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Liu C, Dong N, Zhang Y, Sun Q, Huang Y, Cai C, Chen G, Zhang R. Phenotypic and genomic characteristics of clinical IMP-producing Klebsiella spp. Isolates in China. COMMUNICATIONS MEDICINE 2024; 4:25. [PMID: 38383740 PMCID: PMC10881498 DOI: 10.1038/s43856-024-00439-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND IMP-producing Klebsiella spp. (IMPKsp) strains have spread globally, including in China. Currently, the prevalence and genomic characterization of IMPKsp is largely unknown nationwide. Here we aimed to provide a general overview of the phenotypic and genomic characteristics of IMPKsp strains. METHODS 61 IMPKsp strains were obtained from 13 provinces in China during 2016-2021. All strains were tested for their susceptibility to antimicrobial agents by the microdilution broth method and sequenced with Illumina next-generation sequencing. We performed conjugation experiments on thirteen representative strains which were also sequenced by Oxford nanopore sequencing technology to characterize blaIMP-encoding plasmids. RESULTS We find that all IMPKsp strains display multidrug-resistant (MDR) phenotypes. All strains belong to 27 different STs. ST307 emerges as a principal IMP-producing sublineage. blaIMP-4 is found to be the major isoform, followed by blaIMP-38. Seven incompatibility types of blaIMP-encoding plasmids are identified, including IncHI5 (32/61, 52.5%), IncN-IncR (10/61, 16.4%), IncFIB(K)-HI1B (7/61, 11.5%), IncN (5/61, 8.2%), IncN-IncFII (2/61, 3.3%), IncFII (1/61, 1.6%) and IncP (1/61, 1.6%). The strains carrying IncHI5 and IncN plasmids belong to diverse ST types, indicating that these two plasmids may play an important role in the transmission of blaIMP genes among Klebsiella spp. strains. CONCLUSIONS Our results highlight that multi-clonal transmission, multiple genetic environments and plasmid types play a major role in the dissemination process of blaIMP genes among Klebsiella spp. IncHI5 type plasmids have the potential to be the main vectors mediating the spread of the blaIMP genes in Klebsiella spp.
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Affiliation(s)
- Congcong Liu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Ning Dong
- Department of Medical Microbiology, School of Biology and Basic Medical Science, Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Yanyan Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Qiaoling Sun
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Yonglu Huang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Chang Cai
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Gongxiang Chen
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.
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Pitout JDD, Peirano G, Matsumura Y, DeVinney R, Chen L. Escherichia coli sequence type 410 with carbapenemases: a paradigm shift within E. coli toward multidrug resistance. Antimicrob Agents Chemother 2024; 68:e0133923. [PMID: 38193668 PMCID: PMC10869336 DOI: 10.1128/aac.01339-23] [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] [Indexed: 01/10/2024] Open
Abstract
Escherichia coli sequence type ST410 is an emerging carbapenemase-producing multidrug-resistant (MDR) high-risk One-Health clone with the potential to significantly increase carbapenem resistance among E. coli. ST410 belongs to two clades (ST410-A and ST410-B) and three subclades (ST410-B1, ST410-B2, and ST410-B3). After a fimH switch between clades ST410-A and ST410-B1, ST410-B2 and ST410-B3 subclades showed a stepwise progression toward developing MDR. (i) ST410-B2 initially acquired fluoroquinolone resistance (via homologous recombination) in the 1980s. (ii) ST410-B2 then obtained CMY-2, CTX-M-15, and OXA-181 genes on different plasmid platforms during the 1990s. (iii) This was followed by the chromosomal integration of blaCMY-2, fstl YRIN insertion, and ompC/ompF mutations during the 2000s to create the ST410-B3 subclade. (iv) An IncF plasmid "replacement" scenario happened when ST410-B2 transformed into ST410-B3: F36:31:A4:B1 plasmids were replaced by F1:A1:B49 plasmids (both containing blaCTX-M-15) followed by blaNDM-5 incorporation during the 2010s. User-friendly cost-effective methods for the rapid identification of ST410 isolates and clades are needed because limited data are available about the frequencies and global distribution of ST410 clades. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST410 (including the ability to acquire successive MDR determinants). Such information will aid with management and prevention strategies to curb the spread of carbapenem-resistant E. coli. The medical community can ill afford to ignore the spread of a global E. coli clone with the potential to end the carbapenem era.
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Affiliation(s)
- Johann D. D. Pitout
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Yasufumi Matsumura
- Kyoto University Graduate School of Medicine, Pretoria, Gauteng, South Africa
| | | | - Liang Chen
- Meridian Health Center for Discovery and Innovation, Kyoto, Japan
- Hackensack Meridian School of Medicine at Seton Hall University, Nutley, New Jersey, USA
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Magobo RE, Ismail H, Lowe M, Strasheim W, Mogokotleng R, Perovic O, Kwenda S, Ismail A, Makua M, Bore A, Phayane R, Naidoo H, Dennis T, Ngobese M, Wijnant W, Govender NP. Outbreak of NDM-1- and OXA-181-Producing Klebsiella pneumoniae Bloodstream Infections in a Neonatal Unit, South Africa. Emerg Infect Dis 2023; 29:1531-1539. [PMID: 37486166 PMCID: PMC10370860 DOI: 10.3201/eid2908.230484] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
After an increase in carbapenem-resistant Klebsiella pneumoniae (CRKP) bloodstream infections and associated deaths in the neonatal unit of a South Africa hospital, we conducted an outbreak investigation during October 2019-February 2020 and cross-sectional follow-up during March 2020-May 2021. We used genomic and epidemiologic data to reconstruct transmission networks of outbreak-related clones. We documented 31 cases of culture-confirmed CRKP infection and 14 deaths. Two outbreak-related clones (blaNDM-1 sequence type [ST] 152 [n = 16] and blaOXA-181 ST307 [n = 6]) cocirculated. The major clone blaNDM-1 ST152 accounted for 9/14 (64%) deaths. Transmission network analysis identified possible index cases of blaOXA-181 ST307 in October 2019 and blaNDM-1 ST152 in November 2019. During the follow-up period, 11 new cases of CRKP infection were diagnosed; we did not perform genomic analysis. Sustained infection prevention and control measures, adequate staffing, adhering to bed occupancy limits, and antimicrobial stewardship are key interventions to control such outbreaks.
