Antibiotic-resistant Isolates Research Articles

Aerobic Microbiological Spectrum and Antibiotic Resistance in Children Operated for Anorectal Abscesses.

(1) Background: Anorectal abscesses are a relatively rare pathology in childhood. Most often, male children under 1 year of age are affected. The importance of microbiological examination for the diagnosis and treatment of such patients remains debatable among surgeons, resulting in scarce data being available in the literature. We aimed to identify the aerobic microbiological spectrum and antibiotic resistance of isolates in children undergoing operation to treat anorectal abscesses. (2) Methods: We performed a case series of 102 children diagnosed and operated for anorectal abscesses over a period of 10 years (2010-2019). Purulent wound exudate was used for microbiological evaluation, which was subsequently cultured on 5% sheep-blood agar and eosin-methylene blue agar. For microbiological identification, conventional biochemical tests and semi-automated (API 20, bioMerieux, Marcy-l'Étoile, France) tests were used, as well as automated systems (Vitek-2 Compact, bioMerieux, France). Antimicrobial susceptibility testing was performed by the disk diffusion method of Bauer-Kirby and by determining the minimal inhibitory concentrations for glycopeptides. The results were interpreted according to the EUCAST standard for the corresponding year. (3) Results: Microbiological testing in children operated for anorectal abscesses mainly identified the gut commensals that normally reside in the rectal mucosa. Monocultures were found in just over half of the cases. Escherichia coli, Klebsiella pneumoniae complex, and Proteus mirabilis were the most frequently isolated. In addition, Staphylococcus aureus was found in 7% of patients. In Gram-negative bacteria, antibiotic resistance was most often observed in penicillins, cephalosporins, sulfonamides, and fluoroquinolones. (4) Conclusions: The increasing rates of antimicrobial resistance impose the need for the local monitoring of circulating commensal bacteria associated with anorectal abscesses in children to guide antibiotic therapy when indicated.

Dry and liquid formulations of IBT-V02, a novel multi-component toxoid vaccine, are effective against Staphylococcus aureus isolates from low-to-middle income countries.

Staphylococcus aureus is the leading cause of skin and soft tissue infections (SSTIs) in the U.S. as well as more serious invasive diseases, including bacteremia, sepsis, endocarditis, surgical site infections, osteomyelitis, and pneumonia. These infections are exacerbated by the emergence of antibiotic-resistant clinical isolates such as methicillin-resistant S. aureus (MRSA), highlighting the need for alternatives to antibiotics to treat bacterial infections. We have previously developed a multi-component toxoid vaccine (IBT-V02) in a liquid formulation with efficacy against multiple strains of Staphylococcus aureus prevalent in the industrialized world. However, liquid vaccine formulations are not compatible with the paucity of cold chain storage infrastructure in many low-to-middle income countries (LMICs). Furthermore, whether our IBT-V02 vaccine formulations are protective against S. aureus isolates from LMICs is unknown. To overcome these limitations, we developed lyophilized and spray freeze-dried formulations of IBT-V02 vaccine and demonstrated that both formulations had comparable biophysical attributes as the liquid formulation, including similar levels of toxin neutralizing antibodies and protective efficacy against MRSA infections in murine and rabbit models. To enhance the relevancy of our findings, we then performed a multi-dimensional screen of 83 S. aureus clinical isolates from LMICs (e.g., Democratic Republic of Congo, Palestine, and Cambodia) to rationally down-select strains to test in our in vivo models based on broad expression of IBT-V02 targets (i.e., pore-forming toxins and superantigens). IBT-V02 polyclonal antisera effectively neutralized toxins produced by the S. aureus clinical isolates from LMICs. Notably, the lyophilized IBT-V02 formulation exhibited significant in vivo efficacy in various preclinical infection models against the S. aureus clinical isolates from LMICs, which was comparable to our liquid formulation. Collectively, our findings suggested that lyophilization is an effective alternative to liquid vaccine formulations of our IBT-V02 vaccine against S. aureus infections, which has important implications for protection from S. aureus isolates from LMICs.

Antibiotic resistance of P. aeruginosa in the presence and absence of pyocyanin pigment

