Molecular and descriptive epidemiologyof multidrug-resistant Enterobacteriaceae in hospitalized infants

Application of Next-Generation Sequencing to Enterobacter Hormaechei Subspecies Analysis during a Neonatal Intensive Care Unit Outbreak

INTRODUCTION

The Enterobacter cloacae complex (ECC) species are potential neonatal pathogens, and ECC strains are among the most commonly encountered Enterobacter spp. associated with nosocomial bloodstream infections. Outbreaks caused by ECC can lead to significant morbidity and mortality in susceptible neonates. At the molecular level, ECC exhibits genomic heterogeneity, with six closely related species and subspecies. Genetic variability poses a challenge in accurately identifying outbreaks by determining the clonality of ECC isolates. This difficulty is further compounded by the limitations of the commonly used molecular typing methods, such as pulsed field gel electrophoresis, which do not provide reliable accuracy in distinguishing between ECC strains and can lead to incorrect conclusions. Next-generation sequencing (NGS) offers superior resolution in determining strain relatedness. Therefore, we investigated the clinical pertinence of incorporating NGS into existing bundle measures to enhance patient management during an outbreak of ECC in a level-3 neonatal intensive care unit (NICU) in Germany.

METHODS

As the standard of care, all neonates on the NICU received weekly microbiological swabs (nasopharyngeal and rectal) and analysis of endotracheal secretion, where feasible. During the 2.5-month outbreak, colonisation with ECC was detected in n = 10 neonates. The phylogenetic relationship and potential antimicrobial resistance genes as well as mobile genetic elements were identified via bacterial whole-genome sequencing (WGS) using Illumina MiSeq followed by in silico data analysis.

RESULTS

Although all ECC isolates exhibited almost identical antimicrobial susceptibility patterns, the WGS data revealed the involvement of four different ECC clones. The isolates could be characterised as Enterobacter hormaechei subspecies steigerwaltii (n = 6, clonal), subsp. hoffmannii (n = 3, two clones) and subsp. oharae (n = 1). Despite the collection of environmental samples, no source of this diffuse outbreak could be identified. A new standardised operating procedure was implemented to enhance the management of neonates colonised with MRGN. This collaborative approach involved both parents and medical professionals and successfully prevented further transmission of ECC.

CONCLUSIONS

Initially, it was believed that the NICU outbreak was caused by a single ECC clone due to the similarity in antibiotic resistance. However, our findings show that antibiotic susceptibility patterns can be misleading in investigating outbreaks of multi-drug-resistant ECC. In contrast, bacterial WGS accurately identified ECC at the clonal level, which significantly helped to delineate the nature of the observed outbreak.

Infection control measures against multidrug-resistant Gram-negative bacteria in children and neonates

The increase in infections caused by multidrug-resistant (MDR) Gram-negative bacteria in neonatal and pediatric intensive care units over recent years is alarming. MDR Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii have constituted the main causes of the MDR Gram-negative bacteria problem. The implementation of infection control measures such as hand hygiene, cohorting of patients, contact precautions, active surveillance and environmental cleaning could diminish their spread. Recently, water safety has been identified as a major component of infection control policies. The aim of the current review is to highlight the effectiveness of these infection control measures in managing outbreaks caused by MDR Gram-negative bacteria in neonatal and pediatric intensive care units and highlight future perspectives on the topic.

Infections Caused by Antimicrobial Drug-Resistant Saprophytic Gram-Negative Bacteria in the Environment

Background

Drug-resistance genes found in human bacterial pathogens are increasingly recognized in saprophytic Gram-negative bacteria (GNB) from environmental sources. The clinical implication of such environmental GNBs is unknown.

Objectives

We conducted a systematic review to determine how often such saprophytic GNBs cause human infections.

Methods

We queried PubMed for articles published in English, Spanish, and French between January 2006 and July 2014 for 20 common environmental saprophytic GNB species, using search terms “infections,” “human infections,” “hospital infection.” We analyzed 251 of 1,275 non-duplicate publications that satisfied our selection criteria. Saprophytes implicated in blood stream infection (BSI), urinary tract infection (UTI), skin and soft tissue infection (SSTI), post-surgical infection (PSI), osteomyelitis (Osteo), and pneumonia (PNA) were quantitatively assessed.

