Nested Russian Doll-like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Genebla_KPC

Abstract

The recent widespread emergence of carbapenem resistance in Enterobacteriaceae is a major public health concern, as carbapenems are a therapy of last resort in this family of common bacterial pathogens. Resistance genes can mobilize via various mechanisms including conjugation and transposition, however the importance of this mobility in short-term evolution, such as within nosocomial outbreaks, is currently unknown. Using a combination of short- and long-read whole genome sequencing of 281 blaKPC-positive Enterobacteriaceae isolated from a single hospital over five years, we demonstrate rapid dissemination of this carbapenem resistance gene to multiple species, strains, and plasmids. Mobility of blaKPC occurs at multiple nested genetic levels, with transmission of blaKPC strains between individuals, frequent transfer of blaKPC plasmids between strains/species, and frequent transposition of the blaKPC transposon Tn4401 between plasmids. We also identify a common insertion site for Tn4401 within various Tn2-like elements, suggesting that homologous recombination between Tn2-like elements has enhanced the spread of Tn4401 between different plasmid vectors. Furthermore, while short-read sequencing has known limitations for plasmid assembly, various studies have attempted to overcome this with the use of reference-based methods. We also demonstrate that as a consequence of the genetic mobility observed herein, plasmid structures can be extremely dynamic, and therefore these reference-based methods, as well as traditional partial typing methods, can produce very misleading conclusions. Overall, our findings demonstrate that non-clonal resistance gene dissemination can be extremely rapid, presenting significant challenges for public health surveillance and achieving effective control of antibiotic resistance.ImportanceIncreasing antibiotic resistance is a major threat to human health, as highlighted by the recent emergence of multi-drug resistant “superbugs”. Here, we tracked how one important multi-drug resistance gene spread in a single hospital over five years. This revealed high levels of resistance gene mobility to multiple bacterial species, which was facilitated by various different genetic mechanisms. The mobility occurred at multiple nested genetic levels, analogous to a Russian doll set where smaller dolls may be carried along inside larger dolls. Our results challenge traditional views that drug-resistance outbreaks are due to transmission of a single pathogenic strain. Instead, outbreaks can be “gene-based”, and we must therefore focus on tracking specific resistance genes and their context rather than only specific bacteria.

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

“…This suggests K. pneumoniae receives DNA from a wider diversity of HGT partners; indeed lowest common ancestor analysis of K. pneumoniae accessory genes has implicated >20 distinct genera as DNA donors, including numerous other members of the Enterobacteriaceae but also diverse groups such as Acinetobacter, Burkholderia, Streptomyces, Vibrio, Xanthomonas and Xyella [9]. More direct evidence for K. pneumoniae engaging in inter--species HGT can be found in recent genomic comparisons of carbapenem--resistant Enterobacteriaciae in hospitals, which captured identical or highly similar carbapenemase encoding plasmids and/or transposons from K. pneumoniae and other species originating from the same ward and/or patient (E. coli, E. cloacae, Enterobacter asburiae, Citrobacter freundii, Klebsiella oxytoca, Raoultella ornothinolytica) [73][74][75].…”

Relación clonal y detección del gen blaKPC en cepas de Klebsiella pneumoniae resistentes a carbapenémicos, en un hospital de Venezuela

“…Este resultado es similar al obtenido en otra investigación realizada en Venezuela, donde se reportó un predominio de policlonalidad en cepas de K. pneumoniae productoras de β-lactamasas de espectro extendido 30 . La policlonalidad obtenida entre 2011 y 2014 puede deberse a la aparición de nuevos clones o a la adición sucesiva de eventos genéticos como la transferencia horizontal de genes mediante plásmidos y/o transposones o mutaciones puntuales, producto de la presión selectiva generada por el uso indiscriminado de antimicrobianos en los diferentes servicios del HUAPA, favorecido por la presencia en estas cepas del gen plasmídico bla KPC que, como se ha señalado, se encuentra frecuentemente en un transposón 10,13,14 .…”

“…Las serino-carbapenemasas KPC están codificadas por el gen plasmídico bla KPC . Este gen está localizado principalmente en el elemento transponible Tn4401, que facilita la transferencia entre plásmidos de bacterias de la misma o diferente especie 4,10,12 ; actualmente existen reportes de este gen en otras localizaciones 13,14 . En Latinoamérica el primer reporte de K. pneumoniae con el gen bla KPC fue en Colombia en el año 2006 11 .…”

Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms

“…However, the studies used to inform stewardship decisions generally evaluate the risk of antibiotic resistance associated with singlebacterial species. This single-species view of MDRO epidemiology does not reflect the complex reality; most healthcare facilities have multiple circulating MDRO species (20,21), and individuals are often colonized by more than one MDRO (22-24). Thus, interventions based on a single-species perspective can result in unintended consequences.…”