Klebsiella oxytoca: An emerging pathogen?

Mucosal sugars delineate pyrazine vs pyrazinone autoinducer signaling in Klebsiella oxytoca

Virulent Klebsiella oxytoca strains are associated with gut and lung pathologies, yet our understanding of the molecular signals governing pathogenesis remains limited. Here, we characterized a family of K. oxytoca pyrazine and pyrazinone autoinducers and explored their roles in microbial and host signaling. We identified the human mucin capping sugar Neu5Ac as a selective elicitor of leupeptin, a protease inhibitor prevalent in clinical lung isolates of K. oxytoca, and leupeptin-derived pyrazinone biosynthesis. Additionally, we uncovered a separate pyrazine pathway, regulated by general carbohydrate metabolism, derived from a broadly conserved PLP-dependent enzyme. While both pyrazine and pyrazinone signaling induce iron acquisition responses, including enterobactin biosynthesis, pyrazinone signaling enhances yersiniabactin virulence factor production and selectively activates the proinflammatory human histamine receptor H4 (HRH4). Our findings suggest that the availability of specific carbohydrates delineates distinct autoinducer pathways in K. oxytoca that may have differential effects on bacterial virulence and host immune responses.

Antibiotic resistance: a global crisis, problems and solutions

Healthy state is priority in today's world which can be achieved using effective medicines. But due to overuse and misuse of antibiotics, a menace of resistance has increased in pathogenic microbes. World Health Organization (WHO) has announced ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) as the top priority pathogens as these have developed resistance against certain antibiotics. To combat such a global issue, it is utmost important to identify novel therapeutic strategies/agents as an alternate to such antibiotics. To name certain antibiotic adjuvants including: inhibitors of beta-lactamase, efflux pumps and permeabilizers for outer membrane can potentially solve the antibiotic resistance problems. In this regard, inhibitors of lytic domain of lytic transglycosylases provide a novel way to not only act as an alternate to antibiotics but also capable of restoring the efficiency of previously resistant antibiotics. Further, use of bacteriophages is another promising strategy to deal with antibiotic resistant pathogens. Taking in consideration the alternatives of antibiotics, a green synthesis nanoparticle-based therapy exemplifies a good option to combat microbial resistance. As horizontal gene transfer (HGT) in bacteria facilitates the evolution of new resistance strains, therefore identifying the mechanism of resistance and development of inhibitors against it can be a novel approach to combat such problems. In our perspective, host-directed therapy (HDT) represents another promising strategy in combating antimicrobial resistance (AMR). This approach involves targeting specific factors within host cells that pathogens rely on for their survival, either through replication or persistence. As many new drugs are under clinical trials it is advisable that more clinical data and antimicrobial stewardship programs should be conducted to fully assess the clinical efficacy and safety of new therapeutic agents.

Comprehensive genomics reveals novel sequence types of multidrug resistant Klebsiella oxytoca with uncharacterized capsular polysaccharide K- and lipopolysaccharide O-antigen loci from the National Hospital of Uganda

The Klebsiella oxytoca complex comprises diverse opportunistic bacterial pathogens associated with hospital and community-acquired infections with growing alarming antimicrobial resistance. We aimed to uncover the genomic features underlying the virulence and antimicrobial resistance of isolates from Mulago National Hospital in Uganda. We coupled whole genome sequencing with Pathogenwatch multilocus sequence typing (MLST) and downstream bioinformatic analysis to delineate sequence types (STs) capsular polysaccharide K- and O-antigen loci, along with antimicrobial resistance (AMR) profiles of eight clinical isolates from the National Referral Hospital of Uganda. Our findings revealed that only two isolates (RSM6774 and RSM7756) possess a known capsular polysaccharide K-locus (KL74). The rest carry various unknown K-loci (KL115, KL128, KLI52, KL161 and KLI63). We also found that two isolates possess unknown loci for the lipopolysaccharide O-antigen (O1/O2v1 type OL104 and unknown O1). The rest possess known O1 and O3 serotypes. From MLST, we found four novel sequence types (STs), carrying novel alleles for the housekeeping genes glyceraldehyde-6-phosphate dehydrogenase A (gapA), glucose-6-phosphate isomerase (pgi), and RNA polymerase subunit beta (rpoB). Our AMR analysis revealed that all the isolates are resistant to ampicillin and ceftriaxone, with varied resistance to other antibiotics, but all carry genes for extended-spectrum beta-lactamases (ESBLs). Notably, one strain (RSM7756) possesses outstanding chromosomal and plasmid-encoded AMR to beta-lactams, cephalosporins, fluoroquinolones and methoprims. Conclusively, clinical samples from Mulago National Referral Hospital harbor novel STs and multidrug resistant K. oxytoca strains, with significant public health importance, which could have been underrated.

An Analysis of the Contaminants on Otoscopes of Otolaryngology Residents: An Observational Study

The study was conducted to learn if the otoscope, a noncritical medical device, used by ENT residents harbor pathogenic organism. This study was conducted in a medical teaching hospital in India. Total of 38 otoscopes of ENT residents were examined after taking samples using sterile cotton swabs from otoscope speculum and otoscope head and both bacterial and fungal culture were studied. The study showed that 11 otoscope heads (28.94%) and 11 otoscope speculums (28.94%) out of the 38 otoscopes studied showed bacterial growth. Most commonly isolated bacteria were skin commensals followed by Klebsiella species. Fungal growth was seen in 3 out of 38 otoscope Speculums (7.89%). All 3 fungi isolated during the study belonged to Aspergillus species. Training residents regarding hygiene of medical equipments is necessary. Residents must be periodically assessed regarding their practice in handling medical equipments.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12070-024-04695-8.

Epidemiology and antimicrobial resistance of toxin-producing Klebsiella oxytoca clinical isolates from children admitted to the oncology chemotherapy center in Mofid Children's Hospital in Tehran, Iran: A cross-sectional study

Background and Aims

Klebsiella oxytoca (K. oxytoca) is the second bacterial cause of nosocomial infections in the general population after K. pneumoniae. This study surveyed the frequency of cytotoxin-producing strains of K. oxytoca and their antibiotic susceptibility profile in a cohort of children admitted to a referral hospital with different malignancies.

Methods

The Stool samples of children admitted to the Cancer Chemotherapy Unit of the Mofid Children's Hospital, Tehran, Iran were analyzed using conventional biochemical tests and polymerase chain reaction targeting the pehX gene to identify K. oxytoca. The antibiotic susceptibility profile of isolated K. oxytoca against commonly prescribed antibiotics used in treating infection at the facility was determined using the Kirby-Bauer disk diffusion technique. Also, the prevalence of genes encoding toxins among K. oxytoca was identified by PCR assay.

Results

The Stool samples of 280 participants were taken for the study of which 38 samples [(55.3% (21/38) 42 males and 44.7% (17/38) females)] tested positive for various Klebsiella spp. Out of this, K. oxytoca was identified in 2.5% (7/280) stools using cultures and conventional biochemical tests. Also, the stools of 2.9% (8/280) of the participants tested positive for K. oxytoca using PCR assay. Using PCR, (2/7) of the K. oxytoca isolates tested positive for the npsA and npsB genes and were identified as toxigenic K. oxytoca strains.

Conclusion

The prevalence of toxin-producing K. oxytoca strains in stool samples of children diagnosed with cancer in Iran is relatively low. Most of the K. oxytoca isolates were susceptible to tested antibiotics. Globally, active surveillance of toxigenic K. oxytoca strains in patients with different malignancies or immunocompromised patients is recommended in healthcare settings.

Antimicrobial Potential of Pomegranate and Lemon Extracts Alone or in Combination with Antibiotics against Pathogens

Amidst the growing concern of antimicrobial resistance as a significant health challenge, research has emerged, focusing on elucidating the antimicrobial potential of polyphenol-rich extracts to reduce reliance on antibiotics. Previous studies explored the antifungal effects of extracts as potential alternatives to conventional therapeutic strategies. We aimed to assess the antibacterial and antifungal effects of standardised pomegranate extract (PE) and lemon extract (LE) using a range of Gram-negative and Gram-positive bacteria and two yeast species. Additionally, we assessed the antimicrobial activities of common antibiotics (Ciprofloxacin, Imipenem, Gentamicin, and Ceftazidime), either alone or in combination with extracts, against Staphylococcus aureus and Escherichia coli. PE displayed substantial antibacterial (primarily bactericidal) and antifungal effects against most pathogens, while LE exhibited antibacterial (mostly bacteriostatic) and antifungal properties to a lesser extent. When compared with antibiotics, PE showed a greater zone of inhibition (ZOI) than Ciprofloxacin and Ceftazidime (p < 0.01) and comparable ZOI to Gentamicin (p = 0.4) against Staphylococcus aureus. However, combinations of either PE or LE with antibiotics exhibited either neutral or antagonistic effects on antibiotic activity against Staphylococcus aureus and Escherichia coli. These findings contribute to the existing evidence regarding the antimicrobial effects of PE and LE. They add to the body of research suggesting that polyphenols exert both antagonistic and synergistic effects in antimicrobial activity. This highlights the importance of identifying optimal polyphenol concentrations that can enhance antibiotic activity and reduce antibiotic resistance. Further in vivo studies, starting with animal trials and progressing to human trials, may potentially lead to recommendation of these extracts for therapeutic use.

