NDM-5 and OXA-181 Beta-Lactamases, a Significant Threat Continues To Spread in the Americas

ABSTRACT Among Gram-negative bacteria, carbapenem-resistant infections pose a serious and life-threatening challenge. Here, the CRACKLE network reports a sentinel detection and characterization of a carbapenem-resistant Klebsiella pneumoniae ST147 isolate harboring bla NDM-5 and bla OXA-181 from a young man who underwent abdominal surgery in India. bla NDM-5 was located on an IncFII plasmid of ≈90 kb, whereas bla OXA-181 was chromosomally encoded. Resistome and genome analysis demonstrated multiple copies of the transposable element IS 26 and a “hot-spot region” in the IncFII plasmid

Genomic and Transcriptomic Analyses of Colistin-Resistant Clinical Isolates of Klebsiella pneumoniae Reveal Multiple Pathways of Resistance

ABSTRACT The emergence of multidrug-resistant (MDR) Klebsiella pneumoniae has resulted in a more frequent reliance on treatment using colistin. However, resistance to colistin (Col r ) is increasingly reported from clinical settings. The genetic mechanisms that lead to Col r in K. pneumoniae are not fully characterized. Using a combination of genome sequencing and transcriptional profiling by RNA sequencing (RNA-Seq) analysis, distinct genetic mechanisms were found among nine Col r clinical isolates. Col r was related to mutations in three different genes in K. pneumoniae strains, with distinct impacts on gene expression. Upregulation of the pmrH operon encoding 4-amino-4-deoxy- l -arabinose (Ara4N) modification of lipid A was found in all Col r strains. Alteration of the mgrB gene was observed in six strains. One strain had a mutation in phoQ . Common among these seven strains was elevated expression of phoPQ and unaltered expression of pmrCAB , which is involved in phosphoethanolamine addition to lipopolysaccharide (LPS). In two strains, separate mutations were found in a previously uncharacterized histidine kinase gene that is part of a two-component regulatory system (TCRS) now designated crrAB . In these strains, expression of pmrCAB , crrAB , and an adjacent glycosyltransferase gene, but not that of phoPQ , was elevated. Complementation with the wild-type allele restored colistin susceptibility in both strains. The crrAB genes are present in most K. pneumoniae genomes, but not in Escherichia coli . Additional upregulated genes in all strains include those involved in cation transport and maintenance of membrane integrity. Because the crrAB genes are present in only some strains, Col r mechanisms may be dependent on the genetic background

Genomic heterogeneity underlies multidrug resistance in Pseudomonas aeruginosa: A population-level analysis beyond susceptibility testing.

BACKGROUND: Pseudomonas aeruginosa is a persistent and difficult-to-treat pathogen in many patients, especially those with Cystic Fibrosis (CF). Herein, we describe a longitudinal analysis of a series of multidrug resistant (MDR) P. aeruginosa isolates recovered in a 17-month period, from a young female CF patient who underwent double lung transplantation. Our goal was to understand the genetic basis of the observed resistance phenotypes, establish the genomic population diversity, and define the nature of sequence evolution over time. METHODS: Twenty-two sequential P. aeruginosa isolates were obtained within a 17-month period, before and after a double-lung transplant. At the end of the study period, antimicrobial susceptibility testing, whole genome sequencing (WGS), phylogenetic analyses and RNAseq were performed in order to understand the genetic basis of the observed resistance phenotypes, establish the genomic population diversity, and define the nature of sequence changes over time. RESULTS: The majority of isolates were resistant to almost all tested antibiotics. A phylogenetic reconstruction revealed 3 major clades representing a genotypically and phenotypically heterogeneous population. The pattern of mutation accumulation and variation of gene expression suggested that a group of closely related strains was present in the patient prior to transplantation and continued to change throughout the course of treatment. A trend toward accumulation of mutations over time was observed. Different mutations in the DNA mismatch repair gene mutL consistent with a hypermutator phenotype were observed in two clades. RNAseq performed on 12 representative isolates revealed substantial differences in the expression of genes associated with antibiotic resistance and virulence traits. CONCLUSIONS: The overwhelming current practice in the clinical laboratories setting relies on obtaining a pure culture and reporting the antibiogram from a few isolated colonies to inform therapy decisions. Our analyses revealed significant underlying genomic heterogeneity and unpredictable evolutionary patterns that were independent of prior antibiotic treatment, highlighting the need for comprehensive sampling and population-level analysis when gathering microbiological data in the context of CF P. aeruginosa chronic infection. Our findings challenge the applicability of antimicrobial stewardship programs based on single-isolate resistance profiles for the selection of antibiotic regimens in chronic infections such as CF