Purpose: study of antibiotic resistance of Р. aeruginosa strains in the presence and absence of pyocyanin pigment. Materials and methods. Bacteriological studies of pathological material from "asphyxiated embryos", sick chickens and forcibly killed or dead adult birds were carried out according to generally accepted methods. Cultures from bone, brain, heart, liver, spleen, gall bladder, muscles and other organs were carried out on simple, selective and differential diagnostic nutrient media. The sensitivity of P. aeruginosa isolates to antibacterial drugs was determined by diffusion in agar according to the generally accepted method. The results. The obtained results of studies by the diffusion method in agar indicate that the proportion of resistant to the studied antibiotics among non-pigmented isolates was on average 79.00 % (60-100) %, and among strains that formed pyocyanin - 51.00 % (25-100) %. 60.00 % - 90.00 % of resistant non-pigmented isolates were found to fluoroquinolones, 60.00-70.00 % to cephalosporins, 60.00-97.00 % to aminoglycosides. To representatives of semisynthetic penicillins, tetracyclines, and macrolides - 100 % of resistant isolates that did not synthesize pyocyanin were found. Among P. aeruginosa isolates that synthesized pigment, 25.00-40.00 % were resistant to fluoroquinolones, 30.00-35.00 % to cephalosporins, 25.00-50.00 % to aminoglycosides, representatives semi-synthetic penicillins, tetracyclines, macrolides - 100 % of the studied strains. Conclusions. The absence of pigment formation in P. aeruginosa isolates, obtained in association with bacterial pathogens, is not accompanied by the absence of antibiotic resistance. 28 % more antibiotic-resistant isolates were found among non-pigmented isolates compared to isolates that synthesize pyocyanin pigment. The data presented emphasize the need for the use of differential media for the isolation of P. aeruginosa in order to identify non-pigmented strains and prescribe appropriate treatment, which, accordingly, will prevent the spread of latent forms of infection

Antibiotic Resistance of Streptococcus spp. Isolated from the Root Surface of Extracted Teeth to Penicillin V and Clindamycin Using E-Test

Background: Antibiotics are used to treat and prevent oral infections. Clindamycin and penicillin are widely used drugs in this field. Poor use of antibacterial agents causes the emergence of antibiotic-resistant bacteria. Objectives: The present study examined and compared the frequency distribution of resistance of streptococci isolated from the root surface of extracted teeth to penicillin V and clindamycin. This study was conducted in 2021 in Yazd, Iran. Methods: This was an analytical cross-sectional study performed in vitro. The samples were taken from the root surfaces of 50 teeth immediately after extraction and transferred to the laboratory in a transfer medium. After cultivation, isolation, and identification, the antibiotic resistance of isolates was measured by the E-test method. The data were analyzed using SPSS software (version 23). Results: Streptococci spp. were isolated from 46 samples (92%) without environmental contamination. The minimum inhibitory concentration (MIC) 50 and MIC 90 for penicillin V were 0.5 μg/mL and 1 μg/mL, respectively, and for clindamycin, 0.125 μg/mL and 0.19 μg/mL, respectively, which was significantly (P = 0.0001) lower for clindamycin. Intermediate sensitivity to penicillin V was 95.6%, and resistance to clindamycin was 21.8%. Conclusions: It seems that except in limited cases where there is resistance to clindamycin, this antibiotic is a more effective drug to control the bacteria in the mouth. However, in some cases, aerobic isolates showed intermediate sensitivity to penicillin V; instead, resistance to clindamycin was observed.

Clinical characteristics and outcomes of acute bacterial meningitis in adults at a tertiary university hospital in Thailand.

The epidemiology of acute bacterial meningitis varies among settings, areas, and times. This study aimed to determine the clinical characteristics, the causative organisms and their antibiotic susceptibility, and the outcomes of patients with acute bacterial meningitis in Thai adults. This retrospective study included hospitalized patients aged ≥18 years diagnosed with acute bacterial meningitis at Siriraj Hospital during January 2002-December 2016. Of 390 patients, the median age was 48 years, 51% were male, and 80% had at least 1 underlying illness. Over half (54%) of patients had community-acquired bacterial meningitis (CBM), and 46% had nosocomial bacterial meningitis (NBM). The triad of acute bacterial meningitis (fever, headache, and neck stiffness) was found in 46% of CBM and 15% of NBM (P < .001). The causative organisms were identified in about half (53%) of patients. Most study patients (73%) received antibiotic treatment before the CSF collection. Causative organisms were identified more frequently in CBM (P < .001). Gram-positive cocci were more prevalent in CBM (P < .001), whereas Gram-negative bacilli were more common in NBM (P < .001). Streptococcus agalactiae (29%), Streptococcus pneumoniae (12%), and Streptococcus suis (11%) were most common in CBM, and all of them were sensitive to third-generation cephalosporins. Acinetobacter baumannii (19%), Klebsiella pneumoniae (16%), and Staphylococcus aureus (11%) were the most common organisms in NBM, and antibiotic-resistant isolates were frequently found among these organisms. Ceftriaxone monotherapy and meropenem plus vancomycin were the most common empiric antibiotic in CBM and NBM, respectively. Mortality was 19% among CBM and 23% among NBM (P = .338). HIV infection, alcoholism, pneumonia, shock, and disseminated intravascular coagulation were independent predictors of mortality. Mortality remains high among adults with acute bacterial meningitis in Thailand. A clinical practice guideline for acute bacterial meningitis should be developed that is based on local epidemiology and microbiology data.

Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria

Horizontal gene transfer (HGT) and gene duplication are often considered as separate mechanisms driving the evolution of new functions. However, the mobile genetic elements (MGEs) implicated in HGT can copy themselves, so positive selection on MGEs could drive gene duplications. Here, we use a combination of modeling and experimental evolution to examine this hypothesis and use long-read genome sequences of tens of thousands of bacterial isolates to examine its generality in nature. Modeling and experiments show that antibiotic selection can drive the evolution of duplicated antibiotic resistance genes (ARGs) through MGE transposition. A key implication is that duplicated ARGs should be enriched in environments associated with antibiotic use. To test this, we examined the distribution of duplicated ARGs in 18,938 complete bacterial genomes with ecological metadata. Duplicated ARGs are highly enriched in bacteria isolated from humans and livestock. Duplicated ARGs are further enriched in an independent set of 321 antibiotic-resistant clinical isolates. Our findings indicate that duplicated genes often encode functions undergoing positive selection and horizontal gene transfer in microbial communities.

Culture-independent detection of low-abundant Clostridioides difficile in environmental DNA via PCR.

Clostridioides difficile represents a major burden to public health. As a well-known nosocomial pathogen whose occurrence is highly associated with antibiotic treatment, most examined C. difficile strains originated from clinical specimen and were isolated under selective conditions employing antibiotics. This suggests a significant bias among analyzed C. difficile strains, which impedes a holistic view on this pathogen. In order to support extensive isolation of C. difficile strains from environmental samples, we designed a detection PCR that targets the hpdBCA-operon and thereby identifies low abundances of C. difficile in environmental samples. This operon encodes the 4-hydroxyphenylacetate decarboxylase, which catalyzes the production of the antimicrobial compound para-cresol. Amplicon-based analyses of diverse environmental samples demonstrated that the designed PCR is highly specific for C. difficile and successfully detected C. difficile despite its absence in general 16S rRNA gene-based detection strategies. Further analyses revealed the potential of the hpdBCA detection PCR sequence for initial phylogenetic classification, which allows assessment of C. difficile diversity in environmental samples via amplicon sequencing. Our findings furthermore showed that C. difficile strains isolated under antibiotic treatment from environmental samples were originally dominated by other strains according to PCR amplicon results. This provided evidence for selective cultivation of under-represented but antibiotic-resistant isolates. Thereby, we revealed a substantial bias in C. difficile isolation and research.IMPORTANCEClostridioides difficile is a main cause of diarrheic infections after antibiotic treatment with serious morbidity and mortality worldwide. Research on this pathogen and its virulence has focused on bacterial isolation from clinical specimens under antibiotic treatment, which implies a substantial bias in isolated strains. Comprehensive studies, however, require an unbiased strain collection, which is accomplished by isolation of C. difficile from diverse environmental samples and avoidance of antibiotic-based enrichment strategies. Thus, isolation can significantly benefit from our C. difficile-specific detection PCR, which rapidly verifies C. difficile presence in environmental samples and further allows estimation of the C. difficile diversity by using next-generation sequencing.

MICROBIAL LOAD AND ANTIBIOTICS RESISTANCE PATTERNS OF BACTERIAL ISOLATES FROM NIGERIA NAIRA NOTES

In our society today, exchange of goods and services usually involves exchange of currency notes by hand. This can serve as a means of transferring microorganisms and antibiotics resistant bacterial isolates. This study was aimed at assessing the contamination of Naira notes in Ungwan Rimi area of Kaduna State and to determine the antibiotics resistance patterns of the isolated bacteria. A total of 160 samples of naira notes, were collected randomly from staff and students, marketers, hospital and pharmacies, food vendors and transporters at strategic spots in Ungwan Rimi. Bacteria isolation and identification of samples were carried out using spread plate technique on medium and standard biochemical characterization, respectively. Antibiotics susceptibility testing were carried out using agar disc diffusion method. Isolates that were non-susceptible to at least one antimicrobial agent in three or more antimicrobial classes were classified as multidrug resistant (MDR), those that remain susceptible to agent(s) in only one or two classes as extended drug resistant (XDR) while pandrug resistant (PDR) isolates were classified as those isolates that were resistant to all antibiotics used. Highest bacterial load was observed with N100 notes with marketers (5.33 x 105) while the least bacterial load was 1.2 x 104 in N50 notes from hospitals and pharmacies. The following bacteria were isolated Staphylococcus aureus 70 (26.8%), Bacillus spp 60 (23.0%), Clostridium spp 31 (11.9%), Escherichia coli 30 (11.5%), Streptococcus species 25 (9.6%), Klebsiella spp 24 (9.2%), Salmonella 15 (5.8%), Shigella species 4 (1.5%) and Pseudomonas species 2 (0.8%)...

The prevalence of antibiotic resistance genes of carbopenemases of the metallo-β-lactamase group in enterobacteria strains isolated from patients of a multidisciplinary hospital in a region with a developed petrochemical industry

The research work included strains of Klebsiella pneumonaie (n = 128) isolated from patients of a multidisciplinary hospital in a large industrial city. The antibiotic sensitivity of the isolated pure cultures was studied in relation to the most popular antibacterial drugs in clinical practice (in the amount of 21), by the standard disco-diffusion method. Identification of resistance genes was carried out by PCR using commercial reagent kits «AmpliSens MDR-MBL-FL», «AmpliSens MDR-KPC/OXA-48‑FL». The results of determining the sensitivity of isolates isolated from the lower respiratory tract revealed low activity of amoxicillