Fatal Respiratory Diphtheria Caused by ß-Lactam–Resistant Corynebacterium diphtheriae

2020 ◽  
Author(s):  
Brian M Forde ◽  
Andrew Henderson ◽  
Elliott G Playford ◽  
David Looke ◽  
Belinda C Henderson ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genomic Analysis ◽  
Carbapenem Resistance ◽  
Corynebacterium Diphtheriae ◽  
Penicillin Binding Protein ◽  
Long Read ◽  
Amoxicillin Clavulanic Acid ◽  
Resistance To Penicillin ◽  
High Level

Abstract Background Diphtheria is a potentially fatal respiratory disease caused by toxigenic Corynebacterium diphtheriae. Although resistance to erythromycin has been recognized, β-lactam resistance in toxigenic diphtheria has not been described. Here, we report a case of fatal respiratory diphtheria caused by toxigenic C. diphtheriae resistant to penicillin and all other β-lactam antibiotics, and describe a novel mechanism of inducible carbapenem resistance associated with the acquisition of a mobile resistance element. Methods Long-read whole-genome sequencing was performed using Pacific Biosciences Single Molecule Real-Time sequencing to determine the genome sequence of C. diphtheriae BQ11 and the mechanism of β-lactam resistance. To investigate the phenotypic inducibility of meropenem resistance, short-read sequencing was performed using an Illumina NextSeq500 sequencer on the strain both with and without exposure to meropenem. Results BQ11 demonstrated high-level resistance to penicillin (benzylpenicillin minimum inhibitory concentration [MIC] ≥ 256 μg/ml), β-lactam/β-lactamase inhibitors and cephalosporins (amoxicillin/clavulanic acid MIC ≥ 256 μg/mL; ceftriaxone MIC ≥ 8 μg/L). Genomic analysis of BQ11 identified acquisition of a novel transposon carrying the penicillin-binding protein (PBP) Pbp2c, responsible for resistance to penicillin and cephalosporins. When strain BQ11 was exposed to meropenem, selective pressure drove amplification of the transposon in a tandem array and led to a corresponding change from a low-level to a high-level meropenem-resistant phenotype. Conclusions We have identified a novel mechanism of inducible antibiotic resistance whereby isolates that appear to be carbapenem susceptible on initial testing can develop in vivo resistance to carbapenems with repeated exposure. This phenomenon could have significant implications for the treatment of C. diphtheriae infection, and may lead to clinical failure.

Extended-spectrum resistance to β-lactams/β-lactamase inhibitors (ESRI) evolved from low-level resistant Escherichia coli

2019 ◽  
Author(s):  
Ángel Rodríguez-Villodres ◽  
María Luisa Gil-Marqués ◽  
Rocío Álvarez-Marín ◽  
Rémy A Bonnin ◽  
María Eugenia Pachón-Ibáñez ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Clavulanic Acid ◽  
Genomic Analysis ◽  
E Coli ◽  
Extended Spectrum ◽  
Copy Numbers ◽  
Resistance Patterns ◽  
Amoxicillin Clavulanic Acid

Abstract Objectives Escherichia coli is characterized by three resistance patterns to β-lactams/β-lactamase inhibitors (BLs/BLIs): (i) resistance to ampicillin/sulbactam and susceptibility to amoxicillin/clavulanic acid and piperacillin/tazobactam (RSS); (ii) resistance to ampicillin/sulbactam and amoxicillin/clavulanic acid, and susceptibility to piperacillin/tazobactam (RRS); and (iii) resistance to ampicillin/sulbactam, amoxicillin/clavulanic acid and piperacillin/tazobactam (RRR). These resistance patterns are acquired consecutively, indicating a potential risk of developing resistance to piperacillin/tazobactam, but the precise mechanism of this process is not completely understood. Methods Clinical isolates incrementally pressured by piperacillin/tazobactam selection in vitro and in vivo were used. We determined the MIC of piperacillin/tazobactam in the presence and absence of piperacillin/tazobactam pressure. We deciphered the role of the blaTEM genes in the new concept of extended-spectrum resistance to BLs/BLIs (ESRI) using genomic analysis. The activity of β-lactamase was quantified in these isolates. Results We show that piperacillin/tazobactam resistance is induced in E. coli carrying blaTEM genes. This resistance is due to the increase in copy numbers and transcription levels of the blaTEM gene, thus increasing β-lactamase activity and consequently increasing piperacillin/tazobactam MICs. Genome sequencing of two blaTEM-carrying representative isolates showed that piperacillin/tazobactam treatment produced two types of duplications of blaTEM (8 and 60 copies, respectively). In the clinical setting, piperacillin/tazobactam treatment of patients infected by E. coli carrying blaTEM is associated with a risk of therapeutic failure. Conclusions This study describes for the first time the ESRI in E. coli. This new concept is very important in the understanding of the mechanism involved in the acquisition of resistance to BLs/BLIs.