Results

Thirteen of the 20 queried GNB saprophytic species were implicated in 674 distinct infection episodes from 45 countries. The most common species included Enterobacter aerogenes, Pantoea agglomerans, and Pseudomonas putida. Of these infections, 443 (66%) had BSI, 48 (7%) had SSTI, 36 (5%) had UTI, 28 (4%) had PSI, 21 (3%) had PNA, 16 (3%) had Osteo, and 82 (12%) had other infections. Nearly all infections occurred in subjects with comorbidities. Resistant strains harbored extended-spectrum beta-lactamase (ESBL), carbapenemase, and metallo-β-lactamase genes recognized in human pathogens.

Conclusion

These observations show that saprophytic GNB organisms that harbor recognized drug-resistance genes cause a wide spectrum of infections, especially as opportunistic pathogens. Such GNB saprophytes may become increasingly more common in healthcare settings, as has already been observed with other environmental GNBs such as Acinetobacter baumannii and Pseudomonas aeruginosa.

Intensified colonisation screening according to the recommendations of the German Commission for Hospital Hygiene and Infectious Diseases Prevention (KRINKO): identification and containment of a Serratia marcescens outbreak in the neonatal intensive care unit, Jena, Germany, 2013-2014

PURPOSE

In 2013, the German Commission for Hospital Hygiene and Infectious Disease Prevention (KRINKO) stated that extending weekly colonisation screening from very low birth weight (VLBW) infants (<1500 g) to all patients in the Neonatal Intensive Care Unit (NICU) might be useful.

METHODS

After implementing this recommendation, we detected a previously unnoticed cluster of Serratia marcescens. Strains were typed by Pulsed Field Gel Electrophoresis (PFGE).

RESULTS

Over 6 months, 19 out of 159 infants acquired S. marcescens. Twelve of the nineteen patients with S. marcescens were non-VLBW infants, and they were colonised significantly earlier than were VLBW infants (median 17 vs. 28 days; p < 0.01). Molecular typing revealed a polyclonal outbreak with multiple strain types leading to one or two transmissions each and a dominating outbreak strains being involved in an explosive outbreak involving eight neonates.

CONCLUSION

The revised KRINKO recommendation may help identify unnoticed outbreaks. Colonised non-VLBW patients may be an underestimated source of S. marcescens.

Media Stories on NICU Outbreaks Lead to an Increased Prescription Rate of Third-Line Antibiotics in the Community of Neonatal Care

BACKGROUND Between 2010 and 2012, 3 outbreaks of nosocomial infections in German neonatal intensive care units (NICUs) attracted considerable public interest. Headlines on national television channels and in newspapers had important consequences for the involved institutions and a negative impact on the relationship between families and staff in many German NICUs. OBJECTIVE To determine whether NICU outbreaks reported in the media influenced provider behavior in the community of neonatal care and led to more third-line antibiotic prescribing. DESIGN Observational cohort study. METHODS To investigate secular trends, we evaluated data for very-low-birth-weight infants (VLBWIs, birth weight <1,500 g) enrolled in the German Neonatal Network (GNN) between 2009 and 2014 (N=10,253). For outbreak effects, we specifically analyzed data for VLBWIs discharged 6 months before (n=2,428) and 6 months after outbreaks (n=2,508). RESULTS The exposure of all VLBWIs to third-line antibiotics increased after outbreaks (19.4% before vs 22.5% after; P=.007). This trend particularly affected male infants (4.6% increase; P=.005) and infants with a birth weight between 1,000 and 1,499 g (3.5% increase; P=.001) In a logistic regression analysis, month of discharge as linear variable of time was associated with increased exposure to third-line antibiotics (odds ratio [OR], 1.01; 95% confidence interval [CI], 1.009-1.014; P<.001), and discharge within the 6-month period after outbreak reports independently contributed to this long-term trend (OR, 1.14; 95% CI, 1.017-1.270; P=.024). CONCLUSIONS Media reports directly affect medical practice, eg, overuse of third-line antibiotics. Future communication and management strategies must be based on objective dialogues between the scientific community and investigative journalists. Infect Control Hosp Epidemiol 2016;37:924-930.

Pathogen-Specific Clustering of Nosocomial Blood Stream Infections in Very Preterm Infants

BACKGROUND AND OBJECTIVES

Nosocomial infections in NICUs tend to cluster, sometimes as devastating outbreaks, but pathogen-specific transmission probabilities are unknown. We aimed to quantify the pathogen-specific risk of a blood stream infection (BSI) in preterm infants after an index case with that pathogen in the same department.

