated resistance to carbapenem, tigecycline, and ATM-AVI. Notably, NMP can restore sensitivity to tigecycline. Subsequent analysis revealed that they co-produced blaIMP-1, blaAFM-4, tmexCD-toprJ, and blaOXA-1041, belonging to a novel sequence type ST268. Although they were closely related on the phylogenetic tree, they exhibited different levels of virulence. Genetic environment analysis indicated variations compared to prior studies, particularly regarding the blaIMP-1 and blaAFM-4 genes, which showed limited horizontal transferability. Moreover, it was observed that temperature exerted a specific influence on their biological factors. CONCLUSION: We initially identified two P. putida ST268 strains co-producing blaIMP-1, blaAFM-4, blaOXA-1041, and tmexCD-toprJ. The resistance to tigecycline and ATM-AVI can be attributed to the presence of multiple drug resistance determinants. These findings underscore the significance of P. putida as a reservoir for novel antibiotic resistance genes. Therefore, it is imperative to develop alternative antibiotic therapies and establish effective monitoring of bacterial resistance.
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Antibacterianos , Compostos Azabicíclicos , Aztreonam , Testes de Sensibilidade Microbiana , Pseudomonas putida , Tigeciclina , beta-Lactamases , Pseudomonas putida/genética , Pseudomonas putida/efeitos dos fármacos , Tigeciclina/farmacologia , Antibacterianos/farmacologia , China , Aztreonam/farmacologia , Compostos Azabicíclicos/farmacologia , beta-Lactamases/genética , beta-Lactamases/metabolismo , Farmacorresistência Bacteriana Múltipla/genética , Sequenciamento Completo do Genoma , Humanos , Combinação de Medicamentos , Biofilmes/efeitos dos fármacos , Biofilmes/crescimento & desenvolvimento , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Infecções por Pseudomonas/microbiologia , Carbapenêmicos/farmacologiaRESUMO
Purpose: The isolation rate of carbapenem-resistant Enterobacter cloacae complex (CREC) is continuously increasing. The aims of this study were to investigate the molecular characteristics and risk factors associated with CREC infections. Methods: Bacterial species were identified using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) (Bruker Daltonik GmbH, Bremen, Germany), and the hsp60 gene was utilized for further typing. Antimicrobial susceptibilities were assessed through the MicroScan WalkAway 96 Plus system (Siemens, Germany) and the microbroth dilution method. Antimicrobial resistance genes were screened through polymerase chain reaction (PCR), while the homologous relationship was assessed using multilocus sequence typing (MLST). Conjugation experiments were performed to verify whether the plasmid could be transferred. Additionally, logistic regression model was employed to analyze risk factors for CREC infections. Results: 32 strains of CREC bacteria were isolated during the study, yet only 20 were retained for preservation. While the isolates demonstrated resistance to the majority of antibiotics, they exhibited high sensitivity to polymyxin B and tigecycline. All isolates carried the blaNDM resistance gene, including 13 blaNDM-1 isolates and 7 blaNDM-5 isolates. MLST homology analysis revealed the presence of seven known ST types and one new ST type. Conjugation experiments confirmed that 13 isolates were capable of transferring the blaNDM resistance gene to Escherichia coli strain EC600. Single-factor analysis identified multiple primary risk factors for CREC infection, but multivariate analysis did not reveal independent risk factors. Conclusion: This study investigates the molecular characteristics and risk factors associated with CREC infections. The detection rate of CREC strains in our hospital is continuously rising and homology analysis suggested that strains might spread in our hospital, emphasizing the importance of implementing effective preventive measures to control the horizontal transmission of plasmid-mediated antimicrobial resistance genes.
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Cutaneous mucormycosis with ischemic complications is a life-threatening condition with high mortality rates, particularly in immunocompromised individuals. The incidence of mucormycosis has increased during the COVID-19 pandemic due to reduced immunity. We present the case of a 17-year-old high school student who experienced a sprained left lower extremity, followed by worsening pain and swelling due to the topical application of unknown local herbs. Eighteen days after the injury, she was admitted to our department in a comatose state with left lower limb ischemia. The patient had a history of uncontrolled diabetes mellitus and displayed a necrotic lesion on her left ankle, suggestive of invasive infectious fungi disease. Diagnostic procedures, including tissue staining and molecular analysis, identified Rhizopus oryzae as the causative organism. Administering amphotericin B yielded marked improvement, but the patient necessitated a mid-thigh amputation to curtail the infection's advance, culminating in her successful discharge post-treatment.
