Detection of IncN-pST15 one-health plasmid harbouring blaKPC-2 in a hypermucoviscous Klebsiella pneumoniae CG258 isolated from an infected dog, Brazil

Emergence of carbapenem-resistant Klebsiella pneumoniae species complex from agrifood systems: detection of ST6326 co-producing KPC-2 and NDM-1

BACKGROUND

Klebsiella pneumoniae species complex (KpSC) is an important disseminator of carbapenemase-encoding genes, mainly blaKPC-2 and blaNDM-1, from hospitals to the environment. Consequently, carbapenem-resistant strains can be spread through the agrifood system, raising concerns about food safety. This study therefore aimed to isolate carbapenem-resistant KpSC strains from the agricultural and environmental sectors and characterize them using phenotypic, molecular, and genomic analyses.

RESULTS

Klebsiella pneumoniae and Klebsiella quasipneumoniae strains isolated from soils used for lemon, guava, and fig cultivation, and from surface waters, displayed an extensive drug-resistance profile and carried blaKPC-2, blaNDM-1, or both. In addition to carbapenemase-encoding genes, KpSC strains harbor a broad resistome (antimicrobial resistance and metal tolerance) and present putative hypervirulence. Soil-derived K. pneumoniae strains were assigned as high-risk clones (ST11 and ST307) and harbored the blaKPC-2 gene associated with Tn4401b and Tn3-like elements on IncN-pST15 and IncX5 plasmids. In surface waters, the coexistence of blaKPC-2 and blaNDM-1 genes was identified in K. pneumoniae ST6326, a new carbapenem-resistant regional Brazilian clone. In this case, blaKPC-2 with Tn4401a isoform and blaNDM-1 associated with a Tn125-like transposon were located on different plasmids. Klebsiella quasipneumoniae ST526 also presented the blaNDM-1 gene associated with a Tn3000 transposon on an IncX3 plasmid.

CONCLUSION

These findings provide a warning regarding the transmission of carbapenemase-positive KpSC across the agricultural and environmental sectors, raising critical food safety and environmental issues. © 2024 Society of Chemical Industry.

Tracking intra-species and inter-genus transmission of KPC through global plasmids mining

Klebsiella pneumoniae carbapenemase (KPC) poses a major public health risk. Understanding its transmission dynamics requires examining the epidemiological features of related plasmids. Our study compiled 15,660 blaKPC-positive isolates globally over the past two decades. We found extensive diversity in the genetic background of KPC, with 23 Tn4401-related and 341 non-Tn4401 variants across 163 plasmid types in 14 genera. Intra-K. pneumoniae and cross-genus KPC transmission patterns varied across four distinct periods. In the initial periods, plasmids with narrow host ranges gradually established a survival advantage. In later periods, broad-host-range plasmids became crucial for cross-genera transmission. In total, 61 intra-K. pneumoniae and 66 cross-genus transmission units have been detected. Furthermore, phylogenetic reconstruction dated the origin of KPC transmission back to 1991 and revealed frequent exchanges across countries. Our research highlights the frequent and transient spread events of KPC mediated by plasmids across multiple genera and offers theoretical support for high-risk plasmid monitoring.

Genetic diversity of KPC-2-producing Klebsiella pneumoniae complex from aquatic ecosystems

During the COVID-19 pandemic, the occurrence of carbapenem-resistant Klebsiella pneumoniae increased in human clinical settings worldwide. Impacted by this increase, international high-risk clones harboring carbapenemase-encoding genes have been circulating in different sources, including the environment. The blaKPC gene is the most commonly disseminated carbapenemase-encoding gene worldwide, whose transmission is carried out by different mobile genetic elements. In this study, blaKPC-2-positive Klebsiella pneumoniae complex strains were isolated from different anthropogenically affected aquatic ecosystems and characterized using phenotypic, molecular, and genomic methods. K. pneumoniae complex strains exhibited multidrug-resistant and extensively drug-resistant profiles, spotlighting the resistance to carbapenems, ceftazidime-avibactam, colistin, and tigecycline, which are recognized as last-line antimicrobial treatment options. Molecular analysis showed the presence of several antimicrobial resistance, virulence, and metal tolerance genes. In-depth analysis showed that the blaKPC-2 gene was associated with three different Tn4401 isoforms (i.e., Tn4401a, Tn4401b, and Tn4401i) and NTEKPC elements. Different plasmid replicons were detected and a conjugative IncN-pST15 plasmid harboring the blaKPC-2 gene associated with Tn4401i was highlighted. K. pneumoniae complex strains belonging to international high-risk (e.g., ST11 and ST340) and unusual clones (e.g., ST323, ST526, and ST4216) previously linked to clinical settings. In this context, some clones were reported for the first time in the environmental sector. Therefore, these findings evidence the occurrence of carbapenemase-producing K. pneumoniae complex strains in aquatic ecosystems and contribute to the monitoring of carbapenem resistance worldwide.