Adhesion of Klebsiella oxytoca to bladder or lung epithelial cells is promoted by the presence of other opportunistic pathogens

The intestinal and respiratory tracts of healthy individuals serve as habitats for a diverse array of microorganisms, among which Klebsiella oxytoca holds significance as a causative agent in numerous community- and hospital-acquired infections, often manifesting in polymicrobial contexts. In specific circumstances, K. oxytoca, alongside other constituents of the gut microbiota, undergoes translocation to distinct physiological niches. In these new environments, it engages in close interactions with other microbial community members. As this interaction may progress to co-infection where the virulence of involved pathogens may be promoted and enhance disease severity, we investigated how K. oxytoca affects the adhesion of commonly co-isolated bacteria and vice versa during co-incubation of different biotic and abiotic surfaces. Co-incubation was beneficial for the adhesion of at least one of the two co-cultured strains. K. oxytoca enhanced the adhesion of other enterobacteria strains to polystyrene and adhered more efficiently to bladder or lung epithelial cell lines in the presence of most enterobacteria strains and S. aureus. This effect was accompanied by bacterial coaggregation mediated by carbohydrate-protein interactions occurring between bacteria. These interactions occur only in sessile, but not planktonic populations, and depend on the features of the surface. The data are of particular importance for the risk assessment of the urinary and respiratory tract infections caused by K. oxytoca, including those device-associated. In this paper, we present the first report on K. oxytoca ability to acquire increased adhesive capacities on epithelial cells through interactions with common causal agents of urinary and respiratory tract infections.

Detailed Insight into Photocatalytic Inactivation of Pathogenic Bacteria in the Presence of Visible-Light-Active Multicomponent Photocatalysts

The use of heterogeneous photocatalysis in biologically contaminated water purification processes still requires the development of materials active in visible light, preferably in the form of thin films. Herein, we report nanotube structures made of TiO2/Ag2O/Au0, TiO2/Ag2O/PtOx, TiO2/Cu2O/Au0, and TiO2/Cu2O/PtOx obtained via one-step anodic oxidation of the titanium-based alloys (Ti94Ag5Au1, Ti94Cu5Pt1, Ti94Cu5Au1, and Ti94Ag5Pt1) possessing high visible light activity in the inactivation process of methicillin-susceptible S. aureus and other pathogenic bacteria-E. coli, Clostridium sp., and K. oxytoca. In the samples made from Ti-based alloys, metal/metal oxide nanoparticles were formed, which were located on the surface and inside the walls of the NTs. The obtained results showed that oxygen species produced at the surface of irradiated photocatalysts and the presence of copper and silver species in the photoactive layers both contributed to the inactivation of bacteria. Photocatalytic inactivation of E. coli, S. aureus, and Clostridium sp. was confirmed via TEM imaging of bacterium cell destruction and the detection of CO2 as a result of bacteria cell mineralization for the most active sample. These results suggest that the membrane ruptures as a result of the attack of active oxygen species, and then, both the membrane and the contents are mineralized to CO2.

Use of Hydrogen Peroxide Vapour for Microbiological Disinfection in Hospital Environments: A Review

Disinfection of nosocomial pathogens in hospitals is crucial to combat healthcare-acquired infections, which can be acquired by patients, visitors and healthcare workers. However, the presence of a wide range of pathogens and biofilms, combined with the indiscriminate use of antibiotics, presents infection control teams in healthcare facilities with ongoing challenges in the selection of biocides and application methods. This necessitates the development of biocides and innovative disinfection methods that overcome the shortcomings of conventional methods. This comprehensive review finds the use of hydrogen peroxide vapour to be a superior alternative to conventional methods. Motivated by observations in previous studies, herein, we provide a comprehensive overview on the utilisation of hydrogen peroxide vapour as a superior high-level disinfection alternative in hospital settings. This review finds hydrogen peroxide vapour to be very close to an ideal disinfectant due to its proven efficacy against a wide range of microorganisms, safety to use, lack of toxicity concerns and good material compatibility. The superiority of hydrogen peroxide vapour was recently demonstrated in the case of decontamination of N95/FFP2 masks for reuse to address the critical shortage caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the COVID-19 pandemic. Despite the significant number of studies demonstrating antimicrobial activity, there remains a need to critically understand the mechanism of action by performing studies that simultaneously measure damage to all bacterial cell components and assess the correlation of this damage with a reduction in viable cell count. This can lead to improvement in antimicrobial efficacy and foster the development of superior approaches.

[Study of the growth temperature of ocular surface microorganisms in norm and in infectious keratitis]

Standard bacteriological examinations, which involve culturing microorganisms at 37 °C, are commonly used in clinical practice for diagnosing infectious diseases. However, the growth temperature of microorganisms on the ocular surface (OS) during infectious keratitis (IK) may not coincide with the laboratory standard, which is due to the characteristic features of heat exchange in the eye.

PURPOSE

This exploratory study examines the distribution and properties of OS microorganisms isolated under different temperature cultivation conditions in patients with IK and healthy volunteers without ophthalmic pathology.

MATERIAL AND METHODS

Fifteen participants were divided into two groups. Group 1 (n=10) consisted of patients with signs of unilateral infectious keratitis, while group 2 (n=5) served as the control group. A novel microbiological method was employed to isolate pure cultures of microorganisms. This method involved cultivating microorganisms at two temperature regimes (37 °C and 24 °C) and subsequently identifying them using biochemical, immunological, and physicochemical techniques, including mass spectrometry. Scanning electron microscopy (SEM) with lanthanide staining used as the reference method. The temperature status of the ocular surface was assessed using non-contact infrared thermography.

RESULTS

The study demonstrated the presence of psychrotolerant microorganisms on the ocular surface, which exhibited growth at a relatively low temperature of 24 °C. These psychrotolerant microorganisms were found to be isolated from the ocular surface displaying signs of temperature dysregulation. Among such microorganisms are Acinetobacter lwoffii, Achromobacter xylosoxidans, Bacillus licheniformis, Enterococcus faecalis, Klebsiella oxytoca, Klebsiella pneumoniae, Micrococcus luteus, Pseudomonas luteola, Streptococcus spp.

CONCLUSION

When identifying the causative agent of infectious keratitis, it is crucial to consider the divergence of growth temperature of ocular surface microorganisms. The presence of psychrotolerant microorganisms on the ocular surface, which can effectively grow at room temperature, should be taken into account, especially in cases of temperature dysregulation.

Mapping of conserved immunodominant epitope peptides in the outer membrane porin (Omp) L of prominent Enterobacteriaceae pathogens associated with gastrointestinal infections

BACKGROUND

Members of Enterobacteriaceae such as Escherichia coli O 157:H7, Salmonella sp., Shigella sp., Klebsiella sp., and Citrobacter freundii are responsible for the outbreak of serious foodborne illness and other mucosal infections across the globe. The outer membrane proteins (OMPs) of Enterobacteriaceae are highly immunogenic in eliciting immune responses against pathogens. Moreover, the OMPs are highly conserved in the Enterobacteriaceae family. Sequence homology in the OMPs will ensure the presence of conserved immunodominant regions with predominant epitopes. The OmpL is such an immunogen that is highly conserved among the Enterobacteriaceae pathogens. In this study, we performed computational analysis on the outer membrane porin (Omp) L of prominent Enterobacteriaceae pathogens.

RESULTS

Multiple sequence and structural alignment analysis have revealed that the OmpL protein is highly conserved among the selected Enterobacteriaceae pathogens. This amount of sequence and structural homology uncovered the conserved antibody binding B-cell epitopes in the OmpL protein. The B-cell epitopes predicted in the OmpL of Salmonella typhimurium are highly conserved among the other Enterobacteriaceae pathogens.

CONCLUSION

In conclusion, these conserved B-cell epitopes will vouch for the generation of heterologous humoral immune response in conferring cross protection against the Enterobacteriaceae pathogens and control their outbreaks across the globe.

Cultivable Gut Microbiota in Synanthropic Bats: Shifts of Its Composition and Diversity Associated with Hibernation

The role of bats in the global microbial ecology no doubt is significant due to their unique immune responses, ability to fly, and long lifespan, all contributing to pathogen spread. Some of these animals hibernate during winter, which results in the altering of their physiology. However, gut microbiota shifts during hibernation is little studied. In this research, we studied cultivable gut microbiota composition and diversity of Nyctalus noctula before, during, and after hibernation in a bat rehabilitation center. Gut microorganisms were isolated on a broad spectrum of culture media, counted, and identified with mass spectrometry. Linear modeling was used to investigate associations between microorganism abundance and N. noctula physiological status, and alpha- and beta-diversity indexes were used to explore diversity changes. As a result, most notable changes were observed in Serratia liquefaciens, Hafnia alvei, Staphylococcus sciuri, and Staphylococcus xylosus, which were significantly more highly abundant in hibernating bats, while Citrobacter freundii, Klebsiella oxytoca, Providencia rettgeri, Citrobacter braakii, and Pedicoccus pentosaceus were more abundant in active bats before hibernation. The alpha-diversity was the lowest in hibernating bats, while the beta-diversity differed significantly among all studied periods. Overall, this study shows that hibernation contributes to changes in bat cultivable gut microbiota composition and diversity.