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A novel nucleic acid aptamer nanoprobes-mediated hairpin allosteric and aptamer-assisted CRISPR system for detection of Streptococcus pneumoniae and Staphylococcus aureus is presented. In this fluorescence assay system, utilizing the hairpin allosteric effect caused by the aptamer binding to the target bacteria, the detection of S. pneumoniae is first achieved through changes in fluorescence due to FRET. Subsequently, a Cas12a protein mixture is added to detect S. aureus. The amplified output signal is triggered by two methods to ensure the sensitivity of the method: the synergistic FRET effect is achieved by the assembly of multi-aptamer through the conjugation of streptavidin-biotin, and the trans-cleavage function of CRISPR/Cas 12a. Under the optimized conditions, the proposed hairpin allosteric aptasensor could achieve high sensitivity (a detection limit of 135 cfu/mL) and broad-concentration quantification (dynamic range of 103-107 cfu/mL) of S. pneumoniae. The aptamer-assisted CRISPR system for S. aureus detection showed good linearity (R2 = 0.996) in the concentration range 102-108 cfu/mL, with a detection limit of 39 cfu/mL. No cross-reactivity with other foodborne pathogenic bacteria was observed in both systems. Taking only 55 min, this method of multiple pathogen detection proved to be promising.
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Aptâmeros de Nucleotídeos , Staphylococcus aureus Resistente à Meticilina , Staphylococcus aureus/genética , Aptâmeros de Nucleotídeos/genética , Streptococcus pneumoniae/genética , BactériasRESUMO
Introduction: The prevalence of diabetic foot ulcers (DFUs) is increasing, leading to a huge financial burden and human suffering. Furthermore, antibiotic resistance is an urgent problem in the realm of clinical practice. Antimicrobial peptides are an effective and feasible strategy for combating infections caused by drug-resistant bacteria. Therefore, we investigated the in vitro antimicrobial ability of the lipopeptide surfactin, either alone or in combination with conventional antibiotics, against the standard and clinical strains of Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), isolated from patients with DFUs. Methods: The minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) of surfactin on the selected strains were evaluated by a microbroth dilution technique. The growth curves of the selected strains with and without surfactin were measured, and transmission electron microscopy was used to observe the structure of surfactin-treated bacterial cells. The biofilm inhibitory abilities of surfactin were assessed by crystal violet staining. The antimicrobial interactions between surfactin and conventional antibiotics were established using a checkerboard assay, as well as determining the mutant prevention concentration. The inhibitory effect of surfactin on penicillinase was tested by iodometry. Results: The MIC and MBC values of surfactin ranged from 512 to 1024 µg/mL and 1024 to 2048 µg/mL, respectively. Moreover, surfactin significantly prevented the S. aureus biofilm formation and displayed limited toxicity on human red blood cells. The synergies between surfactin and ampicillin, oxacillin, and tetracycline against S. aureus were revealed. In vitro resistance was not readily produced by surfactin. The action of surfactin may be by disrupting bacterial cell membranes and inhibiting penicillinase. Conclusion: Surfactin appears to be a potential option for the treatment of DFUs infected with MRSA, as it is capable of improving antimicrobial activities and can be used alone or in combination with conventional antibiotics to prevent or postpone the emergence of resistance.
