Outbreak of Klebsiella pneumoniae producing KPC-2 and SHV-12 in a French hospital

Time-series modelling for the quantification of seasonality and forecasting antibiotic-resistant episodes: application to carbapenemase-producing Enterobacteriaceae episodes in France over 2010-20

BACKGROUND

Carbapenemase-producing Enterobacteriaceae (CPE) cause resistant healthcare-associated infections that jeopardize healthcare systems and patient safety worldwide. The number of CPE episodes has been increasing in France since 2009, but the dynamics are still poorly understood.

OBJECTIVES

To use time-series modelling to describe the dynamics of CPE episodes from August 2010 to December 2016 and to forecast the evolution of CPE episodes for the 2017-20 period.

METHODS

We used time series to analyse CPE episodes from August 2010 to November 2016 reported to the French national surveillance system. The impact of seasonality was quantified using seasonal-to-irregular ratios. Seven time-series models and three ensemble stacking models (average, convex and linear stacking) were assessed and compared with forecast CPE episodes during 2017-20.

RESULTS

During 2010-16, 3559 CPE episodes were observed in France. Compared with the average yearly trend, we observed a 30% increase in the number of CPE episodes in the autumn. We noticed a 1 month lagged seasonality of non-imported episodes compared with imported episodes. Average stacking gave the best forecasts and predicted an increase during 2017-20 with a peak up to 345 CPE episodes (95% prediction interval = 124-1158, 80% prediction interval = 171-742) in September 2020.

CONCLUSIONS

The observed seasonality of CPE episodes sheds light on potential factors associated with the increased frequency of episodes, which need further investigation. Our model predicts that the number of CPE episodes will continue to rise in the coming years in France, mainly due to local dissemination, associated with bacterial carriage by patients in the community, which is becoming an immediate challenge with regard to outbreak control.

The Effectiveness of Drying on Residual Droplets, Microorganisms, and Biofilms in Gastrointestinal Endoscope Reprocessing: A Systematic Review

BACKGROUND

Despite endoscope reprocessing, residual droplets remain in gastrointestinal endoscope working channels. Inadequate drying of gastrointestinal endoscope working channels may promote microbial reproduction and biofilm formation, increasing the risk of infection in patients. This review was designed to provide the current status of gastrointestinal endoscope drying, emphasize the importance of gastrointestinal endoscope drying, and evaluate the effectiveness of different drying methods of gastrointestinal endoscope in reducing residual droplets and microbial growth risk.

METHODS

A systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) reporting checklist. The PubMed, Web of Science, Medline, EMBASE, EBSCO, CNKI, CQVIP, and Wanfang Data databases were searched from 2010 to 2020 to identify eligible articles focused on methods of gastrointestinal endoscope drying and the status of endoscope drying. The following key points were analyzed: type of intervention, amount of residual droplets, major microbial types, and effectiveness of biofilm intervention. JBI quality assessment tool was used to determine bias risk for inclusion in the article.

RESULTS

This review included twelve articles. Two of the articles reported lack of drying of gastrointestinal endoscopes while the other ten reported residual droplets, microbial growth, and biofilm formation after different methods of drying. Four articles reported 0 to 4.55 residual droplets; four articles reported that the main microbial types were cocci and bacilli, most commonly Staphylococcus, Escherichia coli, Bacillus maltophilia, and Pseudomonas aeruginosa; and two reported that drying could effectively reduce biofilm regeneration. The type of intervention is as follows: automatic endoscopy reprocessor (AER), manual compressed air drying, and the Dri-Scope Aid for automatic drying and drying cabinet.

CONCLUSIONS

While endoscope reprocessing may not always be effective, an automatic endoscope reprocessor plus the Dri-Scope Aid with automatic drying over 10 min or storage in a drying cabinet for 72 h may be preferred.

