Worsening epidemiological situation of carbapenemase-producing Enterobacteriaceae in Europe, assessment by national experts from 37 countries, July 2018

Characterization of a rare bla VIM-4 metallo-β-lactamase-producing Serratia marcescens clinical isolate in Hungary

A carbapenem-resistant S. marcescens isolate was recovered from a patient with an inflammed pacemaker inplantation pocket from a Cardiac Surgery ward in a Hungarian University Hospital. Phenotypic tests and polymerase chain reaction (PCR) confirmed a very rare gene responsible for production of a carbapenemase ( bla VIM-4 ), which was further characterized by Sanger-sequencing. The characterization of this S. marcescens strain emphasizes the ongoing emergence of novel or rare carbapenemases. Strains expressing a weak carbapenemase like this strain might go unrecognized by routine diagnostics due to low minimum inhibitory concentrations (MICs) for the bacterial strains producing such enzymes.

Epidemiology of carbapenemase-producing Enterobacterales in England, May 2015-March 2019: national enhanced surveillance findings and approach

Background

In response to increasing numbers of carbapenemase-producing Enterobacterales (CPE) in England, Public Health England (PHE) launched an electronic reporting system (ERS) for the enhanced surveillance of carbapenemase-producing Gram-negative bacteria. Our study aimed to describe system engagement and the epidemiology of CPE in England.

Methods

Engagement with the ERS was assessed by calculating the proportion of referrals submitted this system. ERS data were extracted and cases defined as patients with CPE isolated from a screening or clinical specimen in England between 1^st May 2015 to 31^st March 2019. Descriptive summary statistics for each variable were prepared.

Results

The ERS processed 12,656 suspected CPE reports. Uptake of the ERS by local microbiology laboratories varied, with approximately 70% of referrals made via the ERS by April 2016; this steadily decreased after March 2018. Six-thousand eight-hundred and fifty-seven cases were included in the analysis. Most cases were from colonised patients (80.6%) rather than infected, and the majority were inpatients in acute hospital settings (87.3%). Carbapenemases were most frequently detected in Klebsiella pneumoniae (39.1%) and Escherichia coli (30.3%). The most frequently identified carbapenemase families were OXA-48-like (45.1%) and KPC (26.4%). Enhanced data variables were poorly completed.

Conclusions

The ERS has provided some insight into the epidemiology of CPE in England. An increasing number of routine diagnostic laboratories have introduced methods to routinely identify acquired carbapenemases and PHE has modified its approach to ensure robust surveillance, which is an essential aspect of an effective response to prevent and control the spread of CPE.

Institutional Burden of Carbapenemase-Producing Enterobacterales: The Effect of Changes in Surveillance Culture Methodology

An essential part of the Israeli intervention program aimed to contain the spread of carbapenemase-producing Enterobacterales (CPE) has been the establishment of national surveillance system, where the institutional rates are determined by both clinical and surveillance cultures. The objectives of the study were to analyze the effect of changes in surveillance culture media on the rates and microbiological characteristics of CPE in a multicenter study. The rates were compared during 2 years in and between four centers. Two centers (Tel-Aviv and Beilinson) had changed their surveillance media to CHROMagar™ mSuperCARBA™ after 1 year, and two centers (Rambam and Hillel-Yaffe) had continued to use CHROMagar KPC. There was an increase in the rates of surveillance CPE in Tel-Aviv and Beilinson following the change in media, whereas the rates remained the same or declined in Rambam and Hillel-Yaffe, respectively. The rates of clinical CPE remained unchanged in Rambam and Hillel-Yaffe, declined in Tel-Aviv, and increased in Beilinson but to a lesser extent compared with the increase in surveillance CPE. The relative composition of the CPE mechanisms and species changed in Tel-Aviv, with an increase in non-Klebsiella pneumoniae species and in carbapenemase other than KPC. Our study shows that changes in surveillance media may contribute to significant changes in the rate of surveillance CPE that may be irrespective of actual epidemiological changes. Therefore, determination of institutional burden of CPE and the assessment of intervention results should be based primarily on the rate of clinical CPE rather than surveillance culture reports.