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Carbapenemase-Producing Klebsiella pneumoniae in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types. Antibiotics (Basel) 2023; 12:antibiotics12010107. [PMID: 36671308 PMCID: PMC9854421 DOI: 10.3390/antibiotics12010107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/23/2022] [Accepted: 12/30/2022] [Indexed: 01/10/2023] Open
Abstract
During the COVID-19 pandemic, intensive care units (ICUs) operated at or above capacity, and the number of ICU patients coinfected by nosocomial microorganisms increased. Here, we characterize the population structure and resistance mechanisms of carbapenemase-producing Klebsiella pneumoniae (CP-Kpn) from COVID-19 ICU patients and compare them to pre-pandemic populations of CP-Kpn. We analyzed 84 CP-Kpn isolates obtained during the pandemic and 74 CP-Kpn isolates obtained during the pre-pandemic period (2019) by whole genome sequencing, core genome multilocus sequence typing, plasmid reconstruction, and antibiotic susceptibility tests. More CP-Kpn COVID-19 isolates produced OXA-48 (60/84, 71.4%) and VIM-1 (18/84, 21.4%) than KPC (8/84, 9.5%). Fewer pre-pandemic CP-Kpn isolates produced VIM-1 (7/74, 9.5%). Cefiderocol (97.3-100%) and plazomicin (97.5-100%) had the highest antibiotic activity against pandemic and pre-pandemic isolates. Sequence type 307 (ST307) was the most widely distributed ST in both groups. VIM-1-producing isolates belonging to ST307, ST17, ST321 and ST485, (STs infrequently associated to VIM-1) were detected during the COVID-19 period. Class 1 integron Int1-blaVIM-1-aac(6')-1b-dfrB1-aadAI-catB2-qacEΔ1/sul1, found on an IncL plasmid of approximately 70,000 bp, carried blaVIM-1 in ST307, ST17, ST485, and ST321 isolates. Thus, CP-Kpn populations from pandemic and pre-pandemic periods have similarities. However, VIM-1 isolates associated with atypical STs increased during the pandemic, which warrants additional monitoring and surveillance.
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Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122077. [PMID: 36556442 PMCID: PMC9780897 DOI: 10.3390/life12122077] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Multiresistant Escherichia coli has been disseminated worldwide, and it is one of the major causative agents of nosocomial infections. E. coli has a remarkable and complex genomic plasticity for taking up and accumulating genetic elements; thus, multiresistant high-risk clones can evolve. In this review, we summarise all available data about internationally disseminated extraintestinal pathogenic high-risk E. coli clones based on whole-genome sequence (WGS) data and confirmed outbreaks. Based on genetic markers, E. coli is clustered into eight phylogenetic groups. Nowadays, the E. coli ST131 clone from phylogenetic group B2 is the predominant high-risk clone worldwide. Currently, strains of the C1-M27 subclade within clade C of ST131 are circulating and becoming prominent in Canada, China, Germany, Hungary and Japan. The C1-M27 subclade is characterised by blaCTX-M-27. Recently, the ST1193 clone has been reported as an emerging high-risk clone from phylogenetic group B2. ST38 clone carrying blaOXA-244 (a blaOXA-48-like carbapenemase gene) caused several outbreaks in Germany and Switzerland. Further high-risk international E. coli clones include ST10, ST69, ST73, ST405, ST410, ST457. High-risk E. coli strains are present in different niches, in the human intestinal tract and in animals, and persist in environment. These strains can be transmitted easily within the community as well as in hospital settings. WGS analysis is a useful tool for tracking the dissemination of resistance determinants, the emergence of high-risk mulitresistant E. coli clones and to analyse changes in the E. coli population on a genomic level.
