Misidentification and misreporting of antibiotic resistance in Kluyvera bacteremia by blood culture molecular identification panels.

The use of molecular identification panels has advanced the diagnosis for blood stream infections with fast turnaround time and high accuracy. Yet, this technology cannot completely replace conventional blood culture and standardized antibiotic susceptibility testing (AST) given its limitations and occasional false results. Here we present two cases of bacteremia caused by Kluyvera. Its identification and antibiotic resistance were at least partially mispresented by blood culture molecular identification panels on ePlex, Verigene, and Biofire. The detection of CTX-M resistance marker did not align with the susceptibility to the third generation cephalosporins among a wide range of antibiotics for this organism. Conventional extended-spectrum beta-lactamase (ESBL) testing was used to confirm the absence of ESBL. Caution should be taken when managing cases with CTX-M or ESBL detection in blood culture caused by uncommon pathogens. Conventional culture with microbial identification and standardized AST should continue to be the gold standard for routine patient care. IMPORTANCE: This is the first report that highlights the limitations of blood culture molecular identification panels on identifying Kluyvera and its associated antibiotic resistance patterns. Both the false identification and overreporting of antibiotic resistance could mislead the treatment for bacteremia caused by this pathogen. Patient isolation could have been avoided due to the lack of extended-spectrum beta-lactamase (ESBL) activity of the organism. This report emphasizes the importance of confirming rapid identification and antibiotic resistance by molecular technologies with standardized methods. It also provides insight into the development of new diagnostic panels.

Proposing Kluyvera georgiana as the Origin of the Plasmid-Mediated Resistance Gene fosA4.

A putative fosA gene in Kluyvera georgiana 14751 showed 99% nucleotide identity with plasmid-encoded fosA4 Due to a single-nucleotide insertion translating to a truncated protein, K. georgiana 14751 fosA does not confer fosfomycin resistance. However, analysis of another genome deposit (Kluyvera ascorbata WCH1410) that could be recategorized as K. georgiana after phylogenetic analysis revealed a fosA gene 100% identical to the plasmid-borne fosA4 gene. We suggest that Kluyvera georgiana represents the most probable origin of fosA4.

Origin of the plasmid-mediated fosfomycin resistance gene fosA3.

Background: fosA3 is the most commonly reported plasmid-mediated fosfomycin resistance gene among Enterobacteriaceae. Objectives: To identify the origin of fosA3. Methods: The chromosome of Kluyvera georgiana clinical strain YDC799 was fully sequenced with single-molecule real-time sequencing. Comparative genetic analysis was performed for K. georgiana YDC799, K. georgiana type strain ATCC 51603 and representative fosA3-carrying plasmids. fosA genes were cloned in Escherichia coli to confirm function. Results: K. georgiana YDC799 harboured fosA (designated fosAKG) and blaCTX-M-8 on the chromosome. The genetic environments surrounding fosA3 and bounded by IS26 were nearly identical with the corresponding regions of K. georgiana YDC799 and ATCC 51603. The amino acid sequence of FosAKG from YDC799 and K. georgiana ATCC 51603 shared 99% and 94% identity with FosA3, respectively. Cloned FosAKG conferred fosfomycin resistance with an MIC of >1024 mg/L for E. coli. Conclusions: The plasmid-mediated fosA3 gene was likely mobilized from the chromosome of K. georgiana by an IS26-mediated event.

Draft genome sequence of a Kluyvera intermedia isolate from a patient with a pancreatic abscess.

The genus Kluyvera comprises potential pathogens that can cause many infections. This study reports a Kluyvera intermedia strain (FOSA7093) from a pancreatic cyst specimen from a long-term hospitalised patient. Whole-genome sequencing (WGS) of the K. intermedia isolate was performed and the strain was reported as sensitive to Danish-registered antibiotics although it had a fosA-like gene in the genome. There were nine contigs that aligned to a plasmid, and these contigs contained several heavy metal resistance gene homologues. Furthermore, a prophage was discovered in the genome. WGS represents an efficient tool for monitoring Kluyvera spp. and its role as a reservoir of multidrug resistance. Therefore, this susceptible K. intermedia genome has many characteristics that allow comparison of resistant K. intermedia that might be discovered in the future.

