Investigation of Outbreaks of Extended-Spectrum Beta-Lactamase-Producing Klebsiella Pneumoniae in Three Neonatal Intensive Care Units Using Whole Genome Sequencing.
ABSTRACT: Infections caused by extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-KP) are on a constant rise and are a noted cause of outbreaks in neonatal intensive care units (NICUs). We used whole genome sequencing (WGS) to investigate the epidemiology of consecutive and overlapping outbreaks caused by ESBL-KP in NICUs in three hospitals in close proximity. Clonality of 43 ESBL-KP isolates from 40 patients was determined by BOX-PCR. Short-read sequencing was performed on representative isolates from each clone. The dominant clones from each NICU were sequenced using long-read sequencing. Bioinformatics methods were used to define multilocus sequence type (MLST), analyze plasmid content, resistomes, and virulence factors. In each NICU, we found a unique dominant clone (ST985, ST37, and ST35), each belonging to a distinct sequence type (ST), as well as satellite clones. A satellite strain in NICU-2 (ST35) was the dominant strain in NICU-3, where it was isolated four weeks later, suggesting transmission. NICU-1- and NICU-2-dominant strains had blaCTX-M-15 carried on a similar transposable element (Tn3-ISEcp1) but at different locations: on a plasmid and on the chromosome, respectively. We concluded that the overlapping ESBL-KP outbreaks were a combination of clonal transmission within NICUs, possible transposable element transmission between NICUs, and repeated importation of ESBL-KP from the community.
Project description:BackgroundKlebsiella pneumoniae has been responsible for a large number of clonal hospital outbreaks. However, some epidemiological changes have been observed since the emergence of CTX-M enzymes in K. pneumoniae.AimTo analyse the transmission dynamics of Extended Spectrum ?-Lactamase-producing Klebsiella pneumoniae (ESBL-Kp) in an acute care hospital.MethodsIn 2015 a prospective cohort study was conducted. All new consecutive adult patients with ESBL-Kp isolates in all clinical samples were included. Patients with a previous known infection/colonization by ESBL-Kp and patients in high risk areas (e.g., intensive care units) were excluded. Cross-transmission was defined as the carriage of a clonally-related ESBL-Kp between newly diagnosed patients who shared the same ward for ?48?h with another case, within a maximum time window of 4 weeks. ESBL-production was confirmed using the double-disk diffusion method and PCR. Clonal relationships were investigated by rep-PCR and multilocus sequence typing (MLST).ResultsSixty ESBL-Kp isolates from 60 patients were included and analysed. Infections and colonizations were classified as hospital-acquired (52%), healthcare-related (40%) or community-acquired (8%).High genetic diversity was detected. When epidemiological clinical data were combined with the rep-PCR, the patterns identified did not show any cases of cross-transmission. ESBL-Kp were detected in 12.5% of environmental samples. No clonal relationship could be established between environmental reservoirs and patients. The genetic mechanism detected in all strains was associated with bla CTX-M genes, and 97% were CTX-M-15.ConclusionsThe dynamics of ESBL-K. pneumoniae isolated in our setting could not be explained by clonal transmission from an index patient. A polyclonal spread of ESBL-Kp was identified.
Project description:BACKGROUND:The comparisons of molecular characterization and antibiotic resistance of Klebsiella pneumoniae (KP) isolates from humans and other animal hosts are not well studied. Our goal was to compare the molecular epidemiology of KP strains that were isolated from urban rodents, shrews, and healthy people. RESULTS:K. pneumoniae (KP) isolates were isolated from fecal samples of rodents, shrews and healthy adults in 2015 in southern China. In total, 465 fecal samples were collected, of which 85 from rodents, 105 from shrews, and 275 from healthy adults. Antimicrobial susceptibility and production of extended-spectrum ?-lactamases (ESBL) of the isolates were tested. PCR-based methods were used to detect specific genes, including ESBL genes (blaTEM, blaSHV, and blaCTX-M) in ESBL-producing isolates, capsular serotypes (K1, K2, K5, K20, K54, and K57) in hypervirulent KPs (hvKPs), and virulence genes (magA, wcaG, rmpA, uge, kfu, and aerobactin) in hvKP isolates. Multilocus sequence type (MLST) and pulsed-field gel electrophoresis (PFGE) were performed to exclude the homology of these isolates. The carriage rate of KP in urban rodents and shrews (78.42%) was higher than that in healthy adults (66.18%) (?2?=?8.206, P?=?0.004). The prevalence rates of ESBL-producing isolates among rodents, shrews, and humans were 7.94, 12.79, and 17.03%, respectively. The positive rates of CTX-M, TEM and SHV types in ESBL-producing isolates were 29.79, 27.66, and 17.02%, respectively. Serotype K1, K5, K20, and K57 were detected in both small mammals and humans. PFGE typing revealed thirty-six clusters. PFGE cluster A was clustered by samples of shrews and healthy adult, with a similarity of 88.4%. MLST typing revealed thirty-eight types. ST23 and ST35 were detected in samples of shrews and healthy adults. ST37 was detected in samples of 2 rodents and a healthy adult. CONCLUSIONS:Overlapping serotypes of hvKP were observed in both the animals and humans. The same PFGE or MLST types were also found in isolates derived humans, rodents and shrews. Therefore, urban rodents and shrews might play a certain role in the transmission of drug-resistant and hypervirulent KP.