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Colistin is highly promising against multidrug-resistant and extensively drug-resistant bacteria clinically. Bacteria are resistant to colistin mainly through mcr and chromosome-mediated lipopolysaccharide (LPS) synthesis-related locus variation. However, the current understanding cannot fully explain the resistance mechanism in mcr-negative colistin-resistant strains. Significantly, the contribution of efflux pumps to colistin resistance remains to be clarified. This review aims to discuss the contribution of efflux pumps and their related transcriptional regulators to colistin resistance in various bacteria and the reversal effect of efflux pump inhibitors on colistin resistance. Previous studies suggested a complex regulatory relationship between the efflux pumps and their transcriptional regulators and LPS synthesis, transport, and modification. Carbonyl cyanide 3-chlorophenylhydrazone (CCCP), 1-(1-naphthylmethyl)-piperazine (NMP), and Phe-Arg-ß-naphthylamide (PAßN) all achieved the reversal of colistin resistance, highlighting the role of efflux pumps in colistin resistance and their potential for adjuvant development. The contribution of the efflux pumps to colistin resistance might also be related to specific genetic backgrounds. They can participate in colistin tolerance and heterogeneous resistance to affect the treatment efficacy of colistin. These findings help understand the development of resistance in mcr-negative colistin-resistant strains.
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BACKGROUND: Data on persistent candidemia (PC), a recognized complication of candidemia, are lacking in China. This study aimed to investigate the clinical characteristics and risk factors for the mortality of PC among adults in China. METHODS: This 6-year retrospective study analyzed the prevalence, species distribution, antifungal susceptibility, risk factors, and patient mortality of PC among adults in three regional tertiary teaching hospitals in China from 2016 to 2021. We collected electronic laboratory records data of PC and non-PC patients and used the Student test or Mann-Whitney U test for a retrospective study. Logistic regression was used to identify risk factors associated with persistent candidemia. RESULTS: The definition of PC was fulfilled by 36 patients (13.7%, 36/263). The mean age of the patients was 59.9 years (60 years for patients with PC; 59.8 years for those with non-PC; P > 0.05) and 131 (60.1%) were men [16 with PC (44.4%), 115 with non-PC (63.2%), P < 0.05]. The mean annual incidence was 0.15/1000 admissions (including PC 0.03/1000 admissions vs. non-PC 0.12/1000 admissions, P < 0.05). Candida parapsilosis (14/36, 38.9%) and Candida albicans (81/182, 44.5%) were the predominant pathogens in patients with PC and non-PC, respectively. Most isolates were susceptible to flucytosine (99.0%) and amphotericin B (99.5%), and the activity of antifungal agents against Candida species was not statistically significantly different between patients with PC and non-PC (P > 0.05). The 30-day mortality rate was 20.2% (16.7% with PC vs. 20.9% with non-PC, P > 0.05). Multivariable regression analysis showed that use of broad-spectrum antibiotics (odds ratio (OR), 5.925; 95% confidence interval (CI), 1.886-18.616, P = 0.002), fluconazole (OR, 3.389; 95% CI, 1.302-8.820, P = 0.012) and C. parapsilosis infection (OR, 6.143; 95% CI, 2.093-18.031, P = 0.001) were independent predictors of PC, sex (male) (OR, 0.199; 95% CI, 0.077-0.518, P = 0.001) was the protective factor for PC. Respiratory dysfunction (OR, 5.763; 95% CI, 1.592-20.864, P = 0.008) and length of hospital stay(OR, 0.925; 95% CI, 0.880-0.973, P = 0.002) were independent predictors of 30-day mortality in patients with non-PC. C. tropicalis bloodstream infection (OR, 12.642; 95% CI, 1.059-150.951; P = 0.045) was an independent predictor of 30-day mortality in patients with PC. CONCLUSIONS: The epidemiological data of patients with PC and non-PC were different in the distribution of Candida species, the mean annual incidence and independent predictors of 30-day mortality. Flucytosine and amphotericin B could be used as first-choice drugs in the presence of PC infections.
