Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae

Simner, Patricia J.; Antar, Annukka A.R.; Hao, Stephanie; Gurtowski, James; Tamma, Pranita D.; Rock, Clare; Opene, Belita N. A.; Tekle, Tsigereda; Carroll, Karen C.; Schatz, Michael C.; Timp, Winston

doi:10.1093/jac/dky121

Cited by 43 publications

(45 citation statements)

References 27 publications

(29 reference statements)

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“…Since then, bla KPC-2 -bearing K. pneumoniae isolates have become more prevalent and reported in China as well as other countries and areas 28 . Recently, one patient is found to have susceptible K. pneumoniae bacteraemia in US 15 . While that case is relatively specific since the patient might be affected during the visit and hospitalization in India, which would add more complex environmental factors to confound the results.…”

Section: Discussionmentioning

confidence: 99%

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Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance

Zhang

Zhao

et al. 2019

Preprint

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19The enhancing incidence of carbapenem-resistant Klebsiella pneumoniae (CRKP)-mediated 20 infections in Mengchao Hepatobiliary Hospital of Fujian Medical University in 2017 is the 21 motivation behind this investigation to study gene phenotypes and resistance-associated genes of 22 emergence regarding the CRKP strains. In current study, seven inpatients are enrolled in the 23 hospital with complete treatments. The carbapenem-resistant K. pneumoniae whole genome is 24 sequenced using MiSeq short-read and Oxford Nanopore long-read sequencing technology. 25Prophages are identified to assess genetic diversity within CRKP genomes. The investigation 26 encompassed eight CRKP strains that collected from the patients enrolled as well as the 27 environment, which illustrate that blaKPC-2 is responsible for phenotypic resistance in six CRKP 28 strains that K. pneumoniae sequence type (ST11) is informed. The plasmid with IncR, ColRNAI 29 and pMLST type with IncF[F33:A-:B-] co-exist in all ST11 with KPC-2-producing CRKP 30 strains. Along with carbapenemases, all K. pneumoniae strains harbor two or three extended 31 spectrum β-lactamase (ESBL)-producing genes. fosA gene is detected amongst all the CRKP 32 strains. The single nucleotide polymorphisms (SNP) markers are indicated and validated among 33 all CRKP strains, providing valuable clues for distinguishing carbapenem-resistant strains from 34 conventional K. pneumoniae. In conclusion, ST11 is the main CRKP type, and blaKPC-2 is the 35 dominant carbapenemase gene harbored by clinical CRKP isolates from current investigations. 36

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Section: Discussionmentioning

confidence: 99%

“…The antibiotic resistance and virulence genes, plasmids, phenotyping and genotyping of CRKP genomes are scanned using the Bacterial Analysis Pipeline 14 . Carbapenemase-resistance genes are further identified from above annotated sequences according to Simner et al 15 .…”

Section: Methodsmentioning

confidence: 99%

Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance

Zhang

Zhao

et al. 2019

Preprint

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“…Conversely, HGT can provide genetic features that can be easily tracked and identified in clinical outbreaks, such as plasmids. Plasmid conjugation transfers novel genes and, thus, is relatively easy to track by DNA sequencing and PCR (Snitkin et al 2012;Boyd et al 2015;Gorrie et al 2018;Simner et al 2018). Even classic restriction fragment length polymorphism analysis can resolve the presence and absence of plasmids, as in the case of the loss of the Salmonella virulence plasmid in a human infection (Alexander et al 2015).…”

Section: Detecting and Anticipating Hgtmentioning

confidence: 99%

Horizontal transfer of antibiotic resistance genes in clinical environments

2019

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A global medical crisis is unfolding as antibiotics lose effectiveness against a growing number of bacterial pathogens. Horizontal gene transfer (HGT) contributes significantly to the rapid spread of resistance, yet the transmission dynamics of genes that confer antibiotic resistance are poorly understood. Multiple mechanisms of HGT liberate genes from normal vertical inheritance. Conjugation by plasmids, transduction by bacteriophages, and natural transformation by extracellular DNA each allow genetic material to jump between strains and species. Thus, HGT adds an important dimension to infectious disease whereby an antibiotic resistance gene (ARG) can be the agent of an outbreak by transferring resistance to multiple unrelated pathogens. Here, we review the small number of cases where HGT has been detected in clinical environments. We discuss differences and synergies between the spread of plasmid-borne and chromosomal ARGs, with a special consideration of the difficulties of detecting transduction and transformation by routine genetic diagnostics. We highlight how 11 of the top 12 priority antibiotic-resistant pathogens are known or predicted to be naturally transformable, raising the possibility that this mechanism of HGT makes significant contributions to the spread of ARGs. HGT drives the evolution of untreatable “superbugs” by concentrating ARGs together in the same cell, thus HGT must be included in strategies to prevent the emergence of resistant organisms in hospitals and other clinical settings.