Assessing the role of inter-facility patient transfer in the spread of carbapenemase-producing Enterobacteriaceae: the case of France between 2012 and 2015

The spread of carbapenemase-producing Enterobacteriaceae (CPE) in healthcare settings is a major public health threat that has been associated with cross-border and local patient transfers between healthcare facilities. Since the impact of transfers on spread may vary, our study aimed to assess the contribution of a patient transfer network on CPE incidence and spread at a countrywide level, with a case study of France from 2012 to 2015. Our results suggest a transition in 2013 from a CPE epidemic sustained by internationally imported episodes to an epidemic sustained by local transmission events through patient transfers. Incident episodes tend to occur within close spatial distance of their potential infector. We also observe an increasing frequency of multiple spreading events, originating from a limited number of regional hubs. Consequently, coordinated prevention and infection control strategies should focus on transfers of carriers of CPE to reduce regional and inter-regional transmission.

Spread of hospital-acquired infections: A comparison of healthcare networks

Hospital-acquired infections (HAIs), including emerging multi-drug resistant organisms, threaten healthcare systems worldwide. Efficient containment measures of HAIs must mobilize the entire healthcare network. Thus, to best understand how to reduce the potential scale of HAI epidemic spread, we explore patient transfer patterns in the French healthcare system. Using an exhaustive database of all hospital discharge summaries in France in 2014, we construct and analyze three patient networks based on the following: transfers of patients with HAI (HAI-specific network); patients with suspected HAI (suspected-HAI network); and all patients (general network). All three networks have heterogeneous patient flow and demonstrate small-world and scale-free characteristics. Patient populations that comprise these networks are also heterogeneous in their movement patterns. Ranking of hospitals by centrality measures and comparing community clustering using community detection algorithms shows that despite the differences in patient population, the HAI-specific and suspected-HAI networks rely on the same underlying structure as that of the general network. As a result, the general network may be more reliable in studying potential spread of HAIs. Finally, we identify transfer patterns at both the French regional and departmental (county) levels that are important in the identification of key hospital centers, patient flow trajectories, and regional clusters that may serve as a basis for novel wide-scale infection control strategies.

Hospital-acquired infections (HAIs), including emerging multi-drug resistant organisms, threaten healthcare systems worldwide. Efficient containment measures of HAIs must mobilize the entire healthcare network. Thus, to best understand how to reduce the scale of potential HAI epidemic spread, we explore patient transfer patterns in the French healthcare system. We construct and compare the characteristics of three different patient transfer networks based on data on transfers of patients with diagnosed HAIs, suspected HAIs, or of all patients. Our analyses show that these healthcare networks, the patient populations that comprise them and the patient movement patterns are heterogeneous and centralized. Despite the differences in patient populations, the HAI-specific and suspected-HAI healthcare networks have the same underlying structure as that of the general healthcare network. We identify key hospital centers, patient flow trajectories, at both the regional and department (county) level that may serve as a basis for proposing novel wide-scale infection control strategies.

Endoscope drying and its pitfalls

Inadequate drying of endoscope channels is a possible cause of replication and survival of remaining pathogens during storage. The presence during storage of potentially contaminated water in endoscope channels may promote bacterial proliferation and biofilm formation. An incomplete drying procedure or lack of drying and not storing in a vertical position are the most usual problems identified during drying and endoscope storage. Inadequate drying and storage procedures, together with inadequate cleaning and disinfection, are the most important sources of endoscope contamination and post-endoscopic infection. Flexible endoscopes may be dried in automated endoscope reprocessors (AERs), manually, or in drying/storage cabinets. Flushing of the endoscope channels with 70-90% ethyl or isopropyl alcohol followed by forced air drying is recommended by several guidelines. Current guidelines recommend that flexible endoscopes are stored in a vertical position in a closed, ventilated cupboard. Drying and storage cabinets have a drying system that circulates and forces the dry filtered air through the endoscope channels. Endoscope reprocessing guidelines are inconsistent with one another or give no exact recommendations about drying and storage of flexible endoscopes. There is no conclusive evidence on the length of time endoscopes can be safely stored before requiring re-disinfection and before they pose a contamination risk. To minimize the risk of disease transmission and nosocomial infection, modification and revision of guidelines are recommended as required to be consistent with one another.

