Prospects of Using Soil Microbiome of Mine Tips for Remediation of Anthropogenically Disturbed Ecosystems

Introduction. Coal industry increases soil pollution with heavy metals and polycyclic aromatic hydrocarbons. Therefore, resoiling is an urgent problem that requires an immediate solution. The present research objective was to substantiate the use of microorganisms from mine tips in order to decrease soil pollution with heavy metals and oil compounds. Study objects and methods. The review featured five years of publications in Scopus, Web of Science, and Elibrary, which were subjected to analysis, systematization, and generalization. Results and discussion. Coal industry changes landscapes, flora, fauna, and soil microbiome. Bioremediation uses various microorganisms as means of resoiling. Some microorganisms isolated from coal mining waste are resistant to heavy metals and polycyclic aromatic hydrocarbons and are able to utilize them. For instance, such bacteria as Bacillus and Pseudomonas aeruginosa are capable of degrading oil pollutants. Microorganisms of Enterobacter and Klebsiella species were found to be resistant to copper, iron, lead, and manganese. Bacteria of the genera Bacillus, Arthrobacter, Pseudoarthrobacter, and Sinomonas are now to be resistant to nickel, arsenic, and chromium. Arbuscular mycorrhizal fungi increase the activity of soil enzymes, improve soil fertility, and decompose various organic compounds. Conclusion. Sequencing methods make it possible to determine the species composition of soils in mine tips in order to search for new strains capable of restoring former mining areas.

ESBL plasmids in Klebsiella pneumoniae: diversity, transmission, and contribution to infection burden in the hospital setting

Background Resistance to third-generation cephalosporins, often mediated by extended–spectrum beta–lactamases (ESBLs), is a considerable issue in hospital-associated infections as few drugs remain for treatment. ESBL genes are often located on large plasmids that transfer horizontally between strains and species of Enterobacteriaceae and frequently confer resistance to additional drug classes. While plasmid transmission is recognised to occur in the hospital setting, the frequency and impact of plasmid transmission on infection burden, compared to ESBL+ strain transmission, is not well understood. Methods We sequenced the genomes of clinical and carriage isolates of Klebsiella pneumoniae species complex from a year long hospital surveillance study to investigate ESBL burden and plasmid transmission in an Australian hospital. Long term persistence of a key transmitted ESBL+ plasmid was investigated via sequencing of ceftriaxone resistant isolates during four years of follow–up, beginning three years after the initial study. Results We found 25 distinct ESBL plasmids. One (Plasmid A, carrying blaCTX–M–15 in an IncF backbone similar to pKPN–307) was transmitted at least four times into different Klebsiella species/lineages and was responsible for half of all ESBL episodes during the initial one-year study period. Three of the Plasmid A–positive strains persisted locally 3–6 years later, and Plasmid A was detected in two additional strain backgrounds. Overall Plasmid A accounted for 21% of ESBL+ infections in the follow–up period. Conclusions Whilst ESBL plasmid transmission events were rare in this setting, they had a significant and sustained impact on the burden of ceftriaxone resistant and multidrug resistant infections.

Prophylactic role of ciprofloxacin and ceftriaxone in prostate biopsy-related infection: randomized comparative study of bacterial spectrum and antibiotic sensitivities

