Emergence of the New KPC-49 Variant Conferring an ESBL Phenotype with Resistance to Ceftazidime-Avibactam in the ST131-H30R1 Escherichia coli High-Risk Clone

We report the emergence of an isolate belonging to the sequence type (ST)131-Escherichia coli high-risk clone with ceftazidime-avibactam resistance recovered from a patient with bacteremia in 2019. Antimicrobial susceptibility was determined and whole genome sequencing (Illumina-NovaSeq6000) and cloning experiments were performed to investigate its resistance phenotype. A KPC-3-producing E. coli isolate susceptible to ceftazidime-avibactam (MIC = 0.5/4 mg/L) and with non-wild type MIC of meropenem (8 mg/L) was detected in a blood culture performed at hospital admission. Following 10-days of standard ceftazidime-avibactam dose treatment, a second KPC-producing E. coli isolate with a phenotype resembling an extended-spectrum β-lactamase (ESBL) producer (meropenem 0.5 mg/L, piperacillin-tazobactam 16/8 mg/L) but resistant to ceftazidime-avibactam (16/4 mg/L) was recovered. Both E. coli isolates belonged to ST131, serotype O25:H4 and sublineage H30R1. Genomics analysis showed a core genome of 5,203,887 base pair with an evolutionary distance of 6 single nucleotide polymorphisms. A high content of resistance and virulence genes was detected in both isolates. The novel KPC-49 variant, an Arg-163-Ser mutant of blaKPC-3, was detected in the isolate with resistance to ceftazidime-avibactam. Cloning experiments revealed that blaKPC-49 gene increases ceftazidime-avibactam MIC and decreases carbapenem MICs when using a porin deficient Klebsiella pneumoniae strain as a host. Both blaKPC-3 and blaKPC-49 genes were located on the transposon Tn4401a as a part of an IncF [F1:A2:B20] plasmid. The emergence of novel blaKPC genes conferring decreased susceptibility to ceftazidime-avibactam and resembling ESBL production in the epidemic ST131-H30R1-E. coli high-risk clone presents a new challenge in clinical practice.

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Strains of Escherichia coli O157:H7 Differ Primarily by Insertions or Deletions, Not Single-Nucleotide Polymorphisms

Journal of Bacteriology ◽

10.1128/jb.184.7.1873-1879.2002 ◽

2002 ◽

Vol 184 (7) ◽

pp. 1873-1879 ◽

Cited By ~ 71

Author(s):

Indira T. Kudva ◽

Peter S. Evans ◽

Nicole T. Perna ◽

Timothy J. Barrett ◽

Frederick M. Ausubel ◽

...

Keyword(s):

Escherichia Coli ◽

Single Nucleotide Polymorphisms ◽

Epidemiological Surveillance ◽

Escherichia Coli O157 ◽

Nucleotide Polymorphisms ◽

Strain Variation ◽

Single Nucleotide ◽

E Coli ◽

K 12 ◽

Genetic Events

ABSTRACT Escherichia coli O157:H7 (O157) strains demonstrate varied pulsed-field gel electrophoresis patterns following XbaI digestion, which enable epidemiological surveillance of this important human pathogen. The genetic events underlying PFGE differences between strains, however, are not defined. We investigated the mechanisms for strain variation in O157 by recovering and examining nucleotide sequences flanking each of the XbaI restriction enzyme sites in the genome. Our analysis demonstrated that differences between O157 strains were due to discrete insertions or deletions that contained the XbaI sites polymorphic between strains rather than single-nucleotide polymorphisms in the XbaI sites themselves. These insertions and deletions were found to be uniquely localized within the regions of the genome that are specific to O157 compared to E. coli K-12 (O islands), suggesting that strain-to-strain variation occurs in these O islands. These results may be utilized to devise novel strain-typing tools for this pathogen.

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A Novel 7-Single Nucleotide Polymorphism-Based Clonotyping Test Allows Rapid Prediction of Antimicrobial Susceptibility of Extraintestinal Escherichia coli Directly From Urine Specimens

Open Forum Infectious Diseases ◽

10.1093/ofid/ofw002 ◽

2016 ◽

Vol 3 (1) ◽

Cited By ~ 14

Author(s):

Veronika Tchesnokova ◽

Hovhannes Avagyan ◽

Mariya Billig ◽

Sujay Chattopadhyay ◽

Pavel Aprikian ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Susceptibility ◽

