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de Oliveira ÉM, Beltrão EMB, Pimentel MIS, Lopes ACDS. Occurrence of high-risk clones of Klebsiella pneumoniae ST11, ST340, and ST855 carrying the blaKPC-2, blaNDM-1, blaNDM-5, and blaNDM-7 genes from colonized and infected patients in Brazil. J Appl Microbiol 2023; 134:lxad242. [PMID: 37880999 DOI: 10.1093/jambio/lxad242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 10/27/2023]
Abstract
AIMS Determine which sequence type (ST) clones were carrying the blaKPC, blaNDM, blaVIM, blaIMP, and blaGES genes and their variants in clinical isolates of multidrug-resistant Klebsiella pneumoniae. METHODS AND RESULTS Ten K. pneumoniae isolates were obtained from the colonized and infected patients in a public hospital in the city of Recife-PE, in northeastern Brazil, and were further analyzed. The detection of carbapenem resistance genes and the seven housekeeping genes [for multilocus sequence typing (MLST) detection] were done with PCR and sequencing. The blaKPC and blaNDM genes were detected concomitantly in all isolates, with variants being detected blaNDM-1, blaNDM-5, blaNDM-7, and blaKPC-2. The blaKPC-2 and blaNDM-1 combination being the most frequent. Molecular typing by MLST detected three types of high-risk ST clones, associated with the clonal complex 258, ST11/CC258 in eight isolates, and ST855/CC258 and ST340/CC258 in the other two isolates. CONCLUSIONS These findings are worrying, as they have a negative impact on the scenario of antimicrobial resistance, and show the high genetic variability of K. pneumoniae and its ability to mutate resistance genes and risk of dissemination via different ST clones.
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Affiliation(s)
- Érica Maria de Oliveira
- Departamento de Medicina Tropical, Universidade Federal de Pernambuco-UFPE, Recife, PE 50732-970, Brazil
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Flynn E, Papanicolas LE, Anagnostou N, Warner MS, Rogers GB. Carbapenemase-producing Enterobacterales: a profound threat to Australian public health. Med J Aust 2023; 219:290-292. [PMID: 37660307 DOI: 10.5694/mja2.52077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023]
Affiliation(s)
- Erin Flynn
- South Australian Health and Medical Research Institute, Adelaide, SA
- Australian National University, Canberra, ACT
| | - Lito E Papanicolas
- Flinders University, Adelaide, SA
- SA Pathology, Royal Adelaide Hospital, Adelaide, SA
| | - Nicholas Anagnostou
- Flinders University, Adelaide, SA
- Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, SA
| | - Morgyn S Warner
- SA Pathology, Royal Adelaide Hospital, Adelaide, SA
- University of Adelaide, Adelaide, SA
| | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, SA
- Flinders University, Adelaide, SA
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Ko W, Tseng S, Chou C, Li T, Li R, Zhang Y, Li Y, Lv Y. Molecular epidemiology and comparative genomics of carbapenemase-producing Escherichia coli isolates from 19 tertiary hospitals in China from 2019 to 2020. Front Microbiol 2023; 14:1056399. [PMID: 37152734 PMCID: PMC10160391 DOI: 10.3389/fmicb.2023.1056399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/23/2023] [Indexed: 05/09/2023] Open
Abstract
Background The clinical use of carbapenems is facing challenges due to increased carbapenemase-producing Escherichia coli (CP-EC) infections over the past decade. Meanwhile, whole-genome sequencing (WGS) is an important method for bacterial epidemiological research. We aim to provide more gene-based surveys to explore the genomics and occurrence of CP-EC in China. Methods A total of 780 Escherichia coli isolates were collected by the China Antimicrobial Resistance Surveillance Trial (CARST) from 2019 to 2020. An antibacterial susceptibility test was performed by using the agar dilution method. CP-EC were detected by the modified carbapenem inactivation method (mCIM), EDTA-modified carbapenem inactivation method (eCIM), and polymerase chain reaction (PCR). Homology analysis was performed by multilocus sequence typing (MLST). A conjugation experiment was performed to verify the transferability of plasmids carrying carbapenemase genes. WGS was conducted to explore the gene-environment of the carbapenemase gene. Result Of the 780 Escherichia coli isolates, 31 isolates were insensitive to carbapenem with a rate of 4%. Among them, 13 CP-EC isolates had transferability of the bla NDM gene. These isolates belonged to nine distinct sequence types (STs), with some correlation. We found that two (2/13, 15.4%) of the CP-EC isolates that were collected from blood specimens were highly pathogenic and also showed high transferability of the bla NDM gene. In addition, eight (8/13, 61.5%) of the CP-EC isolates were found to be multidrug-resistant. Conclusion With the increasing use of carbapenem, CP-EC isolates accounted for nearly half of the total carbapenem-insensitive Escherichia coli isolates. Our findings highlight the urgent need to pay attention to CP-EC isolates in bloodstream infections and ESBL-producing CP-EC isolates. Based on the One Health concept, we suggest various measures, including the development of bacterial vaccines, antibiotic management, and establishment of better medical environments, to avoid the outbreak of CP-EC.
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Affiliation(s)
- Wehsin Ko
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Songlu Tseng
- Department of Trauma and Orthopaedics, Peking University People's Hospital, Beijing, China
| | - Chiahsin Chou
- Department of General Surgery, Peking University First Hospital, Beijing, China
| | - Tianmeng Li
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Rose Li
- Department of Clinical Medicine, Civil Aviation General Hospital, Beijing, China
| | - Yaqiao Zhang
- Department of Clinical Medicine, Peking University International Hospital, Beijing, China
| | - Yun Li
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
- *Correspondence: Yun Li
| | - Yuan Lv
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
- Yuan Lv
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Rocke T, El Omeiri N, Quiros RE, Hsieh J, Ramon-Pardo P. Reporting on antibiotic use patterns using the WHO Access, Watch, Reserve classification in the Caribbean. Rev Panam Salud Publica 2022; 46:e186. [DOI: 10.26633/rpsp.2022.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Objective.
To assess antibiotic use in three hospitals in three Caribbean countries based on data from 2013 and 2018 using the World Health Organization Essential Medicines List “Access, Watch, Reserve” (AWaRe) classification
Methods.
A retrospective observational study, which analyzed the World Health Organization Point Prevalence Survey data from three hospitals in three Caribbean countries, to examine proportional AWaRe group antibiotic use for the top ten inpatient indications. The Access-to-Watch ratio was calculated, and the top three antibiotics prescribed in each hospital were determined.
Results.
The final data set included 376 prescriptions for the top ten indications in 766 inpatients. The hospital antibiotic use point prevalence for Hospital 1 was 35.6%, Hospital 2 was 48.6%, and Hospital 3 was 47.1%. The Access-to-Watch ratio for the top ten indications was 2.45, 1.36, and 1.72 in the three hospitals. Access group prevalence was 71.0% in Hospital 1, 57.6% in Hospital 2, and 63.2% in Hospital 3. There were no Reserve antibiotics prescribed in any of the institutions. The most common indication for Watch prescription was skin and soft tissue infections in Hospital 1 and pneumonia in Hospital 2 and 3.
Conclusions.
This study draws urgent attention to evidence of a high proportion of Watch antibiotic prescribing and lack of Reserve group antibiotics in three Caribbean countries. This research provides data that may inform national formulary and antimicrobial stewardship policy-making across the settings analyzed and the wider region.
