Commonality of Multidrug-Resistant Klebsiella pneumoniae ST348 Isolates in Horses and Humans in Portugal

Molecular characterization of carbapenemase-producing Enterobacterales in a tertiary hospital in Lima, Peru

Carbapenemase-producing Enterobacterales (CPE) are a growing threat to global health and the economy. Understanding the interactions between resistance and virulence mechanisms of CPE is crucial for managing difficult-to-treat infections and informing outbreak prevention and control programs. Here, we report the characterization of 21 consecutive, unique clinical isolates of CPE collected in 2018 at a tertiary hospital in Lima, Peru. Isolates were characterized by phenotypic antimicrobial susceptibility testing and whole-genome sequencing to identify resistance determinants and virulence factors. Seven Klebsiella pneumoniae isolates were classified as extensively drug-resistant. The remaining Klebsiella, Enterobacter hormaechei, and Escherichia coli isolates were multidrug-resistant. Eighteen strains carried the metallo-β-lactamase NDM-1, two the serine-carbapenemase KPC-2, and one isolate had both carbapenemases. The blaNDM-1 gene was located in the truncated ΔISAba125 element, and the blaKPC-2 gene was in the Tn4401a transposon. ST147 was the most frequent sequence type among K. pneumoniae isolates. Our findings highlight the urgent need to address the emergence of CPE and strengthen control measures and antibiotic stewardship programs in low- and middle-income settings.IMPORTANCEGenomic surveillance of antimicrobial resistance contributes to monitoring the spread of resistance and informs treatment and prevention strategies. We characterized 21 carbapenemase-producing Enterobacterales collected at a Peruvian tertiary hospital in 2018, which exhibited very high levels of resistance and carried numerous resistance genes. We detected the coexistence of carbapenemase-encoding genes (blaNDM-1 and blaKPC-2) in a Klebsiella pneumoniae isolate that also had the PmrB(R256G) mutation associated with colistin resistance. The blaKPC-2 genes were located in Tn4401a transposons, while the blaNDM-1 genes were in the genetic structure Tn125 (ΔISAba125). The presence of high-risk clones among Klebsiella pneumoniae (ST11 and ST147) and Escherichia coli (ST410) isolates is also reported. The study reveals the emergence of highly resistant bacteria in a Peruvian hospital, which could compromise the effectiveness of current treatments and control.

Antimicrobial resistance and genetic diversity of Klebsiella pneumoniae strains from different clinical sources in horses

Introduction

Klebsiella pneumoniae is a major cause of infections and reproductive disorders among horses, ranked in recent French studies as the sixth most frequently isolated bacterial pathogen in equine clinical samples. The proportion of multidrug-resistant (MDR) K. pneumoniae is therefore significant in a context where MDR K. pneumoniae strains are considered a major global concern by the World Health Organization.

Methods

In this study, we used a genomic approach to characterize a population of 119 equine K. pneumoniae strains collected by two laboratories specialized in animal health in Normandy (France). We describe the main antibiotic resistance profiles and acquired resistance genes, and specify the proportion of virulence-encoding genes carried by these strains. The originality of our panel of strains lies in the broad collection period covered, ranging from 1996 to 2020, and the variety of sample sources: necropsies, suspected bacterial infections (e.g., genital, wound, allantochorion, and umbilical artery samples), and contagious equine metritis analyses.

Results

Our results reveal a remarkable level of genomic diversity among the strains studied and we report the presence of 39% MDR and 9% hypervirulent strains (including 5% that are both MDR and hypervirulent).

Discussion

These findings clearly emphasize the importance of improving the surveillance of K. pneumoniae in routine equine diagnostic tests to detect high-risk MDR-hypervirulent Klebsiella pneumoniae strains. The circulation of these worrisome strains reveals that they are not being detected by the simple K1, K2, and K5 serotype approach currently implemented in the French horse-breeding sector.