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Antifúngicos , Candidemia , Humanos , Adulto , Masculino , Pessoa de Meia-Idade , Feminino , Antifúngicos/farmacologia , Antifúngicos/uso terapêutico , Candidemia/tratamento farmacológico , Candidemia/epidemiologia , Candidemia/microbiologia , Anfotericina B , Estudos Retrospectivos , Flucitosina , Testes de Sensibilidade Microbiana , Candida , Candida parapsilosis , Candida tropicalis , Fatores de Risco , China/epidemiologiaRESUMO
A rarely seen butterfly species, the large swallowtail butterfly Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae), endemic to the Chinese mainland, has been declared a state-protected animal in China since 2000, but its genome is not yet available. To obtain high-quality genome assembly and annotation, we sequenced the genome and transcriptome of P. elwesi using the PacBio and PromethION platforms, respectively. The final assembled genome was 358.51 Mb, of which 97.59% was anchored to chromosomes (30 autosomes and 1 Z sex chromosome), with a contig/scaffold N50 length of 6.79/12.32 Mb and 99.0% (n = 1367) BUSCO completeness. The genome annotation pointed to 36.82% (131.99 Mb) repetitive elements and 1296 non-coding RNAs in the genome, along with 13,681 protein-coding genes that cover 98.6% (1348) of the BUSCO genes. Among the 11,499 identified gene families, 104 underwent significantly rapid expansions or contractions, and these rapidly expanding families play roles in detoxification and metabolism. Additionally, strong synteny exists between the chromosomes of P. elwesi and P. machaon. The chromosome-level genome of P. elwesi could serve as an important genomic resource for furthering our understanding of butterfly evolution and for more in-depth genomic analyses.
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Entomobryoidea has been the focus of phylogenetic studies in recent years owing to a divergence between morphological and genetic data. Recent phylogenies have converged on the sister relationship of Orchesellidae with the remaining Entomobryoidea, and on the non-monophyly of the traditional Paronellidae and Entomobryidae, but still lack resolution. Known molecular phylogenies of the superfamily differ greatly between mitogenomic and multilocus markers. For this reason, we designed universal single-copy orthologue (USCO) and ultraconserved element (UCE) marker sets specific for Entomobryoidea, based on 11 genome assemblies. Upon the newly designed 3406 USCOs and 4030 UCEs, we analysed 34 species covering all Entomobryoidea families and major subfamilies. New data for 26 species were mined from whole-genome sequencing. Phylogenetic inference confirmed the Orchesellidae as an independent family and the Entomobryinae remained the most puzzling taxon gathering scaled and unscaled lineages of both traditional Entomobryidae and Paronellidae. To accommodate Paronellides, Zhuqinia and related genera, Paronellidinae subfam. nov. is proposed within Entomobryidae. The sampled representatives of Paronellinae were recovered as the sister group of (Seirinae+Lepidocyrtinae), suggesting that reduction on the dorsal macrochaetotaxy and trunk sensillar pattern may have occurred independently within the Lepidocyrtinae and Paronellinae or represent their symplesiomorphy posteriorly modified in the Seirinae. The current systematics of the superfamily are revised here, with Entomobryidae now comprising six subfamilies, including all taxa with smooth dens. Our data also point out that all the main events of cladogenesis of the families and subfamilies of Entomobryoidea occurred during the Jurassic. Our genome-scale phylogenomics provides a complete, reliable example for systematics of Entomobryoidea, as well as other invertebrates in the big data era.
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Artrópodes , Humanos , Animais , Filogenia , Artrópodes/genética , Especiação GenéticaRESUMO
Callyntrura(s.l.) Börner, 1906 is the largest genus of the subfamily Salininae and contains 11 subgenera and 98 species from all over the world (mainly Asia), with eight species recorded from China. In the present paper, three new species of Callyntrura(s.l.) are described from China: C. (Japonphysa) xinjianensissp. nov.; C. (J.) tongguensissp. nov. and C. (J.) raoisp. nov. Their differences in colour pattern, chaetotaxy and other characters are slight, however distances of COI mtDNA support their validation as three new distinct species. A key to the Chinese Callyntrura(s.l.) is provided.
