Clinical features and microbiological characteristics of hospital- and community-onset Escherichia coli bloodstream infection

Molecular epidemiology of Escherichia coli in bloodstream infections from a general hospital in Ningxia, China, 2022-2023

OBJECTIVE

To analyse the antibiotic resistance, resistance genes and clonal relationship of Escherichia coli in bloodstream infections in Ningxia from 2022 to 2023.

METHODS

We retrospectively analyzed the antibiotic susceptibilities of 257 isolates. PCR was used to detect blaTEM, blaSHV, blaCTX-M, qnrS, qnrA, qnrB, oqxA, qepA, gyrA, gyrB, parC, and parE, and the clonal relationship through multilocus sequence typing (MLST).

RESULTS

One hundred and twenty-nine of 257 patients were male (50.2%). The 257 E. coli isolates were mainly obtained from the Emergency, Hepatobiliary Surgery, and Haematology Departments, accounting for 56.6%, 7.3%, and 6.2%, respectively. There is no significant difference in sex and genes between the two groups over and under 60 years old (P > 0.05), but there is a significant difference in ST between them(P<0.05). The antimicrobial susceptibility testing showed that the 257 isolates had the highest rates of resistance to ampicillin (82.8%), followed by cefazolin (71.6%), and all isolates were susceptible to tigecycline. Based on the antibiotic susceptibility results for ceftriaxone, we tested 126 isolates of E. coli for extended-spectrum beta-lactamase (ESBL) resistance genes. As a result, blaCTX-M was detected in 76 isolates (60.32%), blaSHV in 26 isolates (20.63%), and blaTEM in 38 isolates (30.16%). Based on the ciprofloxacin and levofloxacin antibiotic susceptibility results, we tested for quinolone resistance genes in 148 isolates, revealing 66 isolates of aac(6')-Ib-cr (44.60%), 3 isolates of oqxA (2.02%), 32 isolates of qnrS (21.62%), and 2 isolates of qepA (1.35%). We did not detect qnrA or qnrB. The detection rates of gyrA, gyrB, parC, and parE were 98%, 42.6%, 91.2%, and 87.8%, respectively and the main amino acid mutations were Ser83 to Leu, Asp87 to Asn(75.2%), Leu417 to Ser, Ser418 to Leu (6.3%), Ser80 to Ile (65.2%), and Ser458 to Ala (21.5%), respectively. MLST revealed that the most common sequence types (STs) were ST69 (12.5%), ST131 (8.2%), and ST1193 (7.8%).

CONCLUSION

In our hospital, E. coli was resistant to most commonly used antibiotics, and cefoperazone/sulbactam, cefotetan, amikacin, and tigecycline were empirically selected for the treatment of bloodstream infections. The predominant ESBL genotype in our hospital was blaCTX-M and the major quinolone resistance gene was aac(6')-Ib-cr. Clonal relationship analysis revealed genetic diversity among the isolates.

Escherichia coli ST1193: Following in the Footsteps of E. coli ST131

Escherichia coli ST1193 is an emerging global multidrug (MDR) high-risk clone and an important cause of community-onset urinary and bloodstream infections. ST1193 is imitating E. coli ST131, the most successful MDR clone of all time. Both clones emerged in the early 1990s by acquiring quinolone resistance-determining region (QRDR) mutations, IncF plasmids, virulence factors, and type 1 pilus (fimH) recombination. They are the only MDR clones that are dominant among unselected E. coli populations. ST131 is the most frequent clone and ST1193 the second most frequent clone among fluoroquinolone/cephalosporin-resistant E. coli isolates. Both clones have played pivotal roles in the global spread of MDR E. coli. ST1193 originated from ST clonal complex 14 (STc14), is lactose nonfermenting, belongs to phylogenetic group B2, and contains the O type O75. Global ST1193 prevalence has been increasing since 2012, even replacing ST131 in certain regions. bla_CTX-M genes are rapidly expanding among ST1193 isolates, a scenario that occurred with ST131 during the 2000s. A validated PCR will enable global surveys to determine the extent of ST1193 among One Health E. coli isolates. The rapid emergence of ST1193 is concerning and is adding to the public health burden of MDR E. coli clones. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST1193. Such information will aid with management and prevention strategies. The medical community can ill afford to ignore the spread of another global successful MDR high-risk E. coli clone, especially one that is following in the footsteps of E. coli ST131.

