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Yeo JH, Begam N, Leow WT, Goh JX, Zhong Y, Cai Y, Kwa ALH. Ironing out Persisters? Revisiting the Iron Chelation Strategy to Target Planktonic Bacterial Persisters Harboured in Carbapenem-Resistant Escherichia coli. Microorganisms 2024; 12:972. [PMID: 38792801 PMCID: PMC11123761 DOI: 10.3390/microorganisms12050972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Antibiotic resistance is a global health crisis. Notably, carbapenem-resistant Enterobacterales (CRE) pose a significant clinical challenge due to the limited effective treatment options. This problem is exacerbated by persisters that develop upon antibiotic exposure. Bacteria persisters can tolerate high antibiotic doses and can cause recalcitrant infections, potentially developing further antibiotic resistance. Iron is a critical micronutrient for survival. We aimed to evaluate the utility of iron chelators, alone and in combination with antibiotics, in managing persisters. We hypothesized that iron chelators eradicate CRE persisters in vitro, when administered in combination with antibiotics. Our screening revealed three clinical isolates with bacteria persisters that resuscitated upon antibiotic removal. These isolates were treated with both meropenem and an iron chelator (deferoxamine mesylate, deferiprone or dexrazoxane) over 24 h. Against our hypothesis, bacteria persisters survived and resuscitated upon withdrawing both the antibiotic and iron chelator. Pursuing our aim, we next hypothesized that iron chelation is feasible as a post-antibiotic treatment in managing and suppressing persisters' resuscitation. We exposed bacteria persisters to an iron chelator without antibiotics. Flow cytometric assessments revealed that iron chelators are inconsistent in suppressing persister resuscitation. Collectively, these results suggest that the iron chelation strategy may not be useful as an antibiotic adjunct to target planktonic bacteria persisters.
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Affiliation(s)
- Jia Hao Yeo
- Department of Pharmacy, Singapore General Hospital, Singapore 169608, Singapore; (J.H.Y.)
- SingHealth-Duke-NUS Academic Clinical Programme (Pathology), Singapore 169857, Singapore
| | - Nasren Begam
- Department of Pharmacy, Singapore General Hospital, Singapore 169608, Singapore; (J.H.Y.)
| | - Wan Ting Leow
- Department of Pharmacy, Singapore General Hospital, Singapore 169608, Singapore; (J.H.Y.)
| | - Jia Xuan Goh
- Department of Pharmacy, Singapore General Hospital, Singapore 169608, Singapore; (J.H.Y.)
| | - Yang Zhong
- Department of Pharmacy, Singapore General Hospital, Singapore 169608, Singapore; (J.H.Y.)
- Department of Clinical Translational Research, Singapore General Hospital, Singapore 169856, Singapore
| | - Yiying Cai
- Department of Pharmacy, Singapore General Hospital, Singapore 169608, Singapore; (J.H.Y.)
| | - Andrea Lay-Hoon Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore 169608, Singapore; (J.H.Y.)
- SingHealth-Duke-NUS Academic Clinical Programme (Medicine), Singapore 169857, Singapore
- Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
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2
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Yang X, Wang Y, Zhao S, Huang X, Tian B, Yu R, Ding Q. Clinical characteristics and prognosis of Klebsiella pneumoniae meningitis in adults. Heliyon 2024; 10:e28010. [PMID: 38601552 PMCID: PMC11004708 DOI: 10.1016/j.heliyon.2024.e28010] [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: 12/03/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
Background Klebsiella pneumoniae is a causative agent of bacterial meningitis in adults. However, there is little information regarding this infection. Therefore, this study comprehensively analyzed the clinical characteristics and prognosis of Klebsiella pneumoniae meningitis (KPM) patients. Methods The clinical data of adult hospitalized patients with KPM were retrospectively collected from January 2015 to December 2022. The clinical characteristics and antibiotic resistance of KPM were evaluated. Meanwhile, a set of logistic regression models was constructed to identify prognostic factors for death. These prognostic factors were subsequently combined to develop a nomogram for predicting the risk of in-hospital mortality in individual patients. Finally, the receiver operating characteristic curve and calibrate plot were utilized to verify the performance of the nomogram. Results This study included 80 adult patients with KPM, 58 (72.5%) of whom were males. The mortality rate was 45%. Among them, 74 (92.5%) were diagnosed with healthcare-associated meningitis. Thirty-seven carbapenem-resistant Klebsiella pneumoniae (CRKP) strains were susceptible to tigecycline, polymyxin, and ceftazidime/avibactam. CRKP (OR = 9.825, 95%CI = 2.757-35.011, P < 0.001), length of stay (OR = 0.953, 95%CI = 0.921-0.986, P = 0.005), and C-reactive protein-to-prealbumin ratio (CRP/PA, OR = 3.053, 95%CI = 1.329-7.016, P = 0.009) were identified as predictive factors for mortality using multivariate logistic regression. Finally, a nomogram for death prediction was established. The area under the curve of this nomogram was 0.900 (95% CI = 0.828-0.971). Conclusions KPM is a fatal disease associated with high incidence of healthcare-associated infections and carbapenem resistance. Moreover, CRKP, length of stay, and CRP/PA were found to be independent predictors of mortality.
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Affiliation(s)
- Xin Yang
- Department of Infectious Disease and Hepatic Disease, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Yanjun Wang
- Department of Infectious Disease and Hepatic Disease, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Siqi Zhao
- Department of Infectious Disease and Hepatic Disease, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xiaoya Huang
- Department of Infectious Disease and Hepatic Disease, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Bingxin Tian
- Department of Infectious Disease and Hepatic Disease, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Runli Yu
- Department of Infectious Disease and Hepatic Disease, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Qin Ding
- Department of Infectious Disease and Hepatic Disease, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
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3
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Park JJ, Park H, Na SH, Seo YB, Lee J. Trends of antimicrobial susceptibilities and multidrug-resistant colonization rate in patients transferred from long-term care facilities during 2017-2022: a cross-sectional study. BMC Infect Dis 2024; 24:235. [PMID: 38383425 PMCID: PMC10882737 DOI: 10.1186/s12879-024-09145-y] [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: 11/13/2023] [Accepted: 02/15/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND With the global increase in the older population, the proportion of those receiving care in long-term care facilities (LTCFs) has also been increasing. We assessed the epidemiology, antibiotic susceptibility, and colonization status of drug-resistant organisms in patients transferred from LTCFs. METHODS We retrospectively reviewed the medical records of patients transferred from LTCFs between 2017 and 2022. The reasons for admission, antimicrobial susceptibility, and colonization rates of carbapenem-resistant Enterobacterales (CRE), methicillin-resistant Staphylococcus aureus (MRSA), and carbapenem-resistant Acinetobacter baumannii (CRAB) were recorded. We analyzed the susceptibility and colonization rates by year to identify trends. RESULTS Of the 936 patients transferred from LTCFs, 54.3% were admitted to the intensive care unit and 12.5% died. The most common reason for admission was infection (n = 573, 61.2%), followed by gastrointestinal bleeding (n = 67, 7.2%) and cerebrovascular disorder (n = 65, 6.9%). A total of 452 Enterobacterales strains were isolated, and their susceptibility rates to ciprofloxacin and cefotaxime were 33.3% and 35.6%, respectively. A total of 54.9% were extended-spectrum beta-lactamase-producing strains, and 4.9% of them were carbapenem-resistant, both of which showed an increasing trend (P = 0.024 and P < 0.001, respectively). The prevalence rates of CRE, CRAB, and MRSA colonization were 9.2%, 7.1%, and 23.1%, respectively. CRE colonization showed a significant increase (P < 0.001), with carbapenemase-producing Enterobacterales accounting for 75.9% of cases. CONCLUSIONS Patients transferred from LTCFs are primarily affected by infections and exhibit high resistance rates. The increasing trend in CRE colonization rates each year highlights the need for the implementation of rigorous infection control measures for effective management.
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Affiliation(s)
- Jin Ju Park
- Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, 1 Singil-Ro, Yeongdeungpo-Gu, Seoul, 07441, Republic of Korea
| | - Hyejin Park
- Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, 1 Singil-Ro, Yeongdeungpo-Gu, Seoul, 07441, Republic of Korea
| | - Sun Hee Na
- Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, 1 Singil-Ro, Yeongdeungpo-Gu, Seoul, 07441, Republic of Korea
| | - Yu Bin Seo
- Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, 1 Singil-Ro, Yeongdeungpo-Gu, Seoul, 07441, Republic of Korea.
| | - Jacob Lee
- Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, 1 Singil-Ro, Yeongdeungpo-Gu, Seoul, 07441, Republic of Korea
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Cao S, Jiang X, Suo J, Lu Y, Ju M, Zeng Q, Zheng Q, Zhang Z, Tang W. Molecular Characteristics and Antimicrobial Susceptibility Profiles of blaKPC-Producing Escherichia Coli Isolated from a Teaching Hospital in Shanghai, China. Infect Drug Resist 2024; 17:319-327. [PMID: 38293312 PMCID: PMC10826548 DOI: 10.2147/idr.s444117] [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: 10/11/2023] [Accepted: 01/05/2024] [Indexed: 02/01/2024] Open
Abstract
Introduction Carbapenem-Resistant Enterobacteriaceae (CRE) has posed a significant threat to humans.The aim of this study was to investigate the molecular characteristics of blaKPC-producing Escherichia coli in a university-affiliated tertiary hospital. Methods Polymerase chain reaction (PCR) and BLAST+ software were used to detect the prevalence of blaKPC in E. coli and Klebsiella pneumoniae. Whole-genome sequencing was performed for the blaKPC-harboring clinical E. coli isolates. Antimicrobial resistance genes, MLSTs, KPC-carrying plasmid typing and genetic environment of blaKPC were analyzed. A maximum likelihood core single nucleotide polymorphism (SNP)-based phylogeny tree was constructed to determine the evolutionary relationships within this ST131 collection. Conjugation experiments were performed to determine the mobilization of blaKPC. The minimal inhibitory concentrations of the common antimicrobial agents were determined using the broth microdilution method. Results The prevalence of blaKPC in 424 clinical E. coli isolates and 1636 E. coli strains from GenBank database were 2.2% (45/2060) whereas the detection rate of blaKPC in K. pneumoniae from the GenBank database was 29.8% (415/1394). The blaKPC-harboring conjugants exhibited resistance to multiple β-lactams, except for cefepime-zidebactam and ceftazidime-avibactam. All blaKPC-carring E. coli isolates were susceptible to tigecycline and polymyxin B. ST131 was the dominant sequence type of blaKPC-carring E. coli, accounting for 40.0% (18/45). Most of the blaKPC-producing ST131 E. coli (89.5%,17/19) belonged to clade C ST131 lineage. Genetic environment analysis revealed that 57.8% (26/45) of blaKPC gene was linked to Tn4401-associated structure ISKpn6-blaKPC-ISKpn7. IncN was the most common plasmid type in KPC-producing E. coli whereas IncFII was the dominant plasmid type in KPC-producing K. pneumoniae. Conclusion The detection rate of blaKPC was lower in E. coli compared with K. pneumoniae. The dominant sequence and plasmid types of blaKPC-harboring isolates differed between E. coli and K. pneumoniae. Further studies about the role of the defense system in acquisition of KPC-plasmids in E. coli will be performed to provide new insights into the low prevalence of blaKPC.
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Affiliation(s)
- Shuaijun Cao
- Department of Critical Care Medicine, Shanghai Sixth People’s Hospital, Shanghai, People’s Republic of China
| | - Xiaoying Jiang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Jinshan Suo
- Department of Ophthalmology, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Yanyan Lu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Mohan Ju
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Qixiang Zeng
- Department of Critical Care Medicine, Shanghai Sixth People’s Hospital, Shanghai, People’s Republic of China
| | - Qingru Zheng
- Department of Critical Care Medicine, Shanghai Sixth People’s Hospital, Shanghai, People’s Republic of China
| | - Zuoyan Zhang
- Department of Critical Care Medicine, Shanghai Sixth People’s Hospital, Shanghai, People’s Republic of China
| | - Wenqi Tang
- Department of Critical Care Medicine, Shanghai Sixth People’s Hospital, Shanghai, People’s Republic of China
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Yassin A, Huralska M, Pogue JM, Dixit D, Sawyer RG, Kaye KS. State of the Management of Infections Caused by Multidrug-Resistant Gram-Negative Organisms. Clin Infect Dis 2023; 77:e46-e56. [PMID: 37738671 DOI: 10.1093/cid/ciad499] [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: 02/27/2023] [Indexed: 09/24/2023] Open
Abstract
In the past decade, the prevalence of multidrug-resistant gram-negative (MDR-GN) bacterial infections has increased significantly, leading to higher rates of morbidity and mortality. Treating these infections poses numerous challenges, particularly when selecting appropriate empiric therapy for critically ill patients for whom the margin for error is low. Fortunately, the availability of new therapies has improved the treatment landscape, offering safer and more effective options. However, there remains a need to establish and implement optimal clinical and therapeutic approaches for managing these infections. Here, we review strategies for identifying patients at risk for MDR-GN infections, propose a framework for the choice of empiric and definitive treatment, and explore effective multidisciplinary approaches to managing patients in the hospital while ensuring a safe transition to outpatient settings.
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Affiliation(s)
- Arsheena Yassin
- Department of Pharmacy, Robert Wood Johnson University Hospital, New Brunswick, New Jersey, USA
| | - Mariya Huralska
- Division of Allergy, Immunology and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Jason M Pogue
- Department of Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
- Department of Pharmacy, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Deepali Dixit
- Department of Pharmacy, Robert Wood Johnson University Hospital, New Brunswick, New Jersey, USA
- Ernest Mario School of Pharmacy, Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
| | - Robert G Sawyer
- Department of Surgery, Western Michigan University Homer Stryker School of Medicine, Kalamazoo, Michigan, USA
| | - Keith S Kaye
- Division of Allergy, Immunology and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
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6
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Ng TM, Ang LW, Heng ST, Kwa ALH, Wu JE, Seah XFV, Lee SY, Seah J, Choo R, Lim PL, Thoon KC, Chlebicki MP, Somani J, Lee TH, Lye DC. Antibiotic utilisation and resistance over the first decade of nationally funded antimicrobial stewardship programmes in Singapore acute-care hospitals. Antimicrob Resist Infect Control 2023; 12:82. [PMID: 37612738 PMCID: PMC10464409 DOI: 10.1186/s13756-023-01289-x] [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: 06/16/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
OBJECTIVE The aim of this study was to describe the time series of broad-spectrum antibiotic utilisation and incidence of antibiotic-resistant organisms during the implementation of antimicrobial stewardship programmes (ASP) in Singapore. METHODS An observational study was conducted using data from 2011 to 2020 in seven acute-care public hospitals. We applied joinpoint regressions to investigate changes in antibiotic utilisation rate and incidence density of antibiotic-resistant organisms. RESULTS Across the seven hospitals, quarterly broad-spectrum antibiotic utilisation rate remained stable. Half-yearly incidence density of antibiotic-resistant organisms with two joinpoints at first half (H1) of 2012 and second half (H2) of 2014 decreased significantly in the second and third period with a half-yearly percentage change (HPC) of -2.9% and - 0.5%, respectively. Across the five hospitals with complete data, half-yearly broad-spectrum antibiotic utilisation rate with one joinpoint decreased significantly from H1 of 2011 to H2 of 2018 (HPC - 4.0%) and H2 of 2018 to H2 2020 (HPC - 0.5%). Incidence density of antibiotic-resistant organisms decreased significantly in the two joinpoint periods from H1 of 2012 to H2 of 2014 (HPC - 2.7%) and H2 of 2014 to H2 of 2020 (HPC - 1.0%). Ceftriaxone with one joinpoint decreased significantly from H1 of 2011 to H1 of 2014 (HPC - 6.0%) and H1 of 2014 to H2 of 2020 (HPC - 1.8%) and ceftriaxone-resistant E. coli and K. pneumoniae decreased significantly in later periods, from H2 of 2016 to H2 of 2020 (HPC - 2.5%) and H1 of 2012 to H2 of 2015 (HPC - 4.6%) respectively. Anti-pseudomonal antibiotics with one joinpoint decreased significantly from H1 of 2011 to H2 of 2014 (HPC - 4.5%) and H2 of 2014 to H2 of 2020 (HPC - 0.8%) and that of quinolones with one joinpoint at H1 of 2015 decreased significantly in the first period. C. difficile with one joinpoint increased significantly from H1 of 2011 to H1 of 2015 (HPC 3.9%) and decreased significantly from H1 of 2015 to H2 of 2020 (HPC - 4.9%). CONCLUSIONS In the five hospitals with complete data, decrease in broad-spectrum antibiotic utilisation rate was followed by decrease in incidence density of antibiotic-resistant organisms. ASP should continue to be nationally funded as a key measure to combat antimicrobial resistance in acute care hospitals.
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Affiliation(s)
- Tat Ming Ng
- Tan Tock Seng Hospital, Singapore, Singapore.
| | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore, Singapore
- Ministry of Health, Singapore, Singapore
| | | | - Andrea Lay-Hoon Kwa
- Singapore General Hospital, Singapore, Singapore
- Duke- National University of Singapore Medical School, Singapore, Singapore
| | - Jia En Wu
- National University Hospital, Singapore, Singapore
| | | | | | | | - Robin Choo
- Ng Teng Fong General Hospital, Singapore, Singapore
| | - Poh Lian Lim
- Tan Tock Seng Hospital, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
- Ministry of Health, Singapore, Singapore
| | - Koh Cheng Thoon
- KK Women's and Children's Hospital, Singapore, Singapore
- Duke- National University of Singapore Medical School, Singapore, Singapore
- Lee Kong Chian School of Medicine, Singapore, Singapore
| | | | - Jyoti Somani
- National University Hospital, Singapore, Singapore
- Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Tau Hong Lee
- Tan Tock Seng Hospital, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
| | - David C Lye
- Tan Tock Seng Hospital, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
- Yong Loo Lin School of Medicine, Singapore, Singapore
- Lee Kong Chian School of Medicine, Singapore, Singapore
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7
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Teo JQM, Chang HY, Tan SH, Tang CY, Ong RTH, Ko KKK, Chung SJ, Tan TT, Kwa ALH. Comparative Activities of Novel Therapeutic Agents against Molecularly Characterized Clinical Carbapenem-Resistant Enterobacterales Isolates. Microbiol Spectr 2023; 11:e0100223. [PMID: 37184408 PMCID: PMC10269625 DOI: 10.1128/spectrum.01002-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/01/2023] [Indexed: 05/16/2023] Open
Abstract
Limited treatment options exist for the treatment of carbapenem-resistant Enterobacterales (CRE) bacteria. Fortunately, there are several recently approved antibiotics indicated for CRE infections. Here, we examine the in vitro activity of various novel agents (eravacycline, plazomicin, ceftazidime-avibactam, imipenem-relebactam, and meropenem-vaborbactam) and comparators (tigecycline, amikacin, levofloxacin, fosfomycin, polymyxin B) against 365 well-characterized CRE clinical isolates with various genotypes. Nonduplicate isolates collected from the largest public health hospital in Singapore between 2007 and 2020 were subjected to antimicrobial susceptibility testing (broth microdilution or antibiotic gradient test strips). Susceptibilities were defined using Clinical and Laboratory Standards Institute (CLSI) or Food and Drug Administration (FDA) interpretative criteria. Sequence types and resistance mechanisms were characterized using short-read whole-genome sequencing. Overall, tigecycline and plazomicin exhibited the highest susceptibility rates (89.6% and 80.8%, respectively). However, the tigecycline susceptibility breakpoint utilized here may be outdated in view of prevailing pharmacokinetic-pharmacodynamic (PK/PD) data. Susceptibility varied by carbapenemase genotype; the β-lactam/β-lactamase inhibitor combinations were equally active (92.3 to 99.2% susceptible) against KPC producers, but only ceftazidime-avibactam retained high susceptibility (98.7%) against OXA-48-like producers. Against metallo-β-lactamase producers, only plazomicin exhibited moderate activity (77.0% susceptible). Aminoglycoside activity was also influenced by carbapenemase genotypes. This work provides an insight into the comparative activity and presumptive utility of novel agents in this geographic region. IMPORTANCE This study determined the susceptibilities of carbapenem-resistant Enterobacterales isolates to various novel antimicrobial agents (ceftazidime-avibactam, imipenem-relebactam, meropenem-vaborbactam, eravacycline, and plazomicin). Whole-genome sequencing was performed for all strains. Our study findings provide insights into the comparative activities of novel agents in this geographic region. Plazomicin and ceftazidime-avibactam exhibited the lowest nonsusceptibility rates and may be considered promising agents in the management of carbapenem-resistant Enterobacterales infections. We note also that antibiotic activity is influenced by genotypes and that understanding the geographic region's molecular epidemiology could aid in the definition of the presumptive utility of novel agents and contribute to antibiotic decision-making.
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Affiliation(s)
- Jocelyn Qi-Min Teo
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Hong Yi Chang
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
- Department of Clinical Translational Research, Singapore General Hospital, Singapore, Singapore
| | - Si Hui Tan
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Cheng Yee Tang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Karrie Kwan Ki Ko
- Department of Microbiology, Singapore General Hospital, Singapore, Singapore
| | - Shimin Jasmine Chung
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Thuan Tong Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Andrea Lay-Hoon Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
- Singhealth Duke-NUS Medicine Academic Clinical Programme, Singapore, Singapore
- Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
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8
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Wang S, Wang L, Jin J, Li G, Shao H, Song Y, Sun Y, Zhang Y, Cheng J, Li L. Genomic Epidemiology and Characterization of Carbapenem-Resistant Klebsiella pneumoniae in ICU Inpatients in Henan Province, China: a Multicenter Cross-Sectional Study. Microbiol Spectr 2023; 11:e0419722. [PMID: 37212684 PMCID: PMC10269698 DOI: 10.1128/spectrum.04197-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/19/2023] [Indexed: 05/23/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) has disseminated globally and is difficult to treat, causing increased morbidity and mortality rates in critically ill patients. We conducted a multicenter cross-sectional study of intensive care unit (ICU) inpatients in 78 hospitals to investigate the prevalence and molecular characteristics of CRKP in Henan Province, China, a hyperepidemic region. A total of 327 isolates were collected and downsampled to 189 for whole-genome sequencing. Molecular typing revealed that sequence type 11 (ST11) of clonal group 258 (CG258) was predominant (88.9%, n = 168), followed by ST2237 (5.8%, n = 11) and ST15 (2.6%, n = 5). We used core genome multilocus sequence typing (cgMLST) to further classified the population into 13 subtypes. Capsule polysaccharide (K-antigen) and lipopolysaccharide (LPS; O-antigen) typing revealed that K64 (48.1%, n = 91) and O2a (49.2%, n = 93) were the most common. We studied isolates collected from both the airway and the gut of the same patients and showed that intestinal carriage was associated with respiratory colonization (odds ratio = 10.80, P < 0.0001). Most isolates (95.2%, n = 180) showed multiple drug resistance (MDR), while 59.8% (n = 113) exhibited extensive drug resistance (XDR), and all isolates harbored either blaKPC-2 (98.9%, n = 187) or blaCTX-M and blaSHV extended-spectrum beta-lactamases (ESBLs) (75.7%, n = 143). However, most were susceptible to ceftazidime-avibactam (CZA) (94.7%, n = 179) and colistin (97.9%, n = 185). We found mgrB truncations in isolates conferring resistance to colistin and mutations in blaSHV and OmpK35 and OmpK36 osmoporins in CZA-resistant isolates. Using a regularized regression model, we found that the aerobactin sequence type and the salmochelin sequence type, among others, were predictors of the hypermucoviscosity phenotype. IMPORTANCE In this study, we address the ongoing epidemic of carbapenem-resistant Klebsiella pneumoniae, a critical threat to public health. The alarming genotypic and phenotypic convergence of multidrug resistance and virulence highlights the increasingly aggravated threat posed by K. pneumoniae. This calls for a combined effort of physicians and scientists to study the potential mechanisms and establish guidelines for antimicrobial therapies and interventions. To this end, we have conducted a genomic epidemiology and characterization study using isolates collected in a coordinated effort of multiple hospitals. Innovative biological discoveries of clinical importance are made and brought to the attention of clinical researchers and practitioners. This study presents an important advance in the application of genomics and statistics to recognize, understand, and control an infectious disease of concern.
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Affiliation(s)
- Shanmei Wang
- Department of Clinical Microbiology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| | - Lei Wang
- Department of Bioinformatics Research, Genskey Co., Ltd., Beijing, China
| | - Jing Jin
- Department of Pathogen Biology and Immunology, Henan Medical College, Zhengzhou, Henan, China
| | - Gang Li
- Department of Clinical Microbiology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| | - Huanzhang Shao
- Department of Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| | - Yang Song
- Department of Bioinformatics Research, Genskey Co., Ltd., Beijing, China
| | - Yuanzheng Sun
- Clinical Laboratory, Yuzhou Jundu Hospital, Xuchang, Henan, China
| | - Yan Zhang
- Clinical Laboratory, Yima People’s Hospital, Sanmenxia, Henan, China
| | - Jianjian Cheng
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| | - Lifeng Li
- Department of Bioinformatics Research, Genskey Co., Ltd., Beijing, China
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9
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Ozyurt OK, Cetinkaya O, Ozhak B, Ongut G, Turhan O, Yazisiz H, Donmez L, Kuskucu MA, Midilli K, Ogunc D. Evaluation of the BD Phoenix CPO Detect Test for the detection of carbapenemase-producing Enterobacterales. Future Microbiol 2023; 18:399-405. [PMID: 37256285 DOI: 10.2217/fmb-2022-0071] [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: 03/22/2022] [Accepted: 02/24/2023] [Indexed: 06/01/2023] Open
Abstract
Aims: This study aimed to evaluate the performance of the BD Phoenix CPO Detect Test (BD Diagnostic Systems) for the detection and classification of carbapenemase-mediated carbapenem resistance. Methods: A total of 447 Enterobacterales strains were included in the study. All strains were tested with the BD Phoenix CPO Detect Test and the modified carbapenem inactivation method. Results: Carbapenemase production was detected in 157 of 159 carbapenemase producers, including 95.7% of class B and 99.2% of class D isolates using the BD Phoenix CPO Detect Test. BD Phoenix CPO Detect has a sensitivity of 98.7% and a specificity of 95.5% in detecting carbapenemase production. Conclusion: The classification of OXA-48 and class B carbapenemases, the most common carbapenemases circulating in Turkey, was highly accurate.
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Affiliation(s)
- Ozlem K Ozyurt
- Department of Medical Microbiology, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Ozgul Cetinkaya
- Department of Medical Microbiology, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Betil Ozhak
- Department of Medical Microbiology, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Gozde Ongut
- Department of Medical Microbiology, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Ozge Turhan
- Department of Infectious Diseases & Clinical Microbiology, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Hatice Yazisiz
- Department of Medical Microbiology, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Levent Donmez
- Department of Public Health, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Mert A Kuskucu
- Department of Medical Microbiology, Istanbul University Cerrahpaşa School of Medicine, Istanbul, Turkey
| | - Kenan Midilli
- Department of Medical Microbiology, Istanbul University Cerrahpaşa School of Medicine, Istanbul, Turkey
| | - Dilara Ogunc
- Department of Medical Microbiology, Akdeniz University Faculty of Medicine, Antalya, Turkey
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10
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Ahn JY, Ahn SM, Kim JH, Jeong SJ, Ku NS, Choi JY, Yeom JS, Song JE. Clinical Characteristics and Associated Factors for Mortality in Patients with Carbapenem-Resistant Enterobacteriaceae Bloodstream Infection. Microorganisms 2023; 11:1121. [PMID: 37317095 DOI: 10.3390/microorganisms11051121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Bloodstream infection (BSI) caused by carbapenem-resistant Enterobacteriaceae (CRE) significantly influences patient morbidity and mortality. We aimed to identify the characteristics, outcomes, and risk factors of mortality in adult patients with CRE bacteremia and elucidate the differences between carbapenemase-producing (CP)-CRE BSI and non-CP-CRE BSI. METHODS This retrospective study included 147 patients who developed CRE BSI between January 2016 and January 2019 at a large tertiary care hospital in South Korea. The patient demographic characteristics and clinical and microbiological data including the Enterobacteriaceae species and carbapenemase type were obtained and analyzed. RESULTS Klebsiella pneumoniae was the most commonly detected pathogen (80.3%), followed by Escherichia coli (15.0%). In total, 128 (87.1%) isolates were found to express carbapenemase, and most CP-CRE isolates harbored blaKPC. The 14-day and 30-day mortality rates for CRE BSI were 34.0% and 42.2%, respectively. Higher body mass index (odds ratio (OR), 1.123; 95% confidence interval (CI), 1.012-1.246; p = 0.029), higher sequential organ failure assessment (SOFA) score (OR, 1.206; 95% CI, 1.073-1.356; p = 0.002), and previous antibiotic use (OR, 0.163; 95% CI, 0.028-0.933; p = 0.042) were independent risk factors for the 14-day mortality. A high SOFA score (OR, 1.208; 95% CI; 1.081-0.349; p = 0.001) was the only independent risk factor for 30-day mortality. Carbapenemase production and appropriate antibiotic treatment were not associated with high 14- or 30-day mortality rates. CONCLUSIONS Mortality from CRE BSI was related to the severity of the infection rather than to carbapenemase production or antibiotic treatment, showing that efforts to prevent CRE acquisition rather than treatment following CRE BSI detection would be more effective at reducing mortality.
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Affiliation(s)
- Jin Young Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Sang Min Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung Ho Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Su Jin Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Nam Su Ku
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jun Yong Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Joon Sup Yeom
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Je Eun Song
- Department of Internal Medicine, Inje University Ilsan Paik Hospital, Goyang 10380, Republic of Korea
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11
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Healthcare-associated multispecies outbreaks of OXA-48-positive carbapenemase-producing Enterobacteriaceae in a Singapore tertiary-care hospital. Infect Control Hosp Epidemiol 2023; 44:8-16. [PMID: 35285435 DOI: 10.1017/ice.2022.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To describe OXA-48-like carbapenem-producing Enterobacteriaceae (CPE) outbreaks at Singapore General Hospital between 2018 and 2020 and to determine the risk associated with OXA-48 carriage in the 2020 outbreak. DESIGN Outbreak report and case-control study. SETTING Singapore General Hospital (SGH) is a tertiary-care academic medical center in Singapore with 1,750 beds. METHODS Active surveillance for CPE is conducted for selected high-risk patient cohorts through molecular testing on rectal swabs or stool samples. Patients with CPE are isolated or placed in cohorts under contact precautions. During outbreak investigations, rectal swabs are repeated for culture. For the 2020 outbreak, a retrospective case-control study was conducted in which controls were inpatients who tested negative for OXA-48 and were selected at a 1:3 case-to-control ratio. RESULTS Hospital wide, the median number of patients with healthcare-associated OXA-48 was 2 per month. In the 3-year period between 2018 and 2020, 3 OXA-48 outbreaks were investigated and managed, involving 4 patients with Klebsiella pneumoniae in 2018, 55 patients with K. pneumoniae or Escherichia coli in 2019, and 49 patients with multispecies Enterobacterales in 2020. During the 2020 outbreak, independent risk factors for OXA-48 carriage on multivariate analysis (49 patients and 147 controls) were diarrhea within the preceding 2 weeks (OR, 3.3; 95% CI, 1.1-10.7; P = .039), contact with an OXA-48-carrying patient (OR, 8.7; 95% CI, 1.9-39.3; P = .005), and exposure to carbapenems (OR, 17.2; 95% CI, 2.2-136; P = .007) or penicillin (OR, 16.6; 95% CI, 3.8-71.0; P < .001). CONCLUSIONS Multispecies OXA-48 outbreaks in our institution are likely related to a favorable ecological condition and selective pressure exerted by antimicrobial use. The integration of molecular surveillance epidemiology of the healthcare environment is important in understanding the risk of healthcare-associated infection to patients.
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12
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Sannathimmappa M. Global escalation in carbapenem-resistant Enterobacterales and carbapenem-resistant Acinetobacter baumannii infections: Serious threat to human health from the pink corner. BIOMEDICAL AND BIOTECHNOLOGY RESEARCH JOURNAL (BBRJ) 2023. [DOI: 10.4103/bbrj.bbrj_366_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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13
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Wu AYJ, Chang H, Wang NY, Sun FJ, Liu CP. Clinical and molecular characteristics and risk factors for patients acquiring carbapenemase-producing and non-carbapenemase-producing carbapenem-nonsusceptible-Enterobacterales bacteremia. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1229-1238. [PMID: 34824020 DOI: 10.1016/j.jmii.2021.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND/PURPOSE Carbapenem-nonsusceptible Enterobacterales (CNSE) are a growing global threat. Carbapenemases are often produced by plasmids, which allow rapid transmission. This study aimed to investigate (1) the bacterial type (2) resistant genes (3) antimicrobial susceptibility and (4) risk factors for acquisition of carbapenemase-producing carbapenem-nonsusceptible Enterobacterales (CP-CNSE) and non-carbapenemase-producing carbapenem-nonsusceptible Enterobacterales (non-CP-CNSE) bacteremia. METHODS There were a total of 113 isolates of Enterobacterales from 2013 to 2018. After excluding nonblood isolates and including only one sample from each patient, 99 isolates were analyzed and the medical charts of these patients were reviewed. Carbapenemase genes, β-lactamase genes and antimicrobial susceptibility of the isolates were determined. Multilocus sequence typing (MLST) was performed on CP-CNSE isolates. RESULTS CP-CNSE carried more blaSHV (P = 0.004) and were more resistant to imipenem than non-CP-CNSE (P < 0.001). In the univariate analyses, we found that CP-CNSE bloodstream infection was associated with patient <65 years of age (odds ratio, 3.90; 95% confidence interval [CI], 1.16 to 13.10; P = 0.027), mechanical ventilation at the time of bloodstream infection (BSI) (odds ratio, 3.85; 95% CI, 1.16-12.78; P = 0.028) and exposure to piperacillin/tazobactam (odds ratio, 3.96; 95% CI, 1.09-14.38; P = 0.037). However, on multivariate analyses, no independent predictor for CP-CNSE was identified in this study. CONCLUSION CP-CNSE carried more blaSHV and were more resistant to imipenem when compared to non-CP-CNSE. No independent predictor for CP-CNSE was identified after multivariate analysis. This is the first study conducted in Taiwan comparing risk factors between CP-CNSE and non-CP-CNSE from both clinical and molecular aspects.
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Affiliation(s)
- Alice Ying-Jung Wu
- Division of Infectious Diseases, Department of Internal Medicine, MacKay Memorial Hospital, Taipei, Taiwan
| | - Hsun Chang
- Division of Infectious Diseases, Department of Internal Medicine, MacKay Memorial Hospital, Taipei, Taiwan
| | - Nai-Yu Wang
- Section of Microbiology, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Fang-Ju Sun
- Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan; Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chang-Pan Liu
- Division of Infectious Diseases, Department of Internal Medicine, MacKay Memorial Hospital, Taipei, Taiwan; Section of Microbiology, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan; Department of Medicine, MacKay Medical College, New Taipei, Taiwan.
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14
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Chew KL, Cabang JC, Teo J. Limited in vitro susceptibility of drug-resistant non-fermenting Gram-negative organisms against newer generation antibiotics. Pathology 2022; 55:583-587. [PMID: 36567162 DOI: 10.1016/j.pathol.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 12/05/2022]
Affiliation(s)
- Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore.
| | - Joey Cruz Cabang
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Jeanette Teo
- Department of Laboratory Medicine, National University Hospital, Singapore
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15
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Characterisation of Non-Carbapenemase-Producing Carbapenem-Resistant Klebsiella pneumoniae Based on Their Clinical and Molecular Profile in Malaysia. Antibiotics (Basel) 2022; 11:antibiotics11111670. [PMID: 36421313 PMCID: PMC9686620 DOI: 10.3390/antibiotics11111670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Non-carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae (NC-CRKP) confers carbapenem resistance through a combination of chromosomal mutations and acquired non-carbapenemase resistance mechanisms. In this study, we aimed to evaluate the clinical and molecular profiles of NC-CRKP isolated from patients in a tertiary teaching hospital in Malaysia from January 2013 to October 2019. During the study period, 54 NC-CRKP-infected/colonised patients’ isolates were obtained. Clinical parameters were assessed in 52 patients. The all-cause in-hospital mortality rate among NC-CRKP patients was 46.2% (24/52). Twenty-three (44.2%) patients were infected, while others were colonised. Based on the Charlson Comorbidity Index (CCI) score, 92.3% (48/52) of the infected/colonised patients had a score of ≥ 1. Resistance genes found among the 54 NC-CRKP isolates were blaTEM, blaSHV, blaCTX-M, blaOXA, and blaDHA. Porin loss was detected in 25/54 (46.3%) strains. None of the isolated strains conferred carbapenem resistance through the efflux pumps system. In conclusion, only 25/54 (46.3%) NC-CRKP conferred carbapenem resistance through a combination of porin loss and the acquisition of non-carbapenemase resistance mechanisms. The carbapenem resistance mechanisms for the remaining strains (53.7%) should be further investigated as rapid identification and distinction of the NC-CRKP mechanisms enable optimal treatment and infection control efforts.
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16
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Teo JQM, Tang CY, Tan SH, Chang HY, Ong SM, Lee SJY, Koh TH, Sim JHC, Kwa ALH, Ong RTH. Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae from a Major Public Health Hospital in Singapore. Microbiol Spectr 2022; 10:e0095722. [PMID: 36066252 PMCID: PMC9602435 DOI: 10.1128/spectrum.00957-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/04/2022] [Indexed: 12/30/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global public health threat. In this study, we employed whole-genome sequencing (WGS) to determine the genomic epidemiology of a longitudinal collection of clinical CRKP isolates recovered from a large public acute care hospital in Singapore. Phylogenetic analyses, a characterization of resistance and virulence determinants, and plasmid profiling were performed for 575 unique CRKP isolates collected between 2009 and 2020. The phylogenetic analyses identified the presence of global high-risk clones among the CRKP population (clonal group [CG] 14/15, CG17/20, CG147, CG258, and sequence type [ST] 231), and these clones constituted 50% of the isolates. Carbapenemase production was common (n = 497, 86.4%), and KPC was the predominant carbapenemase (n = 235, 40.9%), followed by OXA-48-like (n = 128, 22.3%) and NDM (n = 93, 16.2%). Hypervirulence was detected in 59 (10.3%) isolates and was most common in the ST231 carbapenemase-producing isolates (21/59, 35.6%). Carbapenemase genes were associated with diverse plasmid replicons; however, there was an association of blaOXA-181/232 with ColKP3 plasmids. This study presents the complex and diverse epidemiology of the CRKP strains circulating in Singapore. Our study highlights the utility of WGS-based genomic surveillance in tracking the population dynamics of CRKP. IMPORTANCE In this study, we characterized carbapenem-resistant Klebsiella pneumoniae clinical isolates collected over a 12-year period in the largest public acute-care hospital in Singapore using whole-genome sequencing. The results of this study demonstrate significant genomic diversity with the presence of well-known epidemic, multidrug-resistant clones amid a diverse pool of nonepidemic lineages. Genomic surveillance involving comprehensive resistance, virulence, and plasmid gene content profiling provided critical information for antimicrobial resistance monitoring and highlighted future surveillance priorities, such as the emergence of ST231 K. pneumoniae strains bearing multidrug resistance, virulence elements, and the potential plasmid-mediated transmission of the blaOXA-48-like gene. The findings here also reinforce the necessity of unique infection control and prevention strategies that take the genomic diversity of local circulating strains into consideration.
