Detection and Whole-Genome Analysis of a High-Risk Clone of Klebsiella pneumoniae ST340/CG258 Producing CTX-M-15 in a Companion Animal

Phylogenomic Analysis of CTX-M-15-Positive Escherichia coli from Companion Animal Reveals Intercontinental Dissemination of ST90 Within a One Health Framework

The global dissemination of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli has been considered a critical issue within a One Health framework. The aim of this study was to perform a genomic investigation of an ESBL-producing E. coli strain belonging to the globally spread sequence type/clonal complex ST90/CC23, isolated from gastrointestinal tract of a dog, in Brazil. Besides CTX-M-15 ESBL, this E. coli isolate carried mutations conferring resistance to human and veterinary fluoroquinolones (GyrA [Ser83Leu, Asp87Asn], ParC [Ser80Ile] and ParE [Ser458Ala]), and resistance determinants to disinfectants and pesticides. Noteworthy, phylogenomic analysis revealed that this multidrug E. coli strain clustered with ST90 lineages isolated from human, dog, and livestock in Brazil. The phylogenetic tree also revealed that this E. coli strain shares a common ancestor with isolates from the United States, Russia, Germany, and China, highlighting the potential global spreading of this clone. In summary, we report genomic data of CTX-M-15-positive E.coli ST90 colonizing a pet. Colonization of companion animals by critical resistant pathogens highlights the need for close monitoring to better understand the epidemiology and genetic factors contributing for successful adaptation of global clones at the human-animal interface.

Emergence of Urease-Negative Klebsiella pneumoniae ST340 Carrying an IncP6 Plasmid-Mediated blaKPC-2 Gene

An unusual biotype of KPC-2-producing Klebsiella pneumoniae (KPC-Kpn) isolates was detected in Corrientes, Argentina, which, to their isolation date, had been free of KPC-Kpn outbreaks. Our aim was to describe the clinical epidemiology focused on genomic characterization of atypical urease-negative KPC-Kpn clinical isolates belonging to the high-risk hospital-associated clonal lineage ST340/CC258. Thirteen isolates were recovered, all of them from inpatients with KPC-Kpn infection (August 2015 to January 2016). These isolates displayed identical enterobacterial repetitive intergenic consensus-PCR electropherotype belonging to a single clonal sequence type ST340. Whole genome sequencing was performed on two KPC-Kpn and the resistome analyses revealed the following acquired resistance genes: bla_KPC-2, bla_CTX-M-15, bla_OXA-1, bla_SHV-11, aac(3)-IId, aph(3')-Ia, aac(6')-Ib-cr, sul1, dfrA14, catB3, fosA, and arr-3. Mutations in GyrA (S83I) and ParC (S80I) were also identified. Among the virulence determinants, yersiniabactin was detected in both strains, specifically the ybt9 locus located in ICEKp3. Five plasmid incompatibility groups were observed in this clone and an unusual IncP6 plasmid bearing bla_KPC-2 gene (named pKpn3KP) was fully characterized. In this study, we present the first draft genome sequences of two clinical isolates of KPC-2/CTX-M-15-producing K. pneumoniae belonging to the high-risk clonal lineage ST340/CC258 associated with nosocomial outbreaks in Argentina.

Pandemic Clones of CTX-M-15 Producing Klebsiella pneumoniae ST15, ST147, and ST307 in Companion Parrots

Psittacine birds are commonly kept as companion birds and the maintenance of these birds in captivity may represent a zoonotic risk and contribute to the propagation of multidrug-resistant and β-lactamase extended-spectrum (ESBLs)-producing pathogens. This study aimed to identify and characterize strains of the Klebsiella pneumoniae complex isolated from diseased psittacine birds, determining virulence and resistance profiles. K. pneumoniae strains were isolated from 16 birds (16/46). All strains carried more than three virulence genes, with a high frequency of fimH and kpn (93.75%), uge (87.52%), and irp-2 (81.25%) genes. The antimicrobial susceptibility revealed that 3/16 strains were ESBL producers. Genomic analysis revealed that CTX-M-15-positive strains belonged to sequence types (STs) ST15, ST147, and ST307, characterized as international clones associated with outbreaks of healthcare-associated infections (HAIs) worldwide.

CTX-M-15-producing Klebsiella pneumoniae ST273 associated with nasal infection in a domestic cat

OBJECTIVE

The aim of the present study was to investigate the genetic context of expanded spectrum beta-lactam resistance in a Klebsiella pneumoniae strain causing hard-to-treat nasal infection in a domestic cat.

METHODS

A K. pneumoniae isolate was recovered from a 4-year-old male cat hospitalized in a Veterinary Hospital in Paraíba, Northeastern Brazil. After phenotypic confirmation of multidrug resistance by the disk diffusion method, the genome was sequenced in Illumina MiSeq. Multilocus sequence typing (MLST), and structural features related to antimicrobial resistance was determined by downstream bioinformatics analyses.