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Affiliation(s)
- Tamarie Rocke
- Pan American Health Organization, Washington, D.C., United States of America
| | - Nathalie El Omeiri
- Pan American Health Organization, Washington, D.C., United States of America
| | | | - Jenny Hsieh
- Pan American Health Organization, Washington, D.C., United States of America
| | - Pilar Ramon-Pardo
- Pan American Health Organization, Washington, D.C., United States of America
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Imai S, Inoue N, Nagai H. Economic and clinical burden from carbapenem-resistant bacterial infections and factors contributing: a retrospective study using electronic medical records in Japan. BMC Infect Dis 2022; 22:581. [PMID: 35768778 PMCID: PMC9241247 DOI: 10.1186/s12879-022-07548-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/17/2022] [Indexed: 11/25/2022] Open
Abstract
Background Antimicrobial resistance is a major threat to global health and the world economy. The economic burden of carbapenem-resistant infections has not previously been evaluated. We aimed to compare the potential economic burden and clinical outcomes between carbapenem-resistant infections and carbapenem-susceptible infections in Japan. Methods We conducted a retrospective cohort study using electronic medical records. Patients aged 15 years or older and with the diagnosis of pneumonia, urinary tract infection, biliary infection, and sepsis were included. Multivariable regression models with random effects were used to estimate the impact of carbapenem resistance on cost, length of hospital stay, and in-hospital mortality. Results Among the 9,517 patients, 86 (0.9%) had carbapenem-resistant (CR) infections. Compared to carbapenem-susceptible (CS) infections, the patients with the CR infections were significantly more likely to receive mechanical ventilation (37.2 vs. 21.2%, P-value = 0.003), antibiotics (88.4 vs. 63.0%, P-value < 0.001), and especially carbapenem (31.4 vs. 8.3%, P-value < 0.001), before the bacterial culture test positive. Significantly higher median costs were found for the CR infections than the CS infections in the categories of medications (3477 US dollars vs. 1609 US dollars), laboratory tests (2498 US dollars, vs. 1845 US dollars), and hospital stay (14,307 US dollars vs. 10,560 US dollars). In the multivariable regression analysis, the length of stay was 42.1% longer and the cost was 50.4% higher in the CR infections than in the CS infections. The risk of in-hospital mortality did not differ between the two groups (odds ratio 1.24, 95% CI 0.72–2.11), due to the small sample size. The result was robust with a similar trend in the analysis using the inverse probability treatment weighting method. Conclusions Compared to carbapenem-susceptible infections, carbapenem-resistant infections were associated with a higher cost and a longer length of stay. Detailed cost analysis showed significant differences in the categories of medication, laboratory tests, and hospital stay. To our knowledge, this study is the first to assess the potential economic burden of carbapenem-resistant infections using a large hospital-based database. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07548-3.
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Affiliation(s)
- Shinobu Imai
- Department of Clinical Data Management and Research, Clinical Research Center, National Hospital Organization Headquarters, 2-5-21, Higashigaoka, Meguroku, Tokyo, 152-8621, Japan.,Department of Drug Safety and Risk Management, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1, Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Norihiko Inoue
- Department of Clinical Data Management and Research, Clinical Research Center, National Hospital Organization Headquarters, 2-5-21, Higashigaoka, Meguroku, Tokyo, 152-8621, Japan. .,Department of Health Policy and Informatics, Tokyo Medical and Dental University Graduate School of Medicine, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| | - Hideaki Nagai
- Center for Pulmonary Diseases, National Hospital Organization Tokyo National Hospital, 3-1-1 Takeoka, Kiyose, Tokyo, 204-8585, Japan
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Epidemiology, Outcomes and Resource Utilisation in Patients with Carbapenem Non-susceptible Gram-Negative Bacteria in the UK: A Retrospective, Observational Study (CARBAR UK). Adv Ther 2022; 39:3602-3615. [PMID: 35701725 PMCID: PMC9309132 DOI: 10.1007/s12325-022-02177-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/29/2022] [Indexed: 11/01/2022]
Abstract
INTRODUCTION Antimicrobial resistance is an urgent medical challenge. In this two-part study, we investigated the epidemiology and management of carbapenem non-susceptible (Carb-NS) Gram-negative bacteria (GNB) in the UK. METHODS We conducted a retrospective review of data from UK hospitals (ten in part 1, nine in part 2). In part 1, epidemiological data were collected from patients hospitalised between April 2017 and March 2018 with any laboratory detection of Carb-NS GNB, encompassing both colonisation and infection. In part 2, diagnosis and management pathways in a randomly selected population of adults from part 1 with confirmed Carb-NS GNB infection were assessed. Data were obtained from a detailed medical chart review for ≥ 3 months from index (collection date of first positive Carb-NS GNB sample). RESULTS Of 42,340 GNB isolates from 36,098 patients colonised/infected with GNB in part 1, 7% were Carb-NS. In 157 patients included in part 2, 234 GNB index samples were collected, of which 197 (82%) were Carb-NS (median number of Carb-NS pathogens per patient, 1; range 1-3). The most frequent Carb-NS isolates were Pseudomonas aeruginosa (36%), Stenotrophomonas maltophilia (29%) and Klebsiella pneumoniae (10%). Median length of hospitalisation was 34 days. Median time from index to appropriate therapy was 3 days, with empirical therapy initiated a median of 1 day before index. Carb-NS infection was believed to contribute to 21 (28%) of 76 deaths during the study. CONCLUSIONS This study highlights the high incidence of Carb-NS GNB colonisation and infection in the UK and the need for improved management of patients with Carb-NS GNB infection.
