The molecular characteristics of carbapenem-resistant Escherichia coli (CREco) remain unclear.
We conducted a multi-center bacterial resistance monitoring project from 2015 to 2017.The minimum ...inhibitory concentrations ofCREco were determined bybroth microdilution method. The genome sequencing of CREcoisolates was performed, and single-nucleotide polymorphism (SNP) was analyzed.
A total of 144CREcoisolatescollected from 10 cities in China were involved in this study. ST167 (n = 43) is the most popular type, followed by ST410(n = 14), ST131(n = 9). There were 102 (70.83%) CREco isolates that produced various NDMs, including NDM-1 (n = 16), NDM-4(n = 1), NDM-5(n = 79), NDM-6(n = 2) and NDM-9(n = 4). In addition, 15 isolates produced KPC-2, three isolates wereIMP-4 positive, and three isolates produced OXA-48. Genetic relatedness and phylogenetic analysis showed that isolates with the same ST had a high degree of homology. Some STs (including ST167, ST410, ST131, ST46, ST405 and ST617) exhibited a trend of outbreak.
The majority of CREco belonged to ST167, followed by ST410 and ST131, and most of them carried various NDM-coding genes. The spread of high-risk clones of CREco has occurred in different regions of China.
In China, the spread and outbreak of OXA-48-producing Enterobacteriaceae remains largely unknown.
OXA-48-producing isolates were analyzed for genetic relatedness by pulsed-field gel electrophoresis ...(PFGE), antimicrobial susceptibility by E-test, and sequence type (ST) by multilocus sequence typing. S1-PFGE and southern blotting were used for plasmid profiling, and PCR and subsequent sequencing were performed to determine the genetic environment of blaOXA-48 gene.
In total, 37 non-duplicated OXA-48-producing K. pneumoniae (OXAKp) isolates were recovered. From December 2013 to August 2014, an outbreak was observed at a respiratory ICU. The 37 isolates of K. pneumoniae were categorized into four PFGE types (A, B, C, and D). The predominant strains associated with the outbreak were strains with PFGE type A and B, which belonged to ST383 and ST147, respectively. Plasmid sequencing revealed that the blaOXA-48-carrying plasmid is 69,069 bp in length and belongs to the IncL/M incompatibility group. Sequence analysis revealed that the IS1999 element was located upstream of the blaOXA-48 gene and was truncated by IS1R.
In this study, the dissemination and outbreak of OXAKp isolates were clonal, and ST147 and ST383 K. pneumoniae were the predominant clones that were associated with the outbreak. Meanwhile, the horizontal transfer of plasmids potentially mediate the spread of blaOXA-48 gene between different K. pneumoniae strains.
Background The Stenotrophomonas maltophilia complex (Smc) has emerged as a significant nosocomial pathogen contributing to increased mortality rates, particularly in case of bloodstream infections. ...Methods This study employed whole-genome sequencing (WGS) to assess the genetic diversity, antimicrobial resistance profiles, molecular epidemiology and frequencies of virulence genes among 55 S. maltophilia isolates obtained from bacteremic cases over a 9-year period. Results Based on the threshold of 95% average nucleotide identity (ANI) and 70% digital DNA–DNA hybridization (dDDH) for genospecies delineation, we classified 37 isolates into 6 known species, all belonging to the Smc. The remaining 18 isolates sequenced in this study were assigned to 6 new genomospecies. Among the 55 isolates, we identified 44 different sequence types (STs), comprising 22 known and 22 novel allele combinations. The resistance rate of Smc against trimethoprim-sulfamethoxazole (TMP/SMX) was found to be 3.6%, with the sul1 and class one integron integrase genes ( intI ) detected in these isolates. All Smc isolates were susceptible to minocycline. Furthermore, all Smc strains harbored the motA, pilU, smf-1 and Stmpr2 genes. Genomospecies 1 (100%, n = 9), Stenotrophomonas maltophilia (84.21%, n = 19) and Stenotrophomonas sepilia (71.43%, n = 7) demonstrated a higher percentage of the afaD gene, which was also associated with a higher separation rate. In addition to motA , pilU , smf-1 , and Stmpr2 genes, all S. maltophilia strains (100%) contained entA , gspD , KatA , and stmPr1 genes, while all genomospecies 1 strains (100%) contained afaD, entA , gspD , and KatA genes. Conclusion Our study highlights the genetic diversity among Smc isolates from patients with bacteremia, revealing 22 novel ST types, 58 new alleles and 6 new genomospecies. S. maltophilia and S. pavanii were found to carry more virulence factors, emphasizing the importance of accurate strain identification. Minocycline emerged as a promising alternative antibiotic for patients who were resistant to TMP/SMX.
Background
Studies on
Citrobacter
spp. are limited, hindering our understanding of its species evolution and medical relevance.