Antimicrobial-Resistant Escherichia coli, Enterobacter cloacae, Enterococcus faecium, and Salmonella Kentucky Harboring Aminoglycoside and Beta-Lactam Resistance Genes in Raw Meat-Based Dog Diets, USA

The practice of feeding raw meat-based diets to dogs has grown in popularity worldwide in recent years. However, there are public health risks in handling and feeding raw meat-based dog diets (RMDDs) to dogs since there are no pathogen reduction steps to reduce the microbial load, which may include antimicrobial-resistant pathogenic bacteria. A total of 100 RMDDs from 63 suppliers were sampled, and selective media were used to isolate bacteria from the diets. Bacterial identification, antimicrobial susceptibility testing, and whole-genome sequencing (WGS) were conducted to identify antimicrobial resistance (AMR). The primary meat sources for RMDDs included in this study were poultry (37%) and beef (24%). Frozen-dry was the main method of product production (68%). In total, 52 true and opportunistic pathogens, including Enterobacterales (mainly Escherichia coli, Enterobacter cloacae) and Enterococcus faecium, were obtained from 30 RMDDs. Resistance was identified to 19 of 28 antimicrobials tested, including amoxicillin/clavulanic acid (23/52, 44%), ampicillin (19/52, 37%), cephalexin (16/52, 31%), tetracycline (7/52, 13%), marbofloxacin (7/52, 13%), and cefazolin (6/52, 12%). All 19 bacterial isolates submitted for WGS harbored at least one type of AMR gene. The identified AMR genes were found to mediate resistance to aminoglycoside (gentamicin, streptomycin, amikacin/kanamycin, gentamicin/kanamycin/tobramycin), macrolide, beta-lactam (carbapenem, cephalosporin), tetracycline, fosfomycin, quinolone, phenicol/quinolone, and sulfonamide. In conclusion, the results of this study suggest that feeding and handling RMDDs may pose a significant public health risk due to the presence of antimicrobial-resistant pathogens, and further research and intervention may be necessary to minimize these risks.

Pyogenic liver abscess associated with Klebsiella oxytoca: Mimicking invasive liver abscess syndrome

A pyogenic liver abscess (PLA) is a space-occupying lesion in the liver that is associated with significant morbidity and mortality. We herein present the case of a Japanese 76-year-old man who visited our hospital with fever and back pain lasting 3 weeks after endoscopic treatment for common bile duct stones. He was accompanied by poorly controlled diabetes mellitus (DM) with an HbA1c of 9.7 %. Laboratory tests disclosed elevated C-reactive protein level (22.1 mg/dL) and white cell count (11,910/μL). Abdominal computed tomography (CT) revealed hypodense lesions in the right liver lobe, with abdominal ultrasonography showing an echogenicity-mixed hypoechoic lesion. Percutaneous needle aspiration of a liver lesion was performed under suspicion of a PLA. Subsequent enhanced CT and magnetic resonance imaging confirmed the hepatic lesions in the right lobe as well as a septic pulmonary embolism, right hepatic vein thrombosis, spondylodiscitis, and a retroperitoneal abscess. Gram staining of the abscess drainage revealed gram-negative bacteria. The above findings indicated invasive liver abscess syndrome (ILAS) caused by Klebsiella pneumoniae. However, further examination of blood, urine, and abscess drainage cultures revealed positivity for Klebsiella oxytoca. This case illustrates that K. oxytoca may cause ILAS-like symptoms. Screening for systemic metastatic infection should be considered in patients with PLA due to K. oxytoca in whom therapeutic intervention has been delayed, especially in patients with poorly controlled DM.

Gut Microbiota Associated with Clostridioides difficile Carriage in Three Clinical Groups (Inflammatory Bowel Disease, C. difficile Infection and Healthcare Workers) in Hospital Field

Clostridioides difficile is an anaerobic spore-forming Gram-positive bacterium. C. difficile carriage and 16S rDNA profiling were studied in three clinical groups at three different sampling times: inflammatory bowel disease (IBD) patients, C. difficile infection (CDI) patients and healthcare workers (HCWs). Diversity analysis was realized in the three clinical groups, the positive and negative C. difficile carriage groups and the three analysis periods. Concerning the three clinical groups, β-diversity tests showed significant differences between them, especially between the HCW group and IBD group and between IBD patients and CDI patients. The Simpson index (evenness) showed a significant difference between two clinical groups (HCWs and IBD). Several genera were significantly different in the IBD patient group (Sutterella, Agathobacter) and in the CDI patient group (Enterococcus, Clostridioides). Concerning the positive and negative C. difficile carriage groups, β-diversity tests showed significant differences. Shannon, Simpson and InvSimpson indexes showed significant differences between the two groups. Several genera had significantly different relative prevalences in the negative group (Agathobacter, Sutterella, Anaerostipes, Oscillospira) and the positive group (Enterococcus, Enterobacteriaceae_ge and Enterobacterales_ge). A microbiota footprint was detected in C. difficile-positive carriers. More experiments are needed to test this microbiota footprint to see its impact on C. difficile infection.

Polyclonal Multidrug ESBL-Producing Klebsiella pneumoniae and Emergence of Susceptible Hypervirulent Klebsiella pneumoniae ST23 Isolates in Mozambique

Globally, antibiotic-resistant Klebsiella spp. cause healthcare-associated infections with high mortality rates, and the rise of hypervirulent Klebsiella pneumoniae (hvKp) poses a significant threat to human health linked to community-acquired infections and increasing non-susceptibility. We investigated the phenotypic and genetic features of 36 Klebsiella isolates recovered from invasive infections at Hospital Central of Maputo in Mozambique during one year. The majority of the isolates displayed multidrug resistance (MDR) (29/36) to cephalosporins, gentamicin, ciprofloxacin, and trimethoprim-sulfamethoxazole but retained susceptibility to amikacin, carbapenems, and colistin. Most isolates were ESBLs-producing (28/36), predominantly carrying the blaCTX-M-15 and other beta-lactamase genes (blaSHV, blaTEM-1, and blaOXA-1). Among the 16 genomes sequenced, multiple resistance genes from different antibiotic classes were identified, with blaCTX-M-15, mostly in the ISEcp1-blaCTX-M-15-orf477 genetic environment, co-existing with blaTEM-1 and aac(3)-IIa in five isolates. Our results highlight the presence of polyclonal MDR ESBL-producing K. pneumoniae from eight sequence types (ST), mostly harbouring distinct yersiniabactin within the conjugative integrative element (ICE). Further, we identified susceptible hvKp ST23, O1-K1-type isolates carrying yersiniabactin (ybt1/ICEKp10), colibactin, salmochelin, aerobactin, and hypermucoid locus (rmpADC), associated with severe infections in humans. These findings are worrying and underline the importance of implementing surveillance strategies to avoid the risk of the emergence of the most threatening MDR hvKp.

Phylogenetic lineages and antimicrobial resistance determinants of clinical Klebsiella oxytoca spanning local to global scales

Klebsiella oxytoca is an opportunistic pathogen causing serious nosocomial infections. Knowledge about the population structure and diversity of healthcare-associated K. oxytoca from a genomic standpoint remains limited. Here, we characterized the phylogenetic relationships and genomic characteristics of 20 K. oxytoca sensu stricto isolates recovered from bloodstream infections at the Dartmouth-Hitchcock Medical Center, New Hampshire, USA from 2017 to 2021. Results revealed a diverse population consisting of 15 sequence types (STs) that together harbored 10 variants of the intrinsic beta-lactamase gene bla OXY-2, conferring resistance to penicillins. Similar sets of antimicrobial resistance (AMR) determinants reside in multiple distinct lineages, with no one lineage dominating the local population. To place the New Hampshire K. oxytoca in a broader context, we compared them to 304 publicly available genomes of clinical isolates from 18 countries. This global clinical K. oxytoca sensu stricto population is represented by over 65 STs that together harbored resistance genes against 14 antimicrobial classes, including eight bla OXY-2 variants. Three dominant STs in the global population (ST2, ST176, ST199) circulate across multiple countries and were also present in the New Hampshire population. The global K. oxytoca population is genetically diverse, but there is evidence for broad dissemination of a few lineages carrying distinct set of AMR determinants. Our findings reveal the clinical diversity of K. oxytoca sensu stricto and its importance in surveillance efforts aimed at monitoring the evolution of this drug-resistant nosocomial pathogen. IMPORTANCE The opportunistic pathogen Klebsiella oxytoca has been increasingly implicated in patient morbidity and mortality worldwide, including several outbreaks in healthcare settings. The emergence and spread of antimicrobial resistant strains exacerbate the disease burden caused by this species. Our study showed that clinical K. oxytoca sensu stricto is phylogenetically diverse, harboring various antimicrobial resistance determinants and bla OXY-2 variants. Understanding the genomic and population structure of K. oxytoca is important for international initiatives and local epidemiological efforts for surveillance and control of drug-resistant K. oxytoca.