METHODS

Data of 44 818 infants below 1500 g birth weight of the German NICU surveillance system (2000-2011) were used to calculate the probability of a BSI in the presence or absence of another infant in the same unit with a same-pathogen BSI.

RESULTS

The relative risk was similar for the more common pathogens, Enterococcus spp (4.3; 95% confidence interval: 2.7-6.9; n = 243), Enterobacter spp (7.9, 5.4-11.4; n = 246), Escherichia coli (7.9; 5.1-12.1; n = 210), Candida albicans (8.7; 5.0-15.4; n = 138), Staphylococcus aureus (9.5; 7.6-12.1; n = 407) and Klebsiella spp (13.1; 9.0-19.1; n = 190) but markedly elevated for Serratia spp (77.5; 41.1-146.1; n = 58) and Pseudomonas aeruginosa (64.5; 25.7-162.1; n = 38). Rates of BSI per 100 exposed infants ranged between 2.21 (Enterococcus) and 8.15 (Serratia). The same pattern emerged after adjustments were made for patients' characteristics or when the analysis was restricted to positive blood cultures during the preceding 30 days.

CONCLUSIONS

Although BSIs with P aeruginosa or Serratia spp in preterm infants are rare, they are associated with a markedly elevated risk of secondary same-pathogen BSI and should prompt intensified active surveillance and infection control measures.

[Update on outbreaks reported from neonatal intensive care units: Serratia marcescens, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa]

In terms of the unique risk profile, the clinical course of nosocomial infections, and the most prevalent bacterial pathogens, literature on outbreaks of potentially pathogenic bacteria on neonatal intensive care units (NICUs) needs to be analyzed separately from reports derived from other intensive care units. With the purpose of updating important information for those involved in outbreak management and fostering preventive efforts, this article summarizes the results of a systematic literature analysis, referring to an earlier publication by Gastmeier et al. This review focuses on NICU outbreaks caused by Serratia marcescens, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa.

Risk factors and outcomes for multidrug-resistant Gram-negative bacteremia in the NICU

OBJECTIVES

To assess the risk factors antibiotic therapy and outcomes of multidrug-resistant (MDR) Gram-negative bacilli (GNB) bacteremia in NICU patients.

METHODS

Episodes of MDR GNB bacteremia were compared with a non-MDR GNB bacteremia group in an 8-year cohort study.

RESULTS

Of 1106 bacteremias, 393 (35.5%) were caused by GNB. Seventy (18.6%) were caused by an MDR strain. The most frequent mechanism of resistance was extended-spectrum β-lactamase production (67.1%), mainly by Klebsiella pneumoniae (59.6%). Previous antibiotic exposure to third-generation cephalosporin (odds ratio [OR]: 5.97; 95% confidence interval [CI]: 2.37-15.08; P < .001) and carbapenem (OR: 3.60; 95% CI: 1.26-10.29; P = .017) and underlying renal disease (OR: 7.08; 95% CI: 1.74-28.83; P = .006) were identified as independent risk factors for MDR GNB acquisition. Patients with MDR GNB bacteremia more likely received inadequate initial antibiotic therapy (72.9% vs 7.8%; P < .001) had higher rates of infectious complication (21.4% vs 10.5%; P = .011) and overall case fatality +rate (28.6% vs 10.5%; P < .001). Independent risk factors for overall mortality were presence of infectious complications after bacteremia (OR: 3.16; 95% CI: 1.41-7.08; P = .005) and underlying secondary pulmonary hypertension with or without cor pulmonale (OR: 6.19; 95% CI: 1.88-20.31; P = .003).

CONCLUSIONS

MDR GNB accounted for 18.6% of all neonatal GNB bacteremia in the NICU, especially in those with previous broad-spectrum antibiotic therapy and underlying renal disease. The most frequent mechanism of resistance was extended-spectrum β-lactamase (ESBL) production. Neonates with MDR GNB were more likely to develop infectious complications, which were independently associated with a higher overall case-fatality rate.

Rectal swabs are suitable for quantifying the carriage load of KPC-producing carbapenem-resistant Enterobacteriaceae

It is more convenient and practical to collect rectal swabs than stool specimens to study carriage of colon pathogens. In this study, we examined the ability to use rectal swabs rather than stool specimens to quantify Klebsiella pneumoniae carbapenemase (KPC)-producing carbapenem-resistant Enterobacteriaceae (CRE). We used a quantitative real-time PCR (qPCR) assay to determine the concentration of the bla(KPC) gene relative to the concentration of 16S rRNA genes and a quantitative culture-based method to quantify CRE relative to total aerobic bacteria. Our results demonstrated that rectal swabs are suitable for quantifying the concentration of KPC-producing CRE and that qPCR showed higher correlation between rectal swabs and stool specimens than the culture-based method.