Co-Occurrence of Multidrug Resistant Klebsiella pneumoniae Pathogenic Clones of Human Relevance in an Equine Pneumonia Case

The global epidemiology of multidrug resistant Klebsiella pneumoniae, a serious threat to both animal and human health, is dominated by the spread of pathogenic clones, each separately evolving via acquisition of transferable antibiotic resistance or niche-specific virulence determinants. In horses, K. pneumoniae infection can lead to severe respiratory illness. Here, we characterized multiple isolates recovered from bronchial aspirates of a mare with pneumonia refractory to antibiotics. First, we used a combination of standard microbiology, bacteriophage cross-susceptibility and antibiotic resistance testing to profile the infecting K. pneumoniae population. The genomes of isolates with distinct fingerprints (pulsed-field gel electrophoresis) and unique combined bacteriophage/antibiotic profiles were then further analyzed using whole-genome sequencing. Adhesion to human epithelial cells and biofilm production were also measured as virulence indicators. Although it is commonly expected for one clone to dominate an infection episode, we identified five coexisting multidrug resistant K. pneumoniae sharing the same niche. One was a novel sequence type (ST4656), while the other four were all members of emerging human pathogenic clonal groups (ST307, ST628, ST893 and ST392). These isolates did not display significant differences from one another in terms of virulence or resistance and differed only in plasmid content from isolates implicated in severe human infections, with equal potential to prolong duration and severity of infection when sharing the same niche. This study highlights the importance of more precise surveillance and detection measures to uncover bacterial heterogeneity, reminding us that the "single clone" concept is not an absolute in invasive bacterial infections. IMPORTANCE Multidrug resistant Klebsiella pneumoniae are agents of life-threatening infections in animals and humans, with several multidrug resistant clones causing outbreaks of disease worldwide. It is generally accepted that only one clone will be dominant in an infection episode. In this study, we investigated K. pneumoniae isolates from a horse with severe pneumonia and demonstrated co-occurrence of multiple sequence types previously identified as emerging human pathogens. The equine isolates are not significantly different from one another in terms of virulence or resistance, with equal potential to prolong duration and severity of infection, and are indistinguishable from isolates recovered from humans, except for plasmid content. Our study highlights how the "one dominant clone" concept is not an absolute in severe infection, illustrating the need for improved diagnostics to track heterogeneity of infection, and reinforces the importance of cross-monitoring of environmental and human reservoirs of multidrug resistant pathogens.

Chromosomal studies on drug resistance genes in extended spectrum β-lactamases producing-Klebsiella pneumoniae isolated from equine

Background

K. pneumoniae is one of the most virulent and multidrug resistant bacteria, of great concern in both human and veterinary medicine. Studies conducted on the drug resistance of Klebsiella pneumoniae in equine are lack in Egypt.

Results

The distribution pattern of ten drug resistance genes were investigated and analyzed among fifteen Klebsiella isolates (previously isolated, identified and antibiogram tested). The targeted determinant genes were coded on the chromosomes, conferring the resistance against β-lactams, carbapenems, fluoroquinolones and aminoglycosides, in addition to the gene determinants of porin protein and efflux pump. The study revealed an incidence rate of 86.7, 100, 23, 7.7, 0, 0, 73.3, 40, 100 and 0% for the genes blaCTX-M, blaTEM, blaKPC, blaNDM-1, blaVIM, qnrB, qnrS, aadA1, AcrAB and ompK35 respectively. The Extended Spectrum β-lactamase-production coding genes were detected in all strains with at least one of their genes. In addition, the efflux pump codding gene and mutation in porin protein gene, which are two important co-factors in the drug resistance mechanism were also detected in all strains. By investigating the association of the drug resistance determinants within a single strain, it was showed that 40% (6/15) of the strains harbored 5 associated genes, 27.7% (4/15) harbored 6 associated genes, 13.3% (2/15) harbored 4 and 7 genes as well and finally only 1 isolate harbored 3 determinants, with complete absence of strains having sole existence of one gene or even two. Pareto chart elucidated that the association of β-lactamases, AcrAB and Qnr with the mutation of the porin protein was the most existed (26.7%). Interestingly, the sequencing results of the CTX-M PCR amplicons were typed as OXY-5 (50%), CTX-M-15 (40%) and CTX-M-27 (10%).

Conclusions

The current study represented the first record of the drug resistance genes’ predominance and their association among the K. pneumoniae strains; recovered from equine in Egypt, offering a helpful guide for scientists seeking new alternatives other-than antibiotics.

Complete Genome Sequence of Klebsiella quasipneumoniae MMCC7, Isolated from an Eclectus Parrot (Eclectus roratus)

Klebsiella quasipneumoniae MMCC7 is a multidrug- and heavy metal-resistant strain isolated from the feces of a pet shop eclectus parrot in Hong Kong. The complete genome, a single chromosome and circular plasmid (5,382,488 bp; G+C content, 57.79%), was determined by hybrid assembly.