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Chen L, Peirano G, Kreiswirth BN, Devinney R, Pitout JDD. Acquisition of genomic elements were pivotal for the success of Escherichia coli ST410. J Antimicrob Chemother 2022; 77:3399-3407. [PMID: 36204996 PMCID: PMC10205468 DOI: 10.1093/jac/dkac329] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/05/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Escherichia coli ST410 is an emerging MDR clone linked to blaCTX-M-15 and blaOXA-181. Limited comprehensive data about the global distribution of ST410 clades and mobile genetic elements associated with different β-lactamases are available. METHODS Short- and long-read WGS were performed on a collection of ST410 producing carbapenemases (n = 45) obtained from 11 countries. The evolutionary history of global E. coli ST410 was also investigated. RESULTS OXA-181 and NDM-5 were the most frequent carbapenemases and used different underlying strategies to ensure their successful association with ST410 clades. Our phylogenetic analysis of publicly available ST410 genomes amended the previously published ST410 B subclades: ST410-B1 is identical to B1/H24, ST410-B2 includes B2/H24R and B3/H24Rx, while ST410-B3 corresponds to B4/H24RxC. Long-read WGS identified the following genomic events that likely shaped the evolution of ST410-B3: (i) gyrA and parC mutations were acquired via homologous recombination events; (ii) chromosomal integration of blaCMY-2 among ST410-B3; (iii) the emergence of ST410-B3 from ST410-B2 was accompanied by the replacement of IncFII plasmids harbouring blaCTX-M-15 (i.e. F36:31:A4:B1 in ST410-B2 with F1:A1:B49 plasmids in ST410-B3); and (iv) the NDM-5 gene was integrated within F1:A1:B49 plasmids over time. CONCLUSIONS The global ST410 population producing carbapenemases is dominated by the ST410-B2 and B3 subclades with varied geographical distribution that requires ongoing genomic surveillance. We provided an updated timeline of pivotal genomic events that have shaped the success of the ST410-B3 subclade.
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Affiliation(s)
- Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Gisele Peirano
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, T2L 2K8 Calgary, Alberta, Canada
| | - Barry N Kreiswirth
- Hackensack Meridian Health Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Rebekah Devinney
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, T2L 2K8 Calgary, Alberta, Canada
| | - Johann D D Pitout
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, T2L 2K8 Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
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OXA-48-Like β-Lactamases: Global Epidemiology, Treatment Options, and Development Pipeline. Antimicrob Agents Chemother 2022; 66:e0021622. [PMID: 35856662 PMCID: PMC9380527 DOI: 10.1128/aac.00216-22] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Modern medicine is threatened by the rising tide of antimicrobial resistance, especially among Gram-negative bacteria, where resistance to β-lactams is most often mediated by β-lactamases. The penicillin and cephalosporin ascendancies were, in their turn, ended by the proliferation of TEM penicillinases and CTX-M extended-spectrum β-lactamases. These class A β-lactamases have long been considered the most important. For carbapenems, however, the threat is increasingly from the insidious rise of a class D carbapenemase, OXA-48, and its close relatives. Over the past 20 years, OXA-48 and "OXA-48-like" enzymes have proliferated to become the most prevalent enterobacterial carbapenemases across much of Europe, Northern Africa, and the Middle East. OXA-48-like enzymes are notoriously difficult to detect because they often cause only low-level in vitro resistance to carbapenems, meaning that the true burden is likely underestimated. Despite this, they are associated with carbapenem treatment failures. A highly conserved incompatibility complex IncL plasmid scaffold often carries blaOXA-48 and may carry other antimicrobial resistance genes, leaving limited treatment options. High conjugation efficiency means that this plasmid is sometimes carried by multiple Enterobacterales in a single patient. Producers evade most β-lactam-β-lactamase inhibitor combinations, though promising agents have recently been licensed, notably ceftazidime-avibactam and cefiderocol. The molecular machinery enabling global spread, current treatment options, and the development pipeline of potential new therapies for Enterobacterales that produce OXA-48-like β-lactamases form the focus of this review.
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Carbapenem-resistant Enterobacterales in patients with bacteraemia at tertiary academic hospitals in South Africa, 2019 - 2020: An update. S Afr Med J 2022; 112:542-552. [DOI: 10.7196/samj.2022.v112i8.16351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Indexed: 11/08/2022] Open
Abstract
Background. The emergence of carbapenem-resistant Enterobacterales (CRE) has become a serious and significant public health threat worldwide, owing to the limited antimicrobial therapy options, and the elevated mortality rates associated with these infections.Objectives. To present an update on the epidemiology of CRE bloodstream infections among hospitalised patients reported under the Group for Enteric, Respiratory and Meningeal Diseases Surveillance in South Africa (GERMS-SA) between January 2019 and December 2020. Methods. Patients of all ages with CRE bacteraemia were included and isolates, when available, were sent to the reference laboratory for confirmatory testing and molecular characterisation. Multivariable logistic regression analysis was performed to assess factors associated with in-hospital mortality.
Results. We included 2 144 patients with CRE bacteraemia with a median age of 33 (interquartile range 1 - 51) years, of whom 1 145 (54.2%) were male. Klebsiella pneumoniae accounted for 79.8% of infections (n=863/1 082), of which 89.5% (n=611/683) were healthcare associated (HA). The most common carbapenemase genes were carbapenem-hydrolysing oxacillinase-48 (blaOXA-48-like) (76.8%; n=761/991), New Delhi metallo-β-lactamase (blaNDM) (21.1%; n=209/991) and Verona integron-encoded metallo-β-lactamase (blaVIM) (1.3%; n=13/991). None of the screened isolates with a colistin minimum inhibitory concentration >2 μg/mL harboured the mobilised colistin resistance (mcr)-1 to mcr-5 genes. The crude in-hospital mortality rate was 36.6% (n=377/1 029). Patients aged ≥60 years (v. 1.6 - 9 years) (adjusted odds ratio (aOR) 4.53; 95% confidence interval (CI) 2.21 - 9.28), those with comorbidities (diabetes, malignancy, renal and/or cardiovascular failure) (aOR 1.72; 95% CI 1.17 - 2.52), those with altered mental state (aOR 5.36; 95% CI 3.21 - 8.92) and those with previous antimicrobial use (aOR 1.88; 95% CI 1.27 - 2.77) had increased odds of in-hospital mortality.