Methods
A total of 164 clinical
Citrobacter
spp. isolates were ...collected from 2017 to 2020 and identified by VITEK MALDI-TOF MS or VITEK-2 Gram-Negative Identification Card. All isolates were further analyzed by whole-genome sequencing using a HiSeq sequencer. All sequences were processed using different modules of the PGCGAP integrated package: Prokka and fastANI were used for annotation and average nucleotide identification (ANI), respectively. Antibiotic resistance and virulence genes were identified by searching CARD, ResFinder, and VFDB databases, respectively. Strains were identified using Ribosomal Multi-locus Sequence Typing (rMLST) classification based on 53 ribosome protein subunits (
rps
). The evolutionary relationship was analyzed using kSNP3 and visualized by iTOL editor v1_1. Genetic environments were compared by BLAST and visualized by Easyfig 2.2.5. The pathogenicity of some
Citrobacter freundii
isolates was confirmed by
Galleria mellonella
larvae infection test.
Results
A total of 14 species of
Citrobacter
spp. were identified from 164 isolates. However, 27 and 11 isolates were incorrectly identified as
C. freundii
and
Citrobacter braakii
by MALDI-TOF MS, respectively. In addition, MS also failed to identify
Citrobacter portucalensis
. The virulence genes mainly encoded proteins related to flagella and iron uptake systems.
Citrobacter koseri
isolates (
n
= 28) contained two iron uptake systems, coding yersiniabactin and aerobactin, respectively.
C. braakii
isolates (
n
= 32), like
Salmonella
, carried Vi capsule polysaccharide synthesis genes. The yersiniabactin gene clusters identified in five
C. freundii
isolates are located on various ICE
kp
elements and have not been reported previously. Moreover, ICE
kp
-carrying
C. freundii
showed diverse pathogenic features.
Conclusion
Conventional methods have significant defects in identifying
Citrobacter
spp. ICE
kp
-like elements-mediated acquirement of the
Yersinia
high-pathogenicity island was identified for the first time in
C. freundii
.
Background
Carbapenem-resistant
Klebsiella pneumoniae
(CRKP) is an important pathogen causing hospital-associated outbreaks worldwide. The spread of
K. pneumoniae
carbapenemase-2 (KPC-2)-producing ...CRKP is primarily associated with sequence type (ST) 11.
Methods
A total of 152 KPC-2-producing
K. pneumoniae
ST11 isolates were collected from the respiratory department of a tertiary care hospital in Beijing, China between 2009 and 2018. The genome sequencing of these isolates was performed on the HiSeq X Ten sequencer. Multilocus sequence typing (MLST), capsular type, plasmid replicon types and resistance genes were identified. Fifteen isolates were selected for the subsequent single-molecule real-time (SMRT) sequencing on the PacBio RS II. Alignment of the complete sequences of the plasmids carrying
bla
KPC–2
and/or virulence genes was performed by using BRIG and Easyfig.
Results
From 2012 to 2018, the detection rate of the
bla
KPC–2
-carrying CRKP rose rapidly from 3.3 to 28.1%. KPC-2-producing
K. pneumoniae
ST11 isolates were dominant in CRKP, which emerged in 2012 and caused several outbreaks. Most isolates exhibited multidrug-resistant to commonly used antibiotics, while all the isolates remained susceptible to tigecycline and polymyxin B. The single nucleotide polymorphism (SNP) analysis showed that all these 152 KPC-2-producing
K. pneumoniae
ST11 isolates could be divided into three genetically distinct clades (A, B, and C) and eleven subclades (A1–A9 and B1–B2). The majority belonged to clade A with KL47 serotype (
n
= 117, 77.0%), while KL64 and KL16 were identified in clades B and C, respectively. The
bla
KPC–2
-carrying plasmids exhibited diverse types, namely, IncFII (pHN7A8)/IncR(6/15), IncFII (pHN7A8)/Inc
pA1763–KPC
(5/15), IncFII (pHN7A8) (1/15), IncR (1/15), and Inc
pA1763–KPC
(1/15). The genetic environment of
bla
KPC–2
showed nine IS
26
-based composite transposons, which had a basic core structure IS
Kpn27-bla
KPC–2
-ΔIS
Kpn6
. About 27.6% (42/152) isolates co-carried 2 to 4 virulence marker genes (namely,
peg344
,
iucA
,
iroB
,
rmpA
, and
rmpA2
) for hvKp strains. At least three isolates were identified to harbor virulence gene-carrying plasmids.
Conclusion
KPC-2-producing
K. pneumoniae
ST11 was highly heterogeneous in our hospital. Transmission of these strains was mainly mediated by twelve high-risk clones. The
bla
KPC–2
-carrying plasmids and genetic environment of
bla
KPC–2
genes exhibited active evolution in
K. pneumoniae
ST11. More attention should be paid to the tendency of KPC-2-ST11 to acquire hypervirulent plasmids.