Etiological Bacterial Spectrum of Purulent Inflammation of Cervical Lymph Nodes in Children With Unknown Causes of Lymphadenopathy

In the management of the non-specific purulent inflammation of the cervical lymph nodes in children, not only surgical treatment to evacuate the available pus but also antibacterial therapy is mandatory. Knowledge of the spectrum of the bacterial causative agents of this disease is of fundamental importance for it. This retrospective study included 66 patients with purulent inflammation of the cervical lymph nodes with a mean age of 5.79 years, ranging from 29 days to 17 years, who were hospitalized for the period 2015-2022 in the three pediatric clinics at the St. Marina University Multispecialty Hospital for Active Treatment in Varna, Bulgaria, and operated by an oral or maxillofacial surgeon, in which for microbiological examination material from the suppurated lymph node was taken and analyzed first by direct microscopy for gram-positivity and then on a biochemical machine identifier VITEK (bioMérieux, Marcy-l'Étoile, France). In all of them, the patients and their parents did not provide anamnestic data explaining the etiology of their infectious diseases of the cervical lymph nodes. There was no clear cause that would explain the occurrence of cervical lymphadenopathy - skin infections, dental diseases, diseases of the ears and upper and lower respiratory tracts, onco-hematological diseases, and others. During the medical examination by pediatricians and surgeons, no entrances to the infection were found, but only local signs of inflammation (redness, swelling, and pain), increased levels of blood markers of inflammation (leukocytes, neutrophils, erythrocyte sedimentation rate, and C-reactive protein) and there was imaging evidence (ultrasound, magnetic resonance imaging, and computed tomography) of a purulent collection in the lymph nodes and/or in the soft tissues surrounding them. Exudate without microbial growth was found in 22 of the cases. The main causative agents of purulent lymphadenopathy are gram-positive bacteria (n=32, 72,73%) - Staphylococcus aureus (n=16), Staphylococcus haemolyticus (n=8), Beta-hemolytic streptococcus (n=2), and gram-positive mixed resident microflora (n=6). However, in 27.27% (n=12) of all 44 patients described in this article with isolated pathogens, cultures were gram-negative. These are Bartonella henselae (n=4), Klebsiella pneumoniae (n=4), Klebsiella oxytoca (n=2), and Flavimonas oryzihabitans (n=2).

Binary CuO\CoO nanoparticles inhibit biofilm formation and reduce the expression of papC and fimH genes in multidrug-resistant Klebsiella oxytoca

BACKGROUND AND AIM

Binary copper-cobalt oxide nanoparticles (CuO\CoO NPs) are modern kinds of antimicrobials, which may get a lot of interest in clinical application. This study aimed to detect the effect of the binary CuO\CoO NPs on the expression of papC and fimH genes in multidrug-resistant (MDR) isolates of Klebsiella oxytoca to reduce medication time and improve outcomes.

METHODS

Ten isolates of K. oxytoca were collected and identified by different conventional tests besides PCR. Antibiotic sensitivity and biofilm-forming ability were carried out. The harboring of papC and fimH genes was also detected. The effect of binary CuO\CoO nanoparticles on the expression of papC and fimH genes was investigated.

RESULTS

Bacterial resistance against cefotaxime and gentamicin was the highest (100%), while the lowest percentage of resistance was to amikacin (30%). Nine of the ten bacterial isolates had the ability to form a biofilm with different capacities. MIC for binary CuO\CoO NPs was 2.5 µg/mL. Gene expression of papC and fimH was 8.5- and 9-fold lower using the NPs.

CONCLUSION

Binary CuO\CoO NPs have a potential therapeutic effect against infections triggered by MDR K. oxytoca strains due to the NPs-related downregulation ability on the virulence genes of K. oxytoca.

Phage therapy of antibiotic-resistant strains of Klebsiella pneumoniae, opportunities and challenges from the past to the future

Klebsiella spp. is a commensal gram-negative bacterium and a member of the human microbiota. It is the leading cause of various hospital-acquired infections. The occurrence of multi-drug drug resistance and carbapenemase-producing strains of Klebsiella pneumoniae producing weighty contaminations is growing, and Klebsiella oxytoca is an arising bacterium. Alternative approaches to tackle contaminations led by these microorganisms are necessary as strains enhance opposing to last-stage antibiotics in the way that Colistin. The lytic bacteriophages are viruses that infect and rapidly eradicate bacterial cells and are strain-specific to their hosts. They and their proteins are immediately deliberate as opportunities or adjuncts to antibiotic therapy. There are several reports in vitro and in vivo form that proved the potential use of lytic phages to combat superbug stains of K. pneumoniae. Various reports dedicated that the phage area can be returned to the elimination of multi-drug resistance and carbapenemase resistance isolates of K. pneumoniae. This review compiles our current information on phages of Klebsiella spp. and highlights technological and biological issues related to the evolution of phage-based therapies targeting these bacterial hosts.

Enterobacteriaceae isolates from clinical and household tap water samples: antibiotic resistance, screening for extended-spectrum, metallo- and ampC-beta-lactamases, and detection of blaTEM,blaSHV and blaCTX-M in Uyo, Nigeria

Introduction

Infections caused by multidrug-resistant (MDR) bacteria, extended spectrum β-lactamase (ESBL), metallo-β-lactamase (MBL) and AmpC-β-lactamase (AmpC-βL)-producers are increasing globally. This study identified bacteria in clinical and tap water samples and determined the prevalence of MDR, and β-lactamase enzymes and genes.

Methods

Isolates were identified by the Vitek 2 (bioMérieux, France) automated system. Antibiotic resistance and screening for β-lactamase enzymes and genes was done using disc diffusion method and Vitek 2 automated system, CHROMagar-ESBL, combined double disc, inhibition-based method and multiplex polymerase chain reaction, respectively.

Results

The Enterobacteriaceae isolates obtained were Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, Salmonella spp., Proteus mirabilis, Enterobacter aerogenes, Shigella sonnei, Proteus vulgaris, Enterobacter sakazakii, Klebsiella oxytoca, Citrobacter diversus, and Serratia liquefaciens. Of the 674 isolates from clinical samples, 36.5%, 28.5%, and 19.9% were ESBL, MBL, and AmpC-βL producers, respectively. A low prevalence of AmpC-βL and MBL producers were obtained, with no significant difference (p<0.05) between the prevalence of ESBL and non-ESBL producers. Isolates exhibited varied levels of resistance to gentamicin, amoxicillin-clavulanic acid, ciprofloxacin, and tetracycline. The results showed that 54.6% of ESBL producers, 57.9% of MBL producers, and 62.8% of AmpC-βL producers were MDR strains. Of the 141 representative isolates tested, 36.9%, 15.6%, and 20.6% had only blaTEM, blaSHV, and blaCTX-M, respectively; 5.7% possessed both blaTEM and blaSHV; 7.1% possessed both blaTEM and blaCTX-M and 4.3% had both blaSHV and blaCTX-M.

Conclusions

This study found a high prevalence of β-lactamase producers, indicating the need for further research on the molecular epidemiology of β-lactamase producers and their impacts in the region.

Zinc-Based Nanoparticles Reduce Bacterial Biofilm Formation

Biofilm formation is important for microbial survival in hostile environments and a phenotype that provides microorganisms with antimicrobial resistance. Zinc oxide (ZnO) and Zinc sulfide (ZnS) nanoparticles (NPs) present potential antimicrobial properties for biomedical and food industry applications. Here, we aimed to analyze, for the first time, the bactericidal and antibiofilm activity of ZnS NPs against Staphylococcus aureus, Klebsiella oxytoca, and Pseudomonas aeruginosa, all medically important bacteria in developed countries. We compared ZnS NPs antimicrobial activity to ZnO NPs, which have been extensively studied. Using the colorimetric XTT reduction assay to observe the metabolic activity of bacterial cells and the crystal violet assay to measure biofilm mass, we demonstrated that ZnS and ZnO had similar efficacy in killing planktonic bacterial cells and reducing biofilm formation, with S. aureus being more susceptible to both therapeutics than K. oxytoca and P. aeruginosa. Crystal violet staining and confocal microscopy validated that Zn NPs inhibit biofilm formation and cause architectural damage. Our findings provide proof of principle that ZnS NPs have antibiofilm activity, and can be potentially used in medical and food industry applications, such as treatment of wound infections or package coating for food preservation. IMPORTANCE Zinc (Zn)-based nanoparticles (NPs) can be potentially used in medical and food preservation applications. As proof of principle, we investigated the bactericidal and antibiofilm activity of zinc oxide (ZnO) and zinc sulfide (ZnS) NPs against medically important bacteria. Zn-based NPs were similarly effective in killing planktonic and biofilm-associated Staphylococcus aureus, Klebsiella oxytoca, and Pseudomonas aeruginosa cells. However, S. aureus was more susceptible to these investigational therapeutics. Although further studies are warranted, our findings suggest the possibility of future use of Zn-based NPs in the treatment of skin infections or preservation of food.