Clinical Diagnostics ◽

Resolving Power ◽

Nucleotide Polymorphisms ◽

Typing Method ◽

Single Nucleotide ◽

E Coli ◽

Specificity And Sensitivity ◽

Urine Specimens

Abstract Background. Escherichia coli is a highly clonal pathogen. Extraintestinal isolates belong to a limited number of genetically related groups, which often exhibit characteristic antimicrobial resistance profiles. Methods. We developed a rapid clonotyping method for extraintestinal E coli based on detection of the presence or absence of 7 single nucleotide polymorphisms (SNPs) within 2 genes (fumC and fimH). A reference set of 2559 E coli isolates, primarily of urinary origin, was used to predict the resolving power of the 7-SNP-based typing method, and 582 representative strains from this set were used to evaluate test robustness. Results. Fifty-four unique SNP combinations (“septatypes”) were identified in the reference strains. These septatypes yielded a clonal group resolution power on par with that of traditional multilocus sequence typing. In 72% of isolates, septatype identity predicted sequence type identity with at least 90% (mean, 97%) accuracy. Most septatypes exhibited highly distinctive antimicrobial susceptibility profiles. The 7-SNP-based test could be performed with high specificity and sensitivity using single or multiplex conventional polymerase chain reaction (PCR) and quantitative PCR. In the latter format, E coli presence and septatype identity were determined directly in urine specimens within 45 minutes with bacterial loads as low as 102 colony-forming units/mL and, at clinically significant bacterial loads, with 100% sensitivity and specificity. Conclusions. 7-SNP-based typing of E coli can be used for both epidemiological studies and clinical diagnostics, which could greatly improve the empirical selection of antimicrobial therapy.

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Genotypic analyses of uropathogenic Escherichia coli based on fimH single nucleotide polymorphisms (SNPs)

Journal of Medical Microbiology ◽

10.1099/jmm.0.47262-0 ◽

2007 ◽

Vol 56 (10) ◽

pp. 1363-1369 ◽

Cited By ~ 25

Author(s):

Sara Y. Tartof ◽

Owen D. Solberg ◽

Lee W. Riley

Keyword(s):

Escherichia Coli ◽

Single Nucleotide Polymorphisms ◽

Screening Test ◽

Epidemiological Studies ◽

Discriminatory Power ◽

Snp Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Discriminatory Ability ◽

E Coli

The application of genotyping techniques for subtyping uropathogenic Escherichia coli has contributed to better understanding of the epidemiology of community-acquired urinary tract infection (UTI). However, the current techniques are hampered by limited reproducibility, poor discriminatory power, labour-intensive performance or high cost. A screening test that is sequence-based would provide an inexpensive, reproducible way to subtype E. coli isolates. Such a test, if also discriminatory, would be highly useful for epidemiological studies. The discriminatory ability of 12 putative virulence genes (fimH, fliD, fliM, iha, motA, papA/H, kpsMTII, fepE, fimA, flgA, malG, purD) was evaluated based on single nucleotide polymorphisms (SNPs) in nine uropathogenic E. coli isolates, all previously found to belong to a single multilocus sequence type (MLST) complex (ST69). An additional 25 epidemiologically well-characterized E. coli isolates belonging to 12 distinct MLST clonal complexes were analysed for fimH SNP. None of the 12 genes except fimH were able to further discriminate the nine ST69-complex strains. Isolates belonging to the 12 non-ST69 MLST groups were separated into 10 fimH SNP subgroups. While fimH SNP analysis may not be an appropriate phylogenetic method, it offers discriminatory power similar to that of MLST and could be used as a simple, inexpensive screening test for epidemiological studies of uropathogenic E. coli.

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Genome-Based Analyses of Fitness Effects and Compensatory Changes Associated with Acquisition of blaCMY-, blaCTX-M-, and blaOXA-48/VIM-1-Containing Plasmids in Escherichia coli

Antibiotics ◽

10.3390/antibiotics10010090 ◽

2021 ◽

Vol 10 (1) ◽

pp. 90

Author(s):

Michael Pietsch ◽

Yvonne Pfeifer ◽

Stephan Fuchs ◽

Guido Werner

Keyword(s):

Escherichia Coli ◽

Growth Rates ◽

Beta Lactamase ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genomic Changes ◽