Infectious complications in gastrointestinal endoscopy and their prevention

Gastrointestinal endoscopes are medical devices that have been associated with outbreaks of health care-associated infections. Because of the severity and limited treatment options of infections caused by multidrug-resistant Enterobacteriaceae and Pseudomonas aeruginosa, considerable attention has been paid to detection and prevention of these post-endoscopic outbreaks. Endoscope reprocessing involves cleaning, high-level disinfection/sterilization followed by rinsing and drying before storage. Failure of the decontamination process implies the risk of settlement of biofilm producing species in endoscope channels. This review covers the infectious complications in gastrointestinal endoscopy and their prevention and highlights the problem of infection risk associated with different steps of endoscope reprocessing.

Molecular epidemiology of KPC-2-producing Enterobacteriaceae (non-Klebsiella pneumoniae) isolated from Brazil

In Brazil, since 2009, there has been an ever increasing widespread of the bla(KPC-2) gene, mainly in Klebsiella pneumoniae. This study aims to assess the molecular epidemiology and genetic background of this gene in Enterobacteriaceae (non-K. pneumoniae) species from 9 Brazilian states between 2009 and 2011. Three hundred eighty-seven isolates were analyzed exhibiting nonsusceptibility to carbapenems, in which the bla(KPC-2) gene was detected in 21.4%. By disk diffusion and E-test, these isolates exhibited high rates of resistance to most of the antimicrobials tested, including tigecycline (45.6% nonsusceptible) and polymyxin B (16.5%), the most resistant species being Enterobacter aerogenes and Enterobacter cloacae. We found great clonal diversity and a variety of bla(KPC-2)-carrying plasmids, all of them exhibiting a partial Tn4401 structure. Therefore, this study demonstrates the dissemination of KPC-2 in 9 Enterobacteriaceae species, including species that were not previously described such as Pantoea agglomerans and Providencia stuartii.

Emergence of blaKPC carbapenemase genes in Australia

blaKPC genes encoding resistance to carbapenems are increasingly widely reported and are now endemic in parts of several countries, but only one Klebsiella pneumoniae isolate carrying blaKPC-2 had previously been reported in Australia, in 2010. Here we characterised this isolate, six additional K. pneumoniae and one Escherichia coli carrying blaKPC and another K. pneumoniae lacking blaKPC, all isolated in Australia in 2012. Seven K. pneumoniae belonged to clonal complex (CC) 292, associated with blaKPC in several countries. Five with blaKPC-2 plus the isolate lacking a blaKPC gene were sequence type 258 (ST258) and the seventh was the closely related ST512 with blaKPC-3. The eighth K. pneumoniae isolate, novel ST1048, and the E. coli (ST131) also carried blaKPC-2. blaKPC genes were associated with the most common Tn4401a variant, which gives the highest levels of expression, in all isolates. The ST258 isolates appeared to share a similar set of plasmids, with IncFIIK, IncX3 and ColE-type plasmids identified in most isolates. All K. pneumoniae isolates had a characteristic insertion in the ompK35 gene resulting in a frameshift and early termination, but only the ST512 isolate had a GlyAsp insertion in loop 3 of OmpK36 that may contribute to increased resistance. The clinical epidemiology of blaKPC emergence in Australia thus appears to reflect the global dominance of K. pneumoniae CC292 (and perhaps E. coli ST131). Some, but not all, patients carrying these isolates had previously been hospitalised outside Australia, suggesting multiple discrete importation events of closely related strains, as well as undetected nosocomial spread.