Oral Microbiome as a Tool of Systemic Disease on Cleft Patients: A New Landscape

The oral cavity microbiome comprises benign and pathogenic bacteria, with more than 700 species identified. However, the current literature regarding resident bacterial flora in the oropharyngeal cavities in cleft lip/palate (CLP) patients still needs to be completed. This review aims to evaluate the role of the oral microbiome of cleft patients as an indicator in systemic diseases for which cleft patients might be at higher risk in the short or long term. A literature review was performed in July 2020 using Biomedical Reference Collection Comprehensive, Cumulative Index to Nursing and Allied Health Literature (CINAHL) Complete, Dentistry & Oral Sciences Source via Elton B. Stephens Company/Online Database (EBSCO), Turning Research into Practice (TRIP), and PubMed. The keywords used were "oral, bacteria, microbiome, biota, flora, cleft, palate." The resulting 466 articles were deduplicated using Endnote. The total amount of articles' abstracts without duplicates was filtered using a set criterion. The title and abstract filter criteria included 1) cleft lip (CL) and/or cleft palate (CP) patients, 2) changes in the oral microbiome in CL and/or CP patients, 3) male and female patients 0-21 years old, and 4) English language. The full-text filter criteria included 1) CL and/or CP patients vs. non-cleft control patients, 2) oral bacteria, 3) nonprocedural measurements of microorganisms, and 4) case-control studies. A Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) flow chart was created using the EndNote data results. The final five articles of the systematic search indicated that the oral cavity of cleft lip and/or palate patients resulted in 1) contradicting levels of Streptococcus mitis and Streptococcus salivarius; 2) lower levels of Streptococcus gordonii, Bordetella dentium, Fusobacterium nucleatum, Veillonella parvula, Bacillus and Lautropia when compared to the control group; 3) higher levels of Staphylococcus epidermidis and Methicillin-sensitive Staphylococcus aureus compared to the control group; 4) presence of Enterobacter cloacae 36.6%, Klebsiella pneumoni 53.3%, and Klebsiella oxytoca 76.6% vs. absence in the control non-cleft group. Patients with CL and/or CP are at higher risk for caries, periodontal diseases, and upper and lower respiratory infections. The results from this review indicate that relative levels of certain bacteria may be associated with these issues. The lower levels of S. mitis, S. salivarius, S. gordini, and F. nucleatum in the oral cavity of cleft patients could be linked as a possible cause of the higher incidence of tooth decay, gingivitis and periodontal disease as high levels of these bacteria are associated with oral disease. Further, the higher incidence of sinusitis in cleft patients might be linked to low levels of S. salivarius in the oral profile of these patients. Likewise, E. cloacae, K. oxycota, and K. pneumoni have been linked with pneumonia and bronchiolitis, both of which are increased in cleft patients. The oral bacterial dysbiosis of cleft patients observed in this review may play a vital function in the oral microbiome's diversity, which could play a role in disease progression and disease markers. The pattern seen in cleft patients potentially demonstrates how structural abnormalities can lead to the onset of severe infection.

The use of carbon dioxide and intense pulsed light laser for the treatment of hypertrophic burn scars: A case series

Introduction

Hypertrophic scarring is a common and debilitating consequence of burn scars. While there is limited evidence for current treatment options, laser therapy has been shown to be effective, low risk and minimally invasive. This study assesses the use of carbon dioxide lasers and intense pulsed light devices in the treatment of hypertrophic burn scars.

Methods

In this case series, patients were recruited from a hypertrophic burn scar waitlist and completed a Patient and Observer Scar Assessment Scale prior to and six weeks after laser therapy. The Nordlys (intense pulsed light) and CO2RE (carbon dioxide) systems from Candela Medical were used, with a range of settings used depending on the assessment of the burn scar. The differences between scores were calculated for the total Patient and Observer Scar Assessment Scale score, pain, itch, colour, stiffness, thickness, irregularity and the overall opinion of the scar. Statistical analysis was completed using a paired, two-tailed student T test.

Results

A total of 31 patients were recruited for this trial with a range of scar locations, surface areas and mechanism of burn injury. The calculated difference in mean showed a significant reduction for the overall Patient and Observer Scar Assessment Scale score (1.93, p < 0.0001), pain (1.39, p  =  0.0002), itch (1.84, p  =  0.0002), colour (1.97, p < 0.0001), stiffness (2.47, p < 0.0001), thickness (2.1, p < 0.0001), irregularity (1.89, p < 0.0001) and overall opinion (1.58, p  =  0.0003).

Conclusion

Current management options for hypertrophic scarring have limited evidence. Laser therapy presents a minimally invasive procedure that can be completed under topical anaesthetic and has shown to be effective following a single treatment of combined carbon dioxide laser and intense pulsed light device therapy.

Lay Summary

Many people will suffer a burn injury throughout their life and up to almost 3 out of 4 people with burn injuries will suffer from hypertrophic scars (a thickened, red and itchy scar). These scars cause distress both due to their appearance and their reduction of function, particularly over a joint or muscle. Laser therapy, in which different wave lengths of light (pulsed light) or gas (carbon dioxide) target the scar, has been found to be effective and have minimal side effects in the management of hypertrophic scars. While individual lasers have been assessed and found to be effective and low risk, the combined use of multiple lasers on the same scar has not been extensively studied. We studied the effectiveness of both light and gas laser therapies on hypertrophic scars. Patients with hypertrophic scars completed a questionnaire that focused on their perspective of their scar (pain, itch, stiffness, thickness, irregularity, overall opinion) prior to the treatment. The patients then underwent laser therapy (with local anaesthetic gel) with either pulsed light and/or carbon dioxide (gas) laser. The type of laser used was decided by the clinician performing the therapy depending on scar location and thickness. Patients then re-completed the subjective survey six weeks following the laser therapy, and the results compared. We learnt that laser therapy (both light, gas and a combination of both) are effective (and low risk) in reducing the subjective burden of the scar for the patient.

A Klebsiella pneumoniae NDM-1+ bacteriophage: Adaptive polyvalence and disruption of heterogenous biofilms

Bacteriophage KL-2146 is a lytic virus isolated to infect Klebsiella pneumoniae BAA2146, a pathogen carrying the broad range antibiotic resistance gene New Delhi metallo-betalactamase-1 (NDM-1). Upon complete characterization, the virus is shown to belong to the Drexlerviridae family and is a member of the Webervirus genus located within the (formerly) T1-like cluster of phages. Its double-stranded (dsDNA) genome is 47,844 bp long and is predicted to have 74 protein-coding sequences (CDS). After challenging a variety of K. pneumoniae strains with phage KL-2146, grown on the NDM-1 positive strain BAA-2146, polyvalence was shown for a single antibiotic-sensitive strain, K. pneumoniae 13,883, with a very low initial infection efficiency in liquid culture. However, after one or more cycles of infection in K. pneumoniae 13,883, nearly 100% infection efficiency was achieved, while infection efficiency toward its original host, K. pneumoniae BAA-2146, was decreased. This change in host specificity is reversible upon re-infection of the NDM-1 positive strain (BAA-2146) using phages grown on the NDM-1 negative strain (13883). In biofilm infectivity experiments, the polyvalent nature of KL-2146 was demonstrated with the killing of both the multidrug-resistant K. pneumoniae BAA-2146 and drug-sensitive 13,883 in a multi-strain biofilm. The ability to infect an alternate, antibiotic-sensitive strain makes KL-2146 a useful model for studying phages infecting the NDM-1+ strain, K. pneumoniae BAA-2146. GRAPHICAL ABSTRACT.

Investigation on the microbiological hazards in an artisanal soft cheese produced in northern Italy and its production environment in different seasonal periods

The present study aimed at assessing the occurrence of microbiological hazards (Listeria monocytogenes, Staphylococcus aureus, Salmonella spp. and Escherichia coli O157) in an artisanal soft cheese produced in northern Italy. In the same product total bacterial count, lactic acid bacteria and Enterobacteriaceae were enumerated, and pH and water activity measured in two batches sampled in summer and winter. Samples of raw materials, environmental swabs from the production processes and cheese during 15 days of storage at 2 and 8°C as well as dynamic temperature of 2°C for 5 days and 8°C for 10 days were collected and tested. The load of total bacterial count was significantly higher in the winter batch in comparison to the summer one, with a significant increase at the end of the storage period also noticed for lactic acid bacteria. Statistical higher values of pH were registered in raw materials and end of storage in winter batch. S. aureus was confirmed only in the winter batch within samples (n=4) of stored cheese. On plates used for E. coli O157 detection, colonies of Klebsiella pneumoniae and Klebsiella oxytoca were isolated. The results suggest that the highest bacterial population in the winter batch was associated to a higher pH in stored cheese and a higher number of biological hazards identified. Their isolation started in the maturation room suggesting this step as relevant for possible cheese contamination.

Moderation of gut microbiota and bile acid metabolism by chlorogenic acid improves high-fructose-induced salt-sensitive hypertension in mice

Chlorogenic acid (CGA) is a natural compound with many important pharmacological effects including anti-hypertension. This study aimed to investigate the anti-hypertensive effect of CGA on high-fructose-induced salt-sensitive hypertension and the underlying mechanism. Hypertension was induced in male C57BL/6 mice by 20% fructose in drinking water plus 4% sodium chloride in the diet (HFS) for 8 weeks. CGA (50, 100 or 200 mg kg^-1 d^-1) was orally administered to HFS-treated mice. The blood pressure of mice was recorded via the tail cuff method. The structure of gut microbiota and profiles of bile acids (BAs) in the serum were determined. Here, we found that HFS-elevated systolic blood pressure was greatly attenuated by CGA. The microbiota analysis showed that CGA restructured the HFS-treated gut microbiota, and markedly enriched Klebsiella. Oral administration of a Klebsiella isolate, Klebsiella oxytoca, also exhibited an anti-hypertensive effect in HFS-fed mice. Furthermore, we found that CGA and CGA-enriched K. oxytoca enhanced the expression of colonic Farnesoid X Receptor (FXR), modulated BA metabolism and enriched some BAs including deoxycholic acid (DCA) in the serum of HFS-fed mice. Treatment with DCA improved phenylephrine-induced vasoconstriction in arterioles of mice and attenuated hypertension in HFS-fed mice, suggesting that DCA serves as a link between gut microbiota and blood pressure. Our results clearly demonstrate that CGA attenuates HFS-induced hypertension in mice by modulating gut microbiota and BA metabolism. These findings provide insights into the potential mechanism of CGA for the treatment of hypertension.

Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials

Plastics are inexpensive and widely used organic polymers, but their high durability hinders biodegradation. Polystyrene, including extruded polystyrene (also known as styrofoam), is among the most commonly produced plastics worldwide and is recalcitrant to microbial degradation. In this study, we assessed changes in the gut microbiome of superworms (Zophobas morio) reared on bran, polystyrene or under starvation conditions over a 3 weeks period. Superworms on all diets were able to complete their life cycle to pupae and imago, although superworms reared on polystyrene had minimal weight gains, resulting in lower pupation rates compared to bran reared worms. The change in microbial gut communities from baseline differed considerably between diet groups, with polystyrene and starvation groups characterized by a loss of microbial diversity and the presence of opportunistic pathogens. Inferred microbial functions enriched in the polystyrene group included transposon movements, membrane restructuring and adaptations to oxidative stress. We detected several encoded enzymes with reported polystyrene and styrene degradation abilities, supporting previous reports of polystyrene-degrading bacteria in the superworm gut. By recovering metagenome-assembled genomes (MAGs) we linked phylogeny and functions and identified genera including Pseudomonas, Rhodococcus and Corynebacterium that possess genes associated with polystyrene degradation. In conclusion, our results provide the first metagenomic insights into the metabolic pathways used by the gut microbiome of superworms to degrade polystyrene. Our results also confirm that superworms can survive on polystyrene feed, but this diet has considerable negative impacts on host gut microbiome diversity and health.

Integrated metagenomic and metatranscriptomic analysis reveals actively expressed antibiotic resistomes in the plastisphere

The plastisphere is viewed as a reservoir for the antibiotic resistome in water environments and may pose health concerns. However, the expression profiles of the resistome in the plastisphere are largely unknown. Here, we profiled the occurrence, abundance, and transcriptional level of antibiotic resistance genes (ARGs), plasmid associated ARGs, microbial composition and ARG bacterial hosts in the plastisphere and urban river water using 16S rRNA gene sequencing, metagenomic sequencing, and metatranscriptomic sequencing methods. A total of 173 ARGs conferring resistance to 24 major classes of antibiotics commonly prescribed to humans and animals were detected in the plastisphere. Of these, 75 genes were observed with transcriptional activity, indicating that the antibiotic resistome in the plastisphere was not only present, but also actively expressed. Human pathogens belonging to family Enterobacteriaceae were identified as bacterial hosts of ARGs in the plastisphere. The opportunistic and multidrug resistant human pathogen Enterobacter cloacae was found to actively express tetG and confer tetracycline resistance to the plastisphere. Furthermore, 39 genes were identified as "plasmid associated ARGs" in the plastisphere, displaying a higher proportion of transcript abundance compared with water. The above results suggest that the plastisphere is a hotspot for antibiotic resistome acquisition, expression, and dissemination.

Improved diagnosis of antibiotic-associated haemorrhagic colitis (AAHC) in faecal specimens by a new qualitative real-time PCR assay detecting relevant toxin genes of Klebsiella oxytoca sensu lato

OBJECTIVE

Toxin-producing Klebsiella oxytoca causes antibiotic-associated haemorrhagic colitis (AAHC). The disease-relevant cytotoxins tilivalline and tilimycine produced by certain K. oxytoca isolates are encoded by the non-ribosomal peptide synthetase genes A (npsA) and B (npsB). In this study, the new LightMix® Modular kit for the detection of relevant K. oxytoca sensu lato (s.l.) toxin genes was evaluated.

METHODS

DNA was extracted on the automated EMAG® platform. Amplification was done on the Light Cycler® 480 II instrument. In total, 130 residual faecal specimens collected from patients with antibiotic-associated diarrhoea were studied to determine the clinical sensitivity and specificity. Toxigenic culture served as reference method.

RESULTS

With the new kit, the limit of detection was 15 CFU/mL for all targets. For the pehX target specific to K. oxytoca s.l., 65 of 130 clinical specimens were positive, while toxin-specific targets (npsA/npsB) were positive in 47 of 130. The npsA/npsB PCR targets showed a clinical sensitivity of 100% (95%CI 80.5-100%) and a specificity of 73.5% (95%CI 64.3-81.3%) with a positive predictive value of 16.5% (95%CI 12.7-21.2%) and a negative predictive value of 100%.

CONCLUSION

Compared with culture, additional clinical specimens positive for K. oxytoca s.l. were detected with real-time PCR. The specificity of the toxin targets appears moderate due to the inferior sensitivity of the culture-based reference method. Since the developed assay is highly sensitive, it may be used as first-line method to improve the diagnosis of AAHC.

Klebsiella species: Taxonomy, hypervirulence and multidrug resistance

Members of the genus Klebsiella have rapidly evolved within the past decade, generating organisms that simultaneously exhibit both multidrug resistance and hypervirulence (MDR-hv) phenotypes; such organisms are associated with severe hospital- and community-acquired infections. Carbapenem-resistant infections with unknown optimal treatment regime were of particular concern among the MDR-hv Klebsiella strains. Recent studies have revealed the molecular features and the mobile resistance elements they harbour, allowing identification of genetic loci responsible for transmission, stable inheritance, and expression of mobile resistance or virulence-encoding elements that confer the new phenotypic characteristics of MDR-hv Klebsiella spp. Here, we provide a comprehensive review on the taxonomic position, species composition and different phylotypes of Klebsiella spp., describing the diversity and worldwide distribution of the MDR-hv clones, the genetic mutation and horizontal gene transfer events that drive the evolution of such clones, and the potential impact of MDR-hv infections on human health.

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.

Inhibition of Several Bacterial Species Isolated from Squid and Shrimp Skewers by Different Natural Edible Compounds

Seafood is an excellent source of nutrients, essential for a healthy diet, ranging from proteins and fatty acids to vitamins and minerals. Seafood products are highly perishable foods due to their nutritional characteristics and composition. The application of nontoxic, natural, and edible preservatives to extend the shelf-life and inhibit bacterial proliferation of several foods has been a hot topic. Consequently, this work aimed to perform the microbiological characterization of squid and shrimp skewers during their shelf-life (five days) and evaluate the susceptibility of randomly isolated microorganisms to several natural edible compounds so that their application for the preservation and shelf-life extension of the product might be analyzed in the future. The product had considerably high total microorganisms loads of about 5 log CFU/g at day zero and 9 log CFU/g at day five. In addition, high bacterial counts of Pseudomonas spp., Enterobacterales, and lactic acid bacteria (LAB) were found, especially on the last day of storage, being Pseudomonas the dominant genus. However, no Escherichia coli or Listeria monocytogenes were detected on the analyzed samples. One hundred bacterial isolates were randomly selected and identified through 16s rRNA sequencing, resulting in the detection of several Enterobacterales, Pseudomonas spp., and LAB. The antibacterial activity of carvacrol, olive leaf extract, limonene, Citrox®, different chitosans, and ethanolic propolis extracts was evaluated by the agar diffusion method, and the minimum inhibitory concentration was determined only for Citrox® since only this solution could inhibit all the identified isolates. At concentrations higher than or equal to 1.69% (v/v), Citrox® demonstrated bacteriostatic and bactericidal activity to 97% and 3% of the isolates, respectively. To our knowledge, there are no available data about the effectiveness of this commercial product on seafood isolates. Although preliminary, this study showed evidence that Citrox® has the potential to be used as a natural preservative in these seafood products, improving food safety and quality while reducing waste. However, further studies are required, such as developing a Citrox®-based coating and its application on this matrix to validate its antimicrobial effect.

Thoracic spondylodiscitis secondary to Klebsiella oxytoca urosepsis-a case report

Spondylodiscitis is an insidious and infectious pathology of the spinal column attributable to pathogenic micro-organisms and occurs in a variety of contexts. These micro-organisms can be inoculated surgically or can metastasise from distant sites of infection. Klebsiella species are important community-acquired and nosocomial pathogens but are uncommonly implicated in spinal infection. Klebsiella oxytoca is more obscure than its generic relative Klebsiella pneumoniae and has only five times previously been reported in spondylodiscitis. It possesses the ability to acquire inducible and recombinant antibiotic resistance, especially in the hospital setting. We describe the case of an elderly man with complex urology and this rare sequela due to incomplete treatment of a K. oxytoca urinary infection. He developed sepsis that recurred after incomplete antibiosis and seeded to his thoracic spine causing overt spondylodiscitis. The infection fulminated and his spinal lesion deteriorated into acute spinal cord compression with neurological compromise, requiring surgical decompression, fixation and long-term antibiotics. This is a sixth documented instance of a rare spinal bacterial infection. We describe the relevant microbiology and pathology, neurosurgical considerations, and general practice points for clinicians. Our report is a novel illustration of the potentially catastrophic consequences of inadequately treated urosepsis and is a stark reminder of the importance of antimicrobial stewardship.