Project description:BACKGROUND: Studies about transmission rates of extended-spectrum ?-lactamase (ESBL)-producing Enterobacteriaceae in hospitals and households are scarce. METHODS: Eighty-two index patients with new carriage of ESBL-producing Escherichia coli (ESBL-Ec; n = 72) or ESBL-producing Klebsiella pneumoniae (ESBL-Kp; n = 10) and their hospital (n = 112) and household (n = 96) contacts were studied prospectively from May 2008 through September 2010. Isolates were phenotypically and molecularly characterized (sequencing of bla genes, repetitive extragenic palindromic polymerase chain reaction, pulse-field gel electrophoresis, and multilocus sequence typing). Transmission was defined as carriage of a clonally-related ESBL producer with identical bla(ESBL) gene(s) in the index patient and his or her contact(s). RESULTS: CTX-M-15 was the most prevalent ESBL in ESBL-Ec (58%) and ESBL-Kp (70%) in the index patients. Twenty (28%) ESBL-Ec isolates were of the hyperepidemic clone ST131. In the hospital, transmission rates were 4.5% (ESBL-Ec) and 8.3% (ESBL-Kp) and the incidences of transmissions were 5.6 (Ec) and 13.9 (Kp) per 1000 exposure days, respectively. Incidence of ESBL-Kp hospital transmission was significantly higher than that of ESBL-Ec (P < .0001), despite implementation of infection control measures in 75% of ESBL-Kp index patients but only 22% of ESBL-Ec index patients. Detection of ESBL producers not linked to an index patient was as frequent (ESBL-Ec, 5.7%; ESBL-Kp, 16.7%) as nosocomial transmission events. In households, transmission rates were 23% for ESBL-Ec and 25% for ESBL-Kp. CONCLUSIONS: Household outweighs nosocomial transmission of ESBL producers. The effect of hospital infection control measures may differ between different species and clones of ESBL producers.
Project description:Antibiotic-resistance of hospital-acquired infections is a major public health issue. The worldwide emergence and diffusion of extended-spectrum ?-lactamase (ESBL)-producing Enterobacteriaceae, including Escherichia coli (ESBL-EC) and Klebsiella pneumoniae (ESBL-KP), is of particular concern. Preventing their nosocomial spread requires understanding their transmission. Using Close Proximity Interactions (CPIs), measured by wearable sensors, and weekly ESBL-EC-and ESBL-KP-carriage data, we traced their possible transmission paths among 329 patients in a 200-bed long-term care facility over 4 months. Based on phenotypically defined resistance profiles to 12 antibiotics only, new bacterial acquisitions were tracked. Extending a previously proposed statistical method, the CPI network's ability to support observed incident-colonization episodes of ESBL-EC and ESBL-KP was tested. Finally, mathematical modeling based on our findings assessed the effect of several infection-control measures. A potential infector was identified in the CPI network for 80% (16/20) of ESBL-KP acquisition episodes. The lengths of CPI paths between ESBL-KP incident cases and their potential infectors were shorter than predicted by chance (P = 0.02), indicating that CPI-network relationships were consistent with dissemination. Potential ESBL-EC infectors were identified for 54% (19/35) of the acquisitions, with longer-than-expected lengths of CPI paths. These contrasting results yielded differing impacts of infection control scenarios, with contact reduction interventions proving less effective for ESBL-EC than for ESBL-KP. These results highlight the widely variable transmission patterns among ESBL-producing Enterobacteriaceae species. CPI networks supported ESBL-KP, but not ESBL-EC spread. These outcomes could help design more specific surveillance and control strategies to prevent in-hospital Enterobacteriaceae dissemination.