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Vibrio cholerae is a bacterium ubiquitous in aquatic environments which can cause widespread infection worldwide. V. cholerae gradually became a rare species of bacteria in clinical microbiology laboratories with the control of the cholera epidemic. In this study, we isolated a V. cholerae strain, named VCHL017, from the blood of an elderly patient without gastrointestinal symptoms. The patient had a history of hookworm infection and multiple myeloma. Furthermore, she was immunocompromised, and received long-term chemotherapy and antimicrobial agents. VCHL017 was inoculated on blood agar and thiosulfate citrate bile salt sucrose plates (TCBS) to observe morphological characteristics. Then this isolate was identified by matrix-assisted laser desorption/ionization time-of-flight spectrometry (MALDI-TOF MS). The minimum inhibitory concentrations (MICs) for cefazolin, ceftazidime, cefepime, meropenem, tetracycline, ciprofloxacin, chloramphenicol, and gentamicin of VCHL017 were determined by the microbroth dilution method. PCR and serum agglutination tests were used to determine whether the serogroups of the isolate belonged to the O1/O139 and cholera toxin encoding genes. Finally, the genomic features and phylogeny of VCHL017 were analyzed by whole genome sequencing (WGS). VCHL017 was a non-O1/O139 V cholerae strain that did not carry the ctxA gene. Antimicrobial susceptibility tests revealed that VCHL017 was susceptive to chloramphenicol and tetracycline. Although it did not carry the genes encoding the cholera toxin, WGS indicated that VCHL017 carried a variety of other virulence factors. By calculating the average nucleotide identity (ANI), we precisely identified the species of VCHL017 as V. cholerae. There are also A171S and A202S missense mutations in gyrA of VCHL017. The phylogenetic analysis indicated that VCHL017 was closely related to V. cholerae strains isolated from aquatic environments. Our results suggest that continuous monitoring is necessary for non-O1/O139 V cholerae strains isolated from outside the digestive tract, which could be pathogenic through multiple virulence factors.
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Carbapenem-resistant Acinetobacter baumannii (CRAB) has become one of the leading causes of healthcare-associated infections globally, particularly in intensive care units (ICUs). Cross-transmission of microorganisms between patients and the hospital environment may play a crucial role in ICU-acquired CRAB colonization and infection. The control and treatment of CRAB infection in ICUs have been recognized as a global challenge because of its multiple-drug resistance. The main concern is that CRAB infections can be disastrous for ICU patients if currently existing limited therapeutic alternatives fail in the future. Therefore, the colonization, infection, transmission, and resistance mechanisms of CRAB in ICUs need to be systematically studied. To provide a basis for prevention and control countermeasures for CRAB infection in ICUs, we present an overview of research on CRAB in ICUs, summarize clinical infections and environmental reservoirs, discuss the drug resistance mechanism and homology of CRAB in ICUs, and evaluate contemporary treatment and control strategies.
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Extensively drug-resistant and hypervirulent Klebsiella pneumoniae (XDR-hvKp) is a new problem for patients in Intensive Care Unit (ICU) and can become an even more severe threat if resistant to tigecycline, considered one of the 'last lines of defense' drugs. This study collected seven non-replicated tigecycline-resistant XDR-hvKp from seven patients and performed genome analysis and epidemiological investigation using whole genome equencing (WGS) and other methods. All strains in this study were identified as ST11-KL64 and showed high resistance to antibiotics such as ß-lactams, aminoglycosides, quinolones, and tigecycline, and one strain was also resistant to colistin. All strains were determined to be hvKp by the results of serum resistance assay and Galleria mellonella infection models. All strains had resistance genes bla CTX-M-65,bla KPC-2,bla LAP-2,bla TEM-1B, rmtB, and qnrS1 and virulence factors such as rmpA, rmpA2, and aerobactin (iucABCD, iutA). The expression of the AcrAB-TolC efflux pump was upregulated in all strains, and the expression levels of the gene pmrK was significantly upregulated in colistin-resistant strain DP compared to colistin-sensitive strain WT in this study. In conclusion, we described an outbreak caused by tigecycline-resistant XDR-hvKp in the ICU of a teaching hospital in southwest China. The spread of these superbugs poses a great threat to patients and therefore requires us to closely monitor these XDR-hvKp and develop relevant strategies to combat them.
