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Antimicrobial Agents and Chemotherapy Feb 2018Carbapenem-resistant (CRE) infection is highly endemic in China, but estimates of the infection burden are lacking. We established the incidence of CRE infection from a...
Carbapenem-resistant (CRE) infection is highly endemic in China, but estimates of the infection burden are lacking. We established the incidence of CRE infection from a multicenter study that covered 25 tertiary hospitals in 14 provinces. CRE cases defined as carbapenem-nonsusceptible , , , or infections during January to December 2015 were collected and reviewed from medical records. Antimicrobial susceptibility testing and carbapenemase gene identification were performed. Among 664 CRE cases, most were caused by (73.9%), followed by (16.6%) and (7.1%). The overall CRE infection incidence per 10,000 discharges was 4.0 and differed significantly by region, with the highest in Jiangsu (14.97) and the lowest in Qinghai (0.34). Underlying comorbidities were found in 83.8% of patients; the median patient age was 62 years (range, 45 to 74 years), and 450 (67.8%) patients were male. Lower respiratory tract infections (65.4%) were the most common, followed by urinary tract infection (16.6%), intra-abdominal infection (7.7%), and bacteremia (7.7%). The overall hospital mortality rate was 33.5%. All isolates showed nonsusceptibility to carbapenems and cephalosporins. The susceptibility rate of polymyxin B was >90%. Tigecycline demonstrated a higher susceptibility rate against than against (90.9% versus 40.2%). Of 155 clinical isolates analyzed, 89% produced carbapenemases, with a majority of isolates producing KPC (50%) or NDM (33.5%)-type beta-lactamases among and The incidence of CRE infection in China was 4.0 per 10,000 discharges. The patient-based disease burden in tertiary hospitals in China is severe, suggesting an urgent need to enhance infection control.
Topics: Aged; Anti-Bacterial Agents; Bacteremia; Bacterial Proteins; Carbapenem-Resistant Enterobacteriaceae; Carbapenems; China; Citrobacter freundii; Enterobacter cloacae; Enterobacteriaceae Infections; Escherichia coli; Female; Humans; Klebsiella Infections; Klebsiella pneumoniae; Male; Microbial Sensitivity Tests; Middle Aged; Polymyxin B; Urinary Tract Infections; beta-Lactamases
PubMed: 29203488
DOI: 10.1128/AAC.01882-17 -
Journal of Microbiological Methods Sep 2022The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated proteins) system is a useful tool to edit genomes quickly and efficiently....
The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated proteins) system is a useful tool to edit genomes quickly and efficiently. However, the use of CRISPR/Cas9 to edit bacterial genomes has been limited to select microbial chassis primarily used for bioproduction of high value products. Thus, expansion of CRISPR/Cas9 tools to other microbial organisms is needed. Here, our aim was to assess the suitability of CRISPR/Cas9 for genome editing of the Citrobacter freundii type strain ATCC 8090. We evaluated the commonly used two plasmid pCas/pTargetF system to enable gene deletions and insertions in C. freundii and determined editing efficiency. The CRISPR/Cas9 based method enabled high editing efficiency (~91%) for deletion of galactokinase (galk) and enabled deletion with various single guide RNA (sgRNA) sequences. To assess the ability of CRISPR/Cas9 tools to insert genes, we used the fluorescent reporter mNeonGreen, an endopeptidase (yebA), and a transcriptional regulator (xylS) and found successful insertion with high efficiency (81-100%) of each gene individually. These results strengthen and expand the use of CRISPR/Cas9 genome editing to C. freundii as an additional microbial chassis.
Topics: CRISPR-Cas Systems; Citrobacter freundii; Gene Editing; Genome, Bacterial
PubMed: 35779647
DOI: 10.1016/j.mimet.2022.106533 -
Journal of Global Antimicrobial... Jun 2022Citrobacter freundii is an important opportunistic pathogen, and carbapenem-resistant strains pose a significant challenge to public health. Here we report the genetic...
OBJECTIVES
Citrobacter freundii is an important opportunistic pathogen, and carbapenem-resistant strains pose a significant challenge to public health. Here we report the genetic features of antimicrobial resistance genes of a carbapenem-resistant C. freundii SCLZS47 from hospital sewage by using whole genome sequencing.
