A hospital outbreak of an NDM-producing ST167 Escherichia coli with a possible link to a toilet

Successful termination of a multi-year wastewater-associated outbreak of NDM-5-carrying E. coli in a hemato-oncological center

BACKGROUND

In May 2018, an outbreak of NDM-5-carrying Escherichia coli (NDM-5-EC) was detected at the hemato-oncology department of a tertiary care center in Austria. This report details the outbreak investigation, control measures and the whole genome sequencing (WGS) data of the outbreak isolates.

METHODS

A total of 15 isolates (seven clinical isolates from allogenic stem cell transplant (SCT) recipients and eight wastewater isolates recovered from patients' toilets) were analyzed by whole genome sequencing.

RESULTS

Genome based typing identified two clusters of the high risk clones ST167/CT12607 and ST617/CT2791. Long-read sequencing of selected isolates from both clusters identified two different plasmids, however with a highly similar genetic context of the blaNDM-5 containing region. Genomic analysis revealed the presence of additional resistance genes, including blaCTX-M-15, and blaOXA-1, and virulence factors. Four patients were colonized with NDM-5-EC, two patients suffered bacteremia caused by the outbreak strain and two deaths were associated with an NDM-5-EC infection. The outbreak source was traced to toilet sewage pipes, which remained persistently contaminated despite extensive cleaning and disinfection. Successful eradication of NDM-5-EC from the installations required disassembly, hot water pressure washing of the sewage pipes and complete replacement of all movable parts. Additionally, colonized patients were instructed to use wheeled commodes instead of toilets, and a pre-admission screening strategy was implemented for all patients undergoing hematologic stem cell transplantation. The outbreak was successfully terminated in November 2020.

CONCLUSION

NDM-5-EC, especially high-risk clones such as ST167 and ST617, can persist in hospital wastewater systems despite cleaning and disinfection efforts and can cause prolonged outbreaks. Therefore, a comprehensive bundle of interventions like the ones applied in our study is essential, especially in clinical settings with heavily immunosuppressed patients.

Hospital toilets and drainage systems as a reservoir for a long-term polyclonal outbreak of clinical infections with multidrug-resistant Klebsiella oxytoca species complex

Background

Nosocomial outbreaks with multidrug-resistant bacteria with a probable reservoir in hospital toilets and drainage systems have been increasingly reported.

Aim

To investigate an increase in bacteraemia with extended-spectrum β-lactamase (ESBL)-producing Klebsiella oxytoca at our hospital in 2021; the epidemiology of the outbreak suggested an environmental source.

Methods

Available clinical K. oxytoca isolates from patient with infection or rectal carriage from 2019 to 2022 were collected. Clinical information was gathered from included patients and sampled sinks, shower drains, and toilet water. Short- and long-read whole-genome sequencing (WGS) was performed on patient and environmental isolates to assess phylogenetic relationships, antibiotic resistance genes/mutations, and plasmid profiles.

Results

WGS revealed four clusters and a polyclonal population consisting of ESBL-producing K. oxytoca and Klebsiella michiganensis. All clusters contained both clinical and environmental isolates. The environmental sampling revealed widespread contamination of the outbreak strains in the outbreak ward, and plasmid analyses indicated possible transfer of plasmids between species and clones. Most environmental findings in the outbreak ward were from toilet water, and enhanced cleaning of bathrooms and toilets was introduced. The following year, a decrease in outbreak strains in systemic infections was observed.

Conclusion

This investigation uncovered a polyclonal outbreak of multidrug-resistant K. oxytoca and K. michiganensis and unveiled a persistent reservoir of outbreak clones in the drainage system and toilet water, facilitating exchange of resistance genes. The risk of toilet water as a source of clinical infections warrants further investigation.

Transmission of clones of carbapenem-resistant Escherichia coli between a hospital and an urban wastewater treatment plant

