Genomic Epidemiology of Carbapenemase-Producing Enterobacterales at a Hospital System in Toronto, Ontario, Canada, 2007 to 2018.
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SUBMITTER: Jamal AJ
PROVIDER: S-EPMC8284452 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundData on household transmission of carbapenemase-producing Enterobacterales (CPE) remain limited. We studied risk of CPE household co-colonization and transmission in Ontario, Canada.MethodsWe enrolled CPE index cases (identified via population-based surveillance from January 2015 to October 2018) and their household contacts. At months 0, 3, 6, 9, and 12, participants provided rectal and groin swabs. Swabs were cultured for CPE until September 2017, when direct polymerase chain reaction (PCR; with culture of specimens if a carbapenemase gene was detected) replaced culture. CPE risk factor data were collected by interview and combined with isolate whole-genome sequencing to determine likelihood of household transmission. Risk factors for household contact colonization were explored using a multivariable logistic regression model with generalized estimating equations.ResultsNinety-five households with 177 household contacts participated. Sixteen (9%) household contacts in 16 (17%) households were CPE-colonized. Household transmission was confirmed in 3/177 (2%) cases, probable in 2/177 (1%), possible in 9/177 (5%), and unlikely in 2/177 (1%). Household contacts were more likely to be colonized if they were the index case's spouse (odds ratio [OR], 6.17; 95% confidence interval [CI], 1.05-36.35), if their index case remained CPE-colonized at household enrollment (OR, 7.00; 95% CI, 1.92-25.49), or if they had at least 1 set of specimens processed after direct PCR was introduced (OR, 6.46; 95% CI, 1.52-27.40).ConclusionsNine percent of household contacts were CPE-colonized; 3% were a result of household transmission. Hospitals may consider admission screening for patients known to have CPE-colonized household contacts.
| S-EPMC8662791 | biostudies-literature
Project description: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 blaNDM-like (35%), blaOXA-48-like (33%), and blaKPC-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 blaOXA-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.
| S-EPMC7427707 | biostudies-literature
Project description:IntroductionIn contrast to countries where carbapenemase-producing Enterobacterales (CPE) are endemic, only sporadic cases were reported in Switzerland until 2013. An aggravation of the epidemiological situation in neighbouring European countries indicated the need for a surveillance study in Switzerland.AimWe aimed to describe CPE distributions in Switzerland and identify epidemiological factors associated with changes in incidence.MethodsData on all human CPE isolates from 2013 to 2018 were collected by the Swiss Centre for Antibiotic Resistance (ANRESIS) and analysed for temporal and regional trends by Generalised Poisson regression. Isolates associated with infection or colonisation were included in a primary analysis; a secondary analysis included invasive isolates only. Statistical detection of regional clusters was performed with WHONET/SaTScan.ResultsWe analysed 731 CPE isolates, of which 325 (44.5%) were associated with screenings and 173 (23.7%) with infections. Yearly detection of CPE isolates increased considerably during the study period from 65 to 212. The most frequently isolated species were Klebsiella pneumoniae (54%) and Escherichia coli (28%). The most frequent genotypes were OXA-48 (43%), KPC (21%) and NDM (14%). In contrast to the French-speaking parts of Switzerland (West, Geneva) where OXA-48 were the predominant genotypes (around 60%), KPC was the most frequently detected genotype in the Italian-speaking region (63%). WHONET/SaTScan outbreak detection analysis identified seven clusters in five regions of Switzerland.ConclusionsIn a first continuous surveillance of CPE in Switzerland, we found that the epidemiological situation aggravated nationwide and that regional patterns of CPE genotypes mirrored the situation in neighbouring European countries.