Background The mainstay for the diagnosis of prostate cancer is transrectal ultrasound-guided prostate biopsy. However, prostate biopsy is associated with a significant risk of complications including urinary tract infection. This study aims to compare the bacterial profile and antibiotic susceptibility pattern in urinary tract infection after prostate biopsy between patients on 2 different antimicrobial prophylactic regimens. Methods This was a comparative cross-sectional study done at the urology unit of our institution, over 13 months. Fifty-six patients who met the inclusion criteria made up the study population and were randomly assigned to two groups. Those in group 1 (28) received intravenous ciprofloxacin (Juhel) 400 mg at induction of anesthesia, while those in group 2 (28) received intravenous ceftriaxone (Rocephin) 1 g at induction of anesthesia. All patients received bisacodyl (dulcolax) rectal suppositories 20 mg nocte starting 2 nights before the procedure as well as intravenous metronidazole (Juhel) at induction of anesthesia. Urine samples were taken for urine culture and sensitivity three days after biopsy. Isolated organisms and their antibiotics sensitivities were documented. Statistical analysis was done using SPSS version 21.0 with the level of significance set at P < 0.05. Results In group 1 the prevalence of urinary tract infection was 61%. Escherichia coli was isolated in 11(64.71%) cases, Klebsiella species in 3(17.65%), staphylococcus aureus in 1(5.88%), Proteus species in 1(5.88%), and non-hemolytic streptococcus species in 1(5.88%). In this group, all isolated bacterial organisms were resistant to ciprofloxacin. In group 2 the prevalence of urinary tract infection was 43%. Klebsiella spp was isolated in 6(50%) cases, Pseudomonas aeruginosa in 3(25%), E. coli in 2(16.67%), Staphylococcus in 1(8.33%). In group 2 all isolated bacterial organisms were resistant to ceftriaxone. Conclusion Ciprofloxacin and ceftriaxone are both associated with a high rate of urinary tract infection when used as prophylaxis for prostate biopsy. The bacterial etiology of prostate biopsy-related urinary tract infection is dependent on the prophylactic antibiotics used. Based on the high rate of urinary tract infection associated with the use of either ciprofloxacin or ceftriaxone, we recommend a combination of both drugs as prophylaxis for prostate biopsy.

Elevators and staircase handrails as potential sources of nosocomial pathogens at Ndola Teaching Hospital, Zambia

This study aimed to assess microbial colonization of elevators and the staircase handrail at Ndola Teaching Hospital. Swabs from elevators and staircase handrail were cultured on Blood, MacConkey and Mannitol Salt agar for 24-48h at 35-37oC. All observed bacterial colonies were sub-cultured for identification. Data analysis was conducted with Microsoft excel 2010 and SPSS version 20 statistical software. A 2-tailed Pearson Correlation test was used to assess for significant differences in colonization prevalence between the two elevators and handrail. A total of 94 bacteria species were isolated, among which 75(78.8%) were isolated from elevators while 19(20.2%) were isolated from the staircase handrail. Most bacteria were isolated from exterior buttons followed by doors and interior of elevators whereas the basement, ground and sixth floor sections of the staircase handrail were largely contaminated with S. aureus, non-spore-forming Gram-positive bacilli, Klebsiella spp, coagulase-negative Staphylococci and Enterobacter spp. Overall, the commonest isolated bacteria were S. aureus (33%) followed by non-spore-forming Gram-positive bacilli (16%), coagulase-negative Staphylococci, and endospore-forming Gram-positive bacilli (13.8% apiece), Streptococci (7.4%), and Klebsiella species (6.4%). A strong relationship existed between the prevalence of bacteria colonizers of elevators and the staircase handrail (p<0.01). Therefore, the study showed that elevators and the staircase handrail possess viable microorganisms and may act as potential sources of nosocomial infections especially to immunocompromised patients in hospitals, and this calls for proper and effective infection control and prevention strategies to lessen microbial population from dry surfaces.

Detection of Carbapenemase Production in Clinical Isolates of Escherichia coli and Klebsiella Species

The increasingly frequent application of carbapenemases induces a selective pressure on bacteria to acquire resistance against carbapenems. A large variety of carbapenemases have been identified in Enterobacteriaceae. The emergence of carbapenemases in E. coli and Klebsiella species possess a serious therapeutic problem in hospitals because carbapenems are often antibiotics of last resort for the treatment of serious infections caused by multidrug-resistant bacteria. The main aim of this study to determine the carbapenem-resistant strains of Escherichia coli and Klebsiella species. Detection of carbapenemase enzyme in the carbapenem-resistant Escherichia coli and Klebsiella species. This is a cross-sectional study, performed in the bacteriological laboratory. A total of 204 strains of Escherichia coli and 122 strains of Klebsiella species were isolated from patients admitted & attending the OPD at Sharda Hospital during the study period. The identification of the clinical isolates was based on morphological and biochemicals characterization. Result: Among the total number of bacterial growth received during the study period, the E. coli (204) was more in number as compared to other bacterial strains followed by Klebsiella species (122), Pseudomonas species (117), Staphylococcus aureus (100) and Enterococcus species (80). Among the following specimen i.e, urine (58.8%), was highly received during the study period followed by pus (15.3%) and sputum (7.5%). Colistin (100%) and Polymyxin B (100%) is found to be the most sensitive drug. Gentamicin (19.6%) and Cefuroxime (12.2%) are the least sensitive drugs. In the present study, we found that the Klebsiella species (75%) and Escherichia coli (64%) was the major reason of carbapenemase production but the organisms incidentally were susceptible to colistin and polymyxins (100%) followed by other antibiotics. This is a welcome finding in times of increasing carbapenem resistance & is reason enough to suggest the use of Polymyxins in the health care settings where the carbapenems to be used for the treatment of infections caused by Enterobacteriaceae.