E Coli ◽

Fitness Effects ◽

Growth Differences

(1) Background: Resistance plasmids are under selective conditions beneficial for the bacterial host, but in the absence of selective pressure, this carriage may cause fitness costs. Compensation of this fitness burden is important to obtain competitive ability under antibiotic-free conditions. In this study, we investigated fitness effects after a conjugative transfer of plasmids containing various beta-lactamase genes transferred into Escherichia coli. (2) Methods: Fourteen beta-lactamase-encoding plasmids were transferred from clinical donor strains to E. coli J53. Growth rates were compared for all transconjugants and the recipient. Selected transconjugants were challenged in long-term growth experiments. Growth rates were assessed at different time points during growth for 500 generations. Whole-genome sequencing (WGS) of initial and evolved transconjugants was determined. Results: Most plasmid acquisitions resulted in growth differences, ranging from −4.5% to 7.2%. Transfer of a single blaCMY-16-carrying plasmid resulted in a growth burden and a growth benefit in independent mating. Long-term growth led to a compensation of fitness burdens and benefits. Analyzing WGS revealed genomic changes caused by Single Nucleotide Polymorphisms (SNPs) and insertion sequences over time. Conclusions: Fitness effects associated with plasmid acquisitions were variable. Potential compensatory mutations identified in transconjugants’ genomes after 500 generations give interesting insights into aspects of plasmid–host adaptations.

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Emergence of NDM-producing Klebsiella pneumoniae and Escherichia coli in Spain: phylogeny, resistome, virulence and plasmids encoding blaNDM-like genes as determined by WGS

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkz366 ◽

2019 ◽

Vol 74 (12) ◽

pp. 3489-3496 ◽

Cited By ~ 10

Author(s):

María Pérez-Vázquez ◽

Pedro J Sola Campoy ◽

Adriana Ortega ◽

Verónica Bautista ◽

Sara Monzón ◽

...

Keyword(s):

Escherichia Coli ◽

Population Structure ◽

High Risk ◽

High Resolution ◽

Klebsiella Pneumoniae ◽

Core Genome ◽

Acquired Resistance ◽

Variable Region ◽

E Coli ◽

The Impact

Abstract Objectives NDM carbapenemases have spread worldwide. However, little information exists about the impact of NDM-producing Enterobacteriaceae in Spain. By WGS, we sought to elucidate the population structure of NDM-like-producing Klebsiella pneumoniae and Escherichia coli in Spain and to determine the plasmids harbouring blaNDM-like genes. Methods High-resolution SNP typing, core-genome MLST and plasmid reconstruction (PlasmidID) were performed on 59 NDM-like-producing K. pneumoniae and 8 NDM-like-producing E. coli isolated over an 8 year period in Spain. Results Five major epidemic clones of NDM-producing K. pneumoniae caused five important nationwide outbreaks: ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1; in contrast, the spread of NDM-producing E. coli was polyclonal. Three blaNDM types were identified: blaNDM-1, 61.2%; blaNDM-7, 32.8%; and blaNDM-5, 6%. Five K. pneumoniae isolates co-produced other carbapenemases (three blaOXA-48 and two blaVIM-1). The average number of acquired resistance genes was higher in K. pneumoniae than in E. coli. The plasmids encoding blaNDM-like genes belonged to IncFII, IncFIB, IncX3, IncR, IncN and IncC types, of which IncF, IncR and IncC were associated with MDR. The genetic surroundings of blaNDM-like genes showed a highly variable region upstream of ISAba125. Conclusions In recent years NDM-producing K. pneumoniae and E. coli have emerged in Spain; the spread of a few high-risk K. pneumoniae clones such as ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1 have caused several interregional outbreaks. In contrast, the spread of NDM-producing E. coli has been polyclonal. Plasmid types IncFII, IncFIB, IncX3, IncR, IncN and IncC carried blaNDM, and the same IncX3 plasmid was detected in K. pneumoniae and E. coli.

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Association between Mannose-Binding Lectin Deficiency and Septic Shock following Acute Pyelonephritis Due to Escherichia coli

Clinical and Vaccine Immunology ◽

10.1128/cvi.00400-06 ◽

2007 ◽

Vol 14 (3) ◽

pp. 256-261 ◽

Cited By ~ 15

Author(s):

Alex Smithson ◽

Ana Muñoz ◽

Belen Suarez ◽

Sara Maria Soto ◽

Rafael Perello ◽

...

Keyword(s):

Escherichia Coli ◽

Septic Shock ◽

Acute Pyelonephritis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

E Coli ◽

Increased Risk ◽

Healthy Control ◽

Low Expression

ABSTRACT Structural and promoter MBL2 gene polymorphisms responsible for low MBL levels are associated with increased risk of infection. The objective of this study was to assess the possible association between polymorphisms of the MBL2 gene and the incidence of septic shock and bacteremia in patients with acute pyelonephritis due to Escherichia coli. The study included 62 female patients with acute pyelonephritis due to E. coli who required hospital admission, as well as 133 healthy control subjects. Six single-nucleotide polymorphisms (−550 G/C, −221 C/G, +4 C/T, codon 52 CGT/TGT, codon 54 GGC/GAC, and codon 57 GGA/GAA) in the MBL2 gene were genotyped by using a sequence-based typing technique. No significant differences were observed in the frequencies for low-expression MBL2 genotypes (O/O and LXA/O) between patients with acute pyelonephritis and healthy controls. Patients with acute pyelonephritis and septic shock had a higher incidence of low-expression MBL2 genotypes than patients with acute pyelonephritis without septic shock (odds ratio = 9.019, 95% confidence interval = 1.23 to 65.93; P = 0.03). No association was found between bacteremic acute pyelonephritis and low-expression MBL2 genotypes. We found that low-expression MBL2 genotypes predispose to septic shock but not to bacteremia in patients with E. coli-induced acute pyelonephritis. Determination of MBL2 polymorphisms could be useful for assessing the risk of septic shock in women undergoing acute pyelonephritis.

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Lineage and Genogroup-Defining Single Nucleotide Polymorphisms of Escherichia coli O157:H7

Applied and Environmental Microbiology ◽

10.1128/aem.02173-13 ◽

2013 ◽

Vol 79 (22) ◽

pp. 7036-7041 ◽

Cited By ~ 15

Author(s):

Woo Kyung Jung ◽

James L. Bono ◽

Michael L. Clawson ◽

Shana R. Leopold ◽

Smriti Shringi ◽

...

Keyword(s):

Escherichia Coli ◽

Reservoir Host ◽

Escherichia Coli O157 ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Content Type ◽

Biologically Relevant ◽

E Coli

ABSTRACTEscherichia coliO157:H7 is a zoonotic human pathogen for which cattle are an important reservoir host. Using both previously published and new sequencing data, a 48-locus single nucleotide polymorphism (SNP)-based typing panel was developed that redundantly identified 11 genogroups that span six of the eight lineages recently described forE. coliO157:H7 (J. L. Bono, T. P. Smith, J. E. Keen, G. P. Harhay, T. G. McDaneld, R. E. Mandrell, W. K. Jung, T. E. Besser, P. Gerner-Smidt, M. Bielaszewska, H. Karch, M. L. Clawson, Mol. Biol. Evol. 29:2047–2062, 2012) and additionally defined subgroups within four of those lineages. This assay was applied to 530 isolates from human and bovine sources. The SNP-based lineage groups were concordant with previously identifiedE. coliO157:H7 genotypes identified by other methods and were strongly associated with carriage of specific Stx genes. Two SNP lineages (Ia and Vb) were disproportionately represented among cattle isolates, and three others (IIa, Ib, and IIb) were disproportionately represented among human clinical isolates. This 48-plex SNP assay efficiently and economically identifies biologically relevant lineages withinE. coliO157:H7.

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Investigation of High-Risk ST131 Clone in Extended Spectrum β-Lactamase–Producing Escherichia coli Isolates in Children

Journal of Pediatric Infectious Diseases ◽

10.1055/s-0041-1730995 ◽

2021 ◽

Author(s):

Mehmet E. Bulut ◽

Gülen Hürkal ◽

Nazan Dalgıç

Keyword(s):

Escherichia Coli ◽

High Risk ◽

Pediatric Patients ◽

Pediatric Population ◽

Maldi Tof Ms ◽

E Coli ◽

Maldi Tof ◽

Extended Spectrum ◽

St131 Clone ◽

Tof Ms

Abstract Objective Antimicrobial resistance poses a serious threat to children's health. In recent years, high-risk Escherichia coli ST131 has become an important target for global surveillance studies. The E.coli ST131 clone is associated with extended spectrum β-lactamase (ESBL) production, as well as multidrug resistance and treatment failure. Studies on this clone in the pediatric age group are limited. We aim to investigate the rate of high-risk E. coli ST131 clone in ESBL-positive E. coli isolates obtained from pediatric patients. Methods A total of 292 ESBL-positive E. coli isolates from clinical samples of pediatric patients was included in the study. MALDI-TOF MS system was used for bacterial identification. Susceptibility tests were performed using BD Phoenix automated system. ST131 detection was done by MALDI-TOF-MS. Fisher's exact test was used to compare the groups (significance <0.05). Results A total of 292 isolates was analyzed. The high-risk ST131 clone was detected in 117 (40%) of the 292 ESBL-positive isolates. ST131 rates were found to be significantly higher in children under the age of 5 years compared with children over the age of 5 years (49.3 vs. 31.1%, p = 0.0019). Ciprofloxacin resistance was higher in ST131 isolates (45.6 vs. 31.7%; p < 0.05). Conclusion The rate of the ST131 clone was found to be high in the pediatric population. The significantly high rate of resistance to ciprofloxacin, which is not commonly used in the pediatric population, in ST131 isolates reveals the importance of the spread of high-risk clones for the development of resistance.