Kluyvera ascorbata Strain from Hospital Sewage Carrying the mcr-1 Colistin Resistance Gene.

The newly identified plasmid-borne colistin resistance gene mcr-1 was found in a Kluyvera ascorbata isolate from hospital sewage in China. mcr-1 was carried by a 57-kb self-transmissible IncI2 plasmid. Unlike in a previous report, mcr-1 was not associated with ISApl1 and was inserted into a gene encoding a putative membrane protein by an unknown mechanism. This study highlights that mcr-1 has spread to multiple bacterial species.

Resistance and inactivation kinetics of bacterial strains isolated from the non-chlorinated and chlorinated effluents of a WWTP.

The microbiological quality of water from a wastewater treatment plant that uses sodium hypochlorite as a disinfectant was assessed. Mesophilic aerobic bacteria were not removed efficiently. This fact allowed for the isolation of several bacterial strains from the effluents. Molecular identification indicated that the strains were related to Aeromonas hydrophila, Escherichia coli (three strains), Enterobacter cloacae, Kluyvera cryocrescens (three strains), Kluyvera intermedia, Citrobacter freundii (two strains), Bacillus sp. and Enterobacter sp. The first five strains, which were isolated from the non-chlorinated effluent, were used to test resistance to chlorine disinfection using three sets of variables: disinfectant concentration (8, 20 and 30 mg·L(-1)), contact time (0, 15 and 30 min) and water temperature (20, 25 and 30 °C). The results demonstrated that the strains have independent responses to experimental conditions and that the most efficient treatment was an 8 mg·L(-1) dose of disinfectant at a temperature of 20 °C for 30 min. The other eight strains, which were isolated from the chlorinated effluent, were used to analyze inactivation kinetics using the disinfectant at a dose of 15 mg·L(-1) with various retention times (0, 10, 20, 30, 60 and 90 min). The results indicated that during the inactivation process, there was no relationship between removal percentage and retention time and that the strains have no common response to the treatments.

The route of antimicrobial resistance from the hospital effluent to the environment: focus on the occurrence of KPC-producing Aeromonas spp. and Enterobacteriaceae in sewage.

We investigated the antimicrobial resistance profile and the occurrence of Klebsiella pneumoniae carbapenemase (KPC)-producing Gram-negative rods in sewage samples obtained from a Brazilian teaching hospital and from the wastewater treatment plant (WWTP) that receives it for treatment. We identified multidrug-resistant bacteria as well as KPC-2-producing Aeromonas spp. and several Enterobacteriaceae species, including Kluyvera spp., in the hospital effluent and in different sites of the WWTP. Most isolates showed the blaKPC-2 gene harbored on a transposon that was carried by conjugative plasmids. The presence of KPC production among Aeromonas spp., Kluyvera spp., and other Enterobacteriaceae indicates the adaptability of such isolates to aquatic environments, not only in the hospital effluent but also throughout the WWTP. Although secondary treatment seems to decrease the amount of KPC producers in sewage, multidrug-resistant isolates are continually disposed in the urban river. Thus, sewage treatment regulations are urgently needed to decelerate the evolution of antimicrobial resistance beyond hospitals.

Identification and characterization of two novel bla(KLUC) resistance genes through large-scale resistance plasmids sequencing.

Plasmids are important antibiotic resistance determinant carriers that can disseminate various drug resistance genes among species or genera. By using a high throughput sequencing approach, two groups of plasmids of Escherichia coli (named E1 and E2, each consisting of 160 clinical E. coli strains isolated from different periods of time) were sequenced and analyzed. A total of 20 million reads were obtained and mapped onto the known resistance gene sequences. As a result, a total of 9 classes, including 36 types of antibiotic resistant genes, were identified. Among these genes, 25 and 27 single nucleotide polymorphisms (SNPs) appeared, of which 9 and 12 SNPs are nonsynonymous substitutions in the E1 and E2 samples. It is interesting to find that a novel genotype of bla(KLUC), whose close relatives, bla(KLUC-1) and bla(KLUC-2), have been previously reported as carried on the Kluyvera cryocrescens chromosome and Enterobacter cloacae plasmid, was identified. It shares 99% and 98% amino acid identities with Kluc-1 and Kluc-2, respectively. Further PCR screening of 608 Enterobacteriaceae family isolates yielded a second variant (named bla(KLUC-4)). It was interesting to find that Kluc-3 showed resistance to several cephalosporins including cefotaxime, whereas bla(KLUC-4) did not show any resistance to the antibiotics tested. This may be due to a positively charged residue, Arg, replaced by a neutral residue, Leu, at position 167, which is located within an omega-loop. This work represents large-scale studies on resistance gene distribution, diversification and genetic variation in pooled multi-drug resistance plasmids, and provides insight into the use of high throughput sequencing technology for microbial resistance gene detection.