Occurrence and Genomic Characterization of Clone ST1193 Clonotype 14-64 in Uncomplicated Urinary Tract Infections Caused by Escherichia coli in Spain

We conducted a prospective, multicenter, specific pilot study on uncomplicated urinary tract infections (uUTI). One-hundred non-duplicated uropathogenic Escherichia coli (UPEC) from uUTI occurred in 2020 in women attending 15 primary care centers of a single health region of northern Spain were characterized using a clonal diagnosis approach. Among the high genetic diversity showed by 59 different phylogroup-clonotype combinations, 11 clones accounted for 46% of the isolates: B2-ST73 (CH24-30); B2-ST73 (CH24-103); B2-ST131 (CH40-30); B2-ST141 (CH52-5); B2-ST372 (CH103-9); B2-ST404 (CH14-27); B2-ST404 (CH14-807); B2-ST1193 (CH14-64); D-ST69 (CH35-27); D-ST349 (CH36-54), and F-ST59 (CH32-41). The screening of the UPEC status found that 69% of isolates carried ≥ 3 of chuA, fyuA, vat, and yfcV genes. Multidrug resistance to at least one antibiotic of ≥ 3 antimicrobial categories were exhibited by 30% of the isolates, with the highest rates of resistance against ampicillin/amoxicillin (48%), trimethoprim (35%), norfloxacin (28%), amoxicillin-clavulanic acid (26%), and trimethoprim-sulfamethoxazole (24%). None extended-spectrum beta-lactamase/carbapenemase producer was recovered. According to our results, fosfomycin and nitrofurantoin should be considered as empirical treatment of choice for uUTI by E. coli (resistance rates 4% and 2%, respectively). We uncover the high prevalence of the pandemic fluoroquinolone-resistant ST1193 clone (6%) in uUTI, which represents the first report in Spain in this pathology. The genomic analysis showed similar key traits than those ST1193 clones disseminated worldwide. Through the SNP comparison based on the core genome, the Spanish ST1193 clustered with isolates retrieved from the Enterobase, showing high genomic similarity than the global ST1193 described in the United States, Canada and Australia.

IMPORTANCE Analyzing the clonal structure and antimicrobial resistance of E. coli isolates implicated in uncomplicated urinary tract infections, one of the most frequent visits managed in primary health care, is of interest for clinicians to detect changes in the dynamics of emerging uropathogenic clones associated with the spread of fluoroquinolone resistance. It can also provide consensus concerning optimal control and antibiotic prescribing.

Investigation of Antibiotic Susceptibility and Virulence Genes in Escherichia coli Strains Isolated from Blood and Urine Samples

Objective Extraintestinal Escherichia coli isolates are the most common gram-negative pathogens in humans and cause urinary tract infections, sepsis, neonatal meningitis, and others. The aim of this study was to investigate the rates of antibiotic resistance and virulence factors (kpsM II, neuc K1, hlyF, fyuA, afa/draBC, sat, chuA, fimH, tsh, yfcv, ibeA, traT, iucD, usp, iutA, cnf1, hlyA, papC, sfa/focDE, and ompT) of E. coli strains isolated from blood and urine samples.

Methods A total of 150 E. coli strains isolated from blood and urine samples sent to the Microbiology Laboratory, Faculty of Medicine Hospital, Selcuk University were included in the study. The identification and antibiotic susceptibility tests were performed with the VITEK 2 automated system. Multiplex polymerase chain reaction was used to detect the virulence genes.

Results Although the highest antibiotic resistance rate found was against ampicillin (73.3%), the lowest rates were against ertapenem and meropenem (0.7%). Extended-spectrum β-lactamase positivity was 38% in E. coli blood isolates and 29% in urine. The highest rates of virulence genes were detected in fimH gene (92%). iutA gene was 91.3%, traT 76%, fyuA 50%, chuA 54.7%, iucD 46.7%, ompT 32.7%, yfcv 31.3%, hlyF 28.7%, sat 22%, papC and sfa/focDE 20%, kpsM II 19.3%, neuc K1 14.7%, tsh 13.3%, cnf1 6.7%, afa/draBC 6%, ibeA 5.3%, usp 4.7%, and hlyA 3.3%. kpsM II, tsh, hlyA, papC, sfa/focDE, and ompT genes were higher in blood isolates.