Non-viral Microbial Keratitis in a Tertiary Care Hospital in Bangladesh

Introduction: Microbial keratitis is a serious ocular infectious disease that can lead to significant visual loss and ophthalmic morbidity. Objectives were to see the profile of non-viral microbial keratitis in a tertiary care hospital in Bangladesh. Materials and Methods: This cross-sectional study was conducted in the Department of Ophthalmology, Sylhet MAG Osmani Medical College Hospital, Sylhet between January 2015 and December 2016. Results: The mean age of the patients was 46.7 ± 16.5 years with male preponderance (54.4%). The most common predisposing factors were trauma (66.7%), and chronic dacryocystitis (25.6%). Fungal growth was more frequent compared to bacterial growth 70 (77.7%) versus 30 (33.3%), p<0.01). Gram positive organisms were Staphylococcus epidermidis (11.1%), Staphylococcus aureus (3.3%); gram negative organisms were Pseudomonas aeruginosa (12.2%), Klebsiella species (3.3%) and Escherichia coli (3.3%). Aspergillus species (71.4%) was the commonest fungus. Others were Penicillium species (7.1%), Fusarium species (8.6%), Mucor (10.0%) and Rhizopus (2.9%). Conclusion: Fungi are more frequent cause of non-viral keratitis. Watering, redness, pain or burning sensation, corneal opacity and dimness of vision are clinical profiles of non-viral microbial keratitis. Medicine Today 2021 Vol.33(2): 133-137

ANI, Mash and Dashing equally differentiate between Klebsiella species

Species of the genus Klebsiella are among the most important multidrug resistant human pathogens, though they have been isolated from a variety of environments. Given the need for quickly and accurately classifying newly sequenced Klebsiella genomes, we compared 982 Klebsiella genomes using different species-delimiting measures: Average Nucleotide Identity (ANI), which is becoming a standard for species delimitation, as well as Mash, Dashing, and DNA compositional signatures, which can be run in a fraction of the time required to run ANI. ROC analyses showed equal quality in species delimitation for ANI, Mash and Dashing (AUC: 0.99), followed by DNA signatures (AUC: 0.96). The groups obtained at optimal cutoffs were largely in agreement with species designation. Using optimized cutoffs, we obtained 17 species-level groups using either ANI, Mash, or Dashing, all containing the same genomes, unlike DNA signatures which broke the dataset into 38 groups. Further use of Mash to map species after adding draft genomes to the dataset also showed excellent results (AUC: 0.99), producing a total of 28 Klebsiella species in the publicly available genome collection. The ecological niches of Klebsiella strains were found to neither be related to species delimitation, nor to protein functional content, suggesting that a single Klebsiella species can have a wide repertoire of ecological functions.