METHODS
Antimicrobial susceptibility was determined by the broth microdilution method. Whole genomic sequences of SCLZS47 were obtained by using the HiSeq 2000 combined with PacBio RSII platforms. Plasmid incompatibility types, resistance genes, and insertion elements were identified using the PlasmidFinder, ResFinder, and ISfinder, respectively.
RESULTS
SCLZS47 has a circular chromosome and three resistance plasmids, and it carries 23 known ARGs. Among them, bla and three copies of bla are located on the chromosome. Sixteen ARGs are clustered in two accessory modules of a multidrug resistance (MDR) plasmid, and homologous recombination and transposition events contribute to the formation of these MDR regions. Carbapenemase genes bla and bla are carried by a pCKPC18-1-like plasmid and a pNDM-HN380-like plasmid, respectively. Conjugation experiments indicated that both KPC-2- and NDM-1-encoding plasmids are transmissible.
CONCLUSION
Analysis of the genetic features of resistance genes would help to better understand their transmission mechanisms and dynamics in bacterial community, which has significant clinical implications.
Topics: Carbapenems; Citrobacter freundii; Genomics; Plasmids; beta-Lactamases
PubMed: 35489677
DOI: 10.1016/j.jgar.2022.04.014 -
AMB Express Oct 2020Fenvalerate is a pyrethroid insecticide with rapid action, strong targeting, broad spectrum, and high efficiency. However, continued use of fenvalerate has resulted in...
Fenvalerate is a pyrethroid insecticide with rapid action, strong targeting, broad spectrum, and high efficiency. However, continued use of fenvalerate has resulted in its widespread presence as a pollutant in surface streams and soils, causing serious environmental pollution. Pesticide residues in the soil are closely related to food safety, yet little is known regarding the kinetics and metabolic behaviors of fenvalerate. In this study, a fenvalerate-degrading microbial strain, CD-9, isolated from factory sludge, was identified as Citrobacter freundii based on morphological, physio-biochemical, and 16S rRNA sequence analysis. Response surface methodology analysis showed that the optimum conditions for fenvalerate degradation by CD-9 were pH 6.3, substrate concentration 77 mg/L, and inoculum amount 6% (v/v). Under these conditions, approximately 88% of fenvalerate present was degraded within 72 h of culture. Based on high-performance liquid chromatography and gas chromatography-mass spectrometry analysis, ten metabolites were confirmed after the degradation of fenvalerate by strain CD-9. Among them, o-phthalaldehyde is a new metabolite for fenvalerate degradation. Based on the identified metabolites, a possible degradation pathway of fenvalerate by C. freundii CD-9 was proposed. Furthermore, the enzyme localization method was used to study CD-9 bacteria and determine that its degrading enzyme is an intracellular enzyme. The degradation rate of fenvalerate by a crude enzyme solution for over 30 min was 73.87%. These results showed that strain CD-9 may be a suitable organism to eliminate environmental pollution by pyrethroid insecticides and provide a future reference for the preparation of microbial degradation agents and environmental remediation.
PubMed: 33125615
DOI: 10.1186/s13568-020-01128-x -
Frontiers in Cellular and Infection... 2022As a common conditional pathogenic bacterium in nature, has posed a threat to crayfish culture and may infect humans through consumption. However, the pathogenic...
As a common conditional pathogenic bacterium in nature, has posed a threat to crayfish culture and may infect humans through consumption. However, the pathogenic mechanism of in crayfish remains unknown, which poses difficulties for the prevention and control of the bacterium. In this study, the effects of on the digestive organs, intestine and hepatopancreas, of crayfish were investigated by high-throughput sequencing technology combined with histological analysis and flow cytometry. The findings suggested that caused disruption of the intestinal microbiota, leading to intestinal inflammation and disrupting intestinal integrity. Meanwhile, infection stimulates bile acid biosynthesis in the intestinal microbiota. Transcriptomic results showed significant upregulation of hepatopancreatic lipid degradation pathway and cytochrome P450-related pathways. Follow-up experiments confirmed a decrease in intracellular lipids and an increase in ROS and apoptosis. All the results indicated the disruption of intestinal-liver axis homeostasis due to disturbed intestinal microbiota may as a potential basis for pathopoiesis in crayfish. These results provide new insights into the pathogenic molecular mechanisms of in the infection of crayfish.
