Design of clone-specific probes from genome sequences for rapid PCR-typing of outbreak pathogens

Dissemination of a single ST11 clone of OXA-48-producing Klebsiella pneumoniae within a large polyclonal hospital outbreak determined by genomic sequencing

The population structure of a set of OXA-48-producing Klebsiella pneumoniae isolates belonging to sequence type 11 (ST11 Kp-OXA) and obtained from two hospitals in Madrid in the period from 2012 to 2015 was studied by genome sequencing. Overall, 97 ST11 Kp-OXA isolates were sequenced and their population structure and demography were studied by Bayesian phylodynamic analysis using core-genome SNVs. In total, 92 isolates were from Hospital La Paz, 57 of them from two selected units. The remaining five isolates were from different units of Hospital Doce de Octubre. Altogether, 96 out of the 97 ST11 Kp-OXA isolates could be ascribed to a single lineage that evolved into three sublineages. Demographic inference showed an expansion of the ST11 Kp-OXA in the first half of 2013 in agreement with the registered incidences. Dated phylogeny showed transmission clusters within hospital wards, between wards and between hospitals. The ST11 Kp-OXA outbreak in Hospital La Paz was largely due to the expansion of a single clone that was transmitted between different units and to Hospital Doce de Octubre. This clone diverged into three sub-lineages and spread out following a mixed mode of neutral core-genome evolution with some features of antibiotic selection, frequent large deletions and plasmid loss and gain events.

Intestinal loads of OXA-48-producing Klebsiella pneumoniae in colonized patients determined from surveillance rectal swabs

OBJECTIVES

To determine quantitatively the extent of intestinal colonization by OXA-48-producing Klebsiella pneumoniae (KpOXA) in hospitalized patients.

METHODS

The load of the OXA-48 β-lactamase gene in rectal swabs from 147 colonized patients was measured by quantitative PCR. The load was calculated relative to the total bacterial population (represented by the 16S rRNA gene) using the ΔΔCt method and pure cultures of OXA-48-producing K. pneumoniae as reference samples. The relative loads of the epidemic K. pneumoniae clones ST11 and ST405 were also measured.

RESULTS

The relative intestinal loads of the OXA-48 β-lactamase gene, RL_OXA-48, in hospitalized patients were high. The median RL_OXA-48 was -0.42 (95% confidence interval (CI): -0.60 to -0.16), close to that of a pure culture of OXA-48-producing K. pneumoniae (RL_OXA-48 = 0). In those patients colonized by the KpOXA clones ST11 (51/147, 34.7%) and ST405 (14/147, 9.5%), the relative loads of these clones were similarly high (median RL_ST11 = -1.1, 95% CI: -1.64 to -0.92; median RL_ST405 = -1.3, 95% CI: -1.76 to -0.96). Patients that had received previous antibiotic treatments and those that developed infections by KpOXA had significantly higher RL_OXA-48 values: -0.32 (95% CI: -0.58 to -0.20) vs -1.07 (95% CI: -2.43 to -0.35) and -0.26 (-0.77 to -0.23) vs -0.47 (-0.74 to -0.28), respectively.

CONCLUSIONS

Colonization by KpOXA in hospital patients involves intestinal loads much higher than the K. pneumoniae loads reported in the normal microbiota, reaching levels close to those of pure KpOXA cultures in many cases and largely replacing the host microbiota.

Carbapenem-Resistant Enterobacteriaceae Outbreak in a Medical Ward in Spain: Epidemiology, Control Strategy, and Importance of Environmental Disinfection

Introduction: Carbapenem-resistant Enterobacteriaceae (CRE) are a growing public health problem. We describe an outbreak by CRE and the measures to control it in a hospitalization unit in Spain. Methods: In June 2015, the system of prevention and control of CRE implemented in the hospital detected an increase in the incidence of patients with CRE in a mixed hospitalization facility (geriatrics, internal medicine, and pneumology), with the appearance of four related patients in 2 weeks, three of them being nosocomial cases. A multidisciplinary group was created and carried out: weekly screenings, general cleaning, four training sessions for personnel, two hand hygiene observation studies and environmental sampling. A higher incidence of new cases was detected in three adjoining rooms, in which environmental decontamination was performed with vaporized hydrogen peroxide. Results: In 5 months, a total of 18 cases were detected, 14 of them were nosocomial. Four different clones of Klebsiella pneumoniae OXA-48 were responsible for 83.3% of the cases. Adherence to hand hygiene increased from 36% to 85% after the training sessions. Seven percent of the environmental samples were positive for CRE in rooms with high incidence, moving to 0% after decontamination with hydrogen peroxide. Three patients died, one of them possibly associated with clinical infection due to CRE. Conclusions: Multidisciplinary information strategies, personnel training, and control of environmental reservoirs are effective to address outbreaks of CRE.

