Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

Current Opinion in Microbiology - Tập 45 - Trang 131-139 - 2018
Kelly L. Wyres1, Kathryn E. Holt1
1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia

Tóm tắt

Từ khóa


Tài liệu tham khảo

Pendleton, 2013, Clinical relevance of the ESKAPE pathogens, Expert Rev Anti Infect Ther, 11, 297, 10.1586/eri.13.12

de Man, 2018, Genomic analysis of a pan-resistant isolate of Klebsiella pneumoniae, United States 2016, MBio, 9, e00440, 10.1128/mBio.00440-18

Jia, 2017, CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database, Nucleic Acids Res, 4, D566, 10.1093/nar/gkw1004

Dcosta, 2011, Antibiotic resistance is ancient, Nature, 477, 457, 10.1038/nature10388

Nesme, 2014, Large-scale metagenomic-based study of antibiotic resistance in the environment, Curr Biol, 24, 1096, 10.1016/j.cub.2014.03.036

Benveniste, 1973, Aminoglycoside antibiotic-inactivating enzymes in Actinomycetes similar to those present in clinical isolates of antibiotic-resistant bacteria, Proc Natl Acad Sci U S A, 70, 2276, 10.1073/pnas.70.8.2276

Lewis, 2013, Platforms for antibiotic discovery, Nat Rev Drug Discov, 12, 371, 10.1038/nrd3975

Holt, 2015, Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health, Proc Natl Acad Sci U S A, 112, E3574, 10.1073/pnas.1501049112

Navon-Venezia, 2017, Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance, FEMS Microbiol Rev, 41, 252, 10.1093/femsre/fux013

Wand, 2015, Characterization of pre-antibiotic era Klebsiella pneumoniae isolates with respect to antibiotic/disinfectant susceptibility and virulence in Galleria mellonella, Antimicrob Agents Chemother, 59, 3966, 10.1128/AAC.05009-14

Wyres, 2016, Klebsiella pneumoniae population genomics and antimicrobial-resistant clones, Trends Microbiol, 24, 944, 10.1016/j.tim.2016.09.007

Rozwandowicz, 2018, Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae, J Antimicrob Chemother, 10.1093/jac/dkx488

Matthew, 1979, Types of beta-lactamase determined by plasmids in gram-negative bacteria, J Bacteriol, 138, 657, 10.1128/jb.138.3.657-662.1979

Roupas, 1974, R factor-mediated and chromosomal resistance to ampicillin in Escherichia coli, Antimicrob Agents Chemother, 5, 186, 10.1128/AAC.5.2.186

Labia, 1988, The kinetics of SHV-2 plasmid-mediated beta-lactamase compared to those of the parent enzyme from which it is derived, Drugs Exp Clin Res, 14, 335

Jacoby, 1991, More extended-spectrum beta-lactamases, Antimicrob Agents Chemother, 35, 1697, 10.1128/AAC.35.9.1697

Liakopoulos, 2016, A review of SHV extended-spectrum β-lactamases: neglected yet ubiquitous, Front Microbiol, 5, 1374

Dai, 2010, Drug-resistant genes carried by Acinetobacter baumanii isolated from patients with lower respiratory tract infection, Chin Med J (Engl), 123, 2571

Naas, 1999, An SHV-derived extended-spectrum beta-lactamase in Pseudomonas aeruginosa, Antimicrob Agents Chemother, 43, 1281, 10.1128/AAC.43.5.1281

D’Andrea, 2013, CTX-M-type β-lactamases: a successful story of antibiotic resistance, Int J Med Microbiol, 303, 305, 10.1016/j.ijmm.2013.02.008

Cantón, 2012, CTX-M enzymes: origin and diffusion, Front Microbiol, 3, 110, 10.3389/fmicb.2012.00110

Mathers, 2015, The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae, Clin Microbiol Rev, 28, 565, 10.1128/CMR.00116-14

Woerther, 2013, Trends in human fecal carriage of extended-spectrum β-lactamases in the community: toward the globalization of CTX-M, Clin Microbiol Rev, 26, 744, 10.1128/CMR.00023-13

Martinez-Martinez, 1998, Quinolone resistance from a transferable plasmid, Lancet, 351, 797, 10.1016/S0140-6736(97)07322-4

Jacoby, 2006, qnrB, another plasmid-mediated gene for quinolone resistance, Antimicrob Agents Chemother, 50, 1178, 10.1128/AAC.50.4.1178-1182.2006

Poirel, 2005, Origin of plasmid-mediated quinolone resistance determinant QnrA, Antimicrob Agents Chemother, 49, 3523, 10.1128/AAC.49.8.3523-3525.2005

Villegas, 2007, First identification of Pseudomonas aeruginosa isolates producing a KPC-type carbapenem-hydrolyzing beta-lactamase, Antimicrob Agents Chemother, 51, 1553, 10.1128/AAC.01405-06

Martinez, 2014, ISEcp1-mediated transposition of blaKPC into the chromosome of a clinical isolate of Acinetobacter baumannii from Puerto Rico, J Med Microbiol, 63, 1644, 10.1099/jmm.0.080721-0