Population Structure of KPC-Producing Klebsiella pneumoniae Isolates from Midwestern U.S. Hospitals

ABSTRACT Genome sequencing of carbapenem-resistant Klebsiella pneumoniae isolates from regional U.S. hospitals was used to characterize strain diversity and the bla KPC genetic context. A phylogeny based on core single-nucleotide variants (SNVs) supports a division of sequence type 258 (ST258) into two distinct groups. The primary differences between the groups are in the capsular polysaccharide locus ( cps ) and their plasmid contents. A strict association between clade and KPC variant was found. The bla KPC gene was found on variants of two plasmid backbones. This study indicates that highly similar K. pneumoniae subpopulations coexist within the same hospitals over time

K2-79b and K2-222b: Mass Measurements of Two Small Exoplanets with Periods beyond 10 days that Overlap with Periodic Magnetic Activity Signals

Abstract We present mass and radius measurements of K2-79b and K2-222b, two transiting exoplanets orbiting active G-type stars observed with HARPS-N and K2. Their respective 10.99 day and 15.39 day orbital periods fall near periods of signals induced by stellar magnetic activity. The two signals might therefore interfere and lead to an inaccurate estimate of exoplanet mass. We present a method to mitigate these effects when radial velocity (RV) and activity-indicator observations are available over multiple observing seasons and the orbital period of the exoplanet is known. We perform correlation and periodogram analyses on subsets composed of each target's two observing seasons, in addition to the full data sets. For both targets, these analyses reveal an optimal season with little to no interference at the orbital period of the known exoplanet. We make a confident mass detection of each exoplanet by confirming agreement between fits to the full RV set and the optimal season. For K2-79b, we measure a mass of 11.8 ± 3.6 M ⊕ and a radius of 4.09 ± 0.17 R ⊕. For K2-222b, we measure a mass of 8.0 ± 1.8 M ⊕ and a radius of 2.35 ± 0.08 R ⊕. According to model predictions, K2-79b is a highly irradiated Uranus analog and K2-222b hosts significant amounts of water ice. We also present a RV solution for a candidate second companion orbiting K2-222 at 147.5 days.</jats:p

The Kepler-454 system : A small, not-rocky inner planet, a Jovian world, and a distant companion

Kepler-454 (KOI-273) is a relatively bright (V = 11.69 mag), Sun-like starthat hosts a transiting planet candidate in a 10.6 d orbit. From spectroscopy, we estimate the stellar temperature to be 5687 +/- 50 K, its metallicity to be [m/H] = 0.32 +/- 0.08, and the projected rotational velocity to be v sin i 10 years and mass >12.1M_J . The twelve exoplanets with radii <2.7 R_Earth and precise mass measurements appear to fall into two populations, with those <1.6 R_Earth following an Earth-like composition curve and larger planets requiring a significant fraction of volatiles. With a density of 2.76 +/- 0.73 g cm-3, Kepler-454b lies near the mass transition between these two populations and requires the presence of volatiles and/or H/He gas.PostprintPeer reviewe

Characterization of a Novel Pathogen in Immunocompromised Patients: Elizabethkingia anophelis-Exploring the Scope of Resistance to Contemporary Antimicrobial Agents and β-lactamase Inhibitors

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