Klebsiella spp. in endoscopy-associated infections: we may only be seeing the tip of the iceberg

PURPOSE

Two endoscopy-associated nosocomial outbreaks caused by carbapenemase-producing Klebsiella pneumoniae (CPKP) were recently observed in two German hospitals. In this study, we performed a systematic search of the medical literature in order to elucidate the epidemiology of Klebsiella spp. in endoscopy-associated outbreaks.

METHODS

Medline, the Outbreak Database ( http://www.outbreak-database.com ) and reference lists of articles extracted from these databases were screened for descriptions of endoscopy-associated nosocomial outbreaks. The data extracted and analysed were: (1) the type of medical department affected; (2) characterisation of pathogen to species and conspicuous resistance patterns (if applicable); (3) type of endoscope and the grade of its contamination; (4) number and the types of infections; (5) actual cause of the outbreak.

RESULTS

A total of seven nosocomial outbreaks were identified, of which six were outbreaks of endoscopic retrograde cholangiopancreatography-related infections and caused by contaminated duodenoscopes. Including our own outbreaks in the analysis, we identified one extended-spectrum beta-lactamase-producing K. pneumoniae strain and six CPKP strains. Insufficient reprocessing after the use of the endoscope was the main reason for subsequent pathogen transmission.

CONCLUSIONS

There were only two reports of nosocomial outbreaks due to Klebsiella spp. in the first three decades of endoscopic procedures, but seven additional outbreaks of this kind have been reported within the last 4 years. It is very likely that many of such outbreaks have been missed in the past because this pathogen belongs to the physiological gut flora. However, with the emergence of highly resistant (carbapenemase-producing) strains, strict adherence to infection control guidelines is more important than ever.

The mechanism of high-level carbapenem resistance in Klebsiella pneumoniae: underlying Ompk36-deficient strains represent a threat of emerging high-level carbapenem-resistant K. pneumoniae with IMP-1 β-lactamase production in Japan

The mechanisms of high-level carbapenem resistance in Klebsiella pneumoniae isolated in Japan were investigated. High-level carbapenem-resistant K. pneumoniae Mkp4437 and a less carbapenem-sensitive K. pneumoniae strain, Mkp4365, were recovered from the same patient. These two strains were found to be homologous by pulsed-field gel electrophoresis, and both strains contained blaIMP-1, blaDHA-1, blaCTXM-14, blaTEM-1, and blaSHV-1. Based on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis, the lack of Ompk36 was observed in Mkp4437. Direct sequencing of the ompK36 gene demonstrated that a new insertional sequence in the open reading frame of the ompK36 gene was found in Mkp4437. Three clinical isolates (minimum inhibitory concentration [MIC] 2-4 mg/L to imipenem) were identified upon screening the strains of K. pneumoniae isolated in the University hospital with MICs of ≥ 1 mg/L to imipenem. Interestingly, these three isolates all lacked OmpK36. Conjugation of the plasmid harboring IMP-1 to these three OmpK36-deficient strains led to the isolation of high-level carbapenem-resistant transconjugants. In conclusion, the mechanisms of high-level carbapenem resistance in K. pneumoniae entail not only the production of IMP-1 β-lactamase but also the lack of OmpK36. It is vital to monitor for the presence of less carbapenem-sensitive K. pneumoniae strains, which lack OmpK36, because blaIMP-1 transmission to these strains may result in isolates with a high-level carbapenem-resistant phenotype.

Complete nucleotide sequence of the first KPC-2- and SHV-12-encoding IncX plasmid, pKpS90, from Klebsiella pneumoniae

We report the complete nucleotide sequence of the pKpS90 plasmid, carrying the bla(KPC-2) and bla(SHV-12) genes. This plasmid was isolated from a sequence type 258 (ST258) Klebsiella pneumoniae strain responsible for an outbreak in a French university hospital in 2009. pKpS90 is a 53,286-bp plasmid that belongs to the IncX incompatibility group. pKpS90 consists of a backbone from IncX plasmids, in which the KPC-2-encoding Tn4401 transposon and a bla(SHV-12)-encoding region have been inserted.