| S-EPMC8167416 | biostudies-literature
Project description:BackgroundNosocomial transmission and outbreaks of carbapenemase-producing Enterobacterales (CPE) represent a challenge to healthcare systems. In July 2018, a CPE hospital ward outbreak was declared. Our aim was to investigate transmission patterns, using social network analysis and genomics in a nosocomial CPE outbreak.MethodsA retrospective descriptive analysis of all patients (cases and contacts) admitted to a ward experiencing a CPE outbreak (2018-2019) was undertaken. A case had a negative CPE admission screen, and subsequent positive test. A contact shared a multi-bed area and/or facility with a case (>4 hours). Social networks, including genomics data and ward locations, were constructed. Network metrics were analysed.FindingsForty-five cases and 844 contacts were analysed. The median age of cases was 78 years (IQR 67-83), 58% (n=26) were male and 100% had co-morbidities. The median outbreak ward length-of-stay (LOS) was 17 days (IQR 10-34). OXA-48 CPE was confirmed in all cases and from 26 environmental samples. Social networks identified clusters by time, gender and species/sequence type/plasmid. Network metrics indicated potential superspreading involving a subset of patients with behavioural issues.ConclusionSocial networks elucidated high resolution transmission patterns involving two related OXA-48 plasmids, multiple species/genotypes and potential super-spreading. Interventions prevented intra-hospital spread. An older patient cohort, extended hospital LOS and frequent intra-ward bed transfers, coupled with suboptimal ward infrastructure, likely prolonged this outbreak. We recommend social network analysis contemporaneously with genomics (on case and environmental samples) for complex nosocomial outbreaks and bespoke care plans for patients with behavioural issues on outbreak wards.
| S-EPMC10164899 | biostudies-literature
Project description:BackgroundThe Netherlands is currently considered a low endemic country for carbapenem-resistant Enterobacterales (CRE) and carbapenemase-producing Enterobacterales (CPE), experiencing only sporadic hospital outbreaks. This study aims to describe susceptibility to carbapenems and the epidemiology of carbapenemase production in Enterobacterales in the Netherlands in 2017-2019.MethodsThree complementary nationwide surveillance systems are in place to monitor carbapenem susceptibility in the Netherlands. Routine antimicrobial susceptibility test results from medical microbiology laboratories were used to study phenotypic susceptibility of Escherichia coli and Klebsiella pneumoniae. Pathogen surveillance (of all Enterobacterales species) and mandatory notifications were used to describe the characteristics of CPE positive isolates and affected persons.ResultsThe prevalence of isolates with gradient strip test-confirmed elevated meropenem (> 0.25 mg/L) or imipenem (> 1 mg/L) minimum inhibitory concentration (MIC) in the Netherlands was very low in 2017-2019, with percentages of 0.06% in E. coli and 0.49% in K. pneumoniae, and carbapenem resistances of 0.02% and 0.18%, respectively. A total of 895 unique species/carbapenemase-encoding allele combinations of CPE from 764 persons were submitted between 2017 and 2019, with the annual number of submissions increasing slightly each year. Epidemiological data was available for 660 persons. Screening because of presumed colonisation risk was the reason for sampling in 70.0% (462/660) of persons. Hospitalization abroad was the most common risk factor, being identified in 45.9% of persons.ConclusionsCarbapenem resistance of E. coli and K. pneumoniae remains low in the Netherlands. The annual number of CPE isolates slightly increased during the period 2017-2019. Recent hospitalization abroad is the main risk factor for acquisition of CPE.
| S-EPMC8994189 | biostudies-literature
Project description:Carbapenemase-producing Enterobacterales (CPE) are a growing threat to global health and the economy. Understanding the interactions between resistance and virulence mechanisms of CPE is crucial for managing difficult-to-treat infections and informing outbreak prevention and control programs. Here, we report the characterization of 21 consecutive, unique clinical isolates of CPE collected in 2018 at a tertiary hospital in Lima, Peru. Isolates were characterized by phenotypic antimicrobial susceptibility testing and whole-genome sequencing to identify resistance determinants and virulence factors. Seven Klebsiella pneumoniae isolates were classified as extensively drug-resistant. The remaining Klebsiella, Enterobacter hormaechei, and Escherichia coli isolates were multidrug-resistant. Eighteen strains carried the metallo-β-lactamase NDM-1, two the serine-carbapenemase KPC-2, and one isolate had both carbapenemases. The blaNDM-1 gene was located in the truncated ΔISAba125 element, and the blaKPC-2 gene was in the Tn4401a transposon. ST147 was the most frequent sequence type among K. pneumoniae isolates. Our findings highlight the urgent need to address the emergence of CPE and strengthen control measures and antibiotic stewardship programs in low- and middle-income settings.IMPORTANCEGenomic surveillance of antimicrobial resistance contributes to monitoring the spread of resistance and informs treatment and prevention strategies. We characterized 21 carbapenemase-producing Enterobacterales collected at a Peruvian tertiary hospital in 2018, which exhibited very high levels of resistance and carried numerous resistance genes. We detected the coexistence of carbapenemase-encoding genes (blaNDM-1 and blaKPC-2) in a Klebsiella pneumoniae isolate that also had the PmrB(R256G) mutation associated with colistin resistance. The blaKPC-2 genes were located in Tn4401a transposons, while the blaNDM-1 genes were in the genetic structure Tn125 (ΔISAba125). The presence of high-risk clones among Klebsiella pneumoniae (ST11 and ST147) and Escherichia coli (ST410) isolates is also reported. The study reveals the emergence of highly resistant bacteria in a Peruvian hospital, which could compromise the effectiveness of current treatments and control.