The Public Health Burden of Virulent Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Strains Isolated from Diseased Horses

Background: Klebsiella pneumoniae has been associated with both nosocomial and community-acquired infections with mounting public health concern throughout the world. The purpose of this study was to investigate the burden of virulent extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae among diarrheic horses or those with respiratory illness to underscore the public health implication of such strains. Materials and Methods: Rectal and nasal swabs were gathered from 100 diseased horses (50 diarrheic and 50 with respiratory illness). The collected swabs were processed for isolation of ESBL-producing K. pneumoniae using a selective medium followed by phenotypic and molecular identification of the isolates. All ESBL-producing K. pneumoniae strains were investigated for six virulence genes (type 3 fimbrial adhesin [mrkD], enterobactin [entB], regulator of mucoid phenotype A [rmpA], Klebsiella ferric iron uptake [kfu], mucoviscosity-associated gene A [magA], and type 2 capsular polysaccharide [K2]). Results: Of the 100 examined animals, ESBL-producing K. pneumoniae was recovered from 13 (13%), with isolation rates in horses suffering from diarrhea and respiratory illness being 20% and 6%, respectively. Among the obtained isolates, bla TEM and bla SHV were found in all strains (100%) followed by bla CTX-M in 92.3%, while none of the isolates had bla OXA. In addition, 13 ESBL-producing K. pneumoniae strains exhibited a multidrug resistance (MDR) pattern. Regarding the occurrence of virulence genes among the isolates, mrkD (100%) and entB (100%) were the most predominant virulence genes followed by rmpA (76.9%) and kfu (46.2%). On the contrary, magA and K2 were negative in all ESBL-producing strains. Furthermore, this work provides four K. pneumoniae mrkD partial sequences that displayed high genetic relatedness with those obtained from human to clarify the public health burden of such isolates. Conclusion: The occurrence of virulent ESBL-producing K. pneumoniae among diseased horses highlights the potential role of this animal in the epidemiology of such virulent and antimicrobial-resistant strains, which may have great public health threat.

Determination of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolated from horses with respiratory manifestation

Background and Aim:

The World Health Organization considers multidrug-resistant (MDR) Klebsiella pneumoniae a major global threat. Horses harbor commensal isolates of this bacterial species and potentially serve as reservoirs for human MDR bacteria. This study investigated antimicrobial resistance in horses caused by extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae.

Materials and Methods:

One hundred fifty-nine nasal swab samples were collected from horses with respiratory distress not treated with cefotaxime and erythromycin. Biochemical and serological identification was performed on all samples. Polymerase chain reaction (PCR) was used to detect 16S-23S ITS, mucoviscosity-associated gene (magA), uridine diphosphate galacturonate 4-epimerase gene (uge), and iron uptake system gene (kfu), bla_TEM, bla_SHV, and bla_CTX genes. Sequence analysis and phylogenetic relatedness of randomly selected K. pneumoniae isolates carrying the bla_TEM gene were performed.

Results:

Ten isolates of Klebsiella spp. were obtained from 159 samples, with an incidence of 6.28% (10 of 159). Based on biochemical and serological identification, K. pneumoniae was detected in 4.4% (7 of 159) of the samples. Using PCR, all tested K. pneumoniae isolates (n=7) carried the 16S-23S ITS gene. By contrast, no isolates carried magA, uge, and kfu genes. The bla_TEM gene was detected in all test isolates. Moreover, all isolates did not harbor the bla_SHV or bla_CTX gene. Sequence analysis and phylogenetic relatedness reported that the maximum likelihood unrooted tree generated indicated the clustering of the test isolate with the other Gram-negative isolate bla_TEM. Finally, the sequence distance of the bla_TEM gene of the test isolate (generated by Lasergene) showed an identity range of 98.4-100% with the bla_TEM gene of the different test isolates.

Conclusion:

The misuse of antimicrobials and insufficient veterinary services might help generate a population of ESBL-producing K. pneumoniae in equines and humans, representing a public health risk.