Direct detection and genotyping of Klebsiella pneumoniae carbapenemases from urine by use of a new DNA microarray test

Klebsiella pneumoniae carbapenemases (KPCs) are considered a serious threat to antibiotic therapy, as they confer resistance to carbapenems, which are used to treat extended-spectrum beta-lactamase (ESBL)-producing bacteria. Here, we describe the development and evaluation of a DNA microarray for the detection and genotyping of KPC genes (bla(KPC)) within a 5-h period. To test the whole assay procedure (DNA extraction plus a DNA microarray assay) directly from clinical specimens, we compared two commercial DNA extraction kits (the QIAprep Spin miniprep kit [Qiagen] and the urine bacterial DNA isolation kit [Norgen]) for the direct DNA extraction from urine samples (dilution series spiked in human urine). Reliable single nucleotide polymorphism (SNP) typing was demonstrated using 1 × 10(5) CFU/ml urine for Escherichia coli (Qiagen and Norgen) and 80 CFU/ml urine, on average, for K. pneumoniae (Norgen). This study presents, for the first time, the combination of a new KPC microarray with commercial sample preparation for detecting and genotyping microbial pathogens directly from clinical specimens; this paves the way toward tests providing epidemiological and diagnostic data, enabling better antimicrobial stewardship.

Overview of the epidemiology and the threat of Klebsiella pneumoniae carbapenemases (KPC) resistance

Klebsiella pneumoniae carbapenemases (KPCs) confer resistance to nearly all β-lactams. This broad-spectrum drug resistance mechanism has rapidly spread in the United States and is reportedly increasing elsewhere in the world. Thus, the emergence of KPC resistance is a major threat to global health. This article reviews the epidemiology and provides an overview of the dissemination of KPC-producing organisms.

Outbreak of pulmonary infection caused by Klebsiella pneumoniae isolates harbouring blaIMP-4 and blaDHA-1 in a neonatal intensive care unit in China

Outbreaks caused by Klebsiella pneumoniae producing carbapenemases and other β-lactamases have been reported. Four neonates admitted to a neonatal intensive care unit (NICU) in a Chinese hospital developed respiratory infection while receiving intensive care. In all four cases, multidrug-resistant K. pneumoniae was isolated from multiple respiratory specimens, leading to additional characterization of these organisms and investigation of the local environment in the NICU. Multiple β-lactamase genes, including bla(TEM-1), bla(IMP-4), bla(DHA-1) and bla(CTX-M-14), as well as the quinolone resistance gene qnrB4, were harboured by transferable plasmids from all four clinical isolates. Furthermore, PFGE confirmed that three of the four clinical isolates from the patients and three K. pneumoniae isolates collected from the hands of health-care workers and an incubator in the NICU belonged to the same PFGE cluster, indicating that an outbreak due to multidrug-resistant K. pneumoniae carrying bla(IMP-4) and bla(DHA-1) occurred in this NICU. As far as is known, this is the first report of the co-existence of bla(IMP-4) and bla(DHA-1) in the same K. pneumoniae isolate. These data suggest that additional precautions are needed to prevent outbreaks of infection caused by multidrug-resistant K. pneumoniae resulting from environmental exposure in NICUs.

Nosocomial outbreak of Klebsiella pneumoniae carbapenemase-producing Klebsiella oxytoca in Austria

To date, no outbreak of carbapenemase-producing bacteria has been reported for Austria. While outbreaks of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae have been increasingly reported, no outbreak caused by KPC-producing Klebsiella oxytoca has been described yet, to the best of our knowledge. We report an outbreak of KPC-producing K. oxytoca. In 5 months, 31 KPC-producing Klebsiella oxytoca strains were isolated from five patients. All patients were admitted to the same medical intensive care unit in Austria.