RESULTS

The strain was confirmed as Sequence Type (ST) 273 Klebsiella pneumoniae harbouring a variety of genes conferring antimicrobial resistance to phenicols tetracyclines, aminoglycosides, β-lactams, fosfomycin, sulphonamides and quinolones. Two plasmids were identified. The plasmid p114PB_I co-harbored a set of plasmid-borne resistance genes [bla_CTX-M-15, bla_TEM-1, qnrS1, tetD, tetR, sul2, aph(6)-Id, aph(3'') and cat2]. Notably, the multi-resistance region was characterized as a chimeric plasmid structure sharing high sequence homology with several plasmids from Enterobacteriaceae. The second plasmid (p114PB_II) was characterized as a plasmid present in many genomes belonging to K. pneumoniae.

CONCLUSION

The genetic context of the plasmid sequences harbored by a veterinary pathogenic K. pneumoniae reveals the high complexity of horizontal gene transfer mechanisms in the acquisition of antimicrobial resistance genes. The emergence, dissemination, and evolution of antimicrobial resistance must be investigated from a One Health perspective.

A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307

Objectives

To use the nationwide Norwegian surveillance programme on resistant microbes in humans (NORM) to address longitudinal changes in the population structure of Klebsiella pneumoniae isolates from 2001–15, focusing on the emergence and dissemination of ESBL-producing K. pneumoniae in Norway.

Methods

Among blood (n = 6124) and urinary tract (n = 5496) surveillance isolates from 2001–15, we used Illumina technology to whole genome sequence 201 ESBL-producing isolates from blood (n = 130) and urine (n = 71), and 667 non-ESBL isolates from blood. Complete genomes for four isolates were resolved with Oxford Nanopore sequencing.

Results

In a highly diverse collection, Klebsiella variicola ssp. variicola caused 24.5% of Klebsiella pneumoniae species complex (KpSC) bacteraemias. ESBL production was limited to K. pneumoniae sensu stricto (98.5%). A diverse ESBL population of 57 clonal groups (CGs) were dominated by MDR CG307 (17%), CG15 (12%), CG70 (6%), CG258 (5%) and CG45 (5%) carrying bla_CTX-M-15. Yersiniabactin was significantly more common in ESBL-positive (37.8%) compared with non-ESBL K. pneumoniae sensu stricto isolates (12.7%), indicating convergence of virulence and resistance determinants. Moreover, we found a significantly lower prevalence of yersiniabactin (3.0%, 37.8% and 17.3%), IncFIB (58.7%, 87.9% and 79.4%) and IncFII plasmid replicons (40.5%, 82.8% and 54.2%) in K. variicola ssp. variicola compared with ESBL- and non-ESBL K. pneumoniae sensu stricto isolates, respectively.

Conclusions

The increase in Norwegian ESBL-producing KpSC during 2010–15 was driven by CG307 and CG15 carrying bla_CTX-M-15. K. variicola ssp. variicola was a frequent cause of invasive KpSC infection, but rarely carried ESBLs.

Detection of a NDM-5-producing Klebsiella pneumoniae sequence type 340 (CG258) high-risk clone in swine

The emergence and rapid increase of carbapenem-resistant Enterobacteriaceae among food-producing animals poses a serious threat to public health. The aim of this study was to investigate the presence and dissemination of bla_NDM-5 in porcine Klebsiella pneumoniae isolates. Of 19 meropenem-resistant K. pneumoniae isolates, 18 were bla_NDM-5-positive and one carried bla_NDM-1. Susceptibility testing indicated that all bla_NDM-carrying K. pneumoniae showed a multiple drug resistance (MDR) profile. The bla_NDM-5 gene was located on a conjugative IncX3 plasmid of ∼46-kb in all 18 bla_NDM-5-carrying isolates. MLST analysis revealed that ST340 (n = 8), a member of the worldwide existing high-risk epidemic clonal group 258 (CG258), was predominant. Furthermore, whole genome sequence (WGS) analysis for one representative ST340 K. pneumoniae Kp19110124 showed a MDR profile for a wide range of antimicrobial agents, including meropenem, various cephalosporins, azteonam, gentamicin, ciprofloxacin, and florfenicol. Phylogenetic analysis exhibited that K. pneumoniae ST340 strains were clustered into one branch, which had spread across host species and across continents. Among them, K. pneumoniae Kp19110124 displayed a very close relationship with a clinical isolate collected from a patient in Canada. In conclusion, these results reveal the presence of a bla_NDM-5-carrying conjugative IncX3 type plasmid into K. pneumoniae ST340 clone, which then may accelerate the dissemination of the bla_NDM-5 gene in porcine K. pneumoniae isolates. The detection of high-risk bla_NDM-5-carrying K. pneumoniae ST340 in food-producing animal poses a serious threat to public health.