Conclusion High antibiotic resistance rates and virulence genes were detected in E. coli strains in Konya, Turkey. This is the first study in Turkey where both a large number and a variety of virulence factors were investigated and compared. Multicenter studies are needed to better understand E. coli virulence.

Prevalence and Molecular Characterization of Fluoroquinolone-Resistant Escherichia coli in Healthy Children

Faecal E. coli can act as reservoirs for resistance genes. Here, we analyzed prevalence of drug resistance in faecal E. coli isolated from healthy children at a single kindergarten in Beijing, China, then used whole genome sequencing to characterize fluoroquinolone-non-susceptible strains. Our results revealed high resistance to ampicillin (54.0%), trimethoprim/sulphurmethoxazole (47.5%) and tetracycline (58.9%) among 576 faecal E. coli isolates, 49.2% of which exhibited multidrug resistance. A total of 113 E. coli isolates were not susceptible to ciprofloxacin, with four sequence types, namely ST1193 (25.7%), ST773 (13.3%), ST648 (8.8%) and ST131 (7.1%) found to be the most prevalent (54.9%). With regards to resistance to quinolones, we detected chromosomal mutations in gyrA, parC, and parE in 111 (98.2%), 105 (92.9%), and 67 (61.1%) isolates, respectively. bla _CTX-M (37.2%) was the major ESBL gene, whereas bla _CTX-M-14 (12.4%) and bla _CTX-M-27 (11.5%) were the most frequent subtypes. A total of 90 (79.6%) ExPEC and 65 (57.5%) UPEC isolates were classified. Overall, these findings revealed clonal spread of certain prevalent STs, namely ST1193, ST773, ST648 and ST131 E. coli isolates in healthy children within a single kindergarten in Beijing, China, affirming the seriousness of the multidrug resistance problem and potential pathogenicity of E. coli isolates in healthy children. Therefore, there is an urgent need for increased surveillance to enhance control of this problem.

Clonal Structure, Virulence Factor-encoding Genes and Antibiotic Resistance of Escherichia coli, Causing Urinary Tract Infections and Other Extraintestinal Infections in Humans in Spain and France during 2016

Escherichia coli is the main pathogen responsible for extraintestinal infections. A total of 196 clinical E. coli consecutively isolated during 2016 in Spain (100 from Lucus Augusti hospital in Lugo) and France (96 from Beaujon hospital in Clichy) were characterized. Phylogroups, clonotypes, sequence types (STs), O:H serotypes, virulence factor (VF)-encoding genes and antibiotic resistance were determined. Approximately 10% of the infections were caused by ST131 isolates in both hospitals and approximately 60% of these infections were caused by isolates belonging to only 10 STs (ST10, ST12, ST58, ST69, ST73, ST88, ST95, ST127, ST131, ST141). ST88 isolates were frequent, especially in Spain, while ST141 isolates significantly predominated in France. The 23 ST131 isolates displayed four clonotypes: CH40-30, CH40-41, CH40-22 and CH40-298. Only 13 (6.6%) isolates were carriers of extended-spectrum beta-lactamase (ESBL) enzymes. However, 37.2% of the isolates were multidrug-resistant (MDR). Approximately 40% of the MDR isolates belonged to only four of the dominant clones (B2-CH40-30-ST131, B2-CH40-41-ST131, C-CH4-39-ST88 and D-CH35-27-ST69). Among the remaining MDR isolates, two isolates belonged to B2-CH14-64-ST1193, i.e., the new global emergent MDR clone. Moreover, a hybrid extraintestinal pathogenic E.coli (ExPEC)/enteroaggregative isolate belonging to the A-CH11-54-ST10 clone was identified.

Spreading of extended-spectrum β-lactamase-producing Escherichia coli ST131 and Klebsiella pneumoniae ST11 in patients with pneumonia: a molecular epidemiological study

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Background:

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) are the important pathogens causing pneumonia. This study aimed to investigate the clinical characteristics and molecular epidemiology of ESBL-producing E. coli and K. pneumoniae causing pneumonia at a large teaching hospital in China.