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Affiliation(s)
- Jocelyn Qi-Min Teo
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Cheng Yee Tang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Si Hui Tan
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Hong Yi Chang
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Sze Min Ong
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | | | - Tse-Hsien Koh
- Department of Microbiology, Singapore General Hospital, Singapore, Singapore
| | | | - Andrea Lay-Hoon Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
- Singhealth Duke-NUS Medicine Academic Clinical Programme, Singapore, Singapore
- Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
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17
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Prevalence and Distribution of mcr Genotypes in a Large Retrospective Collection of Clinical Carbapenemase-Producing Enterobacterales, Singapore. Antimicrob Agents Chemother 2022; 66:e0101922. [PMID: 36036602 PMCID: PMC9487542 DOI: 10.1128/aac.01019-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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18
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Yong M, Chen Y, Oo G, Chang KC, Chu WHW, Teo J, Venkatachalam I, Thevasagayam NM, Sridatta PSR, Koh V, Marcoleta AE, Chen H, Nagarajan N, Kalisvar M, Ng OT, Gan YH. Dominant Carbapenemase-Encoding Plasmids in Clinical Enterobacterales Isolates and Hypervirulent Klebsiella pneumoniae, Singapore. Emerg Infect Dis 2022; 28:1578-1588. [PMID: 35876475 PMCID: PMC9328930 DOI: 10.3201/eid2808.212542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Dissemination of carbapenemase-encoding plasmids by horizontal gene transfer in multidrug-resistant bacteria is the major driver of rising carbapenem-resistance, but the conjugative mechanics and evolution of clinically relevant plasmids are not yet clear. We performed whole-genome sequencing on 1,215 clinical Enterobacterales isolates collected in Singapore during 2010–2015. We identified 1,126 carbapenemase-encoding plasmids and discovered pKPC2 is becoming the dominant plasmid in Singapore, overtaking an earlier dominant plasmid, pNDM1. pKPC2 frequently conjugates with many Enterobacterales species, including hypervirulent Klebsiella pneumoniae, and maintains stability in vitro without selection pressure and minimal adaptive sequence changes. Furthermore, capsule and decreasing taxonomic relatedness between donor and recipient pairs are greater conjugation barriers for pNDM1 than pKPC2. The low fitness costs pKPC2 exerts in Enterobacterales species indicate previously undetected carriage selection in other ecological settings. The ease of conjugation and stability of pKPC2 in hypervirulent K. pneumoniae could fuel spread into the community.
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19
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Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales. Nat Commun 2022; 13:3052. [PMID: 35650193 PMCID: PMC9160272 DOI: 10.1038/s41467-022-30637-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
Carbapenemase-producing Enterobacterales (CPE) infection control practices are based on the paradigm that detected carriers in the hospital transmit to other patients who stay in the same ward. The role of plasmid-mediated transmission at population level remains largely unknown. In this retrospective cohort study over 4.7 years involving all multi-disciplinary public hospitals in Singapore, we analysed 779 patients who acquired CPE (1215 CPE isolates) detected by clinical or surveillance cultures. 42.0% met putative clonal transmission criteria, 44.8% met putative plasmid-mediated transmission criteria and 13.2% were unlinked. Only putative clonal transmissions associated with direct ward contact decreased in the second half of the study. Both putative clonal and plasmid-mediated transmission associated with indirect (no temporal overlap in patients’ admission period) ward and hospital contact did not decrease during the study period. Indirect ward and hospital contact were identified as independent risk factors associated with clonal transmission. In conclusion, undetected CPE reservoirs continue to evade hospital infection prevention measures. New measures are needed to address plasmid-mediated transmission, which accounted for 50% of CPE dissemination. Carbapenemase-producing Enterobacterales cause healthcare-associated infections but modes of transmission are not well understood. Here, the authors find evidence of transmission without direct patient contact, indicating presence of undetected environmental reservoirs, whilst half of the transmission events are likely due to plasmid-mediated transmission.
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20
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Yang WT, Chiu IJ, Huang YT, Liu PY. Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant Escherichia coli. Front Microbiol 2022; 13:886428. [PMID: 35516434 PMCID: PMC9062692 DOI: 10.3389/fmicb.2022.886428] [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: 02/28/2022] [Accepted: 03/22/2022] [Indexed: 12/13/2022] Open
Abstract
Escherichia coli (E. coli) is a major causative organism of complicated urinary tract infections, bloodstream infections, and pneumonia. With the widespread use of antimicrobial agents, the prevalence of carbapenem resistance in E. coli has been increasing with limited therapeutic options. Fluoroquinolone remains a choice in carbapenem-resistant E. coli (CREc) that were once susceptible to the drug. Despite robust studies on the fluoroquinolone-resistant mechanisms of E. coli, few studies focused specifically on the group of CREc. In this study, we used comparative genomics to identify the fluoroquinolone-resistant mechanisms of CREc and detected gyrA D87N mutation in all the fluoroquinolone-resistant and CREc. Moreover, to investigate the mechanism underlying non-carbapenemase-producing carbapenem-resistant E. coli, we targeted the complete genome sequences for in-depth analysis and found a deletion in OmpF (DEL264-269) that might contribute to carbapenem resistance, which has not been reported before. Further studies focusing on the impact of these mutations on the expression levels are warranted. We further investigate the MLST, serotype, fimH type, phylogroup, and clinical characteristics of the CREc. Combination analysis of clinical and genomic characteristics suggests the polyclonal and highly diverse nature of the CREc in Taiwan. This study provides an insight into the molecular epidemiology of CREc in Taiwan.
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Affiliation(s)
- Wan-Ting Yang
- Division of Infection, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - I-Ju Chiu
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan,Yao-Ting Huang
| | - Po-Yu Liu
- Division of Infection, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan,*Correspondence: Po-Yu Liu
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21
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Waddington C, Carey ME, Boinett CJ, Higginson E, Veeraraghavan B, Baker S. Exploiting genomics to mitigate the public health impact of antimicrobial resistance. Genome Med 2022; 14:15. [PMID: 35172877 PMCID: PMC8849018 DOI: 10.1186/s13073-022-01020-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major global public health threat, which has been largely driven by the excessive use of antimicrobials. Control measures are urgently needed to slow the trajectory of AMR but are hampered by an incomplete understanding of the interplay between pathogens, AMR encoding genes, and mobile genetic elements at a microbial level. These factors, combined with the human, animal, and environmental interactions that underlie AMR dissemination at a population level, make for a highly complex landscape. Whole-genome sequencing (WGS) and, more recently, metagenomic analyses have greatly enhanced our understanding of these processes, and these approaches are informing mitigation strategies for how we better understand and control AMR. This review explores how WGS techniques have advanced global, national, and local AMR surveillance, and how this improved understanding is being applied to inform solutions, such as novel diagnostic methods that allow antimicrobial use to be optimised and vaccination strategies for better controlling AMR. We highlight some future opportunities for AMR control informed by genomic sequencing, along with the remaining challenges that must be overcome to fully realise the potential of WGS approaches for international AMR control.
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Affiliation(s)
- Claire Waddington
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Balaji Veeraraghavan
- Department of Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK. .,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
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22
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Molecular Epidemiology, Risk Factors and Clinical Outcomes of Carbapenem-Nonsusceptible Enterobacter cloacae Complex Infections in a Taiwan University Hospital. Pathogens 2022; 11:pathogens11020151. [PMID: 35215096 PMCID: PMC8874368 DOI: 10.3390/pathogens11020151] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 12/24/2022] Open
Abstract
The genus Enterobacter is a member of the ESKAPE group, which contains the major resistant bacterial pathogens. Enterobacter cloacae complex (ECC) has emerged as a clinically significant cause of a wide variety of nosocomial infections. Carbapenem-nonsusceptible Enterobacter cloacae complex (CnsECC) has become an emerging threat to public health but there is still a lack of comprehensive molecular and clinical epidemiological analysis. A total of 157 CnsECC isolates were recovered during October 2011 to August 2017. hsp60 gene sequencing and pulsed-field gel electrophoresis (PFGE) were applied to discriminate the species, genetic clusters and clonal relatedness. All the isolates were subjected to polymerase chain reaction (PCR) analysis for carbapenemase, AmpC-type β-lactamase, and extended spectrum β-lactamase (ESBL) genes. Clinical data were collected on all patients for comparing clinical risks and outcomes between patients with carbapenemase-producing (CP)-CnsECC compared with non-CP-CnsECC infection. The most commonly identified species was E. hormaechei subsp. hoffmannii (47.1%), followed by E. hormaechei subsp. steigerwaltii (24.8%). Different species of CnsECC isolates showed heterogeneity in resistance patterns to piperacillin/tazobactam, cefepime and levofloxacin. In the present study, we observed that E. hormaechei subsp. hoffmannii was characterized with higher cefepime and levofloxacin resistance rate but lower piperacillin/tazobactam resistance rate relative to other species of CnsECC. CP-CnsECC comprised 41.1% (65 isolates) and all of these isolates carried IMP-8. In this study, 98% of patients had antimicrobial therapy prior to culture, with a total of 57/150 (38%) patients being exposed to carbapenems. Chronic pulmonary disease (OR: 2.51, 95% CI: 1.25–5.06), received ventilator support (OR: 5.54, 95% CI: 2.25–12.03), steroid exposure (OR: 3.88, 95% CI: 1.91–7.88) and carbapenems exposure (OR: 2.17, 95% CI: 1.10–4.25) were considered risk factors associated with CP-CnsECC infection. The results suggest that CP-CnsECC are associated with poorer outcomes including in-hospital mortality, 30-day mortality and 100-day mortality. Our study provides insights into the epidemic potential of IMP-8-producing E. cloacae for healthcare-associated infections and underscores the importance of understanding underlying resistance mechanisms of CnsECC to direct antibiotic treatment decisions.
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Jiang Y, Yang S, Deng S, Lu W, Huang Q, Xia Y. Epidemiology and mechanisms of tigecycline- and carbapenem- resistant Enterobacter cloacae in Southwest China: a five-year retrospective study. J Glob Antimicrob Resist 2022; 28:161-167. [PMID: 35021124 DOI: 10.1016/j.jgar.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 07/12/2021] [Accepted: 01/05/2022] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND The prevalence and molecular epidemiology of tigecycline resistance in carbapenem-resistant Enterobacter cloacae (CREC) in mainland China is unknown. In this study, we aimed to investigate the molecular characteristics and resistance mechanism of tigecycline-resistant CREC (TCREC) in Southwest China. METHODS We conducted a five-year retrospective study. TCREC isolates were subjected to antimicrobial susceptibility testing, pulsed-field gel electrophoresis, and multilocus sequence typing. We determined the presence of genes, deficiency of outer membrane proteins, and expression of efflux pumps using polymerase chain reaction (PCR), reverse transcription-polymerase chain reaction (RT-PCR), and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). RESULTS We found that a high incidence rate of 21.7% (36/166) of isolates were positive for TCREC. All isolates were resistant to ertapenem whereas 67% remained susceptible to imipenem and meropenem. ST88 (10/36, 27.8%) was predominant and associated with moderate resistance to tigecycline and high resistance to carbapenems, followed by ST256 (3/36, 8.3%), ST78 (2/36, 5.6%), ST577 (2/36, 5.6%), and ST102 (2/36, 5.6%). blaNDM-1 (6/36, 16.6%) carriers was the most common carbapenemase gene and ST88 (5/6, 83.3%) was the most common type, followed by blaIMP-8 (n=3/36, 8.3%). Coexistence of extensive-spectrum β-lactamase (ESBL) genes and outer membrane protein OmpF and/or OmpC loss were found in 27 out of 36 isolates, in addition, increased co-expression of efflux pump genes acrB and oqxA was identified in 25 out of 36 isolates, which may together contribute to co-resistance to carbapenem and tigecycline. CONCLUSION Most ST88 strains carried carbapenemases, especially New Delhi metallo-β-lactamase 1 (NDM-1). Overexpression of efflux pumps contributed to tigecycline resistance. The presence of carbapenemase and/or ESBL genes and lack of outer membrane proteins, but not overexpression of efflux pumps, may confer carbapenem resistance. Reasonable supervision and management the epidemic of TCREC will help to stem the transmission of the isolates.