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Infecções por Klebsiella , Quinolonas , Aminoglicosídeos , Antibacterianos/farmacologia , China/epidemiologia , Colistina/farmacologia , Surtos de Doenças , Hospitais de Ensino , Humanos , Unidades de Terapia Intensiva , Infecções por Klebsiella/epidemiologia , Klebsiella pneumoniae/genética , Tigeciclina/farmacologia , Virulência/genética , Fatores de Virulência/genética , beta-LactamasRESUMO
Background: Colistin is one of the few options for treating carbapenem-resistant Enterobacterales (CREs). There is little available information about the epidemic status of colistin-resistant CREs in Southern Sichuan, China. This study mainly investigated the genomic and phenotypic characteristics of an extensively drug resistant E. coli LZ00114 isolated from Luzhou, China. Materials and Methods: In 2020, LZ00114 was isolated from the urine of a patient with hydronephrosis and urinary tract infection in Luzhou, China. We assessed the resistance profile of LZ00114 in the presence and absence of the protonophore carbonyl cyano-m-chlorophenylhydrazine (CCCP) and 1-(1-naphthylmethyl)-piperazine (NMP) by antimicrobial susceptibility testing. The growth kinetics, motility, and pathogenicity of LZ00114 were determined to evaluate its microbial characteristics. In combination with whole genome sequencing (WGS) and real-time reverse transcription PCR (RT-PCR), we comprehensively analyzed the resistance mechanisms of LZ00114. Results: LZ00114 was resistant to various antimicrobial agents, including meropenem, tetracycline, ciprofloxacin, gentamicin, fosfomycin, and polymyxin B. Notably, CCCP reversed the resistance of LZ00114 to polymyxin B. LZ00114 displayed high pathogenicity in the infection model (P<0.01) compared with the Lab-WT strain, and its growth rate and motility were not significantly different from the Lab-WT strain. WGS and conjugation revealed that LZ00114 belonged to ST410 and carried a bla NDM-5-harboring self-transmissible IncX3 plasmid and a multi-replicon IncFII/FIA/FIB plasmid carrying bla OXA-1-bla CTX-M-55-tet(B)-aac(6')-Ib-cr-dfrA17-sul1-fosA3. Comparative genomics revealed genetic relatedness between LZ00114 and strains isolated from other regions. Furthermore, there were point mutations in pmrA (S29G, G144S), pmrB (D283G, Y358N), marR (G103S, Y137H), emrA (I219V), and emrD (G323D) of LZ00114. RT-PCR confirmed the overexpression of efflux pumps and PmrABC in LZ00114. Conclusion: This study provides valuable information for the surveillance of antimicrobial resistance and a theoretical basis for the prevention and control of colistin-resistant E. coli. There is still a need to be vigilant about the clone spread of the high-risk clone group E. coli ST410.
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Soil has become a major hotspot of biodiversity studies, yet the pattern and timing of the evolution of soil organisms are poorly known because of the scarcity of paleontological data. To overcome this limitation, we conducted a genome-based macroevolutionary study of an ancient, diversified, and widespread lineage of soil fauna, the elongate-bodied springtails (class Collembola, order Entomobryomorpha). To build the first robust backbone phylogeny of this previously refractory group, we sampled representatives of major higher taxa (6 out of 8 families, 11 out of 16 subfamilies) of the order with an emphasis on the most problematic superfamily Tomoceroidea, applied whole-genome sequencing methods, and compared the performance of different combinations of data sets (universal single-copy orthologs [USCO] vs. ultraconserved elements]) and modeling schemes. The fossil-calibrated timetree was used to reconstruct the evolution of body size, sensory organs, and pigmentation to establish a time frame of the ecomorphological divergences. The resultant trees based on different analyses were congruent in most nodes. Several discordant nodes were carefully evaluated by considering method fitness, morphological information, and topology test. The evaluation favored the well-resolved topology from analyses using USCO amino acid matrices and complex site-heterogeneous models (CAT$+$GTR and LG$+$PMSF (C60)). The preferred topology supports the monophyletic superfamily Tomoceroidea as an early-diverging lineage and a sister relationship between Entomobryoidea and Isotomoidea. The family Tomoceridae was recovered as monophyletic, whereas Oncopoduridae was recovered as paraphyletic, with Harlomillsia as a sister to Tomoceridae and hence deserving a separate family status as Harlomillsiidae Yu and Zhang fam. n. Ancestral Entomobryomorpha were reconstructed as surface-living, supporting independent origins of soil-living groups across the Paleozoic-Mesozoic, and highlighting the ancient evolutionary interaction between aboveground and belowground fauna. [Collembola; phylogenomics; soil-living adaptation; whole-genome sequencing.].