| S-EPMC10846045 | biostudies-literature
Project description:BackgroundThere are no Canadian epidemiological studies of Paediatric Out-of-Hospital Cardiac Arrest (POHCA) for ≥20 years. Understanding the epidemiology of POHCA is key to prevention, education, and management strategies.MethodsWe applied a validated algorithm to hospital administrative databases to describe paediatric (age 1 day to ≤18 years) atraumatic OHCA in Ontario from 2004-2020.ResultsThe cohort included 1,839 paediatric patients with atraumatic POHCA occurring at a median (IQR) age of 2 (0-12) years with 721 (39.2%) POHCA events in <1-year-olds. Males accounted for 71.1% (n = 1123) of the cohort. Crude incidence of children with POHCA who were transported to an Emergency Department was 4.2/100,000 with an increase annually over the study period (p = 0.0065). Thirty percent (n = 560) lived in a neighbourhood with the lowest income quintile, while 13.6% (n = 251) lived in a neighbourhood with the highest income quintile, 78.6% (n = 1444) presented to a non-academic hospital, and the majority (n = 1533, 83.4%) did not have significant comorbidities. Survival to hospital discharge was achieved in 167 (9.1%). Less than 6 (<3.6%) patients had a repeat POHCA in the year following the index event.ConclusionsThis is the largest Canadian POHCA cohort and the first to describe its incidence, comorbidities, and sociodemographic characteristics. We found an increase in annual crude incidence, POHCA mostly occurred in healthy children, and survival was similar to other cohorts. There were more than double the number of POHCA events in children living in the lowest income quintile neighborhoods compared to the highest. Most children presented to non-academic hospitals first.
| S-EPMC10423885 | biostudies-literature
Project description:BACKGROUND:Ontario, Canada introduced a publicly-funded 13-valent pneumococcal conjugate vaccine (PCV13) for infants in 2010, replacing the 10-valent (PCV10, 2009-2010) and the 7-valent (PCV7, 2005-2009) conjugate vaccine programs; a 23-valent pneumococcal polysaccharide vaccine (PPV23) has been available for older adults since 1996. We examined the epidemiology and serotype distribution of invasive pneumococcal disease (IPD) in Ontario in the context of provincial immunization programs. METHODS:We included confirmed IPD cases reported in Ontario between 2007 and 2017. We grouped serotypes according to Ontario's current immunization program (PCV13, PPV23, and non-vaccine-preventable) and calculated incidence rates (per 100,000 population) using population data. RESULTS:Between 2007 and 2017, annual incidence of IPD in Ontario ranged between 7.3 and 9.7/100,000 per year. Measures of illness severity were high throughout the period of surveillance. After PCV13 program implementation in 2010, incidence due to PCV13 serotypes decreased significantly across all age groups, with the greatest reductions in children <5 years and adults ?65 years. Conversely, incidence due to PPV23 unique serotypes increased significantly between 2007 and 2017, with the greatest increases observed in adults 50-64 years (1.4 to 3.5/100,000) and ?65 years (2.3 to 7.2/100,000). Similar increases were observed in incidence due to non-vaccine-preventable serotypes among all age groups, except infants <1 year. Within specific serotypes, incidence due to serotypes 3 (0.42 to 0.98/100,000) and 22F (0.31 to 0.72/100,000) increased significantly between 2007 and 2017, while incidence due to serotypes 19A and 7F decreased significantly during the PCV13 period (2010-2017). CONCLUSIONS:Eight years after PCV13 implementation in Ontario, our data suggest both direct and indirect effects on serotype-specific incidence in young children and older adults. However, overall provincial rates have remained unchanged, and IPD continues to be a severe burden on the population. The rising incidence of IPD due to PPV23 unique and non-vaccine-preventable serotypes, and the growing burden of serotypes 3 and 22F, require further study.
| S-EPMC6910703 | biostudies-literature
Project description:Carbapenemase-producing Enterobacterales (CPE) are being increasingly reported in Australia, and integrated clinical and genomic surveillance is critical to effectively manage this threat. We sought to systematically characterize CPE in Victoria, Australia, from 2012 to 2016. Suspected CPE were referred to the state public health laboratory in Victoria, Australia, from 2012 to 2016 and examined using phenotypic, multiplex PCR and whole-genome sequencing (WGS) methods and compared with epidemiological metadata. Carbapenemase genes were detected in 361 isolates from 291 patients (30.8% of suspected CPE isolates), mostly from urine (42.1%) or screening samples (34.8%). IMP-4 (28.0% of patients), KPC-2 (25.3%), NDM (24.1%), and OXA carbapenemases (22.0%) were most common. Klebsiella pneumoniae (48.8% of patients) and Escherichia coli (26.1%) were the dominant species. Carbapenemase-inactivation method (CIM) testing reliably detected carbapenemase-positive isolates (100% sensitivity, 96.9% specificity), identifying an additional five CPE among 159 PCR-negative isolates (IMI and SME carbapenemases). When epidemiologic investigations were performed, all pairs of patients designated "highly likely" or "possible" local transmission had ≤23 pairwise single-nucleotide polymorphisms (SNPs) by genomic transmission analysis; conversely, all patient pairs designated "highly unlikely" local transmission had ≥26 pairwise SNPs. Using this proposed threshold, possible local transmission was identified involving a further 16 patients for whom epidemiologic data were unavailable. Systematic application of genomics has uncovered the emergence of polyclonal CPE as a significant threat in Australia, providing important insights to inform local public health guidelines and interventions. Using our workflow, pairwise SNP distances between CPE isolates of ≤23 SNPs suggest local transmission.
| S-EPMC6711911 | biostudies-literature
Project description:Hospital wastewater is an increasingly recognized reservoir for resistant Gram-negative organisms. Factors involved in establishment and persistence of Klebsiella pneumoniae carbapenemase-producing organisms (KPCOs) in hospital wastewater plumbing are unclear. This study was conducted at a hospital with endemic KPCOs linked to wastewater reservoirs and robust patient perirectal screening for silent KPCO carriage. Over 5 months, both rooms occupied and rooms not occupied by KPCO-positive patients were sampled at three wastewater sites within each room (sink drain, sink P-trap, and toilet or hopper). Risk factors for KPCO positivity were assessed using logistic regression. Whole-genome sequencing (WGS) identified environmental seeding by KPCO-positive patients. A total of 219/475 (46%) room sampling events were KPCO positive in at least one wastewater site. KPCO-positive patient exposure was associated with increased risk of environmental positivity for the room and toilet/hopper. Previous positivity and intensive care unit room type were consistently associated with increased risk. Tube feeds were associated with increased risk for the drain, while exposure to patients with Clostridioides difficile was associated with decreased risk. Urinary catheter exposure was associated with increased risk of P-trap positivity. P-trap heaters reduced risk of P-trap and sink drain positivity. WGS identified genomically linked environmental seeding in 6 of 99 room occupations by 40 KPCO-positive patients. In conclusion, KPCO-positive patients seed the environment in at least 6% of opportunities; once positive for KPCOs, wastewater sites are at greater risk of being positive subsequently. Increased nutrient exposure, e.g., due to tube food disposal down sinks, may increase risk; frequent flushing may be protective.IMPORTANCE Klebsiella pneumoniae carbapenemase-producing organisms (KPCOs) are bacteria that are resistant to most antibiotics and thus are challenging to treat when they cause infections in patients. These organisms can be acquired by patients who are hospitalized for other reasons, complicating their hospital stay and even leading to death. Hospital wastewater sites, such as sink drains and toilets, have played a role in many reported outbreaks over the past decade. The significance of our research is in identifying risk factors for environmental positivity for KPCOs, which will facilitate further work to prevent transmission of these organisms to patients from the hospital environment.
| S-EPMC7688209 | biostudies-literature