scholarly journals Variant Phasing and Haplotypic Expression from Single-molecule Long-read Sequencing in Maize

2019 ◽  
Author(s):  
Bo Wang ◽  
Elizabeth Tseng ◽  
Primo Baybayan ◽  
Kevin Eng ◽  
Michael Regulski ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genomic Analysis ◽  
Full Length ◽  
Specific Gene ◽  
Population Genetic Analysis ◽  
Functional Genomic Analysis ◽  
Long Read ◽  
Allele Specific ◽  
Regulatory Effects ◽  
Hybrid Lines

AbstractHaplotype phasing of genetic variants in maize is important for interpretation of the genome, population genetic analysis and functional genomic analysis of allelic activity. Accordingly, accurate methods for phasing the full-length isoforms are essential for functional genomics studies. We performed an isoform-level phasing study in maize, using two inbred lines and their reciprocal crosses, based on the single-molecule full-length cDNA sequencing. To phase and analyze the full-length transcripts between hybrids and parents, we developed a tool called IsoPhase. Using this tool, we validated the majority of SNPs called against matching short-read data and identified cases of allele-specific, gene-level and isoform-level expression. Our results revealed that maize parental lines and hybrid lines exhibit different splicing activities. After phasing 6,907 genes in two reciprocal hybrids using embryo, endosperm and root tissues, we annotated the SNPs and identified large-effect genes. In addition, based on single-molecule sequencing, we identified parent-of-origin isoforms in maize hybrids, distinct novel isoforms in maize parent and hybrid lines, and imprinted genes from different tissues. Finally, we characterized variation in cis- and trans-regulatory effects. Our study provides measures of haplotypic expression that could increase accuracy in studies of allelic expression.

scholarly journals SMRT sequencing reveals differential patterns of methylation in two O111:H- Shiga toxigenicEscherichia coliisolates from a historic hemolytic uremic syndrome outbreak in Australia

2017 ◽  
Author(s):  
Brian M. Forde ◽  
Lauren J. McAllister ◽  
James C. Paton ◽  
Adrienne W. Paton ◽  
Scott A. Beatson
Keyword(s):  
Single Molecule ◽  
Genomic Analysis ◽  
Smrt Sequencing ◽  
Promoter Regions ◽  
Food Borne ◽  
Long Reads ◽  
Long Read ◽  
Shiga Toxin 2 ◽  
Uremic Syndrome ◽  
Potential Promoter

AbstractShiga toxigenicEscherichia coli(STEC) are important food-borne pathogens and a major cause of haemorrhagic colitis and haemolytic-uremic syndrome (HUS) worldwide. In 1995 a severe HUS outbreak in Adelaide occurred. A recent genomic analysis of STEC O111:H-strains 95JB1 and 95NR1 from this outbreak found that the more virulent isolate, 95NR1, harboured two additional copies of the Shiga toxin 2 (Stx2) genes although the structure of the Stx2-converting prophages could not be fully resolved due to the fragmented assembly. In this study we have used Pacific Biosciences (PacBio) single molecule real-time (SMRT) long read sequencing to characterise the complete epigenome (genome and methylome) of 95JB1 and 95NR1. Using long reads we completely resolved the structure of two, tandemly inserted, stx2-converting phage in 95NR1. Our analysis of the methylome of 95NR1 and 95JB1 identified hemi-methylation of a novel motif (5’-CTGCm6AG-3’) in more than 4000 sites in the 95NR1 genome. These sites were entirely unmethalyted in the 95JB1, including at least 180 potential promoter regions that could explain regulatory differences between the strains. We identified a Type IIG methyltransferase encoded in both genomes in association with three additional genes in an operon-like arrangement. IS1203mediated disruption of this operon in 95JB1 is the likely cause of the observed differential patterns of methylation between 95NR1 and 95JB1. This study demonstrates the enormous potential of PacBio SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.

scholarly journals Genomic analysis of carbapenemase-encoding plasmids from Klebsiella pneumoniae across Europe highlights three major patterns of dissemination

2019 ◽  
Author(s):  
Sophia David ◽  
Victoria Cohen ◽  
Sandra Reuter ◽  
Anna E. Sheppard ◽  
Tommaso Giani ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Carbapenem Resistance ◽  
Short Read ◽  
Primary Mechanism ◽  
Carbapenemase Gene ◽  
Long Read ◽  
Short Read Sequence ◽  
Stable Association

AbstractThe incidence of Klebsiella pneumoniae infections that are resistant to carbapenems, a last-line class of antibiotics, has been rapidly increasing. The primary mechanism of carbapenem resistance is production of carbapenemase enzymes, which are most frequently encoded on plasmids by blaOXA-48-like, blaVIM, blaNDM and blaKPC genes. Using short-read sequence data, we previously analysed genomes of 1717 isolates from the K. pneumoniae species complex submitted during the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE). Here, we investigated the diversity, prevalence and transmission dynamics of carbapenemase-encoding plasmids using long-read sequencing of representative isolates (n=79) from this collection in combination with short-read data from all isolates. We highlight three major patterns by which carbapenemase genes have disseminated via plasmids. First, blaOXA-48-like genes have spread across diverse lineages primarily via a highly conserved, epidemic pOXA-48-like plasmid. Second, blaVIM and blaNDM genes have spread via transient associations of diverse plasmids with numerous lineages. Third, blaKPC genes have transmitted predominantly by stable association with one clonal lineage (ST258/512) despite frequent mobilisation between pre-existing yet diverse plasmids within the lineage. Despite contrasts in these three modes of carbapenemase gene spread, which can be summarised as using one plasmid/multiple lineages, multiple plasmids/multiple lineages, and multiple plasmids/one lineage, all are underpinned by significant propagation along high-risk clonal lineages.

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

2019 ◽  
Author(s):  
William C. Shropshire ◽  
Samuel L. Aitken ◽  
Reed Pifer ◽  
Jiwoong Kim ◽  
Micah M. Bhatti ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Outer Membrane ◽  
Patient Population ◽  
Carbapenem Resistance ◽  
Carbapenem Resistant ◽  
Outer Membrane Porin ◽  
Long Read ◽  
Vulnerable Patient ◽  
Vulnerable Patient Population

ABSTRACTBackgroundCarbapenem resistant Enterobacterales (CRE) remain urgent antimicrobial resistance threats. Approximately half of CRE clinical isolates lack carbapenem hydrolyzing enzymes and develop carbapenem resistance through alternative mechanisms. The purpose of this study was to elucidate the development of carbapenem resistance mechanisms from clonal, recurrent extended-spectrum β-lactamase positive Enterobacterales (ESBL-E) bacteremia isolates in a vulnerable patient population.MethodsThis study investigated a historical, retrospective cohort of ESBL-E bacteremia cases in the University of Texas MD Anderson Cancer Center (MDACC) from January 2015 to July 2016. Phylogenetic and comparative genomic analyses were performed to identify clonal, recurrent ESBL-E isolates developing carbapenem resistance. Oxford Nanopore Technology (ONT) long-read and Illumina short-read sequencing data were used to generate consensus assemblies and to identify signatures of mobile genetic element mediated amplification and transposition of antimicrobial resistance genes. Serial passaging experiments were performed on a set of clinical ST131 ESBL-E isolates to recapitulate in vivo observations. qPCR and qRT-PCR were used to determine respective copy number and transcript levels of β-lactamase genes.Results116 ESBL-E bacteremia cases were identified, 16 of which had documented recurrent infections. Four serial, recurrent isolates displayed a carbapenem resistant phenotype, three without the acquisition of a known carbapenemase. These three isolates had non-carbapenemase-producing CRE (non-CP-CRE) mechanisms driven by IS26- and ISEcp1-mediated amplification of respective translocatable units (TU) and transposition units (TPU) harboring both blaOXA-1 and blaCTX-M variants with concomitant outer membrane porin disruption. The TU and TPU structures inserted into the open reading frames of outer membrane porin genes in a subset of non-CP-CRE isolates. Serial passage of an index ST131 ESBL-E isolate under selective carbapenem exposure resulted in chromosomal amplification of modular, TUs harboring β-lactamase genes with concomitant porin inactivation, recapitulating the in vivo carbapenem resistance progression. Long-read sequencing of two additional MDACC bacteremia strains identified similar non-CP-CRE mechanisms observed in the serial isolates.ConclusionsNon-CP-CRE de novo mechanisms were the primary driver of CRE development in recurrent bacteremia cases within this vulnerable patient population. The incorporation of long-read ONT data into AMR surveillance platforms is critical to identify high-risk CRE isolates that are difficult to identify with low-resolution phenotypic and molecular characterization methods.