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Characterization of novel ybjG and dacC variants in Escherichia coli

Journal of Medical Microbiology ◽

10.1099/jmm.0.062893-0 ◽

2013 ◽

Vol 62 (11) ◽

pp. 1728-1734 ◽

Cited By ~ 4

Author(s):

Dongguo Wang ◽

Enping Hu ◽

Jiayu Chen ◽

Xiulin Tao ◽

Katelyn Gutierrez ◽

...

Keyword(s):

Escherichia Coli ◽

Multiple Drug Resistance ◽

Multiple Drug ◽

The Novel ◽

Conventional Pcr ◽

E Coli ◽

Novel Variants ◽

Restriction Sites ◽

Genetic Structures

A total of 69 strains of Escherichia coli from patients in the Taizhou Municipal Hospital, China, were isolated, and 11 strains were identified that were resistant to bacitracin, chloramphenicol, tetracycline and erythromycin. These strains were PCR positive for at least two out of three genes, ybjG, dacC and mdfA, by gene mapping with conventional PCR detection. Conjugation experiments demonstrated that these genes existed in plasmids that conferred resistance. Novel ybjG and dacC variants were isolated from E. coli strains EC2163 and EC2347, which were obtained from the sputum of intensive care unit patients. Genetic mapping showed that the genes were located on 8200 kb plasmid regions flanked by EcoRI restriction sites. Three distinct genetic structures were identified among the 11 PCR-positive strains of E. coli, and two contained the novel ybjG and dacC variants. The putative amino acid differences in the ybjG and dacC gene variants were characterized. These results provide evidence for novel variants of ybjG and dacC, and suggest that multiple drug resistance in hospital strains of E. coli depends on the synergistic function of ybjG, dacC and mdfA within three distinct genetic structures in conjugative plasmids.

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Impact of Extended-Spectrum β-Lactamase Production on Treatment Outcomes of Acute Pyelonephritis Caused by Escherichia coli in Patients without Health Care-Associated Risk Factors

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.04821-14 ◽

2015 ◽

Vol 59 (4) ◽

pp. 1962-1968 ◽

Cited By ~ 13

Author(s):

Sun Hee Park ◽

Su-Mi Choi ◽

Dong-Gun Lee ◽

Sung-Yeon Cho ◽

Hyo-Jin Lee ◽

...

Keyword(s):

Risk Factors ◽

Escherichia Coli ◽

Health Care ◽

Treatment Outcomes ◽

Acute Pyelonephritis ◽

Esbl Production ◽

Content Type ◽

E Coli ◽

Extended Spectrum ◽

The Impact

ABSTRACTExtended-spectrum β-lactamase-producingEscherichia coli(ESBL-EC) is increasingly identified as a cause of acute pyelonephritis (APN) among patients without recent health care contact, i.e., community-associated APN. This case-control study compared 75 cases of community-associated ESBL-EC APN (CA-ESBL) to 225 controls of community-associated non-ESBL-EC APN (CA-non-ESBL) to identify the risk factors for ESBL-EC acquisition and investigate the impact of ESBL on the treatment outcomes of community-associated APN (CA-APN) caused byE. coliat a Korean hospital during 2007 to 2013. The baseline characteristics were similar between the cases and controls; the risk factors for ESBL-EC were age (>55 years), antibiotic use within the previous year, and diabetes with recurrent APN. The severity of illness did not differ between CA-ESBL and CA-non-ESBL (Acute Physiology and Chronic Health Evaluation [APACHE] II scores [mean ± standard deviation], 7.7 ± 5.9 versus 6.4 ± 5.3;P= 0.071). The proportions of clinical (odds ratio [OR], 1.76; 95% confidence interval [CI], 0.57 to 5.38;P= 0.323) and microbiological (OR, 1.16; 95% CI, 0.51 to 2.65;P= 0.730) cures were similar, although the CA-ESBL APN patients were less likely to receive appropriate antibiotics within 48 h. A multivariable Cox proportional hazards analysis of the prognostic factors for CA-APN caused byE. colishowed that ESBL production was not a significant factor for clinical (hazard ratio [HR], 0.39; 95% CI, 0.12 to 1.30;P= 0.126) or microbiological (HR, 0.49; 95% CI, 0.21 to 1.12;P= 0.091) failure. The estimates did not change after incorporating weights calculated using propensity scores for acquiring ESBL-EC. Therefore, ESBL production did not negatively affect treatment outcomes among patients with community-associatedE. coliAPN.

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