1247. Molecular Epidemiology of Multi-drug Resistant Klebsiella pneumoniae and K. quasipneumoniae in Qatar

Background The molecular epidemiology of carbapenem-resistant Klebsiella species is not well investigated in Qatar. The objective of this work was to characterize the genetic context of carbapenemase-producing Klebsiella isolates recovered from clinical specimens. Methods Klebsiella isolates (n=100) were collected at 7 tertiary hospitals from 2015-2017. Identification and susceptibility testing were performed using MALDI-TOF MS and BD Phoenix system, respectively. Whole Genome Sequencing was performed on the Illumina NextSeq platform. Phylogenomic analysis, screening of resistance and virulence genes, and comparison of genetic environment of carbapenemase were carried out. Results Klebsiella pneumoniae was common (80), followed by K. quasipneumoniae (16), K. aerogenes (3) and K. oxytoca (1). The most prevalent were genes encoding NDM-1 (39), OXA-48 (20), OXA-232 (10) and OXA-181 (12). KPC-2 (3) and KPC-3 (2) were also identified; no carbapenemase-encoding genes could be identified in 15 isolates. Plasmid locations of 24 carbapenemase-encoding genes were determined; blaNDM-1 was localized on IncFII replicon, while blaOXA-181 and blaOXA-232 were commonly associated with ColKP3 plasmids. pOXA-48-like plasmid was detected in 17/20 isolates harboring blaOXA-48. blaKPC-3 was located on a contig with ‘traditional’ Tn4401a mobile genetic element. Sequence types (STs) were diverse and the ‘traditional’ clonal group (CG) 258 was rare. K. pneumoniae ST147 was predominant (13), followed by ST231 (7) and ST11 (5). Nine K. quasipneumoniae isolates belonged to ST196 and were highly clonal. The virulence loci such as yersiniabactin (ybt) and rmpA were not detected within the study’s K. quasipneumoniae isolates. Amongst K. pneumoniae, there were 50 ybt+ isolates; 8 isolates had rmpA, and of these, 3 belonged to ST383. K. pneumoniae serotype K2, the capsular serotype associated with invasive liver abscess syndrome, was detected in 5 isolates. Genetic relationship of carbapenem-resistant Klebsiella pneumoniae and K. quasipneumoniae isolates in Qatar inferred from core genome SNPs. The tree is overlaid with predicted antimicrobial resistance genes and virulence factors for each isolate. Conclusion The predominant carbapenemases among clinical Klebsiella species isolates in Qatar are NDM and OXA-48 like enzymes, disseminated through various plasmids. The detection of carbapenemase-producing isolate bearing rmpA and serotype K2 reflect the presence of both multidrug resistance and hypervirulence in K. pneumoniae. Disclosures Yohei Doi, MD, PhD, AstraZeneca (Speaker’s Bureau)bioMerieux (Consultant)FujiFilm (Advisor or Review Panel member, Speaker’s Bureau)Gilead (Consultant)GSK (Consultant)Meiji (Consultant)MSD (Consultant)Shionogi (Consultant) Yohei Doi, MD, PhD, Astellas (Individual(s) Involved: Self): Grant/Research Support; AstraZeneca (Individual(s) Involved: Self): Speakers’ bureau; bioMerieux (Individual(s) Involved: Self): Consultant, Speakers’ bureau; Chugai (Individual(s) Involved: Self): Consultant; Entasis (Individual(s) Involved: Self): Consultant; FujiFilm (Individual(s) Involved: Self): Advisor or Review Panel member; Gilead (Individual(s) Involved: Self): Consultant; GSK (Individual(s) Involved: Self): Consultant; Kanto Chemical (Individual(s) Involved: Self): Grant/Research Support; MSD (Individual(s) Involved: Self): Speaking Fee; Pfizer (Individual(s) Involved: Self): Grant/Research Support; Shionogi (Individual(s) Involved: Self): Grant/Research Support, Speakers’ bureau; Teijin Healthcare (Individual(s) Involved: Self): Speakers’ bureau; VenatoRx (Individual(s) Involved: Self): Consultant

Biosynthesis of Smaller-Sized Platinum Nanoparticles Using the Leaf Extract of Combretum erythrophyllum and Its Antibacterial Activities

Nanobiotechnology is a promising field in the development of safe antibiotics to combat the increasing trend of antibiotic resistance. Nature is a vast reservoir for green materials used in the synthesis of non-toxic and environmentally friendly nano-antibiotics. We present for the first time a facile, green, cost-effective, plant-mediated synthesis of platinum nanoparticles (PtNPs) using the extract of Combretum erythrophyllum (CE) plant leaves. The extract of CE served as both a bio-reductant and a stabilizing agent. The as-synthesized PtNPs were characterized using ultraviolet-visible (UV–Vis) absorption spectroscopy, high-resolution transmission electron microscopy (HR-TEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and dynamic light scattering (DLS) techniques. The HR-TEM image confirmed that the PtNPs are ultrasmall, spherical, and well dispersed with an average particle diameter of 1.04 ± 0.26 nm. The PtNPs showed strong antibacterial activities against pathogenic Gram-positive Staphylococcus epidermidis (ATCC 14990) at a minimum inhibitory concentration (MIC) of 3.125 µg/mL and Gram-negative Klebsiella oxytoca (ATCC 8724) and Klebsiella aerogenes (ATCC 27853) at an MIC value of 1.56 µg/mL. The CE-stabilized PtNPs was mostly effective in Klebsiella species that are causative organisms in nosocomial infections.