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“…Conversely, we observed direct inactivation of OmpC and OmpF either through TU/TPU transposition into their respective ORFs or through INDELs that resulted in frame-shift mutations whereas no alterations in OmpR were identified in our cohort. To our knowledge, there have been only two other reports of an IS Ecp1 -mediated TPU harboring a β-lactamase encoding gene causing the disruption of a porin, in both cases OmpK35 from K. pneumoniae (57, 58). While there have been a number of studies that have implicated IS-mediated porin disruptions, including IS 26 mediated disruptions (54, 59–61), to our knowledge, this is the first documented IS 26 -mediated translocatable unit disruption of an outer membrane porin followed by amplification of a β-lactamase gene.…”

Section: Discussionmentioning

confidence: 99%

Concurrence of Porin Loss and Modular Amplification of β-Lactamase Encoding Genes Drives Carbapenem Resistance in a Cohort of Recurrent Enterobacterales Bacteremia

Shropshire

Aitken

Pifer³

et al. 2019

Preprint

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30 Background 31 Carbapenem resistant Enterobacterales (CRE) remain urgent antimicrobial resistance threats. 32 Approximately half of CRE clinical isolates lack carbapenem hydrolyzing enzymes and develop 33 carbapenem resistance through alternative mechanisms. The purpose of this study was to 34 elucidate the development of carbapenem resistance mechanisms from clonal, recurrent 35 extended-spectrum b-lactamase positive Enterobacterales (ESBL-E) bacteremia isolates in a 36 vulnerable patient population. 37 Methods 38 This study investigated a historical, retrospective cohort of ESBL-E bacteremia cases in the 39 University of Texas MD Anderson Cancer Center (MDACC) from January 2015 to July 2016. 40 Phylogenetic and comparative genomic analyses were performed to identify clonal, recurrent 41 ESBL-E isolates developing carbapenem resistance. Oxford Nanopore Technology (ONT) long-42 read and Illumina short-read sequencing data were used to generate consensus assemblies and to 43 identify signatures of mobile genetic element mediated amplification and transposition of 44 antimicrobial resistance genes. Serial passaging experiments were performed on a set of clinical 45 ST131 ESBL-E isolates to recapitulate in vivo observations. qPCR and qRT-PCR were used to 46 determine respective copy number and transcript levels of b-lactamase genes. 47 Results 48 116 ESBL-E bacteremia cases were identified, 16 of which had documented recurrent infections. 49 Four serial, recurrent isolates displayed a carbapenem resistant phenotype, three without the 50 acquisition of a known carbapenemase. These three isolates had non-carbapenemase-producing 51 CRE (non-CP-CRE) mechanisms driven by IS26-and ISEcp1-mediated amplification of 52 4 respective translocatable units (TU) and transposition units (TPU) harboring both blaOXA-1 and 53 blaCTX-M variants with concomitant outer membrane porin disruption. The TU and TPU 54 structures inserted into the open reading frames of outer membrane porin genes in a subset of 55 non-CP-CRE isolates. Serial passage of an index ST131 ESBL-E isolate under selective 56 carbapenem exposure resulted in chromosomal amplification of modular, TUs harboring β-57 lactamase genes with concomitant porin inactivation, recapitulating the in vivo carbapenem 58 resistance progression. Long-read sequencing of two additional MDACC bacteremia strains 59 identified similar non-CP-CRE mechanisms observed in the serial isolates. 60 Conclusions 61 Non-CP-CRE de novo mechanisms were the primary driver of CRE development in recurrent 62 bacteremia cases within this vulnerable patient population. The incorporation of long-read ONT 63 data into AMR surveillance platforms is critical to identify high-risk CRE isolates that are 64 difficult to identify with low-resolution phenotypic and molecular characterization methods. 65 66 Keywords: 67 Non-carbapenemase-producing carbapenem resistant Enterobacterales, Oxford Nanopore 68 Technologies MinION Sequencing, Mobile Genetic Element Amplifications, Mobile Genetic 69 Element Transpositions...

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Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae

Abstract: To the best of our knowledge, we are the first to report a carbapenem-resistant HMV K. pneumoniae strain in the USA. Ultimately, this case demonstrates the role of antibiotic pressure in the acquisition and loss of important genetic elements.

Cited by 43 publications

References 27 publications

Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance

Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance

Horizontal transfer of antibiotic resistance genes in clinical environments

Concurrence of Porin Loss and Modular Amplification of β-Lactamase Encoding Genes Drives Carbapenem Resistance in a Cohort of Recurrent Enterobacterales Bacteremia

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