Implementation of an infection control program with emphasis on cohorting to patients with carbapenemase-producing Enterobacteriaceae. The experience of 2 years in a tertiary teaching hospital in northern Portugal

BACKGROUND

The emergence of carbapenemase-producing Enterobacterales (CPE) represents a major public health threat. Our purpose was to evaluate a surveillance and cohorting program implemented in patients infected or carriers of CPE.

METHODS

A prospective registry of CPE carriers or infected patients was analyzed from October 2015 until December 2017. All inpatients presenting with CPE were included in a hospital cohort with dedicated healthcare staff and contact precaution measures.

RESULTS

A total of 480 patients were identified, of which 15.8% (n = 76) were infected. Men comprised 56.7% of the cohort (n = 272) and 69.2% (n = 332) were elderly. About 46.3% (n = 222) had a previous hospital admission and 81.7% (n = 392) had at least 1 antibiotic course in the previous 90 days. There was a decline in infected patients in 2017. Periodic and admission screenings accounted for 63% and 74% of cases in 2016 and 2017, with increased detection rate comparing with contact/investigation screenings. In 2017, significantly fewer patients were identified outside the admission/point of prevalence screening (P = .009). In 2017 the proportion of invasive carbapenem-resistant Klebsiella pneumoniae amongst CPE in our center was below the national average (2016: 13.3% vs 5.2%; 2017: 6.6% vs 8.6%). A reduction of the consumption of carbapenems was also observed in 2017.

CONCLUSION

The implementation of the program has increased the number of patients identified by the preventive method and stabilized the emergence of new CPE cases. Furthermore, the program cohort compared well with the national picture, with a lower number of infected patients and a lower proportion of carbapenem-resistant K pneumoniae in invasive specimens. These indicators reflect the added value of the CPE surveillance and cohorting program.

Molecular epidemiology of carbapenemase-producing Enterobacterales in Finland, 2012-2018

Carbapenemase-producing Enterobacterales (CPE) pose an increasing threat to patient safety and healthcare systems globally. We present molecular epidemiology of CPE in Finland during 2012–2018 with detailed characteristics of CPE strains causing clusters during the same time period. All Finnish clinical microbiology laboratories send Enterobacterales isolates with reduced susceptibility to carbapenems or isolates producing carbapenemase to the reference laboratory for further characterization by whole genome sequencing (WGS). In total, 231 CPE strains from 202 patients were identified during 2012–2018. Of the strains, 59% were found by screening and 32% from clinical specimens, the latter were most commonly urine. Travel and/or hospitalization history abroad was reported for 108/171 strains (63%). The most common species were Klebsiella pneumoniae (45%), Escherichia coli (40%), and Citrobacter freundii (6%), and the most common carbapenemase genes bla_NDM-like (35%), bla_OXA-48-like (33%), and bla_KPC-like (31%). During 2012–2018, the annual number of CPE strains increased from 9 to 70 and different sequence types from 7 to 33, and bla_OXA-48-like genes became the most prevalent. Of the clusters, 3/8 were linked to traveling or hospitalization abroad and 5/8 were caused by K. pneumoniae clone clonal complex 258. Most of the clusters were caused by K. pneumoniae producing KPC. High variety among different sequence types indicates that majority of CPE cases detected in Finland are likely imported from foreign countries. Nearly one-third of the cases are not found by screening suggesting that there is hidden transmission occurring in the healthcare settings.

Whole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates

Objectives

The first hospital outbreak of carbapenemase-producing Enterobacteriaceae in Slovenia occurred in 2014–2016. Whole genome sequencing was used to analyse the population of carbapenem-resistant Klebsiella pneumoniae collected in Slovenia in 2014–2017, including OXA-48 and/or NDM-1 producing strains from the outbreak.