Continuous surveillance to reduce extended-spectrum β-lactamase Klebsiella pneumoniae colonization in the neonatal intensive care unit

BACKGROUND

Clinical illness caused by resistant bacteria usually represents a wider problem of asymptomatic colonization. Active surveillance with appropriate institution of isolation precautions represents a potential mechanism to control colonization and reduce infection. The neonatal intensive care unit (NICU) is an environment particularly appropriate for such interventions. Neonates are rarely colonized by resistant bacteria on admission and staff enthusiasm for infection control is high.

OBJECTIVE

To reduce extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-KP) acquisition amongst neonates through a continuous active surveillance intervention.

METHODS

Fecal ESBL-KP cultures were performed weekly on all neonates over 4 years. Neonates with positive cultures were managed with contact precautions by dedicated nurses separately from other neonates. ESBL-KP acquisition amongst neonates staying >7 days was compared for the consecutive years. A subset of ESBL-KP isolates was typed with pulsed-field gel electrophoresis (PFGE).

RESULTS

Surveillance cultures were obtained from 1,482/1,763 (84%) neonates over 4 years. ESBL-KP acquisition decreased continuously from 94/397 (24%) neonates in 2006 to 33/304 (11%) in 2009 (p < 0.001, hazard ratio 0.75, 95% confidence interval 0.66-0.85, p < 0.001 for comparison of years). Hospital-wide ESBL-KP acquisition did not decrease outside the NICU. PFGE identified identical ESBL-KP strains from multiple neonates on six occasions and different strains from single neonates on seven occasions.

CONCLUSIONS

ESBL-KP is probably both imported into and spread within the NICU. Continuous long-term surveillance with cohorting was associated with a decrease in ESBL-KP acquisition within the NICU. This low-risk intervention should be considered as a means to decrease neonatal acquisition of resistant bacteria.

Antibiotic resistance in the NICU

Antimicrobial treatment is a mainstay therapy in the neo-natal intensive care unit (NICU). Given the lack of specificity for clinical symptoms of infection in the newborn and the overwhelming impact of infection with rapid multisystem dissemination, NICU providers tend to treat early while awaiting laboratory results. With the high vulnerability of our special population to a variety of potential infecting microbes, a combination of antibiotics is preferred for initial treatment. The selection of these antibiotics is based on the known or presumed environment of exposure. If the newborn is within a week of birth, we can reasonably expect the likely environment of exposure is the community or the mother. If the newborn is older or has undergone numerous procedures, we can presume the exposure is more likely to be hospital-based.

Antibiotic resistance in neonatal intensive care unit pathogens: mechanisms, clinical impact, and prevention including antibiotic stewardship

Antimicrobial-resistant pathogens are of increasing concern in the neonatal intensive care unit population. A myriad of resistance mechanisms exist in microorganisms, and management can be complex because broad-spectrum antibiotics are increasingly needed. Control and prevention of antibiotic-resistant organisms (AROs) require an interdisciplinary team with continual surveillance. Judicious use of antibiotics; minimizing exposure to risk factors, when feasible; and effective hand hygiene are crucial interventions to reduce infection and transmission of AROs.

Physiological characterisation of the efflux pump system of antibiotic-susceptible and multidrug-resistant Enterobacter aerogenes

Enterobacter aerogenes predominates amongst Enterobacteriaceae species that are increasingly reported as producers of extended-spectrum beta-lactamases. Although this mechanism of resistance to beta-lactams is important, other mechanisms bestowing a multidrug-resistant (MDR) phenotype in this species are now well documented. Amongst these mechanisms is the overexpression of efflux pumps that extrude structurally unrelated antibiotics prior to their reaching their targets. Interestingly, although knowledge of the genetic background behind efflux pumps is rapidly advancing, few studies assess the physiological nature of the overall efflux pump system of this, or for that matter any other, bacterium. The study reported here evaluates physiologically the efflux pump system of an E. aerogenes ATCC reference as well as two strains whose MDR phenotypes are mediated by overexpressed efflux pumps. The activities of the efflux pumps in these strains are modulated by pH and glucose, although the effects of the latter are essentially restricted to pH 8, suggesting the presence of two general efflux pump systems, i.e. proton-motive force-dependent and ABC transporter types, respectively.