Topics: Animals; Astacoidea; Citrobacter freundii; Gastrointestinal Microbiome; Homeostasis; Humans; Liver
PubMed: 35865811
DOI: 10.3389/fcimb.2022.940576 -
Annals of Medicine and Surgery (2012) Nov 2023Vaccination against coronavirus disease 2019 (COVID-19) is essential for controlling the ongoing cases of this disease. Citrobacter infections of the bones and joints...
INTRODUCTION
Vaccination against coronavirus disease 2019 (COVID-19) is essential for controlling the ongoing cases of this disease. Citrobacter infections of the bones and joints are extremely uncommon. Thromboembolism and deep vein thrombosis (DVT) are very rare complications.
CASE PRESENTATION
The authors present a rare case of osteomyelitis, septic arthritis, deep venous thrombosis, and pulmonary embolism in a 15-year-old previously healthy boy occurring shortly after receiving the second dose of the Moderna COVID-19 vaccine. He experienced pain, swelling in the right leg, shortness of breath, and fever, followed by chest pain and leg edema. Treatment included anticoagulation, ketorolac for pain management, antipyretics, and intravenous antibiotics (Tazobactam/Piperacillin, Linezolid, Clindamycin) for osteomyelitis.
DISCUSSION
The risk of COVID-19 vaccine-related thrombotic events is minimal. Thrombotic events reported among mRNA is very rare. bone and joint infections are very rare, accounting for a small percentage of cases. Some documented cases include cefotaxime-resistant strains causing necrotizing fascitis and osteomyelitis, including postarthroplasty infections. Due to the diverse range of susceptibility patterns and the widespread occurrence of drug resistance, personalized treatment based on culture and sensitivity testing is recommended. However, in rare cases, severe complications like DVT and joint infections associated with Citrobacter infection may occur and should be reported to the vaccine adverse events reporting system.
CONCLUSION
Administering the COVID-19 vaccine to enhance natural antibodies is crucial, despite the low risk of infection, thromboembolism, and DVT. Healthcare providers should stay vigilant about adverse effects postvaccination and promptly report those cases.
PubMed: 37915646
DOI: 10.1097/MS9.0000000000001351 -
Journal of Microbiology, Immunology,... Aug 2018Multidrug-resistant strains of Citrobacter have emerged, which carry Amp-C β-lactamase (Amp-C), broad-spectrum β-lactamase, extended-spectrum β-lactamase (ESBL), and...
BACKGROUND/PURPOSE
Multidrug-resistant strains of Citrobacter have emerged, which carry Amp-C β-lactamase (Amp-C), broad-spectrum β-lactamase, extended-spectrum β-lactamase (ESBL), and other resistance mechanisms. These strains are associated with a higher rate of in-hospital mortality. The object of this study is to determine the mortality risk factors, susceptibility pattern to antibiotics, and prevalence of resistance genes in patients with Citrobacter freundii bacteremia.
METHODS
From January 2009 to December 2014, blood isolates of C. freundii were collected in MacKay Memorial Hospital, Taipei, Taiwan. PCR technique and sequencing were performed for resistance genes. Pulsed-field gel electrophoresis (PFGE) was done using XbaI restriction enzyme. The clinical characteristics and risk factors for mortality are demonstrated.
RESULTS
The 36 blood isolates of C. freundii belonged to 32 different PFGE pulsotypes, and 15 isolates (41.7%) were polymicrobial. The most common source of infection was intra-abdominal origin (61.1%), followed by unknown sources (22.2%), the urinary tract (8.3%), intravascular catheter (5.6%), and soft tissue (2.8%). High degree of antibiotic resistance was noted for cefazolin (100%), cefoxitin (97.2%), and cefuroxime (66.7%). The bla resistance gene was present in 16.7% isolates. 72.2% isolates carried bla and 5.6% isolates carried ESBL genes (bla or bla). Multivariate analysis indicated that the independent risk factor for 28-day mortality was carrying the bla resistance gene.