Methods

A total of 32 K. pneumoniae isolates were analysed using short-read sequencing. Multi-locus sequence typing and core genome multi-locus sequence typing were used to infer genetic relatedness. Antimicrobial resistance markers, virulence factors, plasmid content and wzi types were determined. Long-read sequencing was used for six isolates for detailed analysis of plasmids and their possible transmission.

Results

Overall, we detected 10 different sequence types (STs), the most common being ST437 (40.6%). Isolates from the initial outbreak belonged to ST437 (12/16) and ST147 (4/16). A second outbreak of four ST15 isolates was discovered. A new ST (ST3390) and two new wzi types (wzi-556, wzi-559) were identified. blaOXA-48 was found in 17 (53.1%) isolates, blaNDM-1 in five (15.6%), and a combination of blaOXA-48/NDM-1 in seven (21.9%) isolates. Identical plasmids carrying blaOXA-48 were found in outbreak isolates sequenced with long-read sequencing technology.

Conclusions

Whole genome sequencing of Slovenian carbapenem-resistant K. pneumoniae isolates revealed multiple clusters of STs, two of which were involved in the first hospital outbreak of carbapenem producing K. pneumoniae in Slovenia. Transmission of the plasmid carrying blaOXA-48 between two STs was likely to have occurred. A previously unidentified second outbreak was also discovered, highlighting the importance of whole genome sequencing in detection and/or characterization of hospital outbreaks and surveillance of drug-resistant bacterial clones.

Surveillance of common infections in the early period after renal transplantation in a national center: 2014-2017

BACKGROUND

Infection prevention and timely and effective treatment are among the major aims of care in kidney transplant recipients. Pre-transplant vaccination and pre-transplant viral screening have been extensively studied and are now considered standard practice. Early post-operative infection surveillance is mandatory in other vulnerable cohorts, but has not been extensively studied in this population. We hypothesized that surveillance of the most common bacterial infection types in the post-transplant setting would be beneficial and identify key areas for improvement.

METHODS

All adult kidney transplant recipients whose surgeries were performed in the Irish national kidney transplant unit over a 1-year period had prospective early post-transplant (first 30 days) infection surveillance in 2014 for surgical site infection, urinary tract infection, and secondary bloodstream infections (Group T0). Several key changes were implemented following scrutiny of infection patterns and clinical practice. Subsequently, infection surveillance was undertaken for 2016 and 2017 (Group T1) to assess the impact of these changes.

RESULTS

Between 2014 and 2017, the number of kidney transplants increased by 32%. The following aspects of clinical practice were the focus of change following analysis of Group T0 data: timing of surgical antimicrobial prophylaxis (SAP) administration, choice of SAP antimicrobial agent, and routine microbiological testing in the peri-operative period. Following implementation of these changes, the timing of SAP administration was greatly improved (45%-100% of cases appropriately timed). The infection rate decreased from 8.9% to 7.4% in 2016, with a further decrease to 4% in 2017 (OR 0.42 (95% CI: 0.16-1.10); P = .08). Compliance with pre-operative microbiological screening improved in Group T1.

CONCLUSIONS

Simple clinical practice changes, implemented upon analysis of common bacterial infection surveillance data in the first 30 days after kidney transplantation resulted in more effective SAP administration and improved compliance with routine microbiological testing in the peri-operative period. These interventions have potentially contributed to reduced early post-operative infection rates, despite increased transplant activity in the unit. Infection surveillance is an important and under-utilized way of reducing infections in this vulnerable patient cohort.