Carbapenem-resistant Enterobacterales (CRE) constitute an urgent threat to worldwide public health. The spread of CRE is facilitated by transmission via the environment. Wastewater treatment plants (WWTPs) are considered to be important sources of antibiotic resistance and hot spots of antibiotic-resistant bacteria (ARB) which can facilitate dissemination of antibiotic resistance genes. In this study, water samples were collected over one year from a WWTP in Jinan, Shandong province, China, from different functional sites in the wastewater treatment process. Carbapenem-resistant Escherichia coli (CREC) were isolated by selective cultivation and whole-genome sequenced to investigate the occurrence and characteristics of CREC in the WWTP. A total of 77 CREC isolates were included in the study and the detection rate of CREC in the WWTP water inlet was found to be 85%. An additional 10 CREC were isolated from a nearby teaching hospital during the sampling period and included for comparison to the environmental isolates. Susceptibility testing showed that all CREC were multidrug-resistant. 6 different carbapenem resistance genes (CRGs) were detected, including blaNDM-5 (n = 75), blaNDM-1 (n = 6), blaNDM-4 (n = 3), blaNDM-6 (n = 1), blaNDM-9 (n = 1), and blaKPC-2 (n = 4). 42 CREC isolates were whole-genome sequenced with Illumina short-read sequencing. 11 of these were also sequenced with Nanopore long-read sequencing. Plasmids carrying CRGs were found to belong to IncX3 (n = 35), IncFII (n = 12), IncFIA (n = 5), IncFIB (n = 2), IncC (n = 1), and IncP6 (n = 1). Clonal dissemination of CREC belonging to ST167, ST448, and ST746 was observed between different parts of the WWTP. Furthermore, isolates from the WWTP, including an isolate belonging to the high-risk ST167 strain, were found to be clonally related to CREC isolated at the hospital. The spread of CRGs is of considerable concern and strategies to prevent environmental dissemination of this contaminant urgently needs to be implemented.

Universal screening or a universal risk assessment combined with risk-based screening for multidrug-resistant microorganisms upon admission: Comparing strategies

OBJECTIVE

Timely identification of patients who carry multidrug-resistant microorganisms (MDRO) is needed to prevent nosocomial spread to other patients and to the hospital environment. We aimed to compare the yield of a universal screening strategy upon admission to the currently installed universal risk assessment combined with risk-based screening upon admission.

METHODS

This observational study was conducted within a prospective cohort study. From January 1, 2018, until September 1, 2019, patients admitted to our hospital were asked to participate. Nasal and perianal samples were taken upon admission and checked for the presence of MDRO. The results of the universal risk assessment and risk-based screening were collected retrospectively from electronic health records.

RESULTS

In total, 1017 patients with 1069 separate hospital admissions participated in the study. Universal screening identified 38 (3.6%) unknown MDRO carriers upon admission (37 individual patients), all carrying extended-spectrum beta-lactamase-producing Enterobacterales. For 946 of 1069 (88.5%) patients, both the universal risk assessment and universal screening were performed. For 19 (2.0%) admissions, ≥1 risk factor was identified. The universal risk assessment identified one (0.1%) unknown carrier, compared to 37 out of 946 carriers for the universal screening (P<0.001). Of the 37 carriers identified through the universal screening, 35 (94.6%) reported no risk factors.

CONCLUSIONS

Our results show that in our low endemic setting, a universal screening strategy identified significantly more MDRO carriers than the currently implemented universal risk-assessment. When implementing a universal risk-assessment, risk factors should be carefully selected to be able to identify ESBL-E carriers. While the universal screening identified more MDRO carriers, further research is needed to determine the cost-effectiveness of this strategy.

The shared NDM-positive strains in the hospital and connecting aquatic environments

The spread of antibiotic-resistant priority pathogens outside hospital settings is, both, a significant public health concern and an environmental problem. In recent years, New Delhi Metallo-β-lactamase (NDM)-positive strains have caused nosocomial infections with high mortality and poor prognosis worldwide. Our study investigated the links of NDM-positive strains between the hospital and the connecting river system in Jinan city, Eastern China by using NDM-producing Escherichia coli (NDM-EC) as an indicator via whole genome sequencing. Thirteen NDM-EC isolates were detected from 187 river water and sediment samples, while 9 isolates were identified from patients at the local hospital. All NDM-EC isolates were resistant to imipenem, meropenem, cefotaxime, cefoxitin, ampicillin, tetracycline, fosfomycin, piperacillin-tazobactam. The bla_NDM-5 (n = 20) and bla_NDM-9 (n = 2) genes were identified, which were predominantly on IncX3 plasmids (n = 13), followed by IncFII plasmids (n = 5) and IncFIA plasmids (n = 2). Conjugation experiments showed that 21 isolates could transfer NDM-harboring plasmids. The well-conserved bla_NDM-5 genetic environment (ISAba125-bla_NDM-5/9-ble_MBL-trpF-dsbD-IS26) of these plasmids suggested a common genetic origin. Nine sequence types (STs) were detected, including three international high-risk clones ST167 (n = 8), ST410 (n = 1), and ST617 (n = 1). Phylogenetic analysis showed ST167 E. coli from the river was genotypically related to clinical isolates recovered from patients. Furthermore, ST167 isolates showed high genetic similarities with other clinical strains from geographically distinct regions. The genetic concordance between isolates from different sampling sites in the same river (ST218 clone), and different rivers (ST448 clone) raises concerns regarding the rapid dissemination of NDM-EC in the aquatic environment. The emergence and spread of the clinically relevant NDM-positive strains, especially for E. coli ST167 clone, an international high-risk clone associated with multi-resistance and virulence capacity, within and between the hospital and aquatic environments were elucidated, highlighting the need for attention and action.