CONCLUSION
For patients with C. freundii bacteremia, carrying the bla resistance gene was an independent risk factor for 28-day mortality. Carbapenems, fourth-generation cephalosporins, amikacin, and quinolones are still reliable agents for drug-resistant strains.
Topics: Adult; Aged; Aged, 80 and over; Anti-Bacterial Agents; Bacteremia; Citrobacter freundii; Drug Resistance, Bacterial; Electrophoresis, Gel, Pulsed-Field; Enterobacteriaceae Infections; Female; Genes, Bacterial; Humans; Male; Microbial Sensitivity Tests; Middle Aged; Polymerase Chain Reaction; Prevalence; Retrospective Studies; Risk Factors; Sequence Analysis, DNA; Survival Analysis; Taiwan; beta-Lactamases
PubMed: 28711438
DOI: 10.1016/j.jmii.2016.08.016 -
Antimicrobial Resistance and Infection... Jun 2023Accumulating evidence shows a role of the hospital wastewater system in the spread of multidrug-resistant organisms, such as carbapenemase producing Enterobacterales...
Sanitary installations and wastewater plumbing as reservoir for the long-term circulation and transmission of carbapenemase producing Citrobacter freundii clones in a hospital setting.
BACKGROUND
Accumulating evidence shows a role of the hospital wastewater system in the spread of multidrug-resistant organisms, such as carbapenemase producing Enterobacterales (CPE). Several sequential outbreaks of CPE on the geriatric ward of the Ghent University hospital have led to an outbreak investigation. Focusing on OXA-48 producing Citrobacter freundii, the most prevalent species, we aimed to track clonal relatedness using whole genome sequencing (WGS). By exploring transmission routes we wanted to improve understanding and (re)introduce targeted preventive measures.
METHODS
Environmental screening (toilet water, sink and shower drains) was performed between 2017 and 2021. A retrospective selection was made of 53 Citrobacter freundii screening isolates (30 patients and 23 environmental samples). DNA from frozen bacterial isolates was extracted and prepped for shotgun WGS. Core genome multilocus sequence typing was performed with an in-house developed scheme using 3,004 loci.
RESULTS
The CPE positivity rate of environmental screening samples was 19.0% (73/385). Highest percentages were found in the shower drain samples (38.2%) and the toilet water samples (25.0%). Sink drain samples showed least CPE positivity (3.3%). The WGS data revealed long-term co-existence of three patient sample derived C. freundii clusters. The biggest cluster (ST22) connects 12 patients and 8 environmental isolates taken between 2018 and 2021 spread across the ward. In an overlapping period, another cluster (ST170) links eight patients and four toilet water isolates connected to the same room. The third C. freundii cluster (ST421) connects two patients hospitalised in the same room but over a period of one and a half year. Additional sampling in 2022 revealed clonal isolates linked to the two largest clusters (ST22, ST170) in the wastewater collection pipes connecting the rooms.
CONCLUSIONS
Our findings suggest long-term circulation and transmission of carbapenemase producing C. freundii clones in hospital sanitary installations despite surveillance, daily cleaning and intermittent disinfection protocols. We propose a role for the wastewater drainage system in the spread within and between rooms and for the sanitary installations in the indirect transmission via bioaerosol plumes. To tackle this problem, a multidisciplinary approach is necessary including careful design and maintenance of the plumbing system.
Topics: Humans; Aged; Citrobacter freundii; Wastewater; Sanitary Engineering; Retrospective Studies; Hospitals; Clone Cells
PubMed: 37337245
DOI: 10.1186/s13756-023-01261-9 -
Annals of Clinical Microbiology and... Apr 2023Carbapenemase-producing gram-negative organisms continue to be a significant healthcare concern and a therapeutic challenge. Members of the genus Citrobacter have...
BACKGROUND
Carbapenemase-producing gram-negative organisms continue to be a significant healthcare concern and a therapeutic challenge. Members of the genus Citrobacter have emerged as increasingly multidrug resistant and versatile healthcare-associated pathogens. In this study we investigated five KPC-producing Citrobacter freundii isolates, from the same patient, that presented unusual phenotypic characteristics including false susceptibility to carbapenems detection by culture-based methods.