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Cuddihy T, Harris PNA, Permana B, Beatson SA, Forde BM. CATHAI: cluster analysis tool for healthcare-associated infections. BIOINFORMATICS ADVANCES 2022; 2:vbac040. [PMID: 36699387 PMCID: PMC9710666 DOI: 10.1093/bioadv/vbac040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/26/2022] [Accepted: 05/24/2022] [Indexed: 01/28/2023]
Abstract
Motivation Whole genome sequencing (WGS) is revolutionizing disease surveillance where it facilitates high-resolution clustering of related organism and outbreak detection. However, visualizing and efficiently communicating genomic data back to clinical staff is crucial for the successful deployment of a targeted infection control response. Results CATHAI (cluster analysis tool for healthcare-associated infections) is an interactive web-based visualization platform that couples WGS informed clustering with associated metadata, thereby converting sequencing data into informative and accessible clinical information for the management of healthcare-associated infections (HAI) and nosocomial outbreaks. Availability and implementation All code associated with this application are free available from https://github.com/FordeGenomics/cathai. A demonstration version of CATHAI is available online at https://cathai.fordelab.com.
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Affiliation(s)
- Thom Cuddihy
- University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD 4029, Australia
| | - Patrick N A Harris
- University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD 4029, Australia,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia,Central Microbiology, Pathology Queensland, Royal Brisbane & Women’s Hospital, Herston, Brisbane, QLD 4029, Australia
| | - Budi Permana
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia,School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
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Effectiveness of Antiepidemic Measures Aimed to Reduce Carbapenemase-Producing Enterobacteriaceae in the Hospital Environment. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:9299258. [PMID: 35528804 PMCID: PMC9072043 DOI: 10.1155/2022/9299258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 11/27/2022]
Abstract
Purpose The objective of this study was to evaluate the effectiveness of hospital-based antiepidemic measures aimed at limiting the spread of symptomatic infections and colonization with carbapenem-resistant Enterobacteriaceae (CPE), mainly NDM-producing Klebsiella pneumoniae, with particular emphasis on microbiological screening tests. Methods This retrospective study was based on data from 168 hospitals under the supervision of the Provincial Sanitary and Epidemiological Station in Warsaw, Poland, in 2016–2017. Analysis of the effectiveness of antiepidemic procedures focused on the type of implemented antiepidemic procedures, the number of microbiological screening tests per year, the geographic location of the hospitals (inside or outside Warsaw), the timing of the screening tests (on admission to hospital or 48 hours later), and the results of the screening tests. Results Rates of proper isolation of patients infected or colonized with an alarm pathogen including NDM-producing K. pneumoniae increased from 38.0% in 2016 to 49.5% in 2017 (p > 0.05). The number of screening tests performed increased by 88% from 68319 in 2016 to 128373 in 2017. The number of epidemic outbreaks of symptomatic infections caused by NDM-producing K. pneumoniae decreased from 11 in 2016 to 7 in 2017 in hospitals in Warsaw, where microbiological screening tests were performed. The number of outbreaks in hospitals outside Warsaw, where the screening tests were not performed or were limited, increased from 8 in 2016 to 24 in 2017. Conclusion Screening tests increase the chance of detecting colonization by CPE. The implementation of microbiological screening decreased the risk of epidemic outbreaks of symptomatic infections caused by CPE.