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Affiliation(s)
- Yuansu Jiang
- Department of Laboratory Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Department of Clinical Laboratory, Daping Hospital of Army Medical University, Chongqing, China
| | - Shuangshuang Yang
- Department of Laboratory Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shaoli Deng
- Department of Clinical Laboratory, Daping Hospital of Army Medical University, Chongqing, China
| | - Weiping Lu
- Department of Clinical Laboratory, Daping Hospital of Army Medical University, Chongqing, China
| | - Qing Huang
- Department of Clinical Laboratory, Daping Hospital of Army Medical University, Chongqing, China.
| | - Yun Xia
- Department of Laboratory Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Cai Y, Hoo GSR, Lee W, Tan BH, Yoong J, Teo YY, Graves N, Lye D, Kwa AL. Estimating the economic cost of carbapenem resistant Enterobacterales healthcare associated infections in Singapore acute-care hospitals. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0001311. [PMID: 36962882 PMCID: PMC10021918 DOI: 10.1371/journal.pgph.0001311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/30/2022] [Indexed: 12/12/2022]
Abstract
Quantifying the costs of hospital associated infections (HAIs) caused by carbapenem-resistant Enterobacterales (CRE) can aid hospital decision makers in infection prevention and control decisions. We estimate the costs of a CRE HAI by infection type and the annual costs of CRE HAIs to acute-care hospitals in Singapore. We used tree diagrams to estimate the costs (in Singapore dollar) of different CRE HAI types from the health service perspective and compared them to the costs of carbapenem-susceptible HAIs. We used two approaches to estimate costs-direct costs of consumables for infection prevention and treatment; and costs associated with lost bed days. Cost of a HAI were extrapolated to annual CRE HAI incidence in Singapore acute-care hospitals to estimate the annual cost to the hospitals. We found that the cost of a CRE HAI based on direct cost and lost bed days are SGD$9,913 (95% CI, SGD$9,431-10,395) and SGD$10,044 (95% CI, SGD$9,789-10,300) respectively. CRE HAIs are markedly higher than the carbapenem-susceptible HAIs for all infection types. In both approaches, CRE pneumonia was the costliest infection. Based on a CRE HAI incidence of 233 per 100,000 inpatient admissions, CRE HAIs costed SGD$12.16M (95% CI, SGD$11.84-12.48M) annually based on direct costs, and SGD$12.33M (95% CI, SGD$12.01-12.64M) annually based on lost bed days. In conclusion, we described the cost of CRE HAIs in Singapore hospitals and identified infections with the highest costs. The findings may be useful in informing future economic evaluations of competing CRE HAI prevention and treatment programmes.
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Affiliation(s)
- Yiying Cai
- Programme in Health Services & Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Grace S R Hoo
- Department of Pharmacy, Tan Tock Seng Hospital, Singapore, Singapore
| | - Winnie Lee
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Ban Hock Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Joanne Yoong
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Research for Impact, Singapore, Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Nicholas Graves
- Programme in Health Services & Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - David Lye
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Infectious Diseases, National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Andrea L Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
- Singhealth Duke-NUS Medicine Academic Clinical Programme, Singapore, Singapore
- Emerging Infectious Diseases, Duke-National University of Singapore, Singapore, Singapore
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Carbapenemase-producing Enterobacterales infections: Recent advances in diagnosis and treatment. Int J Antimicrob Agents 2022; 59:106528. [DOI: 10.1016/j.ijantimicag.2022.106528] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 11/19/2022]
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Cai L, Sun J, Yao F, Yuan Y, Zeng M, Zhang Q, Xie Q, Wang S, Wang Z, Jiao X. Antimicrobial resistance bacteria and genes detected in hospital sewage provide valuable information in predicting clinical antimicrobial resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148815. [PMID: 34247085 DOI: 10.1016/j.scitotenv.2021.148815] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 06/27/2021] [Accepted: 06/29/2021] [Indexed: 02/05/2023]
Abstract
Extensive use of antibiotics is significantly associated with development of antibiotic-resistant (AR) bacteria. However, their causal relationships have not been adequately investigated, especially in human population and hospitals. Our aims were to understand clinical AR through revealing co-occurrence patterns between antibiotic-resistant bacteria and genes (ARB and ARGs), and their association with antibiotic use, and to consider impact of ARB and ARGs on environmental and human health. Antibiotic usage was calculated based on the actual consumption in our target hospital. ARB was identified by culture. In isolates collected from hospital sewage, bacterial-specific DNA sequences and ARGs were determined using metagenomics. Our data revealed that the use of culture-based single-indicator-strain approaches only captured ARB in 16.17% of the infectious samples. On the other hand, 1573 bacterial species and 885 types of ARGs were detected in the sewage. Furthermore, hospital use of antibiotics influenced the resistance profiles, but the strength varied among bacteria. From our metagenomics analyses, ARGs for aminoglycosides were the most common, followed by sulfonamide, tetracycline, phenicol, macrolides, and quinolones, comprising 82.6% of all ARGs. Association analyses indicated that 519 pairs of ARGs were significantly correlated with ARB species (r > 0.8). The co-occurrence patterns of bacteria-ARGs mirrored the AR in the clinic. In conclusion, our systematic investigation further emphasized that antibiotic usage in hospital significantly influenced the abundance and types of ARB and ARGs in dose- and time-dependent manners which, in turn, mirrored clinical AR. In addition, our data provide novel information on development of certain ARB with multiple antibiotic resistance. These ARB and ARGs from sewage can also be disseminated into the environment and communities to create health problems. Therefore, it would be helpful to use such data to develop improved predictive risk model of AR, to enhance effective use of antibiotics, and to reduce environmental pollution.
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Affiliation(s)
- Leshan Cai
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Jiayu Sun
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Fen Yao
- Department of Pharmacology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yumeng Yuan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Mi Zeng
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Qiaoxin Zhang
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Qingdong Xie
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Shiwei Wang
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Medical College of Yangzhou University, Yangzhou, Jiangsu 225000, China
| | - Zhen Wang
- Institute of Marine Sciences, Shantou University, Shantou 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China.
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Zhu C, Li C, Lai CKC, Ng R, Chau KY, Wong KT, Lo NWS, Barua N, Yang Y, Liyanapathirana V, Hui M, Lai RW, Fung KSC, Tsang DN, Ip M. Longitudinal Genomic Characterization of Carbapenemase-producing Enterobacteriaceae (CPE) Reveals Changing Pattern of CPE Isolated in Hong Kong Hospitals. Int J Antimicrob Agents 2021; 58:106430. [PMID: 34525401 DOI: 10.1016/j.ijantimicag.2021.106430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/23/2021] [Accepted: 08/28/2021] [Indexed: 11/30/2022]
Abstract
An active, territory-wide, CPE surveillance program implemented from 2011 showed increasing levels of carbapenemase-producing Enterobacteriaceae (CPE) isolates from patients in Hong Kong hospitals. The molecular epidemiology of 567 CPE from patients of three of seven public hospital clusters in Hong Kong are described. During a 7-year period, the incidence of CPE isolation increased from 0.05 to 9.6/100 000 patient-days. The carbapenemase genes identified were polyclonal, including blaKPC, blaNDM and blaIMP, which were mainly associated with hospitalization overseas in previous years. However, increasing CPE isolation from patients without hospitalization overseas occurred in 2015, with blaNDM (52.6%) predominant followed by blaIMP (30.0%). Escherichia coli (46.4%) and Klebsiella spp. (38.3%) were the dominant species. Whole-genome sequencing was performed on 169 representative isolates with a combination of short and long reads using Illumina and Nanopore technology. Two distinct lineages of blaKPC-2-positive Klebsiella pneumoniae (ST11 and ST258) were identified with ST11 carrying yersiniabactin gene ybt-9 on ICEKp3. ST131 E. coli producing IMP-4 was present throughout the study period. The blaNDM and blaIMP genes were mainly carried in IncX3 and IncN-ST7 plasmids, respectively. blaOXA-48-like gene was carried in the IncX3 plasmid in E. coli and in the ColKP3 plasmid in K. pneumoniae. A lineage of K. pneumoniae with blaNDM-1 plus blaOXA-232 in distinct plasmids of IncF1B/IncHI1B was identified and associated with prior hospitalization overseas. This study highlights the threat of multiple types of CPE, with the predominance of blaNDM and blaIMP among CPE in our hospitals. Enhanced containment strategies are needed to mitigate the trend of rapidly rising CPE in healthcare settings.
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Affiliation(s)
- Chendi Zhu
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, China.
| | - Carmen Li
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, China.
| | - Christopher K C Lai
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, China; Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China.
| | - Rita Ng
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, China; Prince of Wales Hospital, Hong Kong, China.
| | - Ka Yee Chau
- United Christian Hospital, Hong Kong, China.
| | - Kam Tak Wong
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, China.
| | - Norman W S Lo
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, China.
| | - Nilakshi Barua
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, China.
| | - Ying Yang
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, China.
| | | | - Mamie Hui
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, China; Prince of Wales Hospital, Hong Kong, China.
| | | | | | | | - Margaret Ip
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, China; Prince of Wales Hospital, Hong Kong, China.
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Lynch JP, Clark NM, Zhanel GG. Escalating antimicrobial resistance among Enterobacteriaceae: focus on carbapenemases. Expert Opin Pharmacother 2021; 22:1455-1473. [PMID: 33823714 DOI: 10.1080/14656566.2021.1904891] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Introduction: Over the past few decades, antimicrobial resistance (AMR) has skyrocketed globally among bacteria within the Family Enterobacteriaceae (i.e. Enterobacter spp, Klebsiella spp, Escherichia coli, Proteus spp, Serratia marcescens, Citrobacter spp, and others). Enterobacteriaceae are intestinal flora and are important pathogens in nosocomial and community settings. Enterobacteriaceae spread easily between humans and may acquire AMR via plasmids or other mobile resistance elements. The emergence and spread of multidrug resistant (MDR) clones have greatly limited therapeutic options. Some infections are untreatable with existing antimicrobials.Areas covered: The authors discuss the escalation of CRE globally, the epidemiology and outcomes of CRE infections, the optimal therapy, and the potential role of several new antimicrobials to combat MDR organisms. An exhaustive search for literature related to Enterobacteriaceae was performed using PubMed, using the following key words: antimicrobial resistance; carbapenemases; Enterobacterales; Enterobacteriaceae; Klebsiella pneumoniae; Escherichia coli; global epidemiology; metallo-β-lactamases; multidrug resistance; New Delhi Metalloproteinase-1 (NDM-1); plasmidsExpert opinion: Innovation and development of new classes of antibacterial agents are critical to expand effective therapeutic options. The authors encourage the judicious use of antibiotics and aggressive infection-control measures are essential to minimize the spread of AMR.
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Affiliation(s)
- Joseph P Lynch
- Division of Pulmonary, Critical Care Medicine, Allergy, and Clinical Immunology;The David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Nina M Clark
- The Division of Infectious Diseases, Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL
| | - George G Zhanel
- Department of Medical Microbiology/Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
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Epidemiology and Transmission of Carbapenemase-Producing Enterobacteriaceae in a Health Care Network of an Acute-Care Hospital and Its Affiliated Intermediate- and Long-Term-Care Facilities in Singapore. Antimicrob Agents Chemother 2021; 65:e0258420. [PMID: 34001509 PMCID: PMC8284465 DOI: 10.1128/aac.02584-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Movement of patients in a health care network poses challenges for the control of carbapenemase-producing Enterobacteriaceae (CPE). We aimed to identify intra- and interfacility transmission events and facility type-specific risk factors of CPE in an acute-care hospital (ACH) and its intermediate-term and long-term-care facilities (ILTCFs). Serial cross-sectional studies were conducted in June and July of 2014 to 2016 to screen for CPE. Whole-genome sequencing was done to identify strain relatedness and CPE genes (blaIMI, blaIMP-1, blaKPC-2, blaNDM-1, and blaOXA-48). Multivariable logistic regression models, stratified by facility type, were used to determine independent risk factors. Of 5,357 patients, half (55%) were from the ACH. CPE prevalence was 1.3% in the ACH and 0.7% in ILTCFs (P = 0.029). After adjusting for sociodemographics, screening year, and facility type, the odds of CPE colonization increased significantly with a hospital stay of ≥3 weeks (adjusted odds ratio [aOR], 2.67; 95% confidence interval [CI], 1.17 to 6.05), penicillin use (aOR, 3.00; 95% CI, 1.05 to 8.56), proton pump inhibitor use (aOR, 3.20; 95% CI, 1.05 to 9.80), dementia (aOR, 3.42; 95% CI, 1.38 to 8.49), connective tissue disease (aOR, 5.10; 95% CI, 1.19 to 21.81), and prior carbapenem-resistant Enterobacteriaceae (CRE) carriage (aOR, 109.02; 95% CI, 28.47 to 417.44) in the ACH. For ILTCFs, presence of wounds (aOR, 5.30; 95% CI, 1.01 to 27.72), respiratory procedures (aOR, 4.97; 95% CI, 1.09 to 22.71), vancomycin-resistant enterococcus carriage (aOR, 16.42; 95% CI, 1.52 to 177.48), and CRE carriage (aOR, 758.30; 95% CI, 33.86 to 16,982.52) showed significant association. Genomic analysis revealed only possible intra-ACH transmission and no evidence for ACH-to-ILTCF transmission. Although CPE colonization was predominantly in the ACH, risk factors varied between facilities. Targeted screening and precautionary measures are warranted.