Multidrug-resistant Klebsiella pneumoniae harboring extended spectrum β-lactamase encoding genes isolated from human septicemias

Klebsiella pneumoniae is a major pathogen implicated in nosocomial infections. Extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae isolates are a public health concern. We aim to characterize the type of β-lactamases and the associated resistance mechanisms in ESBL-producing K. pneumoniae isolates obtained from blood cultures in a Portuguese hospital, as well as to determine the circulating clones. Twenty-two cefotaxime/ceftazidime-resistant (CTX/CAZ^R) K. pneumoniae isolates were included in the study. Identification was performed by MALDI-TOF MS and the antimicrobial susceptibility testing by disk-diffusion. The screening test for ESBL-production was performed and ESBL-producer isolates were further characterized. The presence of different beta-lactamase genes (bla_CTX-M, bla_SHV, bla_TEM, bla_KPC, bla_NDM,bla_VIM,bla_OXA-48,bla_CMY-2, bla_DHA-1,bla_FOX,bla_MOX, and bla_ACC) was analyzed by PCR/sequencing in ESBL-producer isolates, as well as the presence of other resistance genes (aac(6’)-Ib-cr, tetA/B, dfrA, qnrA/B/S, sul1/2/3) or integron-related genes (int1/2/3). Multilocus-sequence-typing (MLST) was performed for selected isolates. ESBL activity was detected in 12 of the 22 CTX/CAZ^RK. pneumoniae isolates and 11 of them carried the bla_CTX-M-15 gene (together with bla_TEM)_, and the remaining isolate carried the bla_SHV-106 gene. All the bla_CTX-M-15 harboring isolates also contained a bla_SHV gene (bla_SHV-1, bla_SHV-11 or bla_SHV-27 variants). Both bla_SHV-27 and bla_SHV-106 genes correspond to ESBL-variants. Two of the CTX-M-15 producing isolates carried a carbapenemase gene (bla_KPC2/3 and bla_OXA-48) and showed imipenem resistance. The majority of the ESBL-producing isolates carried the int1 gene, as well as sulphonamide-resistance genes (sul2 and/or sul3); the tetA gene was detected in all eight tetracycline-resistant isolates. Three different genetic lineages were found in selected isolates: ST348 (one CTX-M-15/TEM/SHV-27/KPC-2/3-producer isolate), ST11 (two CTX-M-15/TEM/SHV-1- and CTX-M-15-TEM-SHV-11-OXA-48-producer isolates) and ST15 (one SHV-106/TEM-producer isolate). ESBL enzymes of CTX-M-15 or SHV-type are detected among blood K. pneumoniae isolates, in some cases in association with carbapenemases of KPC or OXA-48 type.

Endophytic Lifestyle of Global Clones of Extended-Spectrum β-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization?

The global spread of antibiotic-resistant bacteria and their resistance genes is a critical issue that is no longer restricted to hospital settings, but also represents a growing problem involving environmental and food safety. In this study, we have performed a microbiological and genomic investigation of critical priority pathogens resistant to broad-spectrum cephalosporins and showing endophytic lifestyles in fresh vegetables sold in a country with high endemicity of extended-spectrum β-lactamases (ESBLs). We report the isolation of international high-risk clones of CTX-M-15-producing Escherichia coli, belonging to clonal complexes CC38 and CC648, and Klebsiella pneumoniae of complex CC307 from macerated tissue of surface-sterilized leaves of spinach, cabbage, arugula, and lettuce. Regardless of species, all ESBL-positive isolates were able to endophytically colonize common bean (Phaseolus vulgaris) seedlings, showed resistance to acid pH, and had a multidrug-resistant (MDR) profile to clinically relevant antibiotics (i.e., broad-spectrum cephalosporins, aminoglycosides, and fluoroquinolones). Genomic analysis of CTX-M-producing endophytic Enterobacterales revealed a wide resistome (antibiotics, biocides, disinfectants, and pesticides) and virulome, and genes for endophytic fitness and for withstanding acidic conditions. Transferable IncFIB and IncHI2A plasmids carried bla _CTX-M-15 genes and, additionally, an IncFIB plasmid (named pKP301cro) also harbored genes encoding resistance to heavy metals. These data support the hypothesis that fresh vegetables marketed for consumption can act as a figurative Trojan horse for the hidden spread of international clones of critical WHO priority pathogens producing ESBLs, and/or their resistance genes, to humans and other animals, which is a critical issue within a food safety and broader public and environmental health perspective.IMPORTANCE Extended-spectrum β-lactamases (ESBL)-producing Enterobacterales are a leading cause of human and animal infections, being classified as critical priority pathogens by the World Health Organization. Epidemiological studies have shown that spread of ESBL-producing bacteria is not a problem restricted to hospitals, but also represents a growing problem involving environmental and food safety. In this regard, CTX-M-type β-lactamases have become the most widely distributed and clinically relevant ESBLs worldwide. Here, we have investigated the occurrence and genomic features of ESBL-producing Enterobacterales in surface-sterilized fresh vegetables. We have uncovered that international high-risk clones of CTX-M-15-producing Escherichia coli and Klebsiella pneumoniae harboring a wide resistome and virulome, carry additional genes for endophytic fitness and resistance to acidic conditions. Furthermore, we have demonstrated that these CTX-M-15-positive isolates are able to endophytically colonize plant tissues. Therefore, we believe that fresh vegetables can act as a figurative Trojan horse for the hidden spread of critical priority pathogens exhibiting endophytic lifestyles.