Correlation of fluoroquinolone resistance with expression of qnrA gene in Kluyvera spp.

The objective of the present study was to examine whether the expression of qnrA may contribute to a high level of resistance among parent and induced strains of Kluyvera spp. Two clinical isolates of ciprofloxacin-resistant Kluyvera spp. were obtained from livers of diseased chickens, and upon induction with ciprofloxacin, six strains with increased resistance were produced. Point mutations in qnrA, aac(6')-Ib-cr, gyrA, gyrB, parC, and parE were investigated by polymerase chain reaction (PCR) amplification and DNA sequencing, and expression levels of acrAB and qnrA in all strains were investigated by quantitative real-time PCR (qRT-PCR). The induced strains contained the same mutations in quinolone resistance-determining region as those of the parent strains. qRT-PCR showed that the expression of the acrA gene was not detected in any strain and acrB gene expression was unchanged between induced and parental strains. However, difference in expression of qnrA was observed, which correlated well with the level of quinolone resistance in the parent and induced strains. The induced high resistance was not affected by mutations in qnrA and aac(6')-Ib-cr, by new mutations in the quinolone resistance-determining region of gyrA, gyrB, parC, and parE, or by the expression level of acrAB. These data suggest that the expression of qnrA may be a factor contributing to the high level of resistance among parent and induced strains of Kluyvera spp.

A case of urinary tract infection caused by Kluyvera ascorbata in an infant: case report and review of the literature.

We experienced a case of urinary tract infection in a 3-month-old child caused by Kluyvera ascorbata. The authors report the case and review the literature regarding Kluyvera urinary tract infection exclusively in children. Kluyvera infection, which had been extremely rare, has increasingly been reported, including urinary tract infection. A prompt identification of Kluyvera species in clinical infections is important. Recognition of its disease-producing potential and the subsequent initiation of effective antimicrobial coverage are essential for appropriate management in the pediatric population.

Beta-lactam induction of ISEcp1B-mediated mobilization of the naturally occurring bla(CTX-M) beta-lactamase gene of Kluyvera ascorbata.

ISEcp1B is an insertion element associated with the emerging expanded-spectrum beta-lactamase bla(CTX-M) genes in Enterobacteriaceae. Because ISEcp1B-bla(CTX-M)positive strains may be identified from humans and animals, the ability of this insertion sequence to mobilize the bla(CTX-M-2) gene was tested from its progenitor Kluyvera ascorbata to study the effects of amoxicillin/clavulanic and cefquinome as enhancers of transposition. These beta-lactam molecules are administered parenterally to treat infected animals. ISEcp1B-mediated mobilization of the bla(CTX-M-2) gene from K. ascorbata to a plasmid location in Escherichia coli J53 was studied. Transposition assays were performed with overnight cultures with amoxicillin/clavulanic acid and cefquinome at concentrations expected to mimic those found in feces after parenteral administration (0.4-0.008 mg L(-1) and 0.32-0.064 mg L(-1), respectively). Amoxicillin/clavulanic acid and cefquinome did not modify the transposition frequency (1.85+/-1.7 x 10(-7)) whereas ceftazidime (0.5 mg L(-1)), used as a control, did (5.2+/-2.7 x 10(-5)). Therefore, it is likely that neither amoxicillin/clavulanic acid nor cefquinome concentrations as found in the gut flora may enhance mobilization of the bla(CTX-M) genes in Enterobacteriaceae.

Characterisation of KLUA-9, a beta-lactamase from extended-spectrum cephalosporin-susceptible Kluyvera ascorbata, and genetic organisation of bla(KLUA-9).

This study characterised the genetic environment of the chromosomally encoded bla(KLUA-9) gene from a clinical Kluyvera ascorbata isolate and performed a kinetic characterisation of KLUA-9. Purified KLUA-9 showed the highest catalytic efficacies towards benzylpenicillin, ampicillin, piperacillin, first-generation cephalosporins, cefuroxime and cefoperazone; like other 'cefotaximases', it showed a much higher rate of hydrolysis of cefotaxime than ceftazidime, whilst dicloxacillin, cefoxitin and imipenem behaved as poor substrates. A 9kb insert from K. ascorbata was cloned (Escherichia coli KK68C1) and sequenced. bla(KLUA-9) and its 266bp upstream flanking region (almost identical to the integron-associated bla(CTX-M-2)) are preceded by an aspat variant, a ypdABC-like operon and two open reading frames with unknown functions. Unlike ISCR1-associated bla(CTX-M-2) genes, we failed to detect the putative orf513 recombination sites. Instead, we were able to localise the 5bp target sites for insertion of ISEcp1B, suggesting that this element could be responsible for future (or still undetected) mobilisation of bla(KLUA-9) to more efficiently transferred elements.

Correlation between diverse cyclic lipopeptides production and regulation of growth and substrate utilization by Bacillus subtilis strains in a particular habitat.

The two Bacillus subtilis strains (DM-03 and DM-04) were isolated from two extremely different habitats; one from the traditional fermented food and another one from a petroleum contaminated soil sample. These strains produced quantitatively and qualitatively different cyclic lipopeptides isoforms under laboratory culture conditions. MALDI-TOF mass spectral analysis revealed that lipopeptide profile varied according to the producing B. subtilis strains; iturins and surfactins isoforms were pre-dominant cyclic lipopeptides produced by B. subtilis DM-03 and DM-04 strains, respectively. A comparative study showed that these strains possessed distinct preferences for the carbon and nitrogen substrates, temperature and pH for optimal growth and biosurfactant production. Our study documented that the cyclic lipopeptide isoforms produced by the respective strains played an important role in the utilization of available hydrophobic substrate(s) from their natural habitats and conferred some kind of competitive advantage to the producing B. subtilis strains in their parent ecological niche.

Natural antimicrobial susceptibility patterns of Kluyvera ascorbata and Kluyvera cryocrescens strains and review of the clinical efficacy of antimicrobial agents used for the treatment of Kluyvera infections.

The natural susceptibility of 58 K. ascorbata and 24 K. cryocrescens strains to 71 antimicrobial agents was investigated. MIC values were determined with a microdilution procedure in cation-adjusted Mueller Hinton broth (for all strains) and IsoSensitest broth (for some strains). Both species were naturally sensitive or of intermediate susceptibility to tetracyclines, aminoglycosides, quinolones, antifolates, chloramphenicol, nitrofurantoin, fosfomycin, aminopenicillins plus beta-lactamase inhibitors, acylureidopenicillins, carbapenems, aztreonam and some cephalosporins. Uniform natural resistance was found with several macrolides, lincosamides, streptogramins, glycopeptides, rifampicin, fusidic acid, linezolid, penicillin G, oxacillin, and amoxicillin. To the latter agent, some strains of both species were also of intermediate susceptibility. Species-related differences in natural susceptibility affecting clinical assessment criteria were seen with azithromycin, cethromycin, telithromycin, ticarcillin and some cephalosporins, to which K. ascorbata was less susceptible than K. cryocrescens. Medium-related differences in susceptibility were restricted to a few antibiotics. A data base about the natural susceptibility of the two most common Kluyvera spp. to a wide range of antimicrobial agents is presented. It can be used for the validation of forthcoming susceptibility trials of these microorganisms. Although some susceptibilty patterns might be helpful for the phenotypical separation of K. ascorbata from K. cryocrescens, they do not allow a separation of these species. The literature dealing with the clinical efficacy of antimicrobial agents used for the treatment of Kluyvera infections is discussed.