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Rossi M, Chatenoud L, Gona F, Sala I, Nattino G, D'Antonio A, Castelli D, Itri T, Morelli P, Bigoni S, Aldieri C, Martegani R, Grossi PA, Del Curto C, Piconi S, Rimoldi SG, Brambilla P, Bonfanti P, Van Hauwermeiren E, Puoti M, Gattuso G, Cerri C, Raviglione MC, Cirillo DM, Bandera A, Gori A. Characteristics and Clinical Implications of Carbapenemase-Producing Klebsiella pneumoniae Colonization and Infection, Italy. Emerg Infect Dis 2021; 27:1416-1426. [PMID: 33900910 PMCID: PMC8084501 DOI: 10.3201/eid2705.203662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We found 15-day mortality rates were higher for patients with severe infections than for those with mild infections or colonization. Klebsiella pneumoniae carbapenemase–producing K. pneumoniae (KPC-Kp) has been endemic in Italy since 2013. In a multicenter cohort study, we investigated various aspects of KPC-Kp among patients, including 15-day mortality rates and delays in adequate therapy. Most (77%) KPC-Kp strains were sequence type (ST) ST512 or ST307. During 2017, KPC-Kp prevalence was 3.26 cases/1,000 hospitalized patients. Cumulative incidence of KPC-Kp acquired >48 hours after hospital admission was 0.68% but varied widely between centers. Among patients with mild infections and noninfected colonized patients, 15-day mortality rates were comparable, but rates were much higher among patients with severe infections. Delays of >4 days in receiving adequate therapy more frequently occurred among patients with mild infections than those with severe infections, and delays were less common for patients with known previous KPC-Kp colonization. Italy urgently needs a concerted surveillance system to control the spread of KPC-Kp.
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Chen Y, Marimuthu K, Teo J, Venkatachalam I, Cherng BPZ, De Wang L, Prakki SRS, Xu W, Tan YH, Nguyen LC, Koh TH, Ng OT, Gan YH. Acquisition of Plasmid with Carbapenem-Resistance Gene bla KPC2 in Hypervirulent Klebsiella pneumoniae, Singapore. Emerg Infect Dis 2021; 26:549-559. [PMID: 32091354 PMCID: PMC7045839 DOI: 10.3201/eid2603.191230] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The convergence of carbapenem-resistance and hypervirulence genes in Klebsiella pneumoniae has led to the emergence of highly drug-resistant superbugs capable of causing invasive disease. We analyzed 556 carbapenem-resistant K. pneumoniae isolates from patients in Singapore hospitals during 2010-2015 and discovered 18 isolates from 7 patients also harbored hypervirulence features. All isolates contained a closely related plasmid (pKPC2) harboring blaKPC-2, a K. pneumoniae carbapenemase gene, and had a hypervirulent background of capsular serotypes K1, K2, and K20. In total, 5 of 7 first patient isolates were hypermucoviscous, and 6 were virulent in mice. The pKPC2 was highly transmissible and remarkably stable, maintained in bacteria within a patient with few changes for months in the absence of antimicrobial drug selection pressure. Intrapatient isolates were also able to acquire additional antimicrobial drug resistance genes when inside human bodies. Our results highlight the potential spread of carbapenem-resistant hypervirulent K. pneumoniae in Singapore.
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Liu J, Zhang L, Pan J, Huang M, Li Y, Zhang H, Wang R, Zhao M, Li B, Liu L, Gong Y, Bian J, Li X, Tang Y, Lei M, Chen D. Risk Factors and Molecular Epidemiology of Complicated Intra-Abdominal Infections With Carbapenem-Resistant Enterobacteriaceae: A Multicenter Study in China. J Infect Dis 2021; 221:S156-S163. [PMID: 32176797 DOI: 10.1093/infdis/jiz574] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacteriaceae (CRE) infections are associated with poor patient outcomes. Data on risk factors and molecular epidemiology of CRE in complicated intra-abdominal infections (cIAI) in China are limited. This study examined the risk factors of cIAI with CRE and the associated mortality based on carbapenem resistance mechanisms. METHODS In this retrospective analysis, we identified 1024 cIAI patients hospitalized from January 1, 2013 to October 31, 2018 in 14 intensive care units in China. Thirty CRE isolates were genotyped to identify β-lactamase-encoding genes. RESULTS Escherichia coli (34.5%) and Klebsiella pneumoniae (21.2%) were the leading pathogens. Patients with hospital-acquired cIAI had a lower rate of E coli (26.0% vs 49.1%; P < .001) and higher rate of carbapenem-resistant Gram-negative bacteria (31.7% vs 18.8%; P = .002) than those with community-acquired cIAI. Of the isolates, 16.0% and 23.4% of Enterobacteriaceae and K pneumoniae, respectively, were resistant to carbapenem. Most carbapenemase-producing (CP)-CRE isolates carried blaKPC (80.9%), followed by blaNMD (19.1%). The 28-day mortality was 31.1% and 9.0% in patients with CRE vs non-CRE (P < .001). In-hospital mortality was 4.7-fold higher for CP-CRE vs non-CP-CRE infection (P = .049). Carbapenem-containing combinations did not significantly influence in-hospital mortality of CP and non-CP-CRE. The risk factors for 28-day mortality in CRE-cIAI included septic shock, antibiotic exposure during the preceding 30 days, and comorbidities. CONCLUSIONS Klebsiella pneumoniae had the highest prevalence in CRE. Infection with CRE, especially CP-CRE, was associated with increased mortality in cIAI.
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Affiliation(s)
- Jiao Liu
- Department of Critical Care Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lidi Zhang
- Department of Critical Care Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingye Pan
- Department of Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical School, Wenzhou, Zhejiang, China
| | - Man Huang
- Department of Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yingchuan Li
- Department of Critical Care Medicine, Shanghai the Sixth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hongjin Zhang
- Department of Critical Care Medicine, Dongyang People's Hospital, Dongyang, Zhejiang, China
| | - Ruilan Wang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Mingyan Zhao
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjing, China
| | - Bin Li
- Department of Critical Care Medicine, the First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Long Liu
- Intensive Care Unit, The First People's Hospital of Kunshan, Kunshan, Jiangsu, China
| | - Ye Gong
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinjun Bian
- Department of Critical Care Medicine, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xiang Li
- Department of Critical Care Medicine, Minhang Hospital, Fudan University, Shanghai, China
| | - Yan Tang
- Department of Critical Care Medicine, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ming Lei
- Department of Critical Care Medicine, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dechang Chen
- Department of Critical Care Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zhang G, Zhang M, Sun F, Zhou J, Wang Y, Zhu D, Chen Z, Chen Q, Chang Q, Liu H, Chai W, Pan H. Epidemiology, mortality and risk factors for patients with K. pneumoniae bloodstream infections: Clinical impact of carbapenem resistance in a tertiary university teaching hospital of Beijing. J Infect Public Health 2020; 13:1710-1714. [PMID: 33082112 DOI: 10.1016/j.jiph.2020.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/29/2020] [Accepted: 09/05/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND This study compared the epidemiology of carbapenem-resistant (CRKP) and carbapenem-sensitive (CSKP) K. pneumoniae bloodstream infections (BSIs), and assessed risk factors for 28-day mortality of patients with K. pneumoniae BSIs. METHODS A retrospective cohort study was conducted in a 2000-bed tertiary teaching hospital of Beijing between Jan 1st 2013 to Dec 31st, 2019. All patients with K. pneumoniae BSI were identified through the Hospital Information System. The endpoints included incidence rate, mortality and risk factors for mortality of patients with K. pneumoniae BSIs. RESULTS 496 patients with K. pneumoniae BSIs were included in the analysis, with 108 CRKP BSIs. The incidence rate of K. pneumoniae BSI was 10.6 (CI: 9.7, 11.6) per 100 000 patient-days, with the rate for CRKP BSI was 2.3 (95% CI: 1.9, 2.8). The 28-day mortality was 38.0% for CRKP BSI and 8.8% for CSKP BSI, respectively. Logistic analysis showed, higher Charlson Comorbidity Index score (OR = 1.26, 95%CI 1.12-1.43, p < 0.001), respiratory failure (OR = 2.73, 95%CI1.28-5.84, p = 0.010), renal failure (OR = 4.13, 95%CI1.93-8.83, p < 0.001), septic shock (OR = 8.77, 95%CI3.60-21.32, p < 0.001), mechanical ventilation (OR = 4.41, 95%CI1.59-12.25, p = 0.004) and CRKP infection (OR = 3.04, 95%CI1.28-7.22, p = 0.012) were independently associated with 28-day mortality. CONCLUSIONS Considerable incidence rate and remarkable mortality of patients with K. pneumoniae (especially CRKP) BSI was declared in the study. Patient conditions before (higher CCI) and after presentation (respiratory failure, renal failure, septic shock), and healthcare factors (mechanical ventilation and CRKP infection) were independently associated with 28-day mortality. Understanding these risks helps better establishment of infection control strategies.
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Affiliation(s)
- Guojie Zhang
- Department of Medical Affairs, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Meng Zhang
- Department of Medical Records, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Fangyan Sun
- Department of Medical Affairs, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jiong Zhou
- Department of Medical Affairs, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yao Wang
- Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Dawei Zhu
- China Center for Health Development Studies, Peking University, Beijing 100191, China
| | - Zheng Chen
- Department of Medical Affairs, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Qian Chen
- Department of Medical Affairs, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Qing Chang
- Department of Medical Affairs, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Haimin Liu
- Department of Medical Records, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Wenzhao Chai
- Department of Medical Affairs, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Hui Pan
- Department of Medical Affairs, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.
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Lim FK, Liew YX, Cai Y, Lee W, Teo JQM, Lay WQ, Chung J, Kwa ALH. Treatment and Outcomes of Infections Caused by Diverse Carbapenemase-Producing Carbapenem-Resistant Enterobacterales. Front Cell Infect Microbiol 2020; 10:579462. [PMID: 33178629 PMCID: PMC7591786 DOI: 10.3389/fcimb.2020.579462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/28/2020] [Indexed: 01/02/2023] Open
Abstract
Background: Diverse sequence types (ST) and various carbapenemase-producing carbapenem-resistant Enterobacterales (CP-CRE) infections, which complicate treatment strategies, have emerged in Singapore. We aim to describe these CP-CRE infections and clinical outcomes according to their carbapenemase types and determine the hierarchy of predictors for mortality that are translatable to clinical practice. Methods: Clinically significant CP-CRE infections were identified in Singapore General Hospital between 2013 and 2016. Retrospectively, all clinically relevant data were retrieved from electronic medical records from the hospital. Univariate analysis was performed. To further explore the relationship between the variables and mortality in different subsets of patients with CP-CRE, we conducted recursive partitioning analysis on all study variables using the “rpart” package in R. Results: One hundred and fifty five patients were included in the study. Among them, 169 unique CP-CRE were isolated. Thirty-day all-cause in-hospital mortality was 35.5% (n = 55). There was no difference in the severity of illness, or any clinical outcomes exhibited by patients between the various carbapenemases. Root node began with patients with Acute Physical and Chronic Health Evaluation (APACHEII) score ≥ 15 (n = 98; mortality risk = 52.0%) and <15 (n = 57; mortality risk = 9.0%). Patients with APACHEII score ≥ 15 are further classified based on presence (n = 27; mortality risk = 23.0%) and absence (n = 71, mortality risk = 62.0%) of bacterial eradication. Without bacterial eradication, absence (n = 54) and presence (n = 17) of active source control yielded 70.0 and 35.0% mortality risk, respectively. Without active source control, the mortality risk was higher for the patients with non-receipt of definite combination therapy (n = 36, mortality risk = 83.0%) when compared to those who received (n = 18, mortality risk = 47.0%). Overall, the classification tree has an area under receiver operating characteristic curve of 0.92, with a sensitivity of 0.87 and specificity of 0.91. Conclusion: Different mortality risks were observed with different treatment strategies. Effective source control and microbial eradication were associated with a lower mortality rate but not active empiric therapy for CP-CRE infection. When source control was impossible, definitive antibiotic combination appeared to be associated with a reduction in mortality.
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Affiliation(s)
- Fang Kang Lim
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Yi Xin Liew
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Yiying Cai
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore.,Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Winnie Lee
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Jocelyn Q M Teo
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Wei Qi Lay
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Jasmine Chung
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Andrea L H Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore.,Department of Pharmacy, National University of Singapore, Singapore, Singapore.,Emerging Infectious Diseases Programme, Duke-National University of Singapore Medical School, Singapore, Singapore.,Singhealth Duke-National University of Singapore Medical School, Medicine Academic Clinical Programme, Singapore, Singapore
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Lalaoui R, Javelle E, Bakour S, Ubeda C, Rolain JM. Infections Due to Carbapenem-Resistant Bacteria in Patients With Hematologic Malignancies. Front Microbiol 2020; 11:1422. [PMID: 32765433 PMCID: PMC7379235 DOI: 10.3389/fmicb.2020.01422] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/02/2020] [Indexed: 12/24/2022] Open
Abstract
In developed countries, hematological malignancies (HM) account for 8 to 10% of cancers diagnosed annually and one-third of patients with HM (HMP) are expected to die from their disease. The former wide spectrum “magic bullet,” imipenem, has been ousted by the emergence of carbapenem resistant (CR) pathogens. In endemic areas, infections with CR-bacteria occur in vulnerable patients, notably in HMP, who suffer from high mortality related to infectious complications. In this work, we reviewed epidemiologic and clinical factors associated with CR-infections in adult HMP and data on CR-related mortality and antibiotic treatments in this population. We found that resistance profile of strains involved in HMP infections, mainly bacteremia, reflect local epidemiology. Significant risk factors for infections with CR-bacteria include sex male, age around 50 years old, acute leukemia, selvage chemotherapy, neutropenia, and digestive colonization by CR-bacteria. Mortality rate is high in HMP infected with CR-Enterobacteriaceae, more particularly in case of acute myeloid leukemia and unresolved neutropenia, due to inappropriate empiric management and delayed administration of targeted antibiotics, such as tigecycline, colistin, or new associations of active drugs. Thus, we developed an algorithm for clinicians, assessing the incremental risk for CR-bacterial infection occurrence and mortality in febrile HMP, to guide decisions related to empirical therapeutic strategies.