Genomic features of an extensively drug-resistant and NDM-1-positive Klebsiella pneumoniae ST340 isolated from river water

The environmental contamination plays a significant role in the emergence of antimicrobial resistance. In this study, we report a genomic analysis of an extensively drug-resistant and blaNDM-1-producing Klebsiella pneumoniae (EW807) strain recovered from a surface water sample. Strain EW807 belonged to sequence type (ST) 340 and serotype O4:KL15, a high-risk clone of the clonal group 258. This strain carried a broad resistome, including blaNDM-1 and blaCTX-M-15. The core genome multilocus sequence typing phylogenetic analysis revealed that the EW807 strain was most related to strains from Brazil and the USA. An IncX3 plasmid was identified harboring the blaNDM-1 gene, while an IncFIB(K) plasmid was detected carrying the blaCTX-M-15 in addition to multidrug resistance and multimetal tolerance regions. IncX3 and IncFIB(K) plasmids shared high similarity with plasmids from a human in China and a dog in Brazil, respectively. The regions harboring the blaNDM-1 and blaCTX-M-15 genes contained sequences from the Tn3 family. These findings suggest that IncX3 plasmid could play a role in the spread of NDM-1 in a post-pandemic scenario. To the best of our knowledge, this is the first report of blaNDM-1-producing K. pneumoniae ST340 O4:KL15 strain in the environment. Therefore, the presence of high-risk clones of K. pneumoniae carrying carbapenemases in the environment requires strict surveillance.

Genetic plurality of blaKPC-2-harboring plasmids in high-risk clones of Klebsiella pneumoniae of environmental origin

International high-risk clones of Klebsiella pneumoniae are important human pathogens that are spreading to the environment. In the COVID-19 pandemic scenario, the frequency of carbapenemase-producing strains increased, which can contribute to the contamination of the environment, impacting the surrounding and associated ecosystems. In this regard, KPC-producing strains were recovered from aquatic ecosystems located in commercial, industrial, or agricultural areas and were submitted to whole-genome characterization. K. pneumoniae and Klebsiella quasipneumoniae subsp. quasipneumoniae strains were assigned to high-risk clones (ST11, ST340, ST307) and the new ST6325. Virulome analysis showed genes related to putative hypervirulence. Strains were resistant to almost all antimicrobials tested, being classified as extensively drug-resistant or multidrug-resistant. In this context, a broad resistome (clinically important antimicrobials and hazardous metal) was detected. Single replicon (IncX5, IncN-pST15, IncU) and multireplicon [IncFII(K1)/IncFIB(pQil), IncFIA(HI1)/IncR] plasmids were identified carrying the bla_KPC-2 gene with Tn4401 and non-Tn4401 elements. An unusual association of bla_KPC-2 and qnrVC1 and the coexistence of bla_KPC-2 and mer operon (mercury tolerance) was found. Comparative analysis revealed that bla_KPC-2-bearing plasmids were most similar to plasmids from Enterobacterales of Brazil, China, and the United States, evidencing the long persistence of plasmids at the human-animal-environmental interface. Furthermore, the presence of uncommon plasmids, displaying the interspecies, intraspecies, and clonal transmission, was highlighted. These findings alert for the spread of high-risk clones producing bla_KPC-2 in the environmental sector and call attention to rapid dispersion in a post-pandemic world.

An overview of carbapenem-resistant organisms from food-producing animals, seafood, aquaculture, companion animals, and wildlife