Intestinal persistence of a plasmid harbouring the OXA-48 carbapenemase gene after hospital discharge

To study intestinal colonization by OXA-48-producing Klebsiella pneumoniae (KpO48) after hospital discharge, stool samples from 22 previously colonized subjects were collected. Time from discharge was 33-611 days, without readmissions. Eight subjects (36%) were identified as blaOXA-48 gene carriers. In all of them the hospital-acquired strain of KpO48 had been lost, and the gene was harboured by other strains of K. pneumoniae, Klebsiella oxytoca and/or Escherichia coli. Our findings show intestinal persistence for several months of a plasmid harbouring the OXA-48 carbapenemase gene in a significant proportion of individuals in the absence of antibiotic treatment.

Population structure of OXA-48-producing Klebsiella pneumoniae ST405 isolates during a hospital outbreak characterised by genomic typing

OBJECTIVES

The aim of this study was to investigate the structure of a broad and sustained hospital outbreak of OXA-48-producing Klebsiella pneumoniae (KpO48) belonging to sequence type 405 (ST405).

METHODS

Whole-genome sequencing and comparison of ten ST405 KpO48 isolates obtained from clinical samples in our hospital was performed. Using stringent criteria, 36 single nucleotide polymorphisms (SNPs) were detected (range 0-21 in pairwise comparisons), and allele-specific PCR was used to call the SNPs among a larger set of isolates.

RESULTS

Several haplotypes were identified within the population. The haplotypes did not show a spatial structure, but a temporal evolution of sequential haplotype replacements was observed.

CONCLUSIONS

The dispersed spatial distribution suggests a reservoir formed by a large pool of colonised patients, and the temporal replacement pattern suggests that the sustained outbreak was composed of several small outbreaks that appeared and rapidly dispersed to several units.

Epidemiology and control measures of an OXA-48-producing Enterobacteriaceae hospital-wide oligoclonal outbreak

The main objective of our study was to describe the epidemiological and microbiological features of an oligoclonal hospital-wide outbreak caused by OXA-48-producing Enterobacteriaceae (OXA-48-PE). OXA-48 is a carbapenemase belonging to Ambler class D beta-lactamases, identified frequently in the Mediterranean and Southern European countries, and associated with several Enterobacteriaceae species. An outbreak of OXA-48-PE with a complex epidemic pattern was detected in January 2011. Initial control measures included contact precautions and the reinforcement of infection control practices, but despite all efforts made, the epidemiological situation hardly changed and new measures were implemented during 2013. An observational retrospective study was performed to describe the main features of the outbreak and to analyse the cumulative incidence (CI) trends. Eight hundred and 16 patients colonised or infected by OXA-48-PE were identified during the 2-year period (January 2013-December 2014), female 46%, mean age (s.d.), 71.6 (15.2). The samples isolated in the incident cases were rectal swabs (80%), urine samples (10.7%), blood samples (2.8%) and other clinical samples (6.6%). The most frequent OXA-48-PE was Klebsiella pneumoniae. Eleven different clones were identified, but K. pneumoniae sequence types 11 and 405 were predominant: ST11 (64.2%) and ST405 (29.3%). OXA-48-PE CI trend suffered a statistically significant change in August 2013, which continued the following months. Though we could not eradicate the outbreak, we observed a statistically significant drop in CI after an intervention for OXA-48-PE control, based on patient cohort, active surveillance, electronic alerts and reinforcement of infection control measures in a tertiary hospital.

Successful control of 2 simultaneous outbreaks of OXA-48 carbapenemase-producing Enterobacteriaceae and multidrug-resistant Acinetobacter baumannii in an intensive care unit

BACKGROUND

This report describes a double outbreak of OXA-48-producing Enterobacteriaceae (OXA-48-PE) and multidrug-resistant Acinetobacter baumannii (MRAB) in an intensive care unit (ICU) and the effectiveness of measures implemented, including decontamination with vaporized hydrogen peroxide (VHP).