scholarly journals Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq

DNA Research ◽  
2019 ◽  
Vol 26 (4) ◽  
pp. 353-363 ◽  
Author(s):  
Xiu Feng ◽  
Yintao Jia ◽  
Ren Zhu ◽  
Kang Chen ◽  
Yifeng Chen
Keyword(s):  
Gene Expression ◽  
Single Molecule ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Tibet Plateau ◽  
Comparative Genomic ◽  
Rna Seq ◽  
Gene Expression Atlas ◽  
Expression Atlas ◽  
Long Read

Abstract The lakes on the Qinghai-Tibet Plateau (QTP) are the largest and highest lake group in the world. Gymnocypris selincuoensis is the only cyprinid fish living in lake Selincuo, the largest lake on QTP. However, its genetic resource is still blank, limiting studies on molecular and genetic analysis. In this study, the transcriptome of G. selincuoensis was first generated by using PacBio Iso-Seq and Illumina RNA-seq. A full-length (FL) transcriptome with 75,435 transcripts was obtained by Iso-Seq with N50 length of 3,870 bp. Among all transcripts, 75,016 were annotated to public databases, 64,710 contain complete open reading frames and 2,811 were long non-coding RNAs. Based on all- vs.-all BLAST, 2,069 alternative splicing events were detected, and 80% of them were validated by reverse transcription polymerase chain reaction (RT-PCR). Tissue gene expression atlas showed that the number of detected expressed transcripts ranged from 37,397 in brain to 19,914 in muscle, with 10,488 transcripts detected in all seven tissues. Comparative genomic analysis with other cyprinid fishes identified 77 orthologous genes with potential positive selection (Ka/Ks > 0.3). A total of 56,696 perfect simple sequence repeats were identified from FL transcripts. Our results provide valuable genetic resources for further studies on adaptive evolution, gene expression and population genetics in G. selincuoensis and other congeneric fishes.

scholarly journals Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome

2019 ◽  
Author(s):  
S Arredondo-Alonso ◽  
J Top ◽  
AC Schürch ◽  
A McNally ◽  
S Puranen ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Large Scale ◽  
Population Genomics ◽  
Genomic Analysis ◽  
Adaptive Landscape ◽  
Priority List ◽  
Sequencing Technologies ◽  
Long Read ◽  
Pathogen Populations ◽  
High Level

AbstractEnterococcus faecium is a gut commensal of many mammals but is also recognized as a major nosocomial human pathogen, as it is listed on the WHO global priority list of multi-drug resistant organisms. Previous research has suggested that nosocomial strains have multiple zoonotic origins and are only distantly related to those involved in human commensal colonization. Here we present the first comprehensive population-wide joint genomic analysis of hospital, commensal and animal isolates using both short- and long-read sequencing techniques. This enabled us to investigate the population plasmidome, core genome variation and genome architecture in detail, using a combination of machine learning, population genomics and genome-wide co-evolution analysis. We observed a high level of genome plasticity with large-scale inversions and heterogeneous chromosome sizes, collectively painting a high-resolution picture of the adaptive landscape of E. faecium, and identified plasmids as the main indicator for host-specificity. Given the increasing availability of long-read sequencing technologies, our approach could be widely applied to other human and animal pathogen populations to unravel fine-scale mechanisms of their evolution.

scholarly journals SMRT-Cappable-seq reveals complex operon variants in bacteria

2018 ◽  
Author(s):  
Bo Yan ◽  
Matthew Boitano ◽  
Tyson Clark ◽  
Laurence Ettwiller
Keyword(s):  
Single Molecule ◽  
Gene Network ◽  
Accurate Identification ◽  
E Coli ◽  
Short Read Sequencing ◽  
Genome Wide ◽  
Long Read ◽  
Definition Of ◽  
Bacterial Genes