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Welsh J, Korda RJ, Paige E, Morgan MA, Law HD, Stanton T, Bourne ZM, Tolosa MX, Greaves K. The ATHENA COVID-19 Study: Cohort profile and first findings for people diagnosed with COVID-19 in Queensland, 1 January to 31 December 2020. COMMUNICABLE DISEASES INTELLIGENCE (2018) 2021; 45. [PMID: 34587875 DOI: 10.33321/cdi.2021.45.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background To date, there are limited Australian data on characteristics of people diagnosed with COVID-19 and on how these characteristics relate to outcomes. The ATHENA COVID-19 Study was established to describe health outcomes and investigate predictors of outcomes for all people diagnosed with COVID-19 in Queensland by linking COVID-19 notification, hospital, general practice and death registry data. This paper reports on the establishment and first findings for the ATHENA COVID-19 Study. Methods Part 1 of the ATHENA COVID-19 Study used Notifiable Conditions System data from 1 January 2020 to 31 December 2020, linked to: Emergency Department Collection data for the same period; Queensland Health Admitted Patient Data Collections (from 1 January 2010 to 30 January 2021); and Deaths Registrations data (from 1 January 2020 to 17 January 2021). Results To 31 December 2020, a total of 1,254 people had been diagnosed with SARS-CoV-2 infection in Queensland: half were female (49.8%); two-thirds (67.7%) were aged 20-59 years; and there was an over-representation of people living in less-disadvantaged areas. More than half of people diagnosed (57.6%) presented to an ED; 21.2% were admitted to hospital as an inpatient (median length of stay 11 days); 1.4% were admitted to an intensive care unit (82.4% of these required ventilation); and there were six deaths. Analysis of factors associated with these outcomes was limited due to small case numbers: people living in less-disadvantaged areas had a lower risk of being admitted to hospital (test for trend, p < 0.001), while those living in more remote areas were less likely than people living in major cities to present to an ED (test for trend: p=0.007), which may reflect differential health care access rather than health outcomes per se. Increasing age (test for trend, p < 0.001) and being a current/recent smoker (age-sex-adjusted relative risk: 1.61; 95% confidence interval: 1.00, 2.61) were associated with a higher risk of being admitted to hospital. Conclusion Despite uncertainty in our estimates due to small numbers, our findings are consistent with what is known about COVID-19. Our findings reinforce the value of linking multiple data sources to enhance reporting of outcomes for people diagnosed with COVID-19 and provide a platform for longer term follow-up.
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Affiliation(s)
- Jennifer Welsh
- Research Fellow, Research School of Population Health, Australian National University, Canberra, Australian Capital Territory
| | - Rosemary J Korda
- Senior Fellow, Research School of Population Health, Australian National University, Canberra, Australian Capital Territory
| | - Ellie Paige
- Research Fellow, Research School of Population Health, Australian National University, Canberra, Australian Capital Territory
| | - Mark A Morgan
- Associate Dean, Professor of General Practice, Faculty of Science & Medicine, Bond University, Robina, Gold Coast, Queensland
| | - Hsei-Di Law
- Research Fellow, Research School of Population Health, Australian National University, Canberra, Australian Capital Territory
| | - Tony Stanton
- Senior Staff Specialist, Cardiology, Sunshine Coast University Hospital, Queensland Health, Birtinya, Queensland
| | | | - M Ximena Tolosa
- Senior Epidemiologist, Department of Health, Brisbane, Queensland
| | - Kim Greaves
- Senior Staff Specialist, Cardiologist, Principal Project Lead: The ATHENA COVID-19 Study, Sunshine Coast University Hospital, Birtinya, Queensland.,Senior Fellow, Research School of Population Health, Australian National University, Canberra, Australian Capital Territory
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10
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Roberts LW, Forde BM, Hurst T, Ling W, Nimmo GR, Bergh H, George N, Hajkowicz K, McNamara JF, Lipman J, Permana B, Schembri MA, Paterson D, Beatson SA, Harris PNA. Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care. Microb Genom 2021; 7:mgen000530. [PMID: 33599607 PMCID: PMC8190620 DOI: 10.1099/mgen.0.000530] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/24/2021] [Indexed: 02/01/2023] Open
Abstract
Background. Infections caused by carbapenem-resistant Acinetobacter baumannii (CR-Ab) have become increasingly prevalent in clinical settings and often result in significant morbidity and mortality due to their multidrug resistance (MDR). Here we present an integrated whole-genome sequencing (WGS) response to a persistent CR-Ab outbreak in a Brisbane hospital between 2016-2018.Methods. A. baumannii, Klebsiella pneumoniae, Serratia marcescens and Pseudomonas aeruginosa isolates were sequenced using the Illumina platform primarily to establish isolate relationships based on core-genome SNPs, MLST and antimicrobial resistance gene profiles. Representative isolates were selected for PacBio sequencing. Environmental metagenomic sequencing with Illumina was used to detect persistence of the outbreak strain in the hospital.Results. In response to a suspected polymicrobial outbreak between May to August of 2016, 28 CR-Ab (and 21 other MDR Gram-negative bacilli) were collected from Intensive Care Unit and Burns Unit patients and sent for WGS with a 7 day turn-around time in clinical reporting. All CR-Ab were sequence type (ST)1050 (Pasteur ST2) and within 10 SNPs apart, indicative of an ongoing outbreak, and distinct from historical CR-Ab isolates from the same hospital. Possible transmission routes between patients were identified on the basis of CR-Ab and K. pneumoniae SNP profiles. Continued WGS surveillance between 2016 to 2018 enabled suspected outbreak cases to be refuted, but a resurgence of the outbreak CR-Ab mid-2018 in the Burns Unit prompted additional screening. Environmental metagenomic sequencing identified the hospital plumbing as a potential source. Replacement of the plumbing and routine drain maintenance resulted in rapid resolution of the secondary outbreak and significant risk reduction with no discernable transmission in the Burns Unit since.Conclusion. We implemented a comprehensive WGS and metagenomics investigation that resolved a persistent CR-Ab outbreak in a critical care setting.