Molecular characteristics of KPC-producing Enterobacteriaceae at the early stage of their dissemination in Poland, 2008-2009

After the first report in May 2008, the National Reference Center for Susceptibility Testing confirmed 113 cases of infection or colonization by KPC-producing members of the family Enterobacteriaceae in Poland by the end of 2009. The vast majority of patients were found in 18 hospitals; three patients were diagnosed at outpatient clinics. Most of the institutions were in the Warsaw area, including three hospitals with the highest numbers of cases. When available, the data on previous hospitalizations often indicated that these hospitals were the probable acquisition sites; one patient arrived from New York. The group of 119 unique isolates consisted of Klebsiella pneumoniae (n = 114), followed by Klebsiella oxytoca (n = 3), and Escherichia coli (n = 2). The K. pneumoniae isolates were dominated by the clone sequence type 258 (ST258) (n = 111); others were ST11 and ST23. The ST258 group was heterogeneous, with 28 pulsed-field gel electrophoresis (PFGE) subtypes, ∼25 plasmid profiles, and nine β-lactamase patterns differing by KPC variants (KPC-2 mainly), and SHV-12, CTX-M-3, and TEM-1-like enzymes. Plasmids carrying bla(KPC) genes varied in size (~48 to 250 kb), structure, and conjugation potential. Transferable IncFII(K) plasmids of ~110 to 160 kb, probably pKpQIL or its derivatives, were observed in all K. pneumoniae clones and in K. oxytoca. Also prevalent were nontypeable pETKp50-like plasmids of ~50 kb, found in K. pneumoniae ST258 and E. coli isolates (ST93 and ST224). Two K. pneumoniae-E. coli pairs from single patients might represent the in vivo transfer of such plasmids. The striking diversity of KPC producers at the early stage of dissemination could result from several introductions of these bacteria into the country, their multidirectional evolution during clonal spread, and transfer of the plasmids.

Sensitive and specific phenotypic assay for metallo-beta-lactamase detection in Enterobacteria by use of a moxalactam disk supplemented with EDTA

Moxalactam is highly hydrolyzed by plasmid-mediated metallo-β-lactamases (MBLs), whereas it is poorly inactivated by serine-active carbapenemases. This study demonstrated that moxalactam resistance constituted an effective screen for MBL expression in enterobacteria, which could be confirmed, even in low-MBL-producing isolates, by a disk potentiation test using moxalactam and EDTA.

A call for action: the application of The International Health Regulations to the global threat of antimicrobial resistance

Stephen Harbarth and colleagues argue that the International Health Regulations (IHR) should be applied to the global health threat of antimicrobial resistance.

Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance

Multilocus sequence typing reveals that many bacterial species have a clonal structure and that some clones are widespread. This underlying phylogeny was not revealed by pulsed-field gel electrophoresis, a method better suited to short-term outbreak investigation. Some global clones are multiresistant and it is easy to assume that these have disseminated from single foci. Such conclusions need caution, however, unless there is a clear epidemiological trail, as with KPC carbapenemase-positive Klebsiella pneumoniae ST258 from Greece to northwest Europe. Elsewhere, established clones may have repeatedly and independently acquired resistance. Thus, the global ST131 Escherichia coli clone most often has CTX-M-15 extended-spectrum β-lactamase (ESBL), but also occurs without ESBLs and as a host of many other ESBL types. We explore this interaction of clone and resistance for E. coli, K. pneumoniae, Acinetobacter baumannii- a species where three global lineages dominate--and Pseudomonas aeruginosa, which shows clonal diversity, but includes the relatively 'tight' serotype O12/Burst Group 4 cluster that has proved adept at acquiring resistances--from PSE-1 to VIM-1 β-lactamases--for over 20 years. In summary, 'high-risk clones' play a major role in the spread of resistance, with the risk lying in their tenacity--deriving from poorly understood survival traits--and a flexible ability to accumulate and switch resistance, rather than to constant resistance batteries.