AbstractCurrent methods for genome-wide analysis of gene expression requires shredding original transcripts into small fragments for short-read sequencing. In bacteria, the resulting fragmented information hides operon complexity. Additionally,in-vivoprocessing of transcripts confounds the accurate identification of the 5’ and 3’ ends of operons. Here we developed a novel methodology called SMRT-Cappable-seq that combines the isolation of unfragmented primary transcripts with single-molecule long read sequencing. Applied toE. coli, this technology results in an unprecedented definition of the transcriptome with 34% of the known operons being extended by at least one gene. Furthermore, 40% of transcription termination sites have read-through that alters the gene content of the operons. As a result, most of the bacterial genes are present in multiple operon variants reminiscent of eukaryotic splicing. By providing an unprecedented granularity in the operon structure, this study represents an important resource for the study of prokaryotic gene network and regulation.

scholarly journals Carbapenems drive the collateral resistance to ceftaroline in cystic fibrosis patients with MRSA

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Maria Celeste Varela ◽  
Melanie Roch ◽  
Agustina Taglialegna ◽  
Scott W. Long ◽  
Matthew Ojeda Saavedra ◽  
...  
Keyword(s):  
Risk Factors ◽  
Cystic Fibrosis ◽  
Staphylococcus Aureus ◽  
Therapeutic Strategies ◽  
Penicillin Binding Protein ◽  
Molecular Relationships ◽  
High Level ◽  
Level Resistance

Abstract Chronic airways infection with methicillin-resistant Staphylococcus aureus (MRSA) is associated with worse respiratory disease cystic fibrosis (CF) patients. Ceftaroline is a cephalosporin that inhibits the penicillin-binding protein (PBP2a) uniquely produced by MRSA. We analyzed 335 S. aureus isolates from CF sputum samples collected at three US centers between 2015–2018. Molecular relationships demonstrated that high-level resistance of preceding isolates to carbapenems were associated with subsequent isolation of ceftaroline resistant CF MRSA. In vitro evolution experiments showed that pre-exposure of CF MRSA to meropenem with further selection with ceftaroline implied mutations in mecA and additional mutations in pbp1 and pbp2, targets of carbapenems; no effects were achieved by other β-lactams. An in vivo pneumonia mouse model showed the potential therapeutic efficacy of ceftaroline/meropenem combination against ceftaroline-resistant CF MRSA infections. Thus, the present findings highlight risk factors and potential therapeutic strategies offering an opportunity to both prevent and address antibiotic resistance in this patient population.

scholarly journals Carbapenem resistance in a clinical isolate of Citrobacter freundii.

1997 ◽  
Vol 41 (11) ◽  
pp. 2352-2354 ◽  
Author(s):  
J L Mainardi ◽  
P Mugnier ◽  
A Coutrot ◽  
A Buu-Hoï ◽  
E Collatz ◽  
...  
Keyword(s):  
Clinical Isolate ◽  
Outer Membrane Proteins ◽  
Carbapenem Resistance ◽  
Gram Negative Bacteria ◽  
Citrobacter Freundii ◽  
Resistant Strains ◽  
High Level

Carbapenem resistance was studied in two sets of Citrobacter freundii strains: (i) strain CFr950, resistant to imipenem (MIC, 16 microg/ml) and isolated in vivo during imipenem therapy, and strain CFr950-Rev, the spontaneous, imipenem-susceptible revertant of CFr950 selected in vitro, and (ii) strains CFr801 and CFr802, two imipenem-resistant mutants selected in vitro from the susceptible clinical isolate CFr800. In all strains, whether they were imipenem-susceptible or -resistant strains, production of the cephalosporinase was derepressed and their Km values for cephaloridine were in the range of 128 to 199 microM. No carbapenemase activity was detected in vitro. The role of cephalosporinase overproduction in the resistance was demonstrated after introduction of the ampD gene which decreased the level of production of cephalosporinase at least 250-fold and resulted in an 8- to 64-fold decrease in the MICs of the carbapenems. The role of reduced permeability in the resistance was suggested by the absence, in CFr950 and CFr802, of two outer membrane proteins (the 42- and 40-kDa putative porins whose levels were considerably decreased in CFr801) and the reappearance of the 42-kDa protein in imipenem-susceptible strain CFr950-Rev. This role was confirmed after introduction of the ompF gene of Escherichia coli into the CFr strains, which resulted in 8- to 16-fold decreases in the MICs of carbapenems for CFr802 and CFr950. We infer from these results that the association of reduced, porin-mediated permeability with high-level cephalosporinase production, observed previously in other gram-negative bacteria, may also confer carbapenem resistance on C. freundii.

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