High-risk clones of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolated from the University Hospital Establishment of Oran, Algeria (2011-2012)

The purpose of the study was to characterize the resistome, virulome, mobilome and Clustered Regularly Interspaced Short Palindromic Repeats-associated (CRISPR-Cas) system of extended-spectrum β-lactamase producing Klebsiella pneumoniae (ESBL-KP) clinical isolates and to determine their phylogenetic relatedness. The isolates were from Algeria, isolated at the University Hospital Establishment of Oran, between 2011 and 2012. ESBL-KP isolates (n = 193) were screened for several antibiotic resistance genes (ARGs) using qPCR followed by Pulsed-Field Gel Electrophoresis (PFGE). Representative isolates were selected from PFGE clusters and subjected to whole-genome sequencing (WGS). Genomic characterization of the WGS data by studying prophages, CRISPR-Cas systems, Multi-Locus Sequence Typing (MLST), serotype, ARGs, virulence genes, plasmid replicons, and their pMLST. Phylogenetic and comparative genomic were done using core genome MLST and SNP-Based analysis. Generally, the ESBL-KP isolates were polyclonal. The whole genome sequences of nineteen isolates were taken of main PFGE clusters. Sixteen sequence types (ST) were found including high-risk clones ST14, ST23, ST37, and ST147. Serotypes K1 (n = 1), K2 (n = 2), K3 (n = 1), K31 (n = 1), K62 (n = 1), and K151 (n = 1) are associated with hyper-virulence. CRISPR-Cas system was found in 47.4%, typed I-E and I-E*. About ARGs, from 193 ESBL-KP, the majority of strains were multidrug-resistant, the CTX-M-1 enzyme was predominant (99%) and the prevalence of plasmid-mediated quinolone resistance (PMQR) genes was high with aac(6')-lb-cr (72.5%) and qnr's (65.8%). From 19 sequenced isolates we identified ESBL, AmpC, and carbapenemase genes: blaCTX-M-15 (n = 19), blaOXA-48 (n = 1), blaCMY-2 (n = 2), and blaCMY-16 (n = 2), as well as non-ESBL genes: qnrB1 (n = 12), qnrS1 (n = 1) and armA (n = 2). We found IncF, IncN, IncL/M, IncA/C2, and Col replicon types, at least once per isolate. This study is the first to report qnrS in ESBL-KP in Algeria. Our analysis shows the concerning co-existence of virulence and resistance genes and would support that genomic surveillance should be a high priority in the hospital environment.

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.

Whole Genome Sequencing of Peruvian Klebsiella pneumoniae Identifies Novel Plasmid Vectors Bearing Carbapenem Resistance Gene NDM-1

Background

Klebsiella pneumoniae is a bacterial pathogen with increasing rates of resistance to carbapenem antibiotics, but the population structure and genetic drivers of carbapenem-resistant K pneumoniae (CRKP) remain underexplored in developing countries. Carbapenem-resistant K pneumoniae were recently introduced into Peru but have grown rapidly in prevalence, enabling study of this pathogen as it expands into an unaffected environment.

Methods

In this study, using whole genome sequencing, we show that 3 distinct lineages encompass almost all CRKP identified in the hospital where it was first reported in Peru.

Results

The most prevalent lineage, ST348, has not been described outside of Europe, raising concern for global dissemination. We identified metallo- β -lactamase NDM-1 as the primary carbapenem resistance effector, which was harbored on a novel vector resulting from recombination between 2 different plasmids, pKP1-NDM-1 and pMS7884A.

Conclusions

This study is the first of its kind performed in Peru, and it furthers our understanding of the landscape of CRKP infections in Latin America.

Multidrug-Resistant ESBL/AmpC-Producing Klebsiella pneumoniae Isolated from Healthy Thoroughbred Racehorses in Japan

Simple Summary

Extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases (AmpCs) have been recognized as an emerging global problem in humans and animals. These enzymes provide a mechanism of resistance by inactivating β-lactam antibiotics and are mostly encoded on plasmids, which can be easily transmitted to other bacteria in humans, animals, and the environment. Several clinical diseases caused by Klebsiella spp. infection have been confirmed in the horse community. The emergence of antimicrobial resistance in Klebsiella spp. increases the risk of treatment failure in infected horses. In this study, we investigated the presence of ESBL/AmpC-producing Klebsiella spp. isolated from healthy Thoroughbred racehorses in Japan. The results showed that ESBL/AmpC-producing Klebsiella pneumoniae (ESBL/AmpC-KP) isolated from horses have co-resistance to other β-lactam antibiotics as multidrug-resistant (MDR) bacteria. Genetic relatedness analysis suggested that plasmid-mediated AmpC-KP clones may spread between horses. This is the first study to show K. pneumoniae carrying MDR plasmid-mediated AmpC isolated from racehorses. Continuous monitoring antimicrobial resistance to this species is required in order to control the spread of MDR ESBL/AmpC-KP in the racehorse community.