Conclusion. The epidemiology of CRE bloodstream infections remained similar compared with the previous surveillance report. Most infections were HA and caused by OXA-48-like carbapenemase-producing K. pneumoniae with no plasmid-mediated colistin resistance. Standard infection control measures should be strengthened.
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Håkonsholm F, Hetland MA, Svanevik CS, Lunestad BT, Löhr IH, Marathe NP. Insights into the genetic diversity, antibiotic resistance and pathogenic potential of Klebsiella pneumoniae from the Norwegian marine environment using whole-genome analysis. Int J Hyg Environ Health 2022; 242:113967. [DOI: 10.1016/j.ijheh.2022.113967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/25/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023]
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Shropshire WC, Dinh AQ, Earley M, Komarow L, Panesso D, Rydell K, Gómez-Villegas SI, Miao H, Hill C, Chen L, Patel R, Fries BC, Abbo L, Cober E, Revolinski S, Luterbach CL, Chambers H, Fowler VG, Bonomo RA, Shelburne SA, Kreiswirth BN, van Duin D, Hanson BM, Arias CA. Accessory Genomes Drive Independent Spread of Carbapenem-Resistant Klebsiella pneumoniae Clonal Groups 258 and 307 in Houston, TX. mBio 2022; 13:e0049722. [PMID: 35357213 PMCID: PMC9040855 DOI: 10.1128/mbio.00497-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 12/23/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKp) is an urgent public health threat. Worldwide dissemination of CRKp has been largely attributed to clonal group (CG) 258. However, recent evidence indicates the global emergence of a CRKp CG307 lineage. Houston, TX, is the first large city in the United States with detected cocirculation of both CRKp CG307 and CG258. We sought to characterize the genomic and clinical factors contributing to the parallel endemic spread of CG258 and CG307. CRKp isolates were collected as part of the prospective, Consortium on Resistance against Carbapenems in Klebsiella and other Enterobacterales 2 (CRACKLE-2) study. Hybrid short-read and long-read genome assemblies were generated from 119 CRKp isolates (95 originated from Houston hospitals). A comprehensive characterization of phylogenies, gene transfer, and plasmid content with pan-genome analysis was performed on all CRKp isolates. Plasmid mating experiments were performed with CG307 and CG258 isolates of interest. Dissection of the accessory genomes suggested independent evolution and limited horizontal gene transfer between CG307 and CG258 lineages. CG307 contained a diverse repertoire of mobile genetic elements, which were shared with other non-CG258 K. pneumoniae isolates. Three unique clades of Houston CG307 isolates clustered distinctly from other global CG307 isolates, indicating potential selective adaptation of particular CG307 lineages to their respective geographical niches. CG307 strains were often isolated from the urine of hospitalized patients, likely serving as important reservoirs for genes encoding carbapenemases and extended-spectrum β-lactamases. Our findings suggest parallel cocirculation of high-risk lineages with potentially divergent evolution. IMPORTANCE The prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKp) infections in nosocomial settings remains a public health challenge. High-risk clones such as clonal group 258 (CG258) are particularly concerning due to their association with blaKPC carriage, which can severely complicate antimicrobial treatments. There is a recent emergence of clonal group 307 (CG307) worldwide with little understanding of how this successful clone has been able to adapt while cocirculating with CG258. We provide the first evidence of potentially divergent evolution between CG258 and CG307 with limited sharing of adaptive genes. Houston, TX, is home to the largest medical center in the world, with a large influx of domestic and international patients. Thus, our unique geographical setting, where two pandemic strains of CRKp are circulating, provides an indication of how differential accessory genome content can drive stable, endemic populations of CRKp. Pan-genomic analyses such as these can reveal unique signatures of successful CRKp dissemination, such as the CG307-associated plasmid (pCG307_HTX), and provide invaluable insights into the surveillance of local carbapenem-resistant Enterobacterales (CRE) epidemiology.