Project description:BACKGROUND:Enterobacter cloacae species is responsible for nosocomial outbreaks in vulnerable patients in neonatal intensive care units (NICU). The environment can constitute the reservoir and source of infection in NICUs. Herein we report the impact of preventive measures implemented after an Enterobacter cloacae outbreak inside a NICU. METHODS:This retrospective study was conducted in one level 3 NICU in Lyon, France, over a 6?year-period (2012-2018). After an outbreak of Enterobacter cloacae infections in hospitalized neonates in 2013, several measures were implemented including intensive biocleaning and education of medical staff. Clinical and microbiological characteristics of infected patients and evolution of colonization/infection with Enterobacter spp. in this NICU were retrieved. Moreover, whole genome sequencing was performed on 6 outbreak strains. RESULTS:Enterobacter spp. was isolated in 469 patients and 30 patients developed an infection including 2 meningitis and 12 fatal cases. Preventive measures and education of medical staff were not associated with a significant decrease in patient colonisation but led to a persistent decreased use of cephalosporin in the NICU. Infection strains were genetically diverse, supporting the hypothesis of multiple hygiene defects rather than the diffusion of a single clone. CONCLUSIONS:Grouped cases of infections inside one setting are not necessarily related to a single-clone outbreak and could reveal other environmental and organisational problematics. The fight against implementation and transmission of Enterobacter spp. in NICUs remains a major challenge.
Project description:Background:The methicillin-resistant clone Staphylococcus capitis NRCS-A, involved in sepsis in neonatal intensive care units (NICUs) worldwide, is able to persist and spread in NICUs, suggesting the presence of reservoirs inside each setting. The purpose of the present study was to identify these reservoirs and to investigate the cycle of transmission of NRCS-A in one NICU. Methods:In a single institution study, NRCS-A was sought in 106 consecutive vaginal samples of pregnant women to identify a potential source of NRCS-A importation into the NICU. Additionally NICU caregivers and environmental including incubators were tested to identify putative secondary reservoirs. Finally, the efficacy of disinfection procedure in the elimination of NRCS-A from incubators was evaluated. Results:No S. capitis was isolated from vaginal samples of pregnant women. Three of the 21 tested caregivers (14%) carried S. capitis on their hands, but none remain positive after a five-day wash-out period outside NICU. Moreover, the clone NRCS-A persisted during six consecutive weeks in the NICU environment, but none of the sampled sites was constantly contaminated. Finally in our before/after disinfection study, all of 16 incubators were colonized before disinfection and 10 (62%) incubators remained colonized with NRCS-A after the disinfection procedure. Conclusions:The partial ineffectiveness of incubators' disinfection procedures is responsible for persistence of NRCS-A inside a NICU, and the passive hand contamination of caregivers could be involved in the inter-patient transmission of S. capitis.
Project description:BACKGROUND:Variation in healthcare delivery and outcomes in neonatal intensive care units (NICUs) may be partly explained by differences in safety culture. OBJECTIVE:To describe NICU care giver assessments of safety culture, explore variability within and between NICUs on safety culture domains, and test for association with care giver characteristics. METHODS:NICU care givers in 12 hospitals were surveyed using the Safety Attitudes Questionnaire (SAQ), which has six scales: teamwork climate, safety climate, job satisfaction, stress recognition, perception of management and working conditions. Scale means, SDs and percent positives (percent agreement) were calculated for each NICU. RESULTS:There was substantial variation in safety culture domains among NICUs. Composite mean score across the six domains ranged from 56.3 to 77.8 on a 100-point scale and NICUs in the top four NICUs were significantly different from the bottom four (p<0.001). Across the six domains, respondent assessments varied widely, but were least positive on perceptions of management (3%-80% positive; mean 33.3%) and stress recognition (18%-61% positive; mean 41.3%). Comparisons of SAQ scale scores between NICUs and a previously published adult ICU cohort generally revealed higher scores for NICUs. Composite scores for physicians were 8.2 (p=0.04) and 9.5 (p=0.02) points higher than for nurses and ancillary personnel. CONCLUSION:There is significant variation and scope for improvement in safety culture among these NICUs. The NICU variation was similar to variation in adult ICUs, but NICU scores were generally higher. Future studies should validate whether safety culture measured with the SAQ correlates with clinical and operational outcomes in NICUs.