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Affiliation(s)
- Rym Lalaoui
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Emilie Javelle
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Laveran Military Teaching Hospital, Marseille, France
| | - Sofiane Bakour
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Carles Ubeda
- Centro Superior de Investigación en Salud Pública, FISABIO, Valencia, Spain.,Centers of Biomedical Research Network (CIBER), Epidemiology and Public Health, Madrid, Spain
| | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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Yavor A, Ben-Zvi H, Freeman S, Geffen Y, Adler A. Institutional Burden of Carbapenemase-Producing Enterobacterales: The Effect of Changes in Surveillance Culture Methodology. Microb Drug Resist 2020; 26:1350-1356. [PMID: 32380896 DOI: 10.1089/mdr.2019.0478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An essential part of the Israeli intervention program aimed to contain the spread of carbapenemase-producing Enterobacterales (CPE) has been the establishment of national surveillance system, where the institutional rates are determined by both clinical and surveillance cultures. The objectives of the study were to analyze the effect of changes in surveillance culture media on the rates and microbiological characteristics of CPE in a multicenter study. The rates were compared during 2 years in and between four centers. Two centers (Tel-Aviv and Beilinson) had changed their surveillance media to CHROMagar™ mSuperCARBA™ after 1 year, and two centers (Rambam and Hillel-Yaffe) had continued to use CHROMagar KPC. There was an increase in the rates of surveillance CPE in Tel-Aviv and Beilinson following the change in media, whereas the rates remained the same or declined in Rambam and Hillel-Yaffe, respectively. The rates of clinical CPE remained unchanged in Rambam and Hillel-Yaffe, declined in Tel-Aviv, and increased in Beilinson but to a lesser extent compared with the increase in surveillance CPE. The relative composition of the CPE mechanisms and species changed in Tel-Aviv, with an increase in non-Klebsiella pneumoniae species and in carbapenemase other than KPC. Our study shows that changes in surveillance media may contribute to significant changes in the rate of surveillance CPE that may be irrespective of actual epidemiological changes. Therefore, determination of institutional burden of CPE and the assessment of intervention results should be based primarily on the rate of clinical CPE rather than surveillance culture reports.
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Affiliation(s)
- Amit Yavor
- Department of Epidemiology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Haim Ben-Zvi
- Microbiology Laboratory, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Sarit Freeman
- Microbiology Laboratory, Hillel-Yaffe Medical Center, Hadera, Israel
| | - Yuval Geffen
- Microbiology Laboratory, Rambam Medical Center, Haifa, Israel
| | - Amos Adler
- Department of Epidemiology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
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Yin L, He L, Miao J, Yang W, Wang X, Ma J, Wu N, Cao Y, Wang L, Lu G, Li L, Lu C, Hu J, Zhang L, Zhao B, Zhai X, Wang C. Actively surveillance and appropriate patients placements' contact isolation dramatically decreased Carbapenem-Resistant Enterobacteriaceae infection and colonization in pediatric patients in China. J Hosp Infect 2020; 105:S0195-6701(20)30130-4. [PMID: 32243954 DOI: 10.1016/j.jhin.2020.03.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/24/2020] [Indexed: 11/23/2022]
Abstract
BACKGROUND With the increasing use of carbapenems in clinic practice, carbapenem-resistant Enterobacteriaceae (CRE) has also increased, thus posing a significant threat to human health. AIM To assess the effects of CRE colonization active screening and various CRE patient placements implemented in decreasing CRE infection risk. METHODS CRE colonization screening and various CRE patient placements were performed across CRE high-risk departments (PICU, NICU, neonatal wards and hematology departments) between 2017 and 2018, respectively. FINDING In 2018, more than 80% neonatal CRE positive patients were isolated using single room or same room isolation, and more than 50% non-neonatal patients were, with no cohort placement. The CRE nosocomial infection incidences decreased from 1.96% to 0.63% in NICU, and from 0.57% to 0.30% in neonatal wards (all P<0.05) while no significant changes were found in the other departments. The CRE colonization incidence at different length hospital stay (LOS) decreased at 8-14days and >14days LOS in CRE high-risk departments (all P<0.05). In addition, 62.5% clinical strains, 66.7% screening strains, and 74.1% nosocomial infection strains were belonged to CC17 complex group in neonatal isolates; while, 56.6%, 47.5% and 100% strains mentioned above were belonged to CC11 complex group in non-neonatal isolates respectively. The predominant carbapenemase gene was blaNDM-1 (98%) in neonatal and blaKPC-2 (70%) in non-neonatal CR-KP stains. CONCLUSIONS Active CRE colonization surveillance and CRE positive patient propriety placement may decrease the CRE infection risk. Neonatal and non-neonatal CR-KP isolates showed different CRE molecular characteristics, which could further benefit CRE infection precaution and antibiotic therapy.
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Affiliation(s)
- Lijun Yin
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Leiyan He
- The Clinical Microbiology Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Jin Miao
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Weiqing Yang
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaohua Wang
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Jian Ma
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Nana Wu
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Department of neonatal intensive care unit, Children's Hospital of Fudan University, Shanghai, China
| | - Laishuan Wang
- Department of Neonatal room, Children's Hospital of Fudan University, Shanghai, China
| | - Guoping Lu
- Department of Pediatric Intensive Care Unit, Children's Hospital of Fudan University, Shanghai, China
| | - Liling Li
- Department of Nursing Department, Children's Hospital of Fudan University, Shanghai, China
| | - Chunmei Lu
- Department of Neonatal room, Children's Hospital of Fudan University, Shanghai, China
| | - Jing Hu
- Department of Pediatric Intensive Care Unit, Children's Hospital of Fudan University, Shanghai, China
| | - Lei Zhang
- The Clinical Microbiology Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Bing Zhao
- Shanghai Pudong Center for Disease Control and Prevention, Shanghai, China
| | - Xiaowen Zhai
- Department of Hematology, Children's Hospital of Fudan University, Shanghai, China.
| | - Chuanqing Wang
- Department of Nosocomial Infection Control and the Clinical Microbiology Laboratory, Children's Hospital of Fudan University, Shanghai, China.
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Chia PY, Sengupta S, Kukreja A, S L Ponnampalavanar S, Ng OT, Marimuthu K. The role of hospital environment in transmissions of multidrug-resistant gram-negative organisms. Antimicrob Resist Infect Control 2020; 9:29. [PMID: 32046775 PMCID: PMC7014667 DOI: 10.1186/s13756-020-0685-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 01/23/2020] [Indexed: 12/12/2022] Open
Abstract
Infections by multidrug-resistant (MDR) Gram-negative organisms (GN) are associated with a high mortality rate and present an increasing challenge to the healthcare system worldwide. In recent years, increasing evidence supports the association between the healthcare environment and transmission of MDRGN to patients and healthcare workers. To better understand the role of the environment in transmission and acquisition of MDRGN, we conducted a utilitarian review based on literature published from 2014 until 2019.
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Affiliation(s)
- Po Ying Chia
- National Centre for Infectious Diseases, Jln Tan Tock Seng, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Block H, CHI Level 3, 18, Jalan Tan Tock Seng, 308442, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Nanyang, Singapore
| | - Sharmila Sengupta
- National Centre for Infectious Diseases, Jln Tan Tock Seng, Singapore
| | | | | | - Oon Tek Ng
- National Centre for Infectious Diseases, Jln Tan Tock Seng, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Block H, CHI Level 3, 18, Jalan Tan Tock Seng, 308442, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Nanyang, Singapore
| | - Kalisvar Marimuthu
- National Centre for Infectious Diseases, Jln Tan Tock Seng, Singapore. .,Department of Infectious Diseases, Tan Tock Seng Hospital, Block H, CHI Level 3, 18, Jalan Tan Tock Seng, 308442, Singapore. .,Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge Rd, Singapore.
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Ratnayake L, Ang HZ, Ong CH, Chan DSG. An optimized algorithm with improved turnaround time for detection of carbapenemase-producing Enterobacterales using the NG Test CARBA 5 in a routine laboratory. J Med Microbiol 2020; 69:228-232. [DOI: 10.1099/jmm.0.001132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lasantha Ratnayake
- Department of Laboratory Medicine, Ng Teng Fong General Hospital, 1 Jurong East Street 21, Singapore 609606
| | - Hui Zhen Ang
- Department of Laboratory Medicine, Ng Teng Fong General Hospital, 1 Jurong East Street 21, Singapore 609606
| | - Chiou Horng Ong
- Department of Laboratory Medicine, Ng Teng Fong General Hospital, 1 Jurong East Street 21, Singapore 609606
| | - Douglas Su Gin Chan
- Department of Laboratory Medicine, Ng Teng Fong General Hospital, 1 Jurong East Street 21, Singapore 609606
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40
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Cheng CWR, Ong CH, Chan DSG. Impact of BD Kiestra InoqulA streaking patterns on colony isolation and turnaround time of methicillin-resistant Staphylococcus aureus and carbapenem-resistant Enterobacterale surveillance samples. Clin Microbiol Infect 2020; 26:1201-1206. [PMID: 31935564 DOI: 10.1016/j.cmi.2020.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 11/17/2022]
Abstract
OBJECTIVES To determine if using alternative streaking patterns on the BD Kiestra InoqulA can impact colony isolation and improve turnaround time (TAT) of methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacterales (CRE) screening samples. METHODS A total of 1571 positive MRSA screening samples were studied, of which 755 screening plates were streaked by the standard pattern (4-Quadrant uniform S200) and 816 plates were streaked by an alternative pattern (Zigzag 3.5-1 S200). A total of 424 CRE-positive screening samples were studied, of which 211 screening plates were streaked by the standard pattern (Zigzag 2.5-1 inoc S200) and 213 plates were streaked by an alternative customized pattern (Zigzag 3.5-1 vertstreak s200). RESULTS There was a reduction in the number of MRSA screening plates with insufficient isolated colonies for confirmatory testing from 75 plates (9.9%) when using the standard pattern to 18 plates (2.2%) when using the alternative streaking pattern. MRSA cases with a TAT above 36 hours also reduced significantly from 144 (19.1%) to 20 (2.4%). The number of CRE screening plates with insufficient colonies for same-day confirmatory testing reduced from 16 (7.6%) when using the standard pattern to two plates (1.1%) when using the alternative customized pattern. CRE cases with a TAT above 36 hours also reduced from 16 (7.6%) to seven (3.3%). CONCLUSIONS The change in streaking patterns resulted in more plates with sufficient isolated colonies as well as reduced man-hours and materials required to perform subculture of mixed colonies and overall improvements in TAT.
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Affiliation(s)
- C W R Cheng
- Department of Laboratory Medicine, Ng Teng Fong General Hospital, Singapore.
| | - C H Ong
- Department of Laboratory Medicine, Ng Teng Fong General Hospital, Singapore
| | - D S G Chan
- Department of Laboratory Medicine, Ng Teng Fong General Hospital, Singapore
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Yam ELY, Hsu LY, Yap EPH, Yeo TW, Lee V, Schlundt J, Lwin MO, Limmathurotsakul D, Jit M, Dedon P, Turner P, Wilder-Smith A. Antimicrobial Resistance in the Asia Pacific region: a meeting report. Antimicrob Resist Infect Control 2019; 8:202. [PMID: 31890158 PMCID: PMC6921568 DOI: 10.1186/s13756-019-0654-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/14/2019] [Indexed: 01/01/2023] Open
Abstract
The Asia Pacific region, home to two-thirds of the world's population and ten of the least developed countries, is considered a regional hot-spot for the emergence and spread of antimicrobial resistance (AMR). Despite this, there is a dearth of high-quality regional data on the extent of AMR. Recognising the urgency to close this gap, Singapore organised a meeting to discuss the problems in the region and frame a call for action. Representatives from across the region and beyond attended the meeting on the "Antimicrobial Resistance in the Asia Pacific & its impact on Singapore" held in November 2018. This meeting report is a summary of the discussions on the challenges and progress in surveillance, drivers and levers of AMR emergence, and the promising innovations and technologies that could be used to combat the increasing threat of AMR in the region. Enhanced surveillance and research to provide improved evidence-based strategies and policies are needed. The major themes that emerged for an action plan are working towards a tailored solution for the region by harnessing the One Health approach, enhancing inter-country collaborations, and collaboratively leverage upon new emerging technologies. A regionally coordinated effort that is target-driven, sustainable and builds on a framework facilitating communication and governance will strengthen the fight against AMR in the Asia Pacific region.