Carbapenem resistance (CR) is a major global health concern. CR is a growing challenge in clinical settings due to its rapid dissemination and low treatment options. The characterization of its molecular mechanisms and epidemiology are highly studied. Nevertheless, little is known about the spread of CR in food-producing animals, seafood, aquaculture, wildlife, their environment, or the health risks associated with CR in humans. In this review, we discuss the detection of carbapenem-resistant organisms and their mechanisms of action in pigs, cattle, poultry, seafood products, companion animals, and wildlife. We also pointed out the One Health approach as a strategy to attempt the emergency and dispersion of carbapenem-resistance in this sector and to determine the role of carbapenem-producing bacteria in animals among human public health risk. A higher occurrence of carbapenem enzymes in poultry and swine has been previously reported. Studies related to poultry have highlighted P. mirabilis, E. coli, and K. pneumoniae as NDM-5- and NDM-1-producing bacteria, which lead to carbapenem resistance. OXA-181, IMP-27, and VIM-1 have also been detected in pigs. Carbapenem resistance is rare in cattle. However, OXA- and NDM-producing bacteria, mainly E. coli and A. baumannii, are cattle's leading causes of carbapenem resistance. A high prevalence of carbapenem enzymes has been reported in wildlife and companion animals, suggesting their role in the cross-species transmission of carbapenem-resistant genes. Antibiotic-resistant organisms in aquatic environments should be considered because they may act as reservoirs for carbapenem-resistant genes. It is urgent to implement the One Health approach worldwide to make an effort to contain the dissemination of carbapenem resistance.

Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone

The most common resistance mechanism to carbapenems is the production of carbapenemases. In 2021, the Pan American Health Organization warned of the emergence and increase in new carbapenemase combinations in Enterobacterales in Latin America. In this study, we characterized four Klebsiella pneumoniae isolates harboring bla_KPC and bla_NDM from an outbreak during the COVID-19 pandemic in a Brazilian hospital. We assessed their plasmids' transference ability, fitness effects, and relative copy number in different hosts. The K. pneumoniae BHKPC93 and BHKPC104 strains were selected for whole genome sequencing (WGS) based on their pulsed-field gel electrophoresis profile. The WGS revealed that both isolates belong to ST11, and 20 resistance genes were identified in each isolate, including bla_KPC-2 and bla_NDM-1. The bla_KPC gene was present on a ~56 Kbp IncN plasmid and the bla_NDM-1 gene on a ~102 Kbp IncC plasmid, along with five other resistance genes. Although the bla_NDM plasmid contained genes for conjugational transfer, only the bla_KPC plasmid conjugated to E. coli J53, without apparent fitness effects. The minimum inhibitory concentrations (MICs) of meropenem/imipenem against BHKPC93 and BHKPC104 were 128/64 and 256/128 mg/L, respectively. Although the meropenem and imipenem MICs against E. coli J53 transconjugants carrying the bla_KPC gene were 2 mg/L, this was a substantial increment in the MIC relative to the original J53 strain. The bla_KPC plasmid copy number was higher in K. pneumoniae BHKPC93 and BHKPC104 than in E. coli and higher than that of the bla_NDM plasmids. In conclusion, two ST11 K. pneumoniae isolates that were part of a hospital outbreak co-harbored bla_KPC-2 and bla_NDM-1. The bla_KPC-harboring IncN plasmid has been circulating in this hospital since at least 2015, and its high copy number might have contributed to the conjugative transfer of this particular plasmid to an E. coli host. The observation that the bla_KPC-containing plasmid had a lower copy number in this E. coli strain may explain why this plasmid did not confer phenotypic resistance against meropenem and imipenem.

Carbapenem resistance in critically important human pathogens isolated from companion animals: a systematic literature review

This study aimed to describe the presence and geographical distribution of Gram-negativebacteria considered critical on the priority list of antibiotic-resistant pathogens publishedby the World Health Organization, including carbapenem-resistant Enterobacteriaceae,carbapenem-resistant Acinetobacter spp., and carbapenem-resistant Pseudomonas aeruginosa.A systematic review of original studies published in 5 databases between 2010 and 2021 wasconducted, including genotypically confirmed carbapenem-resistant isolates obtained fromcanines, felines, and their settings. Fifty-one articles met the search criteria. Carbapenemresistant isolates were found in domestic canines and felines, pet food, and on veterinarymedical and household surfaces. The review found that the so-called "big five"-that is, the5 major carbapenemases identified worldwide in Enterobacterales (New Delhi metallo-βlactamase, active-on-imipenem, Verona integron-encoded metallo-β-lactamase, Klebsiellapneumoniae carbapenemase, and oxacillin [OXA]-48-like)-and the 3 most importantcarbapenemases from Acinetobacter spp. (OXA-23-like, OXA-40-like, and OXA-58-like) hadbeen detected in 8 species in the Enterobacteriaceae family and 5 species of glucose nonfermenting bacilli on 5 continents. Two publications used molecular analysis to confirmcarbapenem-resistant bacteria transmission between owners and dogs. Isolating criticallyimportant human carbapenem-resistant Gram-negative bacteria from domestic canines andfelines highlights the importance of including these animal species in surveillance programsand antimicrobial resistance containment plans as part of the One Health approach.