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Affiliation(s)
- Leah W. Roberts
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Disease Research Centre, University of Queensland, Brisbane, QLD, Australia
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Brian M. Forde
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Disease Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Trish Hurst
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
- Infection Monitoring and Prevention Service, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
- Unit of Infectious Diseases, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | - Weiping Ling
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
| | - Graeme R. Nimmo
- Pathology Queensland, Central Laboratory, Brisbane, QLD, Australia
| | - Haakon Bergh
- Pathology Queensland, Central Laboratory, Brisbane, QLD, Australia
| | - Narelle George
- Pathology Queensland, Central Laboratory, Brisbane, QLD, Australia
| | - Krispin Hajkowicz
- Unit of Infectious Diseases, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | - John F. McNamara
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
| | - Jeffrey Lipman
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
- Nimes University Hospital, University of Montpellier, Nimes, France
| | - Budi Permana
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Disease Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Mark A. Schembri
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Disease Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - David Paterson
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
- Unit of Infectious Diseases, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Disease Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Patrick N. A. Harris
- Australian Infectious Disease Research Centre, University of Queensland, Brisbane, QLD, Australia
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
- Pathology Queensland, Central Laboratory, Brisbane, QLD, Australia
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11
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Gordon LG, Elliott TM, Forde B, Mitchell B, Russo PL, Paterson DL, Harris PNA. Budget impact analysis of routinely using whole-genomic sequencing of six multidrug-resistant bacterial pathogens in Queensland, Australia. BMJ Open 2021; 11:e041968. [PMID: 33526501 PMCID: PMC7852923 DOI: 10.1136/bmjopen-2020-041968] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE To predict the cost and health effects of routine use of whole-genome sequencing (WGS) of bacterial pathogens compared with those of standard of care. DESIGN Budget impact analysis was performed over the following 5 years. Data were primarily from sequencing results on clusters of multidrug-resistant organisms across 27 hospitals. Model inputs were derived from hospitalisation and sequencing data, and epidemiological and costing reports, and included multidrug resistance rates and their trends. SETTING Queensland, Australia. PARTICIPANTS Hospitalised patients. INTERVENTIONS WGS surveillance of six common multidrug-resistant organisms (Staphylococcus aureus, Escherichia coli, Enterococcus faecium, Klebsiella pneumoniae, Enterobacter sp and Acinetobacter baumannii) compared with standard of care or routine microbiology testing. PRIMARY AND SECONDARY OUTCOMES Expected hospital costs, counts of patient infections and colonisations, and deaths from bloodstream infections. RESULTS In 2021, 97 539 patients in Queensland are expected to be infected or colonised with one of six multidrug-resistant organisms with standard of care testing. WGS surveillance strategy and earlier infection control measures could avoid 36 726 infected or colonised patients and avoid 650 deaths. The total cost under standard of care was $A170.8 million in 2021. WGS surveillance costs an additional $A26.8 million but was offset by fewer costs for cleaning, nursing, personal protective equipment, shorter hospital stays and antimicrobials to produce an overall cost savings of $30.9 million in 2021. Sensitivity analyses showed cost savings remained when input values were varied at 95% confidence limits. CONCLUSIONS Compared with standard of care, WGS surveillance at a state-wide level could prevent a substantial number of hospital patients infected with multidrug-resistant organisms and related deaths and save healthcare costs. Primary prevention through routine use of WGS is an investment priority for the control of serious hospital-associated infections.