Tacão, 2018, Shewanella species as the origin of blaOXA-48 genes: insights into gene diversity, associated phenotypes and possible transfer mechanisms, Int J Antimicrob Agents, 51, 340, 10.1016/j.ijantimicag.2017.05.014

Poirel, 2004, Emergence of oxacillinase-mediated resistance to imipenem in Klebsiella pneumoniae, Antimicrob Agents Chemother, 48, 15, 10.1128/AAC.48.1.15-22.2004

Mairi, 2018, OXA-48-like carbapenemases producing Enterobacteriaceae in different niches, Eur J Clin Microbiol Infect Dis, 37, 587, 10.1007/s10096-017-3112-7

Yong, 2009, Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India, Antimicrob Agents Chemother, 53, 5046, 10.1128/AAC.00774-09

Kumarasamy, 2010, Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study, Lancet Infect Dis, 10, 597, 10.1016/S1473-3099(10)70143-2

Poirel, 2011, Genetic features of blaNDM-1-positive Enterobacteriaceae, Antimicrob Agents Chemother, 55, 5403, 10.1128/AAC.00585-11

Walsh, 2011, Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study, Lancet Infect Dis, 11, 355, 10.1016/S1473-3099(11)70059-7

Karthikeyan, 2010, Coexistence of blaOXA-23 with blaNDM-1 and armA in clinical isolates of Acinetobacter baumannii in India, J Antimicrob Chemother, 65, 2253, 10.1093/jac/dkq273

Liu, 2016, Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study, Lancet Infect Dis, 16, 161, 10.1016/S1473-3099(15)00424-7

Wang, 2018, The global distribution and spread of the mobilized colistin resistance gene mcr-1, Nat Commun, 9, 1179, 10.1038/s41467-018-03205-z

Popa, 2011, Trends and barriers to lateral gene transfer in prokaryotes, Curr Opin Microbiol, 14, 615, 10.1016/j.mib.2011.07.027

Podschun, 1998, Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors, Clin Microbiol Rev, 11, 589, 10.1128/CMR.11.4.589

Brisse, 2005, Identification and antimicrobial susceptibility of 100 Klebsiella animal clinical isolates, Vet Mirobiol, 105, 307, 10.1016/j.vetmic.2004.11.010

Zhang, 2018, Prevalence and mechanisms of extended-spectrum cephalosporin resistance in clinical and fecal Enterobacteriaceae isolates from dogs in Ontario, Canada, Vet Mirobiol, 213, 82, 10.1016/j.vetmic.2017.11.020

Bowring, 2017, An unusual culprit: Klebsiella pneumoniae causing septicaemia outbreaks in neonatal pigs?, Vet Microbiol, 203, 267, 10.1016/j.vetmic.2017.03.018

He, 2017, Occurrence and characterization of blaNDM-5-positive Klebsiella pneumoniae isolates from dairy cows in Jiangsu, China, J Antimicrob Chemother, 72, 90, 10.1093/jac/dkw357

Sasaki, 2017, Peracute bacterial meningitis due to infection with Klebsiella pneumoniae in captive-bred ruffed lemurs (Varecia variegate), J Comp Pathol, 156, 281, 10.1016/j.jcpa.2016.12.003

Bagley, 1985, Habitat association of Klebsiella species, Infect Control, 6, 52, 10.1017/S0195941700062603

Schadich, 2009, Skin peptide activities against opportunistic bacterial pathogens of the African Clawed Frog (Xenopus laevis) and three Litoria frogs, J Herpetol, 43, 173, 10.1670/08-113R1.1

Davis, 2016, Recent research examining links among Klebsiella pneumoniae from food, food animals, and human extraintestinal infections, Curr Environ Health Rep, 10.1007/s40572-016-0089-9

Gorrie, 2017, Gastrointestinal carriage is a major reservoir of K. pneumoniae infection in intensive care patients, Clin Infect Dis, 65, 208, 10.1093/cid/cix270

Conlan, 2012, Species-level analysis of DNA sequence data from the NIH human microbiome project, PLOS ONE, 7, e47075, 10.1371/journal.pone.0047075

Zadoks, 2011, Sources of Klebsiella and RaoultellaM species on dairy farms: be careful where you walk, J Dairy Sci, 94, 1045, 10.3168/jds.2010-3603

Founou, 2018, Genome sequencing of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae isolated from pigs and abattoir workers in Cameroon, Front Microbiol, 9, 1, 10.3389/fmicb.2018.00188

Stenkat, 2014, Aerobic cloacal and pharyngeal bacterial flora in six species of free-living birds, J Appl Microbiol, 117, 1564, 10.1111/jam.12636

Brahmi, 2017, High prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae in wild fish from the Mediterranean Sea in Algeria, Microb Drug Res, 1

Ranjbar, 2016, Molecular detection and antimicrobial resistance of Klebsiella pneumoniae from house flies (Musca domestica) in kitchens, farms, hospitals and slaughterhouses, J Infect Public Health, 9, 499, 10.1016/j.jiph.2015.12.012