A new cellular automaton (CA) model of abnormal grain growth (AGG) that considers anisotropic grain boundary energies was developed in this paper. The anisotropic grain boundary energy was expressed ...based on two types of grains, which correspond to two components of different crystallographic orientation in textured materials. The CA model was established by assigning different grain boundary energies and grain-growth-driven mechanisms to four types of grain boundaries formed by two types of grains. The grain boundaries formed by different kinds of grains adopted the lowest energy principle, while the grain boundaries formed by the same kind of grains adopted the curvature-driven mechanism. The morphology calculated by the CA model shows the characteristics of AGG. Then, the Johnson–Mehl–Avrami (JMA) model was fitted to predict the growth kinetics. By analyzing the fitting results, the JMA model is capable of predicting the growth kinetics of AGG. The Avrami exponent p decreases from about 1.5 to 1 with the initial number of Type II grains increasing. The investigation of the Hillert model and grain size distribution further indicates that the microstructure evolution is consistent with AGG. Therefore, the analysis of morphology and kinetics indicates that AGG can be fairly well-simulated by the present CA model.
The spread and outbreak of Enterobacteriaceae producing OXA-48-like carbapenemases have become more and more prevalent in China.
A total of 62 non-duplicated OXA-232-producing K. pneumoniae ...(OXA232Kp) were isolated between 2015 and 2017. An outbreak of OXA232Kp was observed in burn ICU. The 62 OXA232Kp isolates were all belongs to ST15 and categorized into two PFGE types (A and B). Type A was dominated of the isolates, which contained 61 clinical isolates and divided into 10 subtypes (A1-A10). In addition, most of OXA232Kp strains exhibited low-level carbapenems resistance. All strains carried a 6141 bp ColKP3 plasmid harboring the bla
gene which is highly homologous to other bla
-bearing plasmids involved in other studies in eastern China.
In this study, clone transmission of OXA232Kp ST15was observed. Highly significant homology among the bla
-bearing plasmids indicated the important role of the 6.1 kb ColE-like plasmid on the prevalence of bla
gene in China.
The modeling of austenite grain growth of 25Cr2Ni4MoV steel for super-large nuclear-power rotors was investigated during the common heating process including the continuous heating and isothermal ...heating process. Based on the isothermal grain growth model considering the steady-state grain size and the rule of additivity, a new grain growth model during the continuous heating process was established. The comparison between experimental and predicted results indicates the model has good predictability. To describe the anisotropic and isotropic grain growth during the different isothermal heating stages of the super-large nuclear-power rotor, a cellular automaton model considering anisotropic grain boundary energy for grain growth of 25Cr2Ni4MoV steel was developed. It is found that the anisotropic grain boundary energy mainly exists in the early isothermal heating stage at lower temperatures, and the normal grain growth occurs under anisotropic grain boundary energy conditions. When the temperature is not less than 1273 K and the cellular automaton step is not less than 15, the normal grain growth containing only isotropic grain boundary energy occurs. The analysis of the morphology, energy variance, topology and growth kinetics further indicates that normal grain growth of 25Cr2Ni4MoV steel can be simulated fairly well by the present CA model.
With the recent evolution of multidrug-resistant strains, the genetic characteristics of foodborne
serovar Enteritidis and clinical isolates have changed. ST11 is now the most common genotype ...associated with
. Enteritidis isolates.
A total of 83 strains of
. Enteritidis were collected at the General Hospital of the People's Liberation Army. Of these, 37 were from aseptic sites in patients, 11 were from the feces of patients with diarrhea, and the remaining 35 were of chicken-origin. The minimum inhibitory concentration of
. Enteritidis was determined by the broth microdilution method. Genomic DNA was extracted using the QiAamp DNA Mini Kit, and whole-genome sequencing (WGS) was performed using an Illumina X-ten platform. Prokka was used for gene prediction and annotation, and bioinformatic analysis tools included Resfinder, ISFinder, Virulence Factor Database, and PlasmidFinder. IQ-TREE was used to build a maximum likelihood phylogenetic tree. The phylogenetic relationship and distribution of resistance genes was displayed using iTOL. Comparative population genomics was used to analyze the phenotypes and genetic characteristics of antibiotic resistance in clinical and chicken-origin isolates of
. Enteritidis.
The chicken-origin
. Enteritidis isolates were more resistant to antibiotics than clinical isolates, and had a broader antibiotic resistance spectrum and higher antibiotic resistance rate. A higher prevalence of antibiotic-resistance genes was observed in chicken-origin
. Enteritidis compared to clinical isolates, along with distinct patterns in the contextual characteristics of these genes. Notably, genes such as
and
were exclusive to plasmids in clinical
. Enteritidis, whereas in chicken-origin
. Enteritidis they were found in both plasmids and chromosomes. Additionally,
was significantly more prevalent in chicken-origin isolates than in clinical isolates. Careful analysis revealed that the delayed isolation of chicken-origin
. Enteritidis contributes to accelerated gene evolution. Of note, certain resistance genes tend to integrate seamlessly and persist steadfastly within the chromosome, thereby expediting the evolution of resistance mechanisms against antibiotics. Our comparative analysis of virulence genes in
. Enteritidis strains from various sources found no substantial disparities in the distribution of other virulence factors. In summary, we propose that chicken-origin
. Enteritidis has the potential to cause clinical infections. Moreover, the ongoing evolution and dissemination of these drug-resistant genes poses a formidable challenge to clinical treatment.
Constant vigilance is needed to monitor the dynamic patterns of drug resistance in
. Enteritidis strains sourced from diverse origins.
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