METHODS
The isolates were tested for antimicrobial susceptibility using broth microdilution and disk diffusion. Production of serine carbapenemase was confirmed with the mCIM (modified carbapenem inactivation method) test. Genotypes were determined by PCR and whole genome sequencing analysis.
RESULTS
The five isolates were susceptible to meropenem by broth microdilution and presented varying colonial morphologies and levels of susceptibility to carbapenems by multiple phenotypic methods, despite being positive for carbapenemase production by mCIM and positive for bla by PCR. Whole genome sequence analysis showed that three of the five highly related isolates harbor an additional gene cassette, including bla, ant(2''), aadA2, dfrA19, catB3, cmlA1, mph(E), msr(E), and qnrA1. The presence of these genes explains the difference in phenotypes observed.
CONCLUSION
Failure to detect and completely eradicate the carbapenemase-producing C. freundii in the urine with ertapenem therapy, likely due to the presence of a heterogeneous population, resulted in the phenotypic and genotypic adaptations of the organism as it disseminated to the bloodstream and kidneys. The fact that carbapenemase-producing C. freundii can elude detection by phenotypic methods and can so easily acquire and transfer resistance gene cassettes is of concern.
Topics: Citrobacter freundii; Anti-Bacterial Agents; Bacterial Proteins; beta-Lactamases; Carbapenems; Genotype; Phenotype; Microbial Sensitivity Tests
PubMed: 37055768
DOI: 10.1186/s12941-023-00579-x -
Applied and Environmental Microbiology Apr 2022Klebsiella pneumoniae carbapenemase (KPC) producers are an emerging threat to global health, and the hospital water environment is considered an important reservoir of...
Klebsiella pneumoniae carbapenemase (KPC) producers are an emerging threat to global health, and the hospital water environment is considered an important reservoir of these life-threatening bacteria. We characterized plasmids of KPC-2-producing Citrobacter freundii and Klebsiella variicola isolates recovered from hospital sewage in Japan. Antimicrobial susceptibility testing, whole-genome sequencing analysis, bacterial conjugation, and transformation experiments were performed for both KPC-2 producers. The gene was located on the Tn transposon-related region from an IncP-6 replicon plasmid that could not be transferred via conjugation. Compared to the -encoding plasmid of the C. freundii isolate, alignment analysis of plasmids with showed that the -encoding plasmid of the K. variicola isolate was a novel IncP-6/IncF-like hybrid plasmid containing a 75,218-bp insertion sequence composed of IncF-like plasmid conjugative transfer proteins. Carbapenem-resistant transformants harboring were obtained for both isolates. However, no IncF-like insertion region was found in the K. variicola donor plasmid of the transformant, suggesting that this IncF-like region is not readily functional for plasmid conjugative transfer and is maintained depending on the host cells. The findings on the KPC-2 producers and novel genetic content emphasize the key role of hospital sewage as a potential reservoir of pathogens and its linked dissemination of through the hospital water environment. Our results indicate that continuous monitoring for environmental emergence of antimicrobial-resistant bacteria might be needed to control the spread of these infectious bacteria. Moreover, it will help elucidate both the evolution and transmission pathways of these bacteria harboring antimicrobial resistance. Antimicrobial resistance is a significant problem for global health, and the hospital environment has been recognized as a reservoir of antimicrobial resistance. Here, we provide insight into the genomic features of -harboring isolates of Citrobacter freundii and Klebsiella variicola obtained from hospital sewage in Japan. The findings of carbapenem-resistant bacteria containing this novel genetic context emphasize that hospital sewage could act as a potential reservoir of pathogens and cause the subsequent spread of via horizontal gene transfer in the hospital water environment. This indicates that serial monitoring for environmental bacteria possessing antimicrobial resistance may help us control the spread of infection and also lead to elucidating the evolution and transmission pathways of these bacteria.
Topics: Anti-Bacterial Agents; Carbapenems; Citrobacter freundii; Hospitals; Japan; Klebsiella; Plasmids; Sewage; Water
PubMed: 35380451
DOI: 10.1128/aem.00019-22