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Affiliation(s)
- William C. Shropshire
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, Texas, USA
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - An Q. Dinh
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
| | - Michelle Earley
- The Biostatistics Center, The George Washington University, Rockville, Maryland, USA
| | - Lauren Komarow
- The Biostatistics Center, The George Washington University, Rockville, Maryland, USA
| | - Diana Panesso
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
| | - Kirsten Rydell
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
| | - Sara I. Gómez-Villegas
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
| | - Hongyu Miao
- Department of Biostatistics and Data Science, School of Public Health, University of Texas Health Science Center, Houston, Texas, USA
| | - Carol Hill
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Bettina C. Fries
- Department of Medicine, Infectious Disease Division, Stony Brook University, Stony Brook, New York, USA
- Veteran’s Administration Medical Center, Northport, New York, USA
| | - Lilian Abbo
- Division of Infectious Diseases, Department of Medicine, University of Miami Miller School of Medicine and Jackson Health System, Miami, Florida, USA
| | - Eric Cober
- Department of Infectious Diseases, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sara Revolinski
- School of Pharmacy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Courtney L. Luterbach
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Raleigh, North Carolina, USA
| | - Henry Chambers
- Department of Medicine, University of California San Francisco, San Francisco, USA
| | - Vance G. Fowler
- Division of Infectious Diseases, Duke University, Durham, North Carolina, USA
| | - Robert A. Bonomo
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
| | - Samuel A. Shelburne
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Barry N. Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Raleigh, North Carolina, USA
| | - Blake M. Hanson
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, Texas, USA
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - Cesar A. Arias
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
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Peirano G, Chen L, Nobrega D, Finn TJ, Kreiswirth BN, DeVinney R, Pitout JDD. Genomic Epidemiology of Global Carbapenemase-Producing Escherichia coli, 2015-2017. Emerg Infect Dis 2022; 28. [PMID: 35451367 PMCID: PMC9045447 DOI: 10.3201/eid2805.212535] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We describe the global molecular epidemiology of 229 carbapenemase-producing Escherichia coli in 36 countries during 2015-2017. Common carbapenemases were oxacillinase (OXA) 181 (23%), New Delhi metallo-β-lactamase (NDM) 5 (20%), OXA-48 (17%), Klebsiella pneumoniae carbapenemase 2 (15%), and NDM-1 (10%). We identified 5 dominant sequence types (STs); 4 were global (ST410, ST131, ST167, and ST405), and 1 (ST1284) was limited to Turkey. OXA-181 was frequent in Jordan (because of the ST410-B4/H24RxC subclade) and Turkey (because of ST1284). We found nearly identical IncX3-blaOXA-181 plasmids among 11 STs from 12 countries. NDM-5 was frequent in Egypt, Thailand (linked with ST410-B4/H24RxC and ST167-B subclades), and Vietnam (because of ST448). OXA-48 was common in Turkey (linked with ST11260). Global K. pneumoniae carbapenemases were linked with ST131 C1/H30 subclade and NDM-1 with various STs. The global carbapenemase E. coli population is dominated by diverse STs with different characteristics and varied geographic distributions, requiring ongoing genomic surveillance.
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12
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Charalampous T, Alcolea-Medina A, Snell LB, Williams TGS, Batra R, Alder C, Telatin A, Camporota L, Meadows CIS, Wyncoll D, Barrett NA, Hemsley CJ, Bryan L, Newsholme W, Boyd SE, Green A, Mahadeva U, Patel A, Cliff PR, Page AJ, O'Grady J, Edgeworth JD. Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units. Genome Med 2021; 13:182. [PMID: 34784976 PMCID: PMC8594956 DOI: 10.1186/s13073-021-00991-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 10/14/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity. METHODS CMg using nanopore sequencing was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave. RESULTS An 8-h CMg workflow was 92% sensitive (95% CI, 75-99%) and 82% specific (95% CI, 57-96%) for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of β-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from 4 positive and 39 negative samples. Molecular typing using 24-h sequencing data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak involving 14 patients across three ICUs. CONCLUSION CMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg.
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Affiliation(s)
- Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Infection Sciences, Viapath, St Thomas' Hospital, London, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Tom G S Williams
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Christopher Alder
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Luigi Camporota
- Critical Care Directorate, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | | | - Duncan Wyncoll
- Critical Care Directorate, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Nicholas A Barrett
- Critical Care Directorate, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Carolyn J Hemsley
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Lisa Bryan
- Infection Sciences, Viapath, St Thomas' Hospital, London, UK
| | - William Newsholme
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Sara E Boyd
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Anna Green
- Department of Cellular Pathology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Ula Mahadeva
- Department of Cellular Pathology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Amita Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | | | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Justin O'Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK.
- Infection Sciences, Viapath, St Thomas' Hospital, London, UK.
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK.
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13
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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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Labi AK, Nielsen KL, Marvig RL, Bjerrum S, Enweronu-Laryea C, Bennedbæk M, Newman MJ, Ayibor PK, Andersen LP, Kurtzhals JAL. Oxacillinase-181 Carbapenemase-Producing Klebsiella pneumoniae in Neonatal Intensive Care Unit, Ghana, 2017-2019. Emerg Infect Dis 2021; 26:2235-2238. [PMID: 32818427 PMCID: PMC7454046 DOI: 10.3201/eid2609.200562] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We sequenced 29 carbapenemase-producing Klebsiella pneumoniae isolates from a neonatal intensive care unit in Ghana. Twenty-eight isolates were sequence type 17 with blaOXA-181 and differed by 0–32 single-nucleotide polymorphisms. Improved surveillance and infection control are needed to characterize and curb the spread of multidrug-resistant organisms in sub-Saharan Africa.
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15
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Ma P, He LL, Pironti A, Laibinis HH, Ernst CM, Manson AL, Bhattacharyya RP, Earl AM, Livny J, Hung DT. Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics. eLife 2021; 10:e67310. [PMID: 33871353 PMCID: PMC8079144 DOI: 10.7554/elife.67310] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/15/2021] [Indexed: 02/07/2023] Open
Abstract
In this era of rising antibiotic resistance, in contrast to our increasing understanding of mechanisms that cause resistance, our understanding of mechanisms that influence the propensity to evolve resistance remains limited. Here, we identified genetic factors that facilitate the evolution of resistance to carbapenems, the antibiotic of 'last resort', in Klebsiella pneumoniae, the major carbapenem-resistant species. In clinical isolates, we found that high-level transposon insertional mutagenesis plays an important role in contributing to high-level resistance frequencies in several major and emerging carbapenem-resistant lineages. A broader spectrum of resistance-conferring mutations for select carbapenems such as ertapenem also enables higher resistance frequencies and, importantly, creates stepping-stones to achieve high-level resistance to all carbapenems. These mutational mechanisms can contribute to the evolution of resistance, in conjunction with the loss of systems that restrict horizontal resistance gene uptake, such as the CRISPR-Cas system. Given the need for greater antibiotic stewardship, these findings argue that in addition to considering the current efficacy of an antibiotic for a clinical isolate in antibiotic selection, considerations of future efficacy are also important. The genetic background of a clinical isolate and the exact antibiotic identity can and should also be considered as they are determinants of a strain's propensity to become resistant. Together, these findings thus provide a molecular framework for understanding acquisition of carbapenem resistance in K. pneumoniae with important implications for diagnosing and treating this important class of pathogens.