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Affiliation(s)
- Esabelle Lo Yan Yam
- 1Centre for Global Health, Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232 Singapore
| | - Li Yang Hsu
- 2Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Eric Peng-Huat Yap
- 1Centre for Global Health, Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232 Singapore
| | - Tsin Wen Yeo
- 1Centre for Global Health, Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232 Singapore
| | - Vernon Lee
- 2Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,3Public Health Group, Ministry of Health, Singapore, Singapore
| | - Joergen Schlundt
- 4Nanyang Technological University Food Technology Centre and School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - May O Lwin
- 5Wee Kim Wee School of Communication and Information and Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Direk Limmathurotsakul
- 6Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,7Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mark Jit
- 8Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.,9Modelling and Economics Unit, Public Health England, London, UK.,10School of Public Health, University of Hong Kong, Hong Kong, SAR China
| | - Peter Dedon
- 11Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.,12Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Paul Turner
- 13Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,14Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Annelies Wilder-Smith
- 1Centre for Global Health, Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232 Singapore.,15Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK.,16Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
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Malchione MD, Torres LM, Hartley DM, Koch M, Goodman JL. Carbapenem and colistin resistance in Enterobacteriaceae in Southeast Asia: Review and mapping of emerging and overlapping challenges. Int J Antimicrob Agents 2019; 54:381-399. [DOI: 10.1016/j.ijantimicag.2019.07.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/16/2019] [Accepted: 07/21/2019] [Indexed: 01/21/2023]
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Antecedent Carbapenem Exposure as a Risk Factor for Non-Carbapenemase-Producing Carbapenem-Resistant Enterobacteriaceae and Carbapenemase-Producing Enterobacteriaceae. Antimicrob Agents Chemother 2019; 63:AAC.00845-19. [PMID: 31383670 DOI: 10.1128/aac.00845-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/01/2019] [Indexed: 11/20/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) can be mechanistically classified into carbapenemase-producing Enterobacteriaceae (CPE) and non-carbapenemase-producing carbapenem nonsusceptible Enterobacteriaceae (NCPCRE). We sought to investigate the effect of antecedent carbapenem exposure as a risk factor for NCPCRE versus CPE. Among all patients with CRE colonization and infection, we conducted a case-control study comparing patients with NCPCRE (cases) and patients with CPE (controls). The presence of carbapenemases was investigated with phenotypic tests followed by PCR for predominant carbapenemase genes. We included 843 unique patients with first-episode CRE, including 387 (45.9%) NCPCRE and 456 (54.1%) CPE. The resistance genes detected in CPEs were bla NDM (42.8%), bla KPC (38.4%), and bla OXA-48-like (12.1%). After adjusting for confounders and clustering at the institutional level, the odds of prior 30-day carbapenem exposure was three times higher among NCPCRE than CPE patients (adjusted odds ratio [aOR], 3.48; 95% confidence interval [CI], 2.39 to 5.09; P < 0.001). The odds of prior carbapenem exposure and NCPCRE detection persisted in stratified analyses by Enterobacteriaceae species (Klebsiella pneumoniae and Escherichia coli) and carbapenemase gene (bla NDM and bla KPC). CPE was associated with male gender (aOR, 1.45; 95% CI, 1.07 to 1.97; P = 0.02), intensive care unit stay (aOR, 1.84; 95% CI, 1.24 to 2.74; P = 0.003), and hospitalization in the preceding 1 year (aOR, 1.42; 95% CI, 1.01 to 2.02; P = 0.05). In a large nationwide study, antecedent carbapenem exposure was a significant risk factor for NCPCRE versus CPE, suggesting a differential effect of antibiotic selection pressure.
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Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016. J Clin Microbiol 2019; 57:JCM.00573-19. [PMID: 31315956 PMCID: PMC6711911 DOI: 10.1128/jcm.00573-19] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/08/2019] [Indexed: 12/28/2022] Open
Abstract
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. 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.
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Chua AQ, Kwa ALH, Tan TY, Legido-Quigley H, Hsu LY. Ten-year narrative review on antimicrobial resistance in Singapore. Singapore Med J 2019; 60:387-396. [PMID: 31482178 PMCID: PMC6717780 DOI: 10.11622/smedj.2019088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Antimicrobial resistance (AMR) results in drug-resistant infections that are harder to treat, subsequently leading to increased morbidity and mortality. In 2008, we reviewed the problem of AMR in Singapore, limiting our discussion to the human healthcare sector. Ten years later, we revisit this issue again, reviewing current efforts to contain it in order to understand the progress made as well as current and emerging challenges. Although a significant amount of work has been done to control AMR and improve antibiotic prescribing in Singapore, most of it has focused on the hospital setting, with mixed impact. The role of antibiotic use and AMR in food animals and the environment - and the link to human health - is better understood today. This issue of AMR encompasses both human health as well as animal/food safety, and efforts to control it will need to continually evolve to maintain or improve on current gains.
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Affiliation(s)
- Alvin Qijia Chua
- Department of Pharmacy, Singapore General Hospital, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Andrea Lay-Hoon Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Thean Yen Tan
- Duke-NUS Medical School, National University of Singapore, Singapore
- Department of Laboratory Medicine, Changi General Hospital, Singapore
| | | | - Li Yang Hsu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- National Centre for Infectious Diseases, Singapore
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Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. Nat Biotechnol 2019; 37:937-944. [PMID: 31359005 DOI: 10.1038/s41587-019-0191-2] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
Abstract
Characterization of microbiomes has been enabled by high-throughput metagenomic sequencing. However, existing methods are not designed to combine reads from short- and long-read technologies. We present a hybrid metagenomic assembler named OPERA-MS that integrates assembly-based metagenome clustering with repeat-aware, exact scaffolding to accurately assemble complex communities. Evaluation using defined in vitro and virtual gut microbiomes revealed that OPERA-MS assembles metagenomes with greater base pair accuracy than long-read (>5×; Canu), higher contiguity than short-read (~10× NGA50; MEGAHIT, IDBA-UD, metaSPAdes) and fewer assembly errors than non-metagenomic hybrid assemblers (2×; hybridSPAdes). OPERA-MS provides strain-resolved assembly in the presence of multiple genomes of the same species, high-quality reference genomes for rare species (<1%) with ~9× long-read coverage and near-complete genomes with higher coverage. We used OPERA-MS to assemble 28 gut metagenomes of antibiotic-treated patients, and showed that the inclusion of long nanopore reads produces more contiguous assemblies (200× improvement over short-read assemblies), including more than 80 closed plasmid or phage sequences and a new 263 kbp jumbo phage. High-quality hybrid assemblies enable an exquisitely detailed view of the gut resistome in human patients.
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Liu H, Jia X, Zou H, Sun S, Li S, Wang Y, Xia Y. Detection and characterization of tigecycline heteroresistance in E. cloacae: clinical and microbiological findings. Emerg Microbes Infect 2019; 8:564-574. [PMID: 30945610 PMCID: PMC6455127 DOI: 10.1080/22221751.2019.1601031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tigecycline is regarded as a last-resort treatment for carbapenem-resistant Enterobacteriaceae (CRE), however, the emergence of tigecycline heteroresistance has posted the therapeutic challenge to combat this “nightmare bacteria”. The primary purpose of this study was to demonstrate the existence of tigecycline heteroresistance in carbapenem-resistant E. cloacae (TH-CRECL) and further to explore the epidemiological characteristics and underlying molecular mechanisms. Our study identified a relative low prevalence of carbapenem-resistant E. cloacae (CRECL) isolates, about 20.0% (28/140), as heteroresistance to tigecycline. Molecular genetic relatedness of these heteroresistant isolates were characterized epidemiologically sporadic. In addition, mechanistic analysis revealed that Phe-Arg-β-naphthylamide (PAβN) significantly reversed tigecycline MIC levels of resistant colonies in heteroresistant strains, as primarily related to the marked overproduction of efflux pump genes acrAB and oqxAB, as well as overexpression of transcriptional regulators (soxS and ramA). Moreover, logistic regression analysis showed that previous fluoroquinolone therapy was identified as the only potential independent risk factor for the acquisition of TH-CRECL. Most importantly, our data indicated that patients with TH-CRECL infection might lead to a remarkably prolonged hospital stay and deterioration in functional status. These findings emphasized the necessity of timely detection and intervention of patients infected with TH-CRECL.
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Affiliation(s)
- Hang Liu
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Xiaojiong Jia
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Hua Zou
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Shan Sun
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Shuang Li
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Yonghong Wang
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Yun Xia
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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Goudarzi H, Mirsamadi ES, Ghalavand Z, Hakemi Vala M, Mirjalali H, Hashemi A. Rapid detection and molecular survey of blaVIM, blaIMP and blaNDM genes among clinical isolates of Acinetobacter baumannii using new multiplex real-time PCR and melting curve analysis. BMC Microbiol 2019; 19:122. [PMID: 31182026 PMCID: PMC6558830 DOI: 10.1186/s12866-019-1510-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 06/03/2019] [Indexed: 11/15/2022] Open
Abstract
Background Acinetobacter baumannii is a cosmopolitan bacterium that is frequently reported from hospitalized patients, especially those patients who admitted in the intensive care unit. Recently, multiplex real-time PCR has been introduced for rapid detection of the resistance genes in clinical isolates of bacteria. The current study aimed to develop and evaluate multiplex real-time PCR to detect common resistance genes among clinical isolates of A. baumannii. Results Multiplex real-time PCR based on melting curve analysis showed different Tm corresponding to the amplified fragment consisted of 83.5 °C, 93.3 °C and 89.3 °C for blaIMP, blaVIM and blaNDM, respectively. Results of multiplex real-time PCR showed that the prevalence of blaIMP, blaVIM and blaNDM among the clinical isolates of A. baumannii were 5/128(3.9%), 9/128(7.03%) and 0/128(0%), respectively. Multiplex real-time PCR was able to simultaneously identify the resistance genes, while showed 100% concordance with the results of conventional PCR. Conclusions The current study showed that blaVIM, was the most prevalent MBL gene among the clinical isolates of A. baumannii while no amplification of blaNDM was seen. Multiplex real-time PCR can be sensitive and reliable technique for rapid detection of resistance genes in clinical isolates.
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Affiliation(s)
- Hossein Goudarzi
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elnaz Sadat Mirsamadi
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran. .,Department of Microbiology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Zohreh Ghalavand
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojdeh Hakemi Vala
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamed Mirjalali
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Hashemi
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Chotiprasitsakul D, Srichatrapimuk S, Kirdlarp S, Pyden AD, Santanirand P. Epidemiology of carbapenem-resistant Enterobacteriaceae: a 5-year experience at a tertiary care hospital. Infect Drug Resist 2019; 12:461-468. [PMID: 30863128 PMCID: PMC6390851 DOI: 10.2147/idr.s192540] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Purpose The incidence of carbapenem-resistant Enterobacteriaceae (CRE) has been increasing worldwide. Ertapenem resistance is mediated by non-carbapenemase mechanisms, and has less of an effect on susceptibility to imipenem and meropenem. This study aimed to study the epidemiology of CRE, and to compare risk factors and related mortality between non-susceptibility to ertapenem alone Enterobacteriaceae (NSEE), with non-susceptibility to other carbapenems (imipenem, meropenem, or doripenem) Enterobacteriaceae (NSOCE) at a tertiary care hospital in Thailand. Methods All CRE isolated were identified between December 2011 and December 2016. Quarterly incidence rate was estimated. Hospital-wide carbapenem consumption was calculated as defined daily doses (DDD). Relationships between hospital-wide carbapenem consumption and incidence of CRE were tested. Factors associated with NSEE and NSOCE, and risk factors associated with 14- and 30-day mortality in patients with CRE infection were determined. Results The quarterly CRE incidence increased significantly from 3.37 per 100,000 patient-days in the last quarter of 2011 to 32.49 per 100,000 patient-days in the last quarter of 2016. (P for trend <0.001). Quarterly hospital-wide carbapenem consumption increased 1.58 DDD per 1,000 patient-days (P for trend=0.004). The Poisson regression showed the expected increase of CRE incidence was 1.02 per 100,000 patient-days for a 1 DDD per 1,000 patient-days increase in carbapenem consumption (P<0.001). There were 40 patients with NSEE and 134 patients with NSOCE in the 5-year study period. The NSEE group had significantly lower carbapenem exposure compared with the NSOCE group (adjusted odds ratio: 0.25; P=0.001). No difference in 14-day and 30-day all-cause mortality between the two groups was observed. Conclusion The incidence of CRE has risen significantly at our institution. Previous carbapenem use was associated with NSOCE. This hospital-wide carbapenem use was significantly associated with the increasing incidence of CRE.
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Affiliation(s)
- Darunee Chotiprasitsakul
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand,
| | - Sirawat Srichatrapimuk
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samutprakan, Thailand
| | - Suppachok Kirdlarp
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand,
| | - Alexander D Pyden
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Pitak Santanirand
- Clinical Microbiology Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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Lee SY, Octavia S, Chew KL. Detection of OXA-carbapenemase-producing Enterobacteriaceae with chromID CARBA SMART screening plate. Pathology 2019; 51:108-110. [DOI: 10.1016/j.pathol.2018.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/28/2018] [Accepted: 08/31/2018] [Indexed: 11/28/2022]
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