Project description:<h4>Objective</h4>Our objective was to incorporate social and built environment factors into a compendium of multilevel factors among a cohort of very low birth weight infants to understand their contributions to inequities in NICU quality of care and support providers and NICUs in addressing these inequities via development of a health equity dashboard.<h4>Study design</h4>We examined bivariate associations between NICU patient pool and NICU catchment area characteristics and NICU quality of care with data from a cohort of 15,901 infants from 119 NICUs in California, born 2008-2011.<h4>Result</h4>NICUs with higher proportion of minority racial/ethnic patients and lower SES patients had lower quality scores. NICUs with catchment areas of lower SES, higher composition of minority residents, and more household crowding had lower quality scores.<h4>Conclusion</h4>Multilevel social factors impact quality of care in the NICU. Their incorporation into a health equity dashboard can inform providers of their patients' potential resource needs.
Project description:Importance:Racial and ethnic minorities receive lower-quality health care than white non-Hispanic individuals in the United States. Where minority infants receive care and the role that may play in the quality of care received is unclear. Objective:To determine the extent of segregation and inequality of care of very low-birth-weight and very preterm infants across neonatal intensive care units (NICUs) in the United States. Design, Setting, and Participants:This cohort study of 743 NICUs in the Vermont Oxford Network included 117?982 black, Hispanic, Asian, and white infants born at 401 g to 1500 g or 22 to 29 weeks' gestation from January 2014 to December 2016. Analysis began January 2018. Main Outcomes and Measures:The NICU segregation index and NICU inequality index were calculated at the hospital level as the Gini coefficients associated with the Lorenz curves for black, Hispanic, and Asian infants compared with white infants, with NICUs ranked by proportion of white infants for the NICU segregation index and by composite Baby-MONITOR (Measure of Neonatal Intensive Care Outcomes Research) score for the NICU inequality index. Results:Infants (36?359 black [31%], 21?808 Hispanic [18%], 5920 Asian [5%], and 53?895 white [46%]) were segregated among the 743 NICUs by race and ethnicity (NICU segregation index: black: 0.50 [95% CI, 0.46-0.53], Hispanic: 0.58 [95% CI, 0.54-0.61], and Asian: 0.45 [95% CI, 0.40-0.50]). Compared with white infants, black infants were concentrated at NICUs with lower-quality scores, and Hispanic and Asian infants were concentrated at NICUs with higher-quality scores (NICU inequality index: black: 0.07 [95% CI, 0.02-0.13], Hispanic: -0.10 [95% CI, -0.17 to -0.04], and Asian: -0.26 [95% CI, -0.32 to -0.19]). There was marked variation among the census regions in weighted mean NICU quality scores (range: -0.69 to 0.85). Region of residence explained the observed inequality for Hispanic infants but not for black or Asian infants. Conclusions and Relevance:Black, Hispanic, and Asian infants were segregated across NICUs, reflecting the racial segregation of minority populations in the United States. There were large differences between geographic regions in NICU quality. After accounting for these differences, compared with white infants, Asian infants received care at higher-quality NICUs and black infants, at lower-quality NICUs. Explaining these patterns will require understanding the effects of sociodemographic factors and public policies on hospital quality, access, and choice for minority women and their infants.
Project description:Invasive syndrome caused by Klebsiella pneumoniae (KP), including liver abscess, is mainly caused by community-acquired strains with characteristics of positive hypermucoviscosity (HV) phenotype and regulator of mucoid phenotype A (rmpA) and transcriptional activator (rmpA2) genes. Extended- spectrum ?-lactamase-producing KP (ESBL-KP) is commonly nosocomial and rarely HV-positive. We aimed to explore the reasons of the rarer prevalence of HV phenotype, rmpA and rmpA2 as well as the virulence phenotype among the ESBL-KP isolates from clinical specimens than those non-ESBL isolates. The ?-lactamase genes, rmpA, rmpA2 and genes for K capsule serotype of 440 KP isolates were analyzed. The virulence of the isolates was characterized by the mouse lethality experiments. The prevalence rates of HV phenotype (? 50% vs. < 10%) as well as rmpA and rmpA2 genes (? 50-60% vs. < 20-30%) were significantly higher in non-ESBL group than in the ESBL group (p < 0.0001). Expression of HV phenotype in the rmpA-positive KP isolates was significantly rarer in the ESBL group than in non-ESBL group (33.3% vs. 91.9%, p < 0.0001). The frameshift mutations of rmpA and/or rmpA2 corresponded to negative HV phenotype of KP isolates that harbored the rmpA and/or rmpA2, resulting in variable mouse lethality (LD50, ? 10(3) - >5 × 10(7) CFU). The mutation rates might significantly differ among KP isolates from various sources. Virulence was dependent on rmpA-related HV phenotype. In conclusion, ESBL-KP isolates were less hypermucoviscous and less virulent than non-ESBL KP isolates, mostly due to concurrently lower carriage and higher mutation rates of the rmpA and rmpA2 genes.