Detection of IMP-4 and SFO-1 co-producing ST51 Enterobacter hormaechei clinical isolates

Purpose

To explore the genetic characteristics of the IMP-4 and SFO-1 co-producing multidrug-resistant (MDR) clinical isolates, Enterobacter hormaechei YQ13422hy and YQ13530hy.

Methods

MALDI-TOF MS was used for species identification. Antibiotic resistance genes (ARGs) were tested by PCR and Sanger sequencing analysis. In addition to agar dilution, broth microdilution was used for antimicrobial susceptibility testing (AST). Whole-genome sequencing (WGS) analysis was conducted using the Illumina NovaSeq 6000 and Oxford Nanopore platforms. Annotation was performed by RAST on the genome. The phylogenetic tree was achieved using kSNP3.0. Plasmid characterization was conducted using S1-pulsed-field gel electrophoresis (S1-PFGE), Southern blotting, conjugation experiments, and whole genome sequencing (WGS). An in-depth study of the conjugation module was conducted using the OriTFinder website. The genetic context of bla IMP-4 and bla SFO-1 was analyzed using BLAST Ring Image Generator (BRIG) and Easyfig 2.3.

Results

YQ13422hy and YQ13530hy, two MDR strains of ST51 E. hormaechei harboring bla IMP-4 and bla SFO-1, were identified. They were only sensitive to meropenem, amikacin and polymyxin B, and were resistant to cephalosporins, aztreonam, piperacillin/tazobactam and aminoglycosides, intermediate to imipenem. The genetic context surrounding bla IMP-4 was 5'CS-hin-1-IS26-IntI1-bla IMP-4-IS6100-ecoRII. The integron of bla IMP-4 is In823, which is the array of gene cassettes of 5'CS-bla IMP-4. Phylogenetic analysis demonstrated that E. hormaechei YQ13422hy and YQ13530hy belonged to the same small clusters with a high degree of homology.

Conclusion

This observation revealed the dissemination of the bla IMP-4 gene in E. hormaechei in China. We found that bla IMP-4 and bla SFO-1 co-exist in MDR clinical E. hormaechei isolates. This work showed a transferable IncN-type plasmid carrying the bla IMP-4 resistance gene in E. hormaechei. We examined the potential resistance mechanisms of pYQ13422-IMP-4 and pYQ13422-SFO-1, along with their detailed genetic contexts.

Conjugative transfer of multi-drug resistance IncN plasmids from environmental waterborne bacteria to Escherichia coli

Watersheds contaminated with municipal, hospital, and agricultural residues are recognized as reservoirs for bacteria carrying antibiotic resistance genes (ARGs). The objective of this study was to determine the potential of environmental bacterial communities from the highly contaminated La Paz River basin in Bolivia to transfer ARGs to an Escherichia coli lab strain used as the recipient. Additionally, we tested ZnSO4 and CuSO4 at sub-inhibitory concentrations as stressors and analyzed transfer frequencies (TFs), diversity, richness, and acquired resistance profiles. The bacterial communities were collected from surface water in an urban site close to a hospital and near an agricultural area. High transfer potentials of a large set of resistance factors to E. coli were observed at both sites. Whole-genome sequencing revealed that putative plasmids belonging to the incompatibility group N (IncN, IncN2, and IncN3) were predominant among the transconjugants. All IncN variants were verified to be mobile by a second conjugation step. The plasmid backbones were similar to other IncN plasmids isolated worldwide and carried a wide range of ARGs extensively corroborated by phenotypic resistance patterns. Interestingly, all transconjugants also acquired the class 1 integron intl1, which is commonly known as a proxy for anthropogenic pollution. The addition of ZnSO4 and CuSO4 at sub-inhibitory concentrations did not affect the transfer rate. Metal resistance genes were absent from most transconjugants, suggesting a minor role, if any, of metals in the spread of multidrug-resistant plasmids at the investigated sites.

First Belgian Report of Ertapenem Resistance in an ST11 Klebsiella Pneumoniae Strain Isolated from a Dog Carrying blaSCO-1 and blaDHA-1 Combined with Permeability Defects