METHODS

Affected patients were isolated in a confined area and cared for by dedicated personnel. Four percent chlorhexidine soap was used for patient daily hygiene. All patients are subjected to contact precautions. An in-depth cleaning of the ICU was performed with a chlorine solution, followed by decontamination with VHP. Environmental samples were taken before and after the decontamination.

RESULTS

From July-October 2015, 13 patients were colonized or infected by OXA-48-PE and 18 by MRAB in the ICU. The cumulative incidence of OXA-48-PE and MRAB was 3.48% and 4.81%, respectively. In the period after the intervention, they were 0.8% and 0%, respectively (P < .001). Before the VHP biodecontamination, 4.5% of environmental samples were positive for OXA-48-PE and none for MRAB. After biodecontamination, 1.4% of samples were positive for OXA-48-PE.

CONCLUSIONS

This study emphasizes the importance of environmental hygiene in the control of outbreaks caused by microorganisms of high environmental impact. The rapid effect after the VHP treatment suggests an influence of this measure in eradication.

Bla-OXA48 gene microorganisms outbreak, in a tertiary Children's Hospital, Over 3 years (2012-2014): Case Report

RATIONALE

Carbapenem-resistant Enterobacteriaceae are an emerging problem in children. Nosocomial spread remains the principal risk factor for acquisition of these microorganisms.

PATIENTS CONCERNS

We describe an outbreak of Klebsiella pneumoniae OXA48 (KOXA48) in a tertiary children's hospital during the years 2012 to 2014, as well as the preventive measures put in place in colonized and infected cases.

DIAGNOSES

We studied, "in vitro," the KOXA48 susceptibility to antiseptics and surface disinfectants. Moreover, an epidemiological surveillance of infection or colonization by these microorganisms, with molecular typing of the KOXA48, was performed, and carbapenemase genes were confirmed by polymerase chain reaction (PCR).

INTERVENTIONS

The bundles recommended (early detection, cohorting of children and health care workers [HCW], contact precautions, etc.) to control the KOXA48 outbreak were taken from those described in the centers for disease control (CDC) 2012 guide, and adapted according to our experience in controlling other outbreaks.

OUTCOMES

All the KOXA48 microorganisms isolated from children belonged to the same strain (ST11) and were susceptible to alcohol solutions but not the surface disinfectant previously employed in our hospital (tensoactive). We reinforced the surface disinfection using a double application (tensoactive + alcohol). The outbreak of KOXA48 begun in 2012 (16 cases in neonatal intensive care unit [NICU] and 1 in pediatric intensive care unit [PICU]) ended before the end of the same year and was not transmitted to new patients in 2013 to 2014, despite readmission of some colonized cases, in intensive care units (ICUs) and other units, of our children hospital.

LESSONS

Infected children are the tip of the iceberg (3/17) of KOXA48 prevalence making it necessary to identify the cases colonized by these bacteria. At the beginning of the outbreak, the susceptibility of the epidemic strain to antiseptics and surface disinfectants should be studied. Moreover, the measures taken (cohorts, contact precautions, etc.) must be thorough in both colonized and infected cases, immediately, after microbiological diagnosis.

Community-Onset Bloodstream and Other Infections, Caused by Carbapenemase-Producing Enterobacteriaceae: Epidemiological, Microbiological, and Clinical Features

Background. Because most infections caused by carbapenemase-producing Enterobacteriaceae (CPE) begin during hospitalization, there are limited data about community-onset (CO) infections caused by CPE. Our aim is to describe the frequency of CO infections caused by CPE as well as the clinical features of CO bloodstream infections (CO-BSIs).

Methods. This study includes retrospective case series of CO infections caused by CPE in a tertiary hospital from January 2010 to July 2014. Any clinical sample with a positive culture for CPE that had been ordered by primary care doctors or by doctors at the emergency room (ER) were classified as CO. Epidemiological and microbiological features of CO cases were assessed as were clinical features of CO-BSIs.

Results. Of 780 clinical samples with CPE, 180 were requested at the ER or by primary care doctors (22.9%), 150 of which were produced by Klebsiella pneumoniae (83.3%). The bla_OXA−48 gene was detected in 149 isolates (82.8%) followed by the bla_VIM gene, 29 (16.1%). Sixty-one patients (33.9%) had a prior history of CPE infection/colonization. Thirty-four of the 119 (28.6%) patients without prior history of CPE infection/colonization did not fulfill Friedman criteria for healthcare-associated infections (HAIs). Considering previous hospitalization of up to 12 months as a criterion for defining HAI, only 16 (13.4%) cases were identified as community-acquired infections. The most frequent positive sample was urine (133 of 180; 73.9%). Twenty-one (11.7%) patients had a BSI, 9 of them secondary to urinary tract infections (42.9%). Thirty-day crude mortality among patients with BSI was 23.8% (5 of 21).