Caseinolytic Proteins (Clp) in the Genus Klebsiella: Special Focus on ClpK

Caseinolytic proteins (Clp), which are present in both prokaryotes and eukaryotes, play a major role in cell protein quality control and survival of bacteria in harsh environmental conditions. Recently, a member of this protein family, ClpK was identified in a pathogenic strain of Klebsiella pneumoniae which was responsible for nosocomial infections. ClpK is linked to the thermal stress survival of this pathogen. The genome wide analysis of Clp proteins in Klebsiella spp. indicates that ClpK is present in only 34% of the investigated strains. This suggests that the uptake of the clpk gene is selective and may only be taken up by a pathogen that needs to survive harsh environmental conditions. In silico analyses and molecular dynamic simulations show that ClpK is mainly α-helical and is highly dynamic. ClpK was successfully expressed and purified to homogeneity using affinity and anion exchange chromatography. Biophysical characterization of ClpK showed that it is predominantly alpha-helical, and this is in agreement with in silico analysis of the protein structure. Furthermore, the purified protein is biologically active and hydrolyses ATP in a concentration- dependent manner.

Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch

BACKGROUND

Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting.

METHODS

We developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR.

RESULTS

Using Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1-O3) represented 88.9% of all genomes, whereas capsule types were much more diverse.

CONCLUSIONS

Pathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance.

Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition

Gut colonization with multidrug-resistant (MDR) bacteria enhances the risk of bloodstream infections in susceptible individuals. We demonstrate highly variable degrees of ex vivo colonization resistance against a carbapenem-resistant Klebsiella pneumoniae strain in human feces samples and subsequently isolate diverse K. oxytoca strains from protected donors. Several of these K. oxytoca strains reduce gut colonization of MDR K. pneumoniae strains in antibiotic-treated and gnotobiotic mouse models. Comparative analysis of K. oxytoca strains coupled with CRISPR-Cas9-mediated deletion of casA, a protein essential for utilization of selected beta-glucosides, identified competition for specific carbohydrates as key in promoting colonization resistance. In addition to direct competition between K. oxytoca and K. pneumoniae, cooperation with additional commensals is required to reestablish full colonization resistance and gut decolonization. Finally, humanized microbiota mice generated from K. pneumoniae-susceptible donors are protected by K. oxytoca administration, demonstrating the potential of commensal K. oxytoca strains as next-generation probiotics.

First Experimental Evidence for the Presence of Potentially Virulent Klebsiella oxytoca in 14 Species of Commonly Consumed Aquatic Animals, and Phenotyping and Genotyping of K. oxytoca Isolates

Klebsiella oxytoca is a recently emerging pathogen that can cause necrotizing enterocolitis, hemorrhagic colitis, sepsis-associated purpura fulminans, and infective endocarditis in humans. The bacterium is ubiquitous in water and soil environments. Nevertheless, current literature on K. oxytoca in aquatic products is rare. In this study, we surveyed K. oxytoca contamination in 41 species of consumable aquatic animals sold in July, August, and September of 2018 and 2019 in Shanghai, China, 40 of which had no history of carrying this bacterium. K. oxytoca was for the first time isolated from 14 species with high abundance in benthic animals. None of the K. oxytoca isolates (n = 125) harbored toxin genes mviM, tisB, and yqgB. However, a high occurrence of virulence-associated genes was observed, including brkB (73.6%), cdcB (66.4%), pduV (64.8%), and virk (63.2%). Resistance to sulphamethoxazole-trimethoprim (56.0%) was the most predominant among the isolates, followed by chloramphenicol (6.4%), tetracycline (5.6%), and kanamycin (3.2%). Approximately 8.0% of the isolates displayed multidrug resistant phenotypes. Meanwhile, high percentages of the isolates tolerated the heavy metals Cu²⁺ (84.8%), Pb²⁺ (80.8%), Cr³⁺ (66.4%), Zn²⁺ (66.4%), and Hg²⁺ (49.6%). Different virulence and resistance profiles were observed among K. oxytoca isolates in 3 types and 14 species of aquatic animals. The ERIC-PCR-based genome fingerprinting of the 125 K. oxytoca isolates revealed 108 ERIC genotypes with 79 singletons, which demonstrated the genetic diversity of the isolates. The results of this study fill gaps for policy and research in the risk assessment of K. oxytoca in consumable aquatic animals.

Diffuse-Type Tenosynovial Giant Cell Tumor of the Knee with Concurrent Polymicrobial Infection (Klebsiella oxytoca and Group B Streptococcus)

Tenosynovial giant cell tumors (TGCT) are a rare class of benign proliferative tumors that are classified according to their presentation: localized-type (L-TGCT) or diffuse-type (D-TGCT). TGCT is synonymous with pigmented villonodular synovitis (PVNS). We describe the unique case of a 56-year-old obese male with type 2 diabetes who had polymicrobial septic arthritis of his left knee joint with concurrent D-TGCT in the same knee. While on a vacation, he noticed spontaneous left knee pain and swelling with an acute onset of fever. He was diagnosed with septic arthritis that was attributed to hematogenous spread from a leg laceration. The septic arthritis was treated with arthroscopic lavage and debridement, including simultaneous excision of the D-TGCT lesions, followed by intravenous ceftriaxone. Cultures of the synovial tissue that were obtained during arthroscopy grew Klebsiella oxytoca and beta-hemolytic (group B) Streptococcus agalactiae. We were not able to find another reported case of any joint with (1) a polymicrobial bacterial infection that included Klebsiella oxytoca and (2) concurrent bacterial septic arthritis and TGCT.

Subtractive Proteomics and Immuno-informatics Approaches for Multi-peptide Vaccine Prediction Against Klebsiella oxytoca and Validation Through In Silico Expression

Klebsiella oxytoca is a gram-negative bacterium. It is opportunistic in nature and causes hospital acquired infections. Subtractive proteomics and reverse vaccinology approaches were employed to screen out the best proteins for vaccine designing. Whole proteome of K. oxytoca strain ATCC 8724, consisting of 5483 proteins, was used for designing the vaccine. Total 1670 cytotoxic T lymphocyte (CTL) epitope were predicted through NetCTL while 1270 helper T lymphocyte (HTL) epitopes were predicted through IEDB server. The epitopes were screened for non-toxicity, allergenicity, antigenicity and water solubility. After epitope screening 300 CTL and 250 HTL epitopes were submitted to IFN-γ epitope server to predict their Interferon-γ induction response. The selected IFN-γ positive epitopes were tested for their binding affinity with MHCI-DRB1 by MHCPred. The 15 CTL and 13 HTL epitopes were joined by linkers AAY and GPGPG respectively in vaccine construct. Chain C of Pam3CSK4 (PDB ID; 2Z7X) was linked to the vaccine construct as an adjuvant. A 450aa long vaccine construct was submitted to I-TASSER server for 3D structure prediction. Thirteen Linear B cells were predicted by ABCPred server and 10 sets of discontinues epitopes for 3D vaccine structure were predicted by DiscoTope server. The modeled 3D vaccine construct was docked with human Toll-like receptor 2 (PDB ID: 6NIG) by PatchDock. The docked complexes were refined by FireDock. The selected docked complex showed five hydrogen bonds and one salt bridge. The vaccine sequence was reverse transcribed to get nucleotide sequence for In silico cloning. The reverse transcribed sequence strand was cloned in pET28a(+) expression vector. A clone containing 6586 bp was constructed including the 450 bp of query gene sequence.

African nightshades (Solanum nigrum complex): The potential contribution to human nutrition and livelihoods in sub-Saharan Africa

Achieving zero hunger in sub-Saharan Africa (SSA) without minimizing postharvest losses of agricultural products is impossible. Therefore, a holistic approach is vital to end hunger, simultaneously improving food security, diversity, and livelihoods. This review focuses on the African nightshades (ANS) Solanum spp. contribution to improving food and nutrition security in SSA. Different parts of ANS are utilized as food and medicine; however, pests and diseases hinder ANS utilization. African nightshade is rich in micronutrients such as β-carotene, vitamins C and E, minerals (iron, calcium, and zinc), and dietary fiber. The leaves contain a high amount of nutrients than the berries. Proper utilization of ANS can contribute to ending hidden hunger, mainly in children and pregnant women. Literature shows that ANS contains antinutritional factors such as oxalate, phytate, nitrate, and alkaloids; however, their quantities are low to cause potential health effects. Several improved varieties with high yields, rich in nutrients, and low alkaloids have been developed in SSA. Various processing and preservation techniques such as cooking, drying, and fermentation are feasible techniques for value addition on ANS in SSA; moreover, most societies are yet to adopt them effectively. Furthermore, promoting value addition and commercialization of ANS is of importance and can create more jobs. Therefore, this review provides an overview of ANS production and challenges that hinder their utilization, possible solutions, and future research suggestions. This review concludes that ANS is an essential nutritious leafy vegetable for improving nutrition and livelihoods in SSA.

Microbial contamination profile change over a 4-year period in nonoperated cleft soft palate

AIMS

Surgical site infection is a major concern in cleft soft palate. Knowledge of the type, number and antimicrobial resistance of pathogens present preoperatively contribute to treatment success. The aim of this study is to determine whether or not the microbial contamination (diversity) preoperatively has changed since 2015.

METHODS AND RESULTS

Swabs were taken from the surgical site in 103 consecutive patients who presented for primary repair of the soft palate cleft. These were sent for microscopy, culture and sensitivity testing. Swabs were taken before disinfecting the site. Results were tabled and compared with two previous studies from the same facility. Out of 103 patients, 100 patients showed positive cultures with 42 different pathogenic micro-organisms identified. Most dominant pathogen was Klebsiella pneumoniae, 45.6%, increased by 28% from the previous two studies, with 93.6% of these pathogens resistant to one or more antimicrobials. Most of the other identified pathogens showed an alarming increase in occurrence, with a wide resistance to antimicrobials.