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Artrópodes , Animais , Ecossistema , Fósseis , Filogenia , SoloRESUMO
Hypervirulent Klebsiella pneumoniae (hvKp) has been globally disseminated recently, especially in Asia. The purpose of this study was to identify the molecular characteristics, clinical manifestations, and clinical risk factors of hvKp infections among patients in a large teaching hospital. A retrospective study was conducted in 123 patients infected with K. pneumoniae at the Affiliated Hospital of Southwest Medical University (Luzhou, China) from October 2016 to November 2018. An isolate that positive for both PCR amplification of aerobactin gene and Galleria mellonella infection model was defined as hvKp. Overall, 43.1% (53/123) of K. pneumoniae isolates were hvKp. String tests were performed on all isolates, and MLSTs of all hvKp were conducted. The K1 ST23 isolates were the dominant clone of hvKp (35.8%). Univariate analysis revealed the following risk factors for hvKp: hepatic abscess (OR = 41.818 [95% CI, 5.379-335.086]), bacteremia (OR = 19.94 [95% CI, 5.565-71.446]), metastatic spread (OR = 19.938 [95% CI, 6.344-62.654]), CRP (OR = 1.008 [95% CI, 1.001-1.015]), nitroimidazole treatment (OR = 7.907 [95% CI, 1.652-37.843]), diabetes (OR = 3.067 [95% CI, 1.38-6.817]), and admission to positive culture interval (OR = 3.636 [95% CI, 1.524-8.678]). Moreover, Multivariate analysis implicated hepatic abscess (OR = 74.332 [95% CI, 3.121-1769.588]), bacteremia (OR = 28.388 [95% CI, 3.039-264.200]), and metastatic spread (OR = 19.391 [95% CI, 3.633-103.498]) as independent risk factors for hvKp infections. Thirteen of twenty-one tested antibiotics were founded resistant to non-hvKp, which is significantly greater than hvKp. Importantly, the ESBL-hvKp and MDR-hvKp were responsible for 7.5% and 15.1% in the hvKp group, respectively.
Assuntos
Infecções por Klebsiella , Klebsiella pneumoniae , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , China/epidemiologia , Hospitais de Ensino , Humanos , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/epidemiologia , Klebsiella pneumoniae/genética , Estudos Retrospectivos , Fatores de Risco , VirulênciaRESUMO
OBJECTIVE: This study aimed to determine the clinical manifestations, antimicrobial resistance, molecular characteristics, and risk factors for ESKAPE pathogens infection in burn patients. METHODS: A retrospective study of 187 burn patients infected with ESKAPE pathogens was conducted at the Department of Plastic and Burn Surgery of the Affiliated Hospital of Southwest Medical University (Luzhou, China) from October 2018 to June 2021. All strains were identified using a MicroScan WalkAway 96 Plus System, and antimicrobial susceptibilities were determined using the VITEK system or the disk diffusion method. The antimicrobial resistance genes of multi-drug resistant ESKAPE (MDR-ESKAPE) were detected by polymerase chain reaction (PCR). The multivariable logistic regression analysis was used to estimate the risk factors for ESKAPE infection and MDR-ESKAPE infection. RESULTS: A total of 255 strains were isolated in various types of clinical specimens from 187 burn patients, of which 47.5% were ESKAPE pathogens (121/255). Among these, MDR-ESKAPE pathogens accounted for 55% (67/121). Additionally, aph3'III, mecA, bla SHV, bla TEM, bla PDC, and bla SHV were the most prevalent genes detected in Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp., respectively. The independent risk factors for ESKAPE infection were total body surface area (TBSA) >30-50% (odds ratio [OR] = 10.428; 95% confidence interval [CI], 2.047 to 53.108), TBSA >50% (OR = 15.534; 95% CI, 1.489 to 162.021), and parenteral nutrition (OR = 3.597; 95% CI, 1.098 to 11.787). No independent risk factors were found for MDR-ESKAPE infection. CONCLUSION: Clinical staff should be alert to the risk of nosocomial infection with ESKAPE pathogens in burn patients receiving parenteral nutrition and under TBSA >30%. Full attention should also be paid to the ESKAPE resistance, strict adherence to infection control protocols for the rational use of antimicrobial agents, and enhanced clinical standardization of antimicrobial agents management.