Outbreaks of Serratia marcescens in neonatal and pediatric intensive care units: clinical aspects, risk factors and management

The following recommendations are derived from a systematic analysis of 34 Serratia marcescens outbreaks described in 27 publications from neonatal and pediatric intensive care units (NICU, PICU), in which genotyping methods were used to confirm or exclude clonality. The clinical observation of two or more temporally related cases of nosocomial S. marcescens infection should raise the suspicion of an outbreak, particularly in the NICU or PICU setting. Since colonized or infected patients represent the most important reservoir for cross transmission, hygienic barrier precautions (contact isolation/cohortation, the use of gloves and gowns in addition to strictly performed hand disinfection, enhanced environmental disinfection) should immediately be implemented and staff education given. Well-planned sampling of potential environmental sources should only be performed when these supervised barrier precautions do not result in containment of the outbreak. The current strategy of empiric antibiotic treatment should be reevaluated by a medical microbiologist or an infectious disease specialist. Empiric treatment of colonized children should use combination therapy informed by in vitro susceptibility data; in this context the high propensity of S. marcescens to cause meningitis and intracerebral abscess formation should be considered. In vitro susceptibility patterns do not reliably prove or exclude the clonality of the outbreak isolate. Genotyping of the isolates by pulse-field gel electrophoresis or PCR-based methods should be performed, but any interventions to interrupt further nosocomial spread should be carried out without waiting for the results.

Isolation precautions for antibiotic-resistant bacteria in healthcare settings

PURPOSE OF REVIEW

Emergence of drug-resistant bacteria and new or changing infectious pathogens is an important public health problem. Transmission of these pathogens in an acute care setting may occur frequently if proper precautions are not taken. Despite several guidelines and an abundance of literature on the prevention of transmission of epidemiologically important organisms in the healthcare setting, substantial controversy exists. This review focuses on recent data regarding the use of infection control and isolation precautions.

RECENT FINDINGS

New data are available, but the conflict surrounding the use of active surveillance of methicillin-resistant Staphylococcus aureus (MRSA) has not been resolved. The emergence of multidrug-resistant Gram-negative bacteria has prompted a greater interest in infection control strategies for prevention of their spread. Outbreaks of Clostridium difficile have responded to broad infection control initiatives, but further research is required to determine whether the best infection control precautions are being utilized.

SUMMARY

Effective prevention of the transmission of pathogens within the healthcare system requires a multifaceted approach. Existing guidelines should be used to create institutional policies specific to individual patient populations, problem pathogens and the ability to practically implement various infection control procedures. Despite ongoing study, the use of active surveillance to prevent transmission of MRSA continues to be a complex, controversial and challenging issue.

Carbapenem-resistant Enterobacter cloacae and the emergence of metallo-beta-lactamase-producing strains in a third-level hospital (Santiago de Compostela, NW Spain)

The purpose of this paper was to investigate the occurrence of carbapenem-resistant Enterobacter cloacae in our institution, to detect the carbapenemase-associated resistance and to determine the genetic relatedness of the isolates. Species identification and antimicrobial susceptibility testing were performed using the Vitek 2 system and Etest. Multiplex polymerase chain reaction-enzyme linked immunosorbent assay (PCR-ELISA) was used for the detection of extended-spectrum beta-lactamase (ESBL)-producers. The bla (IMP) and bla (VIM) genes were amplified by PCR and sequenced. The DiversiLab System was used for strain-typing. During the period 2006-2008, 12 different isolates of carbapenem-resistant E. cloacae (2.3 %) were recovered in our laboratory. Only two positive isolates for the bla (VIM) gene were detected. The minimum inhibitory concentration (MIC) values were higher for all carbapenems in the group of non-metallo-beta-lactamase (MBL)-producers. All isolates showed MIC values <or=2 against this tigecycline. The two bla (VIM-1)-carrying isolates showed different genotypes. For non-MBL-producers, two clonally related clusters were observed. Different mechanisms can be associated with carbapenem-resistance in E. cloacae. MBL-producing strains are less prevalent than those with other mechanisms of resistance. The clonal relationship confirms the risk of spread of these organisms with the transfer of patients to different wards and the persistence of these clones over time or the 'de novo' acquisition of the resistance caused by the selective pressure exerted by antibiotics treatments.