Parthasarathi, 2007, Diversity of microflora in the gut and casts of tropical composting earthworms reared on different substrates, J Environ Biol, 28, 87

Singh, 2017, Association study of multiple antibiotic resistance and virulence: a strategy to assess the extent of risk posed by bacterial population in aquatic environment, Environ Monit Assess, 189, 320, 10.1007/s10661-017-6005-4

Lagkouvardos, 2016, IMNGS: a comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies, Sci Rep, 6, 33721, 10.1038/srep33721

Stolle, 2013, Emergence of OXA-48 carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in dogs, J Antimicrob Chemother, 68, 2802, 10.1093/jac/dkt259

Donati, 2014, Extended-spectrum-berta-lactamases and plasmid mediated quinolone resistance in Klebsiella spp. from companion animals in Italy, PLOS ONE, 9, 1, 10.1371/journal.pone.0090564

Sato, 2017, Tigecycline susceptibility of Klebsiella pneumoniae complex and Escherichia coli isolates from companion animals: the prevalence of tigecycline-nonsusceptible K. pneumoniae complex, including internationally expanding human pathogenic, Microb Drug Res, 1

Anzai, 2017, First case report of non-human primates (Alouatta clamitans) with the hypervirulent Klebsiella pneumoniae serotype K1 strain ST23: a possible emerging wildlife pathogen, J Med Primatol, 46, 337, 10.1111/jmp.12296

Lam, 2018, Population genomics of hypervirulent Klebsiella pneumoniae clonal group 23 reveals early emergence and rapid global dissemination, bioRxiv

Runcharoen, 2017, Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae, Genome Med, 9, 6, 10.1186/s13073-017-0397-1

Vernikos, 2015, Ten years of pan-genome analyses, Curr Opin Microbiol, 23, 148, 10.1016/j.mib.2014.11.016

Blin, 2017, Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae, Environ Microbiol, 19, 1881, 10.1111/1462-2920.13689

Gordienko, 2013, Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica, J Bacteriol, 195, 2786, 10.1128/JB.02285-12

Liu, 2013, Comparative genome analysis of Enterobacter cloacae, PLOS ONE, 8, e74487, 10.1371/journal.pone.0074487

Chan, 2015, A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii, Genome Biol, 16, 143, 10.1186/s13059-015-0701-6

Mosquera-Rendón, 2016, Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species, BMC Genomics, 17, 45, 10.1186/s12864-016-2364-4

Mann, 2010, Bacterial genomic G+C composition-eliciting environmental adaptation, Genomics, 95, 7, 10.1016/j.ygeno.2009.09.002

Conlan, 2016, Plasmid dynamics in KPC-positive Klebsiella pneumoniae during long-term patient colonization, MBio, 7, e00742, 10.1128/mBio.00742-16

Sheppard, 2016, Nested Russian doll-like genetic mobility drives rapid dissemination of the carbapenem resistance gene blaKPC, Antimicrob Agents Chemother, 60, 3767, 10.1128/AAC.00464-16

Martin, 2017, Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission, J Antimicrob Chemother, 72, 3025, 10.1093/jac/dkx264

Popa, 2011, Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes, Genome Res, 21, 599, 10.1101/gr.115592.110

Klümper, 2015, Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community, ISME J, 9, 934, 10.1038/ismej.2014.191

Ramirez, 2014, Plasmid-mediated antibiotic resistance and virulence in gram-negatives: the Klebsiella pneumoniae paradigm, Microbiol Spectr, 2, 1, 10.1128/microbiolspec.PLAS-0016-2013

Liu, 2012, Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum, J Bacteriol, 194, 1841, 10.1128/JB.00043-12

Gorrie, 2018, Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital, Clin Infect Dis, 10.1093/cid/ciy027

Wick, 2017, Completing bacterial genome assemblies with multiplex MinION sequencing, MGen, 3

Göttig, 2016, Impact of blaNDM-1 on fitness and pathogenicity of Escherichia coli and Klebsiella pneumoniae, Int J Antimicrob Agents, 47, 430, 10.1016/j.ijantimicag.2016.02.019

Löhr, 2015, Persistence of a pKPN3-like CTX-M-15-encoding IncFIIK plasmid in a Klebsiella pneumoniae ST17 host during two years of intestinal colonization, PLOS ONE, 10, e0116516, 10.1371/journal.pone.0116516

Bouma, 1988, Evolution of a bacteria/plasmid association, Nature, 35, 351, 10.1038/335351a0

Loftie-Eaton, 2017, Compensatory mutations improve general permissiveness to antibiotic resistance plasmids, Nat Ecol Evol, 10.1038/s41559-017-0243-2

De Gelder, 2005, Plasmid donor affects host range of promiscuous IncP-1β plasmid pB10 in an activated-sludge microbial community, Appl Environ Microbiol, 71, 5309, 10.1128/AEM.71.9.5309-5317.2005