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Affiliation(s)
- Peijun Ma
- The Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Molecular Biology, Massachusetts General HospitalBostonUnited States
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Center for Computational and Integrative Biology, Massachusetts General HospitalBostonUnited States
| | - Lorrie L He
- The Broad Institute of MIT and HarvardCambridgeUnited States
| | | | | | - Christoph M Ernst
- The Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Molecular Biology, Massachusetts General HospitalBostonUnited States
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Center for Computational and Integrative Biology, Massachusetts General HospitalBostonUnited States
| | | | - Roby P Bhattacharyya
- The Broad Institute of MIT and HarvardCambridgeUnited States
- Division of Infectious Diseases, Massachusetts General HospitalBostonUnited States
| | - Ashlee M Earl
- The Broad Institute of MIT and HarvardCambridgeUnited States
| | - Jonathan Livny
- The Broad Institute of MIT and HarvardCambridgeUnited States
| | - Deborah T Hung
- The Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Molecular Biology, Massachusetts General HospitalBostonUnited States
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Center for Computational and Integrative Biology, Massachusetts General HospitalBostonUnited States
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16
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High Prevalence of Carbapenemase-Producing Acinetobacter baumannii in Wound Infections, Ghana, 2017/2018. Microorganisms 2021; 9:microorganisms9030537. [PMID: 33807838 PMCID: PMC7998214 DOI: 10.3390/microorganisms9030537] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 01/01/2023] Open
Abstract
Three years after a prospective study on wound infections in a rural hospital in Ghana revealed no emergence of carbapenem-resistant bacteria we initiated a new study to assess the prevalence of multidrug-resistant pathogens. Three hundred and one samples of patients with wound infections were analysed for the presence of resistant bacteria in the period August 2017 till March 2018. Carbapenem-resistant Acinetobacter (A.) baumannii were further characterized by resistance gene sequencing, PCR-based bacterial strain typing, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST “Oxford scheme”). A. baumanni was detected in wound infections of 45 patients (15%); 22 isolates were carbapenem-resistant. Carbapenemases NDM-1 and/or OXA-23 were detected in all isolates; two isolates harboured additionally OXA-420. PFGE and MLST analyses confirmed the presence of one A. baumannii strain in 17 patients that was assigned to the worldwide spread sequence type ST231 and carried NDM-1 and OXA-23. Furthermore, two new A. baumannii STs (ST2145 and ST2146) were detected in two and three patients, respectively. Within three years the prevalence of carbapenem-resistant A. baumannii increased dramatically in the hospital. The early detection of multidrug-resistant bacteria and prevention of their further spread are only possible if continuous surveillance and molecular typing will be implemented.
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17
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Schmitt K, Kuster SP, Zurfluh K, Jud RS, Sykes JE, Stephan R, Willi B. Transmission Chains of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae at the Companion Animal Veterinary Clinic-Household Interface. Antibiotics (Basel) 2021; 10:antibiotics10020171. [PMID: 33572066 PMCID: PMC7914568 DOI: 10.3390/antibiotics10020171] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022] Open
Abstract
Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) among animals and humans are a public health threat. This study analyzed the occurrence of ESBL-E in a high-risk environment in a companion animal clinic and two animal patients’ households. In an intensive care unit (ICU), rectal swabs from 74 dogs and cats, 74 hand swabs from staff and 298 swabs from surfaces were analyzed for ESBL-E. Seventeen hospitalized patients (23%) and ten (3%) surfaces in the ICU tested ESBL-E positive. Transmission chains for Klebsiella pneumoniae ST307 blaCTX-M-15 and Escherichia coli ST38 blaCTX-M-14, ST88 blaCTX-M-14 and ST224 blaCTX-M-1 were observed over extended periods of time (14 to 30 days) with similar strains isolated from patients and the clinical environment. After discharge, two colonized dogs (dogs 7 and 12) and their household contacts were resampled. Dog 7 tested repeatedly positive for 77 days, dog 12 tested negative; six (24%) surfaces in the household of the persistently colonized dog tested ESBL-E positive. The owner of dog 7 and one of the owners of dog 12 were colonized. Based on whole genome sequencing, isolates from the owners, their dogs and other ICU patients belonged to the same clusters, highlighting the public health importance of ESBL-E in companion animal clinics.
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Affiliation(s)
- Kira Schmitt
- Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, CH-8057 Zurich, Switzerland; (K.S.); (K.Z.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, CH-3012 Bern, Switzerland
| | - Stefan P. Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland;
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, CH-8057 Zurich, Switzerland; (K.S.); (K.Z.)
| | - Rahel S. Jud
- Division of Critical Care Medicine, Department of Small Animals, University of Zurich, Winterthurerstrasse 260, CH-8057 Zurich, Switzerland;
| | - Jane E. Sykes
- Department of Medicine & Epidemiology, University of California-Davis, 2108 Tupper Hall, Davis, CA 95618, USA;
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, CH-8057 Zurich, Switzerland; (K.S.); (K.Z.)