Klebsiella pneumoniae of sequence type (ST) 11 is a hyper-epidemic nosocomial clone, which is spreading worldwide among humans and emerging in pets. This is the first report, to the best of our knowledge, of multidrug-resistant (MDR) K. pneumoniae ST11 carrying blaSCO-1 and blaDHA-1, isolated from a four-month-old dog in Belgium. Antimicrobial susceptibility testing (AST) of the isolate, performed via broth microdilution following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines, revealed resistance to eight different classes of antimicrobials, including carbapenems, in particular ertapenem, third-generation cephalosporins and fluoroquinolones. A hybrid approach, combining long- and short-read sequencing, was employed for in silico plasmid characterization, multi-locus sequence typing (MLST) and the identification and localization of antimicrobial resistance (AMR) and virulence-associated genes. Three plasmids were reconstructed from the whole-genome sequence (WGS) data: the conjugative IncFIB(K), the non-mobilizable IncR and the mobilizable but unconjugative ColRNAI. The IncFIB(K) plasmid carried the blaSCO-1 gene, whereas IncR carried blaDHA-1, both alongside several other antimicrobial resistance genes (ARGs). No virulence genes could be detected. Here, we suggest that the resistance to ertapenem associated with susceptibility to imipenem and meropenem in K. pneumoniae could be related to the presence of blaSCO-1 and blaDHA-1, combined with permeability defects caused by point mutations in an outer membrane porin (OmpK37). The presence of the blaSCO-1 gene on a conjugative IncFIB(K) plasmid is worrisome as it can increase the risk of transmission to humans, to animals and to the environment.

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.

Companion Animals—An Overlooked and Misdiagnosed Reservoir of Carbapenem Resistance

The dissemination of antimicrobial-resistance is a major global threat affecting both human and animal health. Carbapenems are human use β-lactams of last resort; thus. the dissemination of carbapenemase-producing (CP) bacteria creates severe limitations for the treatment of multidrug-resistant bacteria in hospitalized patients. Even though carbapenems are not routinely used in veterinary medicine, reports of infection or colonization by carbapenemase-producing Enterobacterales in companion animals are being reported. NDM-5 and OXA-48-like carbapenemases are among the most frequently reported in companion animals. Like in humans, Escherichia coli and Klebsiella pneumoniae are the most represented CP Enterobacterales found in companion animals, alongside with Acinetobacter baumannii. Considering that the detection of carbapenemase-producing Enterobacterales presents several difficulties, misdiagnosis of CP bacteria in companion animals may lead to important animal and public-health consequences. It is of the upmost importance to ensure an adequate monitoring and detection of CP bacteria in veterinary microbiology in order to safeguard animal health and minimise its dissemination to humans and the environment. This review encompasses an overview of the carbapenemase detection methods currently available, aiming to guide veterinary microbiologists on the best practices to improve its detection for clinical or research purposes.

Characterization of 2 Klebsiella pneumoniae carbapenemase-producing Enterobacterales isolated from canine rectal swabs

Globally, carbapenemase-producing Enterobacterales (CPE) cause life-threatening, hospital-acquired infections in people, and have been reported recently among veterinary patients. Organisms that produce a Klebsiella pneumoniae carbapenemase (KPC) are one of the most common CPE isolated from people but have been reported only rarely in animals. We characterized 2 KPC-producing Enterobacterales isolated from companion animal rectal swabs during the response to an outbreak caused by a strain of blaNDM-5 Escherichia coli. Both isolates were characterized by whole-genome sequencing (WGS) and analysis. The first isolate (case A) was from an immunosuppressed 6-y-old Yorkshire Terrier and was identified as E. coli (ST372) with a blaKPC-18 gene and an IncFII plasmid. The second isolate (case B) was from a 3-y-old Labrador Retriever with acute diarrhea and was identified as Citrobacter koseri with a blaKPC-2 gene, multiple plasmids (ColRNAI, pKPC-CAV1193), and a putative enterotoxin gene (senB). Further research is needed to determine what role animals might play in the epidemiology of CPE in communities. It is imperative that all CPE isolated from companion animals be fully characterized by WGS and the associated case examined. All veterinary isolates should be sequenced and shared for surveillance, monitoring, and investigation purposes.

Rapid spread of critical priority carbapenemase-producing pathogens in companion animals: a One Health challenge for a post-pandemic world

The COVID-19 pandemic has increased relationships and interactions between human and companion animals, supported by widespread social distancing and isolation measures. Additionally, the COVID-19 pandemic has led to an exponential growth in antibiotic and biocide use worldwide, possibly inducing further pressure, contributing to the selection of antibiotic-resistant bacteria, including WHO critical priority pathogens. While data from global surveillance studies reveal a linear trend of increasing carbapenem resistance among Gram-negative pathogens from companion animals, the acquisition of carbapenemase-producing Enterobacterales through direct contact with colonized hosts and contaminated veterinary hospital environments has been documented. This article highlights the rapid spread of WHO critical priority carbapenemase-producing pathogens in companion animals, which is a One Health challenge for a post-pandemic world.