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Affiliation(s)
- Louisa G Gordon
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Nursing, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- School of Public Health, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas M Elliott
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Brian Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland, Centre for Clinical Research, Brisbane, Queensland, Australia
| | - Brett Mitchell
- School of Nursing and Midwifery, The University of Newcastle, Newcastle, New South Wales, Australia
| | - Philip L Russo
- School of Nursing and Midwifery, Monash University, Melbourne, Victoria, Australia
| | - David L Paterson
- The University of Queensland, Centre for Clinical Research, Brisbane, Queensland, Australia
| | - Patrick N A Harris
- The University of Queensland, Centre for Clinical Research, Brisbane, Queensland, Australia
- Pathology Queensland, Queensland Health, Brisbane, Queensland, Australia
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Healthcare resource use in hospitalized patients with carbapenem-resistant Gram-negative infections. J Hosp Infect 2021; 110:7-14. [PMID: 33428999 DOI: 10.1016/j.jhin.2020.12.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 11/21/2022]
Abstract
OBJECTIVES Antimicrobial resistance (AMR) is a threat to global public health. Infections with resistant organisms are more challenging to treat, often delay patient recovery and can increase morbidity and mortality. Healthcare costs associated with treating patients with AMR organisms are poorly described. In particular, data for specific organisms, such as those harbouring carbapenem resistance, are lacking. METHODS This was a retrospective, matched (1:1), single-centre, cohort study at a Central London hospital, comparing costs and resource use of 442 adult inpatients infected with either carbapenem-sensitive (CSO) or carbapenem-resistant organisms (CRO) over a two-year period. Resource use and micro-costing data were obtained from the hospital Patient, Education and Research Costing System (PERCS), and included both direct and indirect costs. RESULTS Overall, the median healthcare-related cost of treating a patient with a CRO was more than double (£49,537 vs £19,299) that of treating a patient with a CSO. There were statistically significant increases in expenditure across 21 of 44 measured parameters including critical care costs, which accounted for the greatest proportion of overall costs in both groups. Infections were predominantly of the respiratory tract (41%) and caused by Pseudomonas aeruginosa (76%). CONCLUSIONS Infection with CROs increases healthcare expenditure significantly. Many of the costs, including patient support, portering and catering, have been underappreciated in previous work. We additionally note that patients infected with CROs have longer hospital stays, and increased theatre operating times compared with patients infected with CSOs.
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Camphor HS, Viney K, Polkinghorne B, Pennington K. Retrospective analysis of multidrug-resistant tuberculosis case notifications in Australia (1999-2018). ACTA ACUST UNITED AC 2020; 44. [PMID: 32829704 DOI: 10.33321/cdi.2020.44.68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This study describes the epidemiology and treatment outcomes of multidrug-resistant tuberculosis (MDR-TB) cases notified in Australia between 1999 and 2018, and investigates whether current data fields in the national tuberculosis (TB) dataset allow description and measurement of surveillance information pertaining to the diagnosis and clinical management of MDR-TB. In May 2019, de-identified demographic, clinical, laboratory, drug susceptibility, treatment, risk factor and outcome data for all MDR-TB case notifications were extracted from the Australian National Notifiable Disease Surveillance System. The dataset included ten treatment outcome categories, which were aggregated to four categorical outcomes for descriptive and inferential analyses. The majority of cases were overseas-born (91%). Absolute case numbers increased over time; however, the MDR-TB notification rate remained fairly stable during the study period. Treatment success was achieved in nearly two-thirds of cases (62.1%). Whilst timeframes between initial presentation, specimen collection, case notification and treatment commencement were calculated, current data fields in the national dataset precluded measurement and description of other parameters deemed important for MDR-TB surveillance. This study demonstrates that while Australia's MDR-TB burden is low, cases will continue to occur until TB control improves in countries with which Australia shares cultural and migration links. Australia should continue to support national and regional TB control programmes to sustain progress towards national elimination of TB. This study's findings support a review of data fields in the national TB dataset with potential expansion or adjustment to improve national data reporting, including the monitoring of evidence-based recommendations for the prevention and management of MDR-TB.