- Correspondence:
| | - Barbara Willi
- Clinic for Small Animal Internal Medicine, University of Zurich, Winterthurerstrasse 260, CH-8057 Zurich, Switzerland;
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18
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Confronting Ceftolozane-Tazobactam Susceptibility in Multidrug-Resistant Enterobacterales Isolates and Whole-Genome Sequencing Results (STEP Study). Int J Antimicrob Agents 2020; 57:106259. [PMID: 33310115 DOI: 10.1016/j.ijantimicag.2020.106259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 10/05/2020] [Accepted: 11/28/2020] [Indexed: 01/04/2023]
Abstract
Ceftolozane-tazobactam (C/T) is frequently used for infections caused by multidrug-resistant (MDR)-Enterobacterales isolates. Whole-genome sequencing (WGS, Illumina-Hiseq 4000/NovaSeq 6000, OGC, UK) was used to study the population structure, the resistome and the virulome of C/T-susceptible and -resistant MDR Escherichia spp. (n=30) and Klebsiella spp. (n=78) isolates, recovered from lower respiratory, intra-abdominal and urinary tract infections of ICU patients from 11 Portuguese Hospitals (STEP study, 2017-2018). Minimum inhibitory concentrations (MICs) were determined (ISO-broth microdilution, breakpoints EUCAST-2020). In Escherichia spp., a weak concordance between the phenotypic and the WGS method (P=0.051) was observed in the carbapenemase detection (3/30) [blaVIM-2 (2/3), blaKPC-3 (1/3)]; VIM-2-Escherichia coli isolates were C/T-susceptible and only the KPC-3-Escherichia marmotae producer showed C/T-resistance. Overall, CTX-M-15-E. coli-ST131-O25:H4-H30-Rx (11/30) was the most frequent subclone, followed by CTX-M-27-E. coli-ST131-O25:H4-H30 (4/4). Moreover, a wide resistome and virulome were detected in all E. coli isolates. Among Klebsiella spp. isolates [K. pneumoniae (67/78), K. aerogenes (7/78), K. oxytoca (2/78), K. variicola (2/78)], concordance (P<0.001) was observed between the phenotypic and the genomic carbapenemase detection (21/78) [blaKPC-3 (14/21), blaOXA-48 (3/21), blaOXA-181 (3/21)]. A high correlation between C/T-resistance and carbapenemase detection was established (P<0.05). Overall, a high clonal diversity was observed, mainly in KPC-3-producing K. pneumoniae isolates. An extensive resistome was detected in Klebsiella spp. isolates, whereas virulence determinants were mostly identified in carbapenemase producers (P<0.001). WGS is a powerful tool for typing characterization and microbiological study of MDR-Enterobacterales pathogens. Furthermore, carbapenemase genes are associated with C/T-resistance in Klebsiella spp., but other mechanisms might also be involved.
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19
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Wang X, Kang Q, Zhao J, Liu Z, Ji F, Li J, Yang J, Zhang C, Jia T, Dong G, Liu S, Hu G, Qin J, Wang C. Characteristics and Epidemiology of Extended-Spectrum β-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae From Red Kangaroo, China. Front Microbiol 2020; 11:560474. [PMID: 33162947 PMCID: PMC7591395 DOI: 10.3389/fmicb.2020.560474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/13/2020] [Indexed: 11/20/2022] Open
Abstract
Due to its drug resistant nature, β-lactamase represents a serious challenge for public health. Extended-spectrum β-lactamase (ESBL) producing Klebsiella pneumoniae clones are increasingly reported worldwide. Little is known about the prevalence and biological characteristics of drug-resistant strains in zoos. During routine surveillance at the Zhengzhou Zoo of China, we found Klebsiella pneumoniae isolate in healthy Red Kangaroos (Macropus Rufus) with severe MDR. The Klebsiella pneumoniae were especially resistant to Cefuroxime Sodium (MIC, > 64 μg/mL), Ceftriaxone (MIC, >8 μg/mL) and Cefepime (MIC, >64 μg/mL), and belonged to ST290. Subsequently, whole genome sequencing (WGS) showed that the Chrome Chr-M297-1 harbored blaDHA–3, blaSHV–1, blaCTX–M–14, fosA5, dfrA3, sul3, etc., and pM297-1.1 [222,864 bp, IncFIB(K)], which carried nine antimicrobial genes including blaCTX–M–14, blaTEM–191, aph(3″)-Ib, aph(6)-Id and qnrS1, etc., and pM297-1.2 [225,763 bp, IncFII(K)] carried 22 antimicrobial genes including blaTEM–1, blaCTX–M–3, aph(3′)-Ia, aac(3)-IIa, aac(6′)-Ib-cr, aadA16, qnrB2, qnrS1, qacEΔ1, mphA, sul1, and dfrA27, etc. A traceability analysis then revealed that these two plasmids were highly similar to those recovered from human clinical samples in some southern cities in Sichuan Province, China (>99%), suggesting that these plasmids are spreading in China. Furthermore, two plasmids harboring conjugal transfer genes facilitated the transmission of antimicrobial genes by conjugation with E. coli J53. Our research shows that the transmission and adaptation of Klebsiella pneumoniae producing ESBLs is occurring in zoo environments, suggesting that zoos may be becoming important potential reservoirs for clinically important drug-resistant genes. It is therefore necessary to monitor the emergence and spread of drug-resistant gene strains in captive wild animals held in zoo environments.