Conclusions. Community-onset infections caused by CPE are an important subgroup of all CPE infections. The urinary tract is the main source. Bloodstream infections accounted for more than 10% of the cases.

Phylogeny, resistome and mobile genetic elements of emergent OXA-48 and OXA-245 Klebsiella pneumoniae clones circulating in Spain

OBJECTIVES

The global emergence of OXA-48-producing Klebsiella pneumoniae clones is a significant threat to public health. We used WGS and phylogenetic analysis of Spanish isolates to investigate the population structure of blaOXA-48-like-expressing K. pneumoniae ST11 and ST405 and to determine the distribution of resistance genes and plasmids encoding blaOXA-48-like carbapenemases.

METHODS

SNPs identified in whole-genome sequences were used to reconstruct phylogenetic trees, identify resistance determinants and de novo assemble the genomes of 105 blaOXA-48-like-expressing K. pneumoniae isolates.

RESULTS

Genome variation was generally lower in outbreak-associated isolates compared with those associated with sporadic infections. The relatively limited variation observed within the outbreak-associated isolates was on average 7-10 SNPs per outbreak. Of 24 isolates from suspected sporadic infections, 7 were very closely related to isolates causing hospital outbreaks and 17 were more diverse and therefore probably true sporadic cases. On average, 14 resistance genes were identified per isolate. The 17 ST405 isolates from sporadic cases of infection had four distinct resistance gene profiles, while the resistance gene profile differed in all ST11 isolates from sporadic cases. Sequence analysis of 94 IncL/M plasmids carrying blaOXA-48-like genes revealed an average of two SNP differences, indicating a conserved plasmid clade.

CONCLUSIONS

Whole-genome sequence analysis enabled the discrimination of outbreak and sporadic isolates. Significant inter-regional spread within Spain of highly related isolates was evident for both ST11 and ST405 K. pneumoniae. IncL/M plasmids carrying blaOXA-48-like carbapenemase genes were highly conserved geographically and across the outbreaks, sporadic cases and clones.

Risk factors for colonization by carbapenemase-producing enterobacteria at admission to a Surgical ICU: A retrospective study

INTRODUCTION

In 2011, a hospital-wide outbreak of OXA-48 producing Klebsiella pneumoniae occurred in our hospital, an epidemiological setting of high ESBL-producing K. pneumoniae rates. This study identifies risk factors for colonization with carbapenemase-producing enterobacteria (CPE) at Surgical Intensive Care Unit (SICU) admission.

METHODS

A 2-year retrospective study was performed in all patients admitted to the SICU that following routine had a rectal swab collected upon admission.

RESULTS

Of 254 patients admitted, 41 (16.1%) harbored CPE (five showing two carbapenemase-producing isolates). Most frequent carbapenemase-producing isolates and carbapenemases were K. pneumoniae (39/46, 84.8%) and OXA-48 (31/46; 76.1%), respectively. Carriers significantly had higher rates of chronic renal disease, previous digestive/biliary endoscopy, hospitalization, ICU/SICU admission, intraabdominal surgery, and antibiotic intake, as well as higher median values of clinical scores (SOFA, SAPS II and APACHE II). In the multivariate analysis (R²=0.309, p<0.001), CPE carriage was associated with prior administration of 3rd-4th generation cephalosporins (OR=27.96, 95%CI=6.88, 113.58, p<0.001), β-lactam/β-lactamase inhibitor (OR=11.71, 95%CI=4.51, 30.43, p<0.001), abdominal surgery (OR=6.33, 95%CI=2.12, 18.89, p=0.001), and prior digestive/biliary endoscopy (OR=3.88, 95%CI=1.56, 9.67, p=0.004).

CONCLUSIONS

A strong association between production of ESBLs and carriage of CPE (mainly OXA-48 producing K. pneumoniae) was found. According to the model, the co-selection of β-lactamases by previous exposure to broad-spectrum cephalosporins and β-lactam/β-lactamase inhibitors (with lower relative risk), abdominal surgery and prior digestive/biliary endoscopy were factors associated with CPE carriage.