CONCLUSIONS

The increase in number and diversity of microbial contamination as well as their resistance to antimicrobials is a real concern. Ways of preventing postoperative infection in a natural way need to be explored.

SIGNIFICANCE

Surgeons need to be aware of constant changes in micro-organisms.

Genotypic Characterization of Clinical Klebsiella spp. Isolates Collected From Patients With Suspected Community-Onset Sepsis, Sweden

Klebsiella is a genus of Gram-negative bacteria known to be opportunistic pathogens that may cause a variety of infections in humans. Highly drug-resistant Klebsiella species, especially K. pneumoniae, have emerged rapidly and are becoming a major concern in clinical management. Although K. pneumoniae is considered the most important pathogen within the genus, the true clinical significance of the other species is likely underrecognized due to the inability of conventional microbiological methods to distinguish between the species leading to high rates of misidentification. Bacterial whole-genome sequencing (WGS) enables precise species identification and characterization that other technologies do not allow. Herein, we have characterized the diversity and traits of Klebsiella spp. in community-onset infections by WGS of clinical isolates (n = 105) collected during a prospective sepsis study in Sweden. The sequencing revealed that 32 of the 82 isolates (39.0%) initially identified as K. pneumoniae with routine microbiological methods based on cultures followed by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS) had been misidentified. Of these, 23 were identified as Klebsiella variicola and nine as other members of the K. pneumoniae complex. Comparisons of the number of resistance genes showed that significantly fewer resistance genes were detected in Klebsiella oxytoca compared to K. pneumoniae and K. variicola (both values of p < 0.001). Moreover, a high proportion of the isolates within the K. pneumoniae complex were predicted to be genotypically multidrug-resistant (MDR; 79/84, 94.0%) in contrast to K. oxytoca (3/16, 18.8%) and Klebsiella michiganensis (0/4, 0.0%). All isolates predicted as genotypically MDR were found to harbor the combination of β-lactam, fosfomycin, and quinolone resistance markers. Multi-locus sequence typing (MLST) revealed a high diversity of sequence types among the Klebsiella spp. with ST14 (10.0%) and ST5429 (10.0%) as the most prevalent ones for K. pneumoniae, ST146 for K. variicola (12.0%), and ST176 for K. oxytoca (25.0%). In conclusion, the results from this study highlight the importance of using high-resolution genotypic methods for identification and characterization of clinical Klebsiella spp. isolates. Our findings indicate that infections caused by other members of the K. pneumoniae complex than K. pneumoniae are a more common clinical problem than previously described, mainly due to high rates of misidentifications.

A Multispecies Cluster of GES-5 Carbapenemase-Producing Enterobacterales Linked by a Geographically Disseminated Plasmid

BACKGROUND

Early and accurate treatment of infections due to carbapenem-resistant organisms is facilitated by rapid diagnostics, but rare resistance mechanisms can compromise detection. One year after a Guiana Extended-Spectrum (GES)-5 carbapenemase-positive Klebsiella oxytoca infection was identified by whole-genome sequencing (WGS; later found to be part of a cluster of 3 cases), a cluster of 11 patients with GES-5-positive K. oxytoca was identified over 18 weeks in the same hospital.

METHODS

Bacteria were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry, antimicrobial susceptibility testing followed European Committee on Antimicrobial Susceptibility Testing guidelines. Ertapenem-resistant isolates were referred to Public Health England for characterization using polymerase chain reaction (PCR) detection of GES, pulsed-field gel electrophoresis (PFGE), and WGS for the second cluster.

RESULTS

The identification of the first GES-5 K. oxytoca isolate was delayed, being identified by WGS. Implementation of a GES-gene PCR informed the occurrence of the second cluster in real time. In contrast to PFGE, WGS phylogenetic analysis refuted an epidemiological link between the 2 clusters; it also suggested a cascade of patient-to-patient transmission in the later cluster. A novel GES-5-encoding plasmid was present in K. oxytoca, Escherichia coli, and Enterobacter cloacae isolates from unlinked patients within the same hospital group and in human and wastewater isolates from 3 hospitals elsewhere in the United Kingdom.

CONCLUSIONS

Genomic sequencing revolutionized the epidemiological understanding of the clusters; it also underlined the risk of covert plasmid propagation in healthcare settings and revealed the national distribution of the resistance-encoding plasmid. Sequencing results also informed and led to the ongoing use of enhanced diagnostic tests for detecting carbapenemases locally and nationally.

Klebsiella oxytoca and Emerging Nosocomial Infections

Klebsiella oxytoca is rising as a significant opportunistic pathogen causing nosocomial infections in neonates as well as adults. This pathogen's prevalence varies from 2 to 24%, but outbreaks of infections due to multidrug-resistant strains can be fatal in immunocompromised individuals with comorbidities. Klebsiella oxytoca is responsible for a wide range of ailments from colitis to infective endocarditis, other than the common urinary and respiratory tract infections. The microbe's pathogenicity has been attributed to cytotoxins' production- Tilivalline and Tilimycin, in some intestinal disorders. Klebsiella oxytoca is reported to be resistant to a wide range of antibiotics. Here, we have tried to showcase a brief overview of the emergence of Klebsiella oxytoca in healthcare facilities and the nature of resistance in this species of Klebsiella.

Animal Models in the Evaluation of the Effectiveness of Phage Therapy for Infections Caused by Gram-Negative Bacteria from the ESKAPE Group and the Reliability of Its Use in Humans

The authors emphasize how extremely important it is to highlight the role played by animal models in an attempt to determine possible phage interactions with the organism into which it was introduced as well as to determine the safety and effectiveness of phage therapy in vivo taking into account the individual conditions of a given organism and its physiology. Animal models in which phages are used make it possible, among other things, to evaluate the effective therapeutic dose and to choose the possible route of phage administration depending on the type of infection developed. These results cannot be applied in detail to the human body, but the knowledge gained from animal experiments is invaluable and very helpful. We would like to highlight how useful animal models may be for the possible effectiveness evaluation of phage therapy in the case of infections caused by gram-negative bacteria from the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species) group of pathogens. In this review, we focus specifically on the data from the last few years.

Variation in Accessory Genes Within the Klebsiella oxytoca Species Complex Delineates Monophyletic Members and Simplifies Coherent Genotyping

Members of the Klebsiella oxytoca species complex (KoSC) are emerging human pathogens causing infections of increasing significance especially in healthcare settings. KoSC strains are affiliated with distinct phylogroups based on genetic variation at the beta-lactamase gene (bla _OXY) and it has been proposed that each major phylogroup represents a unique species. However, since the typing methods applied in clinical settings cannot differentiate every species within the complex, existing clinical, epidemiological and DNA sequence data is frequently misclassified. Here we systematically examined the phylogenetic relationship of KoSC strains to evaluate robustness of existing typing methods and to provide a simple typing strategy for KoSC members that cannot be differentiated biochemically. Initial analysis of a collection of K. oxytoca, K. michiganensis, K. pasteurii, and K. grimontii strains of environmental origin showed robust correlation of core phylogeny and blaOXY grouping. Moreover, we identified species-specific accessory gene loci for these strains. Extension of species correlation using database entries initially failed. However, assessment of average nucleotide identities (ANI) and phylogenetic validations showed that nearly one third of isolates in public databases have been misidentified. Reclassification resulted in a robust reference strain set for reliable species identification of new isolates or for retyping of strains previously analyzed by multi-locus sequence typing (MLST). Finally, we show convergence of ANI, core gene phylogeny, and accessory gene content for available KoSC genomes. We conclude that also the monophyletic members K. oxytoca, K. michiganensis, K. pasteurii and K. grimontii can be simply differentiated by a PCR strategy targeting bla _OXY and accessory genes defined here.

Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli

Every year millions of people die due to fatal waterborne diseases around the world especially in developing countries like India. Sikkim, a northeastern state of India, greatly depends on natural water sources. About 80% of the population of Sikkim depends on natural spring water for domestic as well as agricultural use. Recent waterborne disease outbreaks in the state raises a concerning question on water quality. In this study, we analyzed water quality especially for the detection of Enterobacteriaceae members from four districts of the state. Isolation with selective culture media techniques and taxonomic characterization of Enterobacteriaceae bacteria with 16S rRNA gene showed the prevalence of Escherichia coli (37.50%), Escherichia fergusonii (29.41%), Klebsiella oxytoca (36.93%), Citrobacter freundii (37.92%), Citrobacter amalonaticus (43.82%), Enterobacter sp. (43.82%), Morganella morganii (43.82%), Hafnia alvei (32.42%), Hafnia paralvei (38.74%), and Shigella flexneri (30.47%) in the spring water of Sikkim. Antibiotic susceptibility test (AST) showed resistance of the isolates to common antibiotics like ampicillin, amoxicillin as well as to third generation antibiotics like ceftazidime and carbapenem. None of the isolates showed resistance to chloramphenicol. E. coli isolated from spring water of Sikkim showed presence of different virulence genes such as stx1 (81.81%), elt (86.66%), and eae (66.66%) along with resistance gene for ampicillin (CITM) (80%), quinolones (qnrB) (44.44%), tetracycline (tetO) (66.66%), and streptomycin (aadA1) (66.66%). The data indicates a high incidence rate of multiple antibiotic resistant enteric bacteria in the spring water of Sikkim. Additionally, the presence of enteric bacteria in the water samples indicates widespread fecal contamination of the spring water.