Detection of OXA-48-like-producing Enterobacterales in Irish recreational water

The rapid dissemination of carbapenemase-producing Enterobacterales (CPE) is a major public health concern. The role that the aquatic environment plays in this dissemination is underexplored. This study aimed to examine seawater as a reservoir for CPE. Seawater sampling took place at a bathing site throughout the 2017 bathing season. Each 30 L sample (n = 6) was filtered using the CapE filtration system. Wastewater samples (200 mL) (pre-treatment (n = 3) and post-treatment (n = 3)) were obtained from a nearby secondary wastewater treatment plant, during the same time period. All samples were examined for CPE. Whole genome sequencing of confirmed CPE was carried out using Illumina sequencing. Isolate genomes were hosted in corresponding BIGSdb databases and analyses were performed using multiple web-based tools. CPE was detected in 2/6 seawater samples. It was not detected in any wastewater samples. OXA-48-like-producing ST131 Escherichia coli (Ec_BM707) was isolated from a seawater sample collected in May 2017 and OXA-48-like-producing ST101 Klebsiella pneumoniae (Kp_BM758) was isolated from a seawater sample collected in August 2017. The genomes of the environmental isolates were compared to a collection of previously described Irish clinical OXA-48-like-producing Enterobacterales (n = 105). Ec_BM707 and Kp_BM758 harboured bla_OXA-48 on similar mobile genetic elements to those identified in the clinical collection (pOXA-48 fragment in Ec_BM707 and IncL(pOXA-48) plasmid in Kp_BM758). Genetic similarities were observed between Ec_BM707 and several of the clinical ST131 E. coli, with allele matches at up to 98.2% of 2513 core genome multilocus sequence type (cgMLST) loci. In contrast, Kp_BM758 and the 34 clinical K. pneumoniae were genetically distant. The source of the CPE at this site was not identified. The detection of OXA-48-like-producing ST131 E. coli and OXA-48-like-producing ST101 K. pneumoniae in Irish recreational water is a concern. The potential for contamination of the aquatic environment to contribute to dissemination of CPE in Europe warrants further study.

Decreasing and stabilising trends of antimicrobial consumption and resistance in Escherichia coli and Klebsiella pneumoniae in segmented regression analysis, European Union/European Economic Area, 2001 to 2018

Investments to reduce the spread of antimicrobial resistance (AMR) in the European Union have been made, including efforts to strengthen prudent antimicrobial use. Using segmented regression, we report decreasing and stabilising trends in data reported to the European Surveillance of Antimicrobial Consumption Network and stabilising trends in data reported to the European Antimicrobial Resistance Surveillance Network. Our results could be an early indication of the effect of prioritising AMR on the public health agenda.

High prevalence of colonisation with carbapenem-resistant Enterobacteriaceae among patients admitted to Vietnamese hospitals: Risk factors and burden of disease

BACKGROUND

Carbapenem-resistant Enterobacteriaceae (CRE) is an increasing problem worldwide, but particularly problematic in low- and middle-income countries (LMIC) due to limitations of resources for surveillance of CRE and infection prevention and control (IPC).

METHODS

A point prevalence survey (PPS) with screening for colonisation with CRE was conducted on 2233 patients admitted to neonatal, paediatric and adult care at 12 Vietnamese hospitals located in northern, central and southern Vietnam during 2017 and 2018. CRE colonisation was determined by culturing of faecal specimens on selective agar for CRE. Risk factors for CRE colonisation were evaluated. A CRE admission and discharge screening sub-study was conducted among one of the most vulnerable patient groups; infants treated at an 80-bed Neonatal ICU from March throughout June 2017 to assess CRE acquisition, hospital-acquired infection (HAI) and treatment outcome.

RESULTS

A total of 1165 (52%) patients were colonised with CRE, most commonly Klebsiella pneumoniae (n = 805), Escherichia coli (n = 682) and Enterobacter spp. (n = 61). Duration of hospital stay, HAI and treatment with a carbapenem were independent risk factors for CRE colonisation. The PPS showed that the prevalence of CRE colonisation increased on average 4.2% per day and mean CRE colonisation rates increased from 13% on the day of admission to 89% at day 15 of hospital stay. At the NICU, CRE colonisation increased from 32% at admission to 87% at discharge, mortality was significantly associated (OR 5·5, P < 0·01) with CRE colonisation and HAI on admission.

CONCLUSION

These data indicate that there is an epidemic spread of CRE in Vietnamese hospitals with rapid transmission to hospitalised patients.