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Affiliation(s)
- Hendrik S Camphor
- Research School of Population Health, Australian National University, Canberra, Australia; Communicable Diseases Epidemiology and Surveillance Section, Office of Health Protection, Australian Government Department of Health
| | - Kerri Viney
- Research School of Population Health, Australian National University, Canberra, Australia; Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Ben Polkinghorne
- Research School of Population Health, Australian National University, Canberra, Australia
| | - Kate Pennington
- Communicable Diseases Epidemiology and Surveillance Section, Office of Health Protection, Australian Government Department of Health
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14
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Zhen X, Stålsby Lundborg C, Sun X, Gu S, Dong H. Clinical and Economic Burden of Carbapenem-Resistant Infection or Colonization Caused by Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii: A Multicenter Study in China. Antibiotics (Basel) 2020; 9:antibiotics9080514. [PMID: 32823707 PMCID: PMC7459498 DOI: 10.3390/antibiotics9080514] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022] Open
Abstract
Background: Carbapenem resistant Klebsiella pneumoniae (CRKP), Pseudomonas aeruginosa (CRPA), and Acinetobacter baumannii (CRAB) pose significant threats to public health. However, the clinical and economic impacts of CRKP, CRPA, and CRAB remain largely uninvestigated in China. This study aimed to examine the clinical and economic burden of CRKP, CRPA, and CRAB compared with carbapenem susceptible cases in China. Method: We conducted a retrospective and multicenter study among inpatients hospitalized at four tertiary hospitals between 2013 and 2015 who had K. pneumoniae, P. aeruginosa, and A. baumannii positive clinical samples. Propensity score matching (PSM) was used to balance the impact of potential confounding variables, including age, sex, insurance, number of diagnosis, comorbidities (disease diagnosis, and Charlson comorbidity index), admission to intensive care unit, and surgeries. The main indicators included economic costs, length of stay (LOS), and mortality rate. Results: We included 12,022 inpatients infected or colonized with K. pneumoniae, P. aeruginosa, and A. baumannii between 2013 and 2015, including 831 with CRKP and 4328 with carbapenem susceptible K. pneumoniae (CSKP), 1244 with CRPA and 2674 with carbapenem susceptible P. aeruginosa (CSPA), 1665 with CRAB and 1280 with carbapenem susceptible A. baumannii (CSAB). After PSM, 822 pairs, 1155 pairs, and 682 pairs, respectively were generated. Compared with carbapenem-susceptible cases, those with CRKP, CRPA, and CRAB were associated with statistically significantly increased total hospital cost ($14,252, p < 0.0001; $4605, p < 0.0001; $7277, p < 0.0001) and excess LOS (13.2 days, p < 0.0001; 5.4 days, p = 0.0003; 15.8 days, p = 0.0004). In addition, there were statistically significantly differences in hospital mortality rate between CRKP and CSKP, and CRAB and CSAB group (2.94%, p = 0.024; 4.03%, p = 0.03); however, the difference between CRPA and CSPA group was marginal significant (2.03%, p = 0.052). Conclusion: It highlights the clinical and economic impact of CRKP, CRPA, and CRAB to justify more resources for implementing antibiotic stewardship practices to improve clinical outcomes and to reduce economic costs.
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Affiliation(s)
- Xuemei Zhen
- Centre for Health Management and Policy Research, School of Public Health, Cheeloo College of Medicine, Shandong University, (NHC Key Lab of Health Economics and Policy Research, Shandong University), Jinan 250012, China;
- Center for Health Policy Studies, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (X.S.); (S.G.)
| | | | - Xueshan Sun
- Center for Health Policy Studies, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (X.S.); (S.G.)
| | - Shuyan Gu
- Center for Health Policy Studies, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (X.S.); (S.G.)
- Center for Health Policy and Management Studies, School of Government, Nanjing University, Nanjing 210023, China
| | - Hengjin Dong
- Center for Health Policy Studies, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (X.S.); (S.G.)
- Correspondence: ; Tel./Fax: +86-571-8820-6098
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