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Affiliation(s)
- Xue Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China.,College of Veterinary Medicine, Agricultural University of Hebei, Baoding, China
| | - Qian Kang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Jianan Zhao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Zhihui Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China.,College of Veterinary Medicine, Agricultural University of Hebei, Baoding, China
| | - Fang Ji
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | | | - Jianchun Yang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Ting Jia
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Guoying Dong
- College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Shelan Liu
- Department of Infectious Diseases, Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou, China
| | - Guocheng Hu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, China
| | - Jianhua Qin
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding, China
| | - Chengmin Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, China
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20
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Emerging Antimicrobial-Resistant High-Risk Klebsiella pneumoniae Clones ST307 and ST147. Antimicrob Agents Chemother 2020; 64:AAC.01148-20. [PMID: 32747358 DOI: 10.1128/aac.01148-20] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
There is an enormous global public health burden due to antimicrobial-resistant (AMR) Klebsiella pneumoniae high-risk clones. K. pneumoniae ST307 and ST147 are recent additions to the family of successful clones in the species. Both clones likely emerged in Europe during the early to mid-1990s and, in a relatively short time, became prominent global pathogens, spreading to all continents (with the exception of Antarctica). ST307 and ST147 consist of multiple clades/clusters and are associated with various carbapenemases (i.e., KPCs, NDMs, OXA-48-like, and VIMs). ST307 is endemic in Italy, Colombia, the United States (Texas), and South Africa, while ST147 is endemic in India, Italy, Greece, and certain North African countries. Both clones have been introduced into regions of nonendemicity, leading to worldwide nosocomial outbreaks. Genomic studies showed ST307 and ST147 contain identical gyrA and parC mutations and likely obtained plasmids with bla CTX-M-15 during the early to mid-2000s, which aided in their global distribution. ST307 and ST147 then acquired plasmids with various carbapenemases during the late 2000s, establishing themselves as important AMR pathogens in certain regions. Both clones are likely underreported due to restricted detection methodologies. ST307 and ST147 have the ability to become major threats to public health due to their worldwide distribution, ability to cause serious infections, and association with AMR, including panresistance. The medical community at large, especially those concerned with antimicrobial resistance, should be aware of the looming threat posed by emerging AMR high-risk clones such as K. pneumoniae ST307 and ST147.
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Abstract
PURPOSE OF REVIEW To describe current antimicrobial resistance in ESKAPE Gram-negative microorganisms and their situation in the ICUs, the implication of the so-called high-risk clones (HiRCs) involved in the spread of antimicrobial resistance as well as relevance of the COVID-19 pandemic in the potential increase of resistance. RECENT FINDINGS Extended-spectrum and carbapenemase producing Enterobacterales and multidrug and extensive drug-resistant Pseudomonas aeruginosa and Acinetobacter baumannii have increased worldwide. Sequence type (ST)131 Escherichia coli, ST258, ST11, ST10, ST147 and ST307 Klebsiella pneumoniae, ST111, ST175, ST235 and ST244 P. aeruginosa HiRCs are responsible for this increase in the ICUs, and some of them are implicated in the emergence of resistance mechanisms affecting new antimicrobials. A similar situation can be found with European clonal complex 1 and clonal complex 2 of A. baumannii. The high use of antimicrobials during the COVID-19 pandemic, particularly in ICUs, might have a negative influence in future trends of antimicrobial resistance. SUMMARY The increase of antimicrobial resistance in ICUs is mainly due to the spread of HiRCs and is exemplified with the ESKAPE Gram-negative microorganisms. The COVID-19 pandemic might have a negative impact in the increase of antimicrobial resistance and should be monitored through specific surveillance studies in ICUs.
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Chan WW, Campbell L, Doyle D, Pitout JD. Rapid detection of Enterobacterales that produce carbapenemases. Diagn Microbiol Infect Dis 2020; 98:115120. [PMID: 32688297 DOI: 10.1016/j.diagmicrobio.2020.115120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/08/2020] [Accepted: 06/20/2020] [Indexed: 12/27/2022]
Abstract
PURPOSE The rapid detection of carbapenemases among Enterobacterales in clinical laboratories is critical for management of patients, and infection prevention and control efforts. METHODS A study was designed to evaluate the performances of the RAPIDEC CARBA NP®, β-CARBA®, NG-Test CARBA 5®, modified carbapenem-inactivation method, and EDTA version (eCIM) assays against a global collection of Enterobacterales (n = 216) with diverse carbapenemases. RESULTS The RAPIDEC CARBA NP® assay had a sensitivity of 98.6% and specificity of 19.6% and β-CARBA® a sensitivity of 94% and specificity of 97.8%, but showed low sensitivity with Klebsiella Pneumoniae Carbapenemase (KPC)-containing isolates. The NG-Test CARBA 5® had an overall sensitivity of 96.3% and specificity of 100% and failed to detect isolates with blaIMP-13, blaIMP-14. The eCIM gave false- positive results with Oxacillinase (OXA)-48-like enzymes. CONCLUSION The NG-Test CARBA 5® assay was technically simple and provided rapid accurate results on the types of carbapenemases. Such information has potential treatment benefits for patients.
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Affiliation(s)
- Wilson W Chan
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada; Clinical section of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada
| | - Lorraine Campbell
- Clinical section of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada
| | - Diana Doyle
- Clinical section of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada
| | - Johann Dd Pitout
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada; Clinical section of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
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