Abstract

Extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (AmpC)-producing Klebsiella spp. have become a major health problem, leading to treatment failure in humans and animals. This study aimed to evaluate the presence of ESBL/AmpC-producing Klebsiella spp. isolated from racehorses in Japan. Feces samples from 212 healthy Thoroughbred racehorses were collected from the Japan Racing Association Training Centers between March 2017 and August 2018. ESBL/AmpC-producing Klebsiella spp. were isolated using selective medium containing 1 µg/mL cefotaxime. All isolates were subjected to bacterial species identification (MALDI-TOF MS), antimicrobial susceptibility test (disk diffusion test), characterization of resistance genes (PCR), conjugation assay, and genetic relatedness (multilocus sequence typing/MLST). Twelve ESBL/AmpC-producing Klebsiella pneumoniae (ESBL/AmpC-KP) were isolated from 3.3% of horse samples. Antimicrobial resistance profiling for 17 antimicrobials showed all ESBL/AmpC-KP were multidrug-resistant (MDR). Only 1 isolate was confirmed as an ESBL producer (bla_CTX-M-2-positive), whereas the other 11 isolates were plasmid-mediated AmpC (pAmpC) producers (bla_CMY positive). On the basis of MLST analysis, the ESBL-KP isolate was identified as sequence type (ST)-133 and four different STs among AmpC-KP isolates, ST-145, ST-4830, ST-4831, and ST-4832, were found to share six of the seven loci constituting a single-locus variant. This is the first study to show K. pneumoniae carrying MDR pAmpC isolated from a racehorse.

Broad-Spectrum Cephalosporin-Resistant Klebsiella spp. Isolated from Diseased Horses in Austria

Simple Summary

Broad-spectrum cephalosporin-resistant Klebsiella pneumoniae is considered as a serious problem for public human health. To date, only a few broad-spectrum cephalosporin-resistant Klebsiella have been isolated from horses. Considering the zoonotic potential of the Klebsiella spp., and the close relationship between man and horse, this study intended to generate data on the genetic background of broad-spectrum cephalosporin-resistant Klebsiella spp. isolated from horses in Austria. Overall, samples isolated between 2012 and 2019 from 1541 horses underwent bacteriological testing, resulting in 51 specimens tested positive for Klebsiella ssp. Antimicrobial susceptibility tests revealed that seven Klebsiella ssp. isolates were not only cefotaxime-resistant but also showed resistance against other classes of antibiotics so that they were considered to be multidrug-resistant. Data from whole genome sequencing and mating experiments strongly suggest that the majority of antibiotic resistance genes is encoded on plasmids in these seven multidrug-resistant Klebsiella ssp. Considering the potential threat when commensal Klebsiella inhabiting a healthy human gut acquire new antibiotic resistances due to the exchange of plasmids with multidrug-resistant Klebsiella ssp. from horses, further monitoring of horses and other domestic animals for the presence of broad-spectrum cephalosporin-resistant Klebsiella, not only in Austria but worldwide is therefore advisable.

Abstract

The aim of the present study was to investigate the diversity of broad-spectrum cephalosporin-resistant Klebsiella spp. isolated from horses in Austria that originated from diseased horses. A total of seven non-repetitive cefotaxime-resistant Klebsiella sp. isolates were obtained during diagnostic activities from autumn 2012 to October 2019. Antimicrobial susceptibility testing was performed. The isolates were genotyped by whole-genome sequencing (WGS). Four out of seven Klebsiella isolates were identified as K. pneumoniae, two as K. michiganensis and one as K. oxytoca. All isolates displayed a multi-drug resistant phenotype. The detection of resistance genes reflected well the phenotypic resistance profiles of the respective isolates. All but one isolate displayed the extended-spectrum β-lactamases (ESBL) phenotype and carried CTX-M cefotaximases, whereas one isolate displayed an ESBL and AmpC phenotype and carried cephamycinase (CMY)-2 and sulfhydryl variable (SHV)-type b and Temoniera (TEM) β-lactamases. Among Klebsiella pneumoniae isolates, for different sequence types (ST) could be detected (ST147, ST307, ST1228, and a new ST4848). Besides resistance genes, a variety of virulence genes, including genes coding for yersiniabactin were detected. Considering the high proximity between horses and humans, our results undoubtedly identified a public health issue. This deserves to be also monitored in the years to come.