Methods:

We collected patient's clinical data and ESBL-producing E. coli and K. pneumoniae strains causing pneumonia (from December 2015 to June 2016) at a hospital in Wuhan. The susceptibilities, multi-locus sequence typing, homologous analysis, ESBL genes by polymerase chain reaction and sequencing were determined.

Results:

A total of 59 ESBL-producing strains (31 E. coli and 28 K. pneumoniae) isolated from patients with pneumonia were analyzed. The majority of strains were isolated from patients were with hospital-acquired pneumonia (37/59, 62.7%), followed by community-acquired pneumonia (13/59, 22.0%), and ventilator-related pneumonia (9/59, 15.3%). The E. coli ST131 (9 isolates, 29.0%) and K. pneumoniae ST11 (5 isolates, 17.9%) were the predominant sub-types. The most prevalent ESBL gene was CTX-M-14, followed by SHV-77, CTX-M-3, SHV-11, and CTX-M-27. At least 33 (55.9%) of the ESBL-producing strains carried two or more ESBL genes. The ISEcp1 and IS26 were found upstream of all blaCTX-M (CTX-Ms) and of most blaSHV (SHVs) (57.6%), respectively. Moreover, three ESBL-producing K. pneumoniae ST11 strains which were resistant to carbapenems carried the bla_NDM-1 and bla_KPC-2, two of which also bearing bla_OXA-48 were resistant to all antibiotics (including Tigecycline).

Conclusions:

Hospital-acquired pneumonia is more likely correlated with ESBL-producing E. coli and K. pneumoniae. ESBL-producing E. coli ST131 and multi-drug resistance ESBL-producing, as well as New Delhi metallo-β-lactamase-1 (NDM-1) and Klebsiella pneumoniae carbapenemases-2 (KPC-2) bearing K. pneumoniae ST11 are spreading in patients with pneumonia in hospital.

Antimicrobial resistance of bacteraemia in the emergency department of a German university hospital (2013-2018): potential carbapenem-sparing empiric treatment options in light of the new EUCAST recommendations

Background

This study investigated predominant microorganisms causing community-onset bacteraemia at the medical emergency department (ED) of a tertiary-care university hospital in Germany from 2013 to 2018 and their antimicrobial susceptibility patterns.

Methods

Antimicrobial resistance patterns in patients with positive blood cultures presenting to an internal medicine ED were retrospectively analysed.

Results

Blood cultures were obtained at 5191 of 66,879 ED encounters, with 1013 (19.5%) positive results, and true positive results at 740 encounters (diagnostic yield, 14.3%). The most frequently isolated relevant microorganisms were Enterobacterales (n = 439, 59.3%), Staphylococcus aureus (n = 92, 12.4%), Streptococcus pneumoniae (n = 34, 4.6%), Pseudomonas aeruginosa (n = 32, 4.3%), Streptococcus pyogenes (n = 16, 2.2%), Enterococcus faecalis (n = 18, 2.4%), and Enterococcus faecium (n = 12, 1.6%). Antimicrobial susceptibility testing revealed a high proportion of resistance against ampicillin-sulbactam in Enterobacterales (42.2%). The rate of methicillin-resistant Staphylococcus aureus was low (0.4%).

Piperacillin-tazobactam therapy provided coverage for 83.2% of all relevant pathogens using conventional breakpoints. Application of the new European Committee on Antimicrobial Susceptibility Testing (EUCAST) recommendations increased the percentage of susceptible isolates to high-dose piperacillin-tazobactam to 92.8% (p < 0.001). Broad-spectrum carbapenems would only cover an additional 4.8%. The addition of vancomycin or linezolid extended coverage by just 1.7%.

Conclusions

Using an ureidopenicillin-beta-lactamase inhibitor combination at the high dose suggested by the new EUCAST recommendations provided nearly 93% coverage for relevant pathogens in patients with suspected bloodstream infection in our cohort. This might offer a safe option to reduce the empiric use of carbapenems. Our data support the absence of a general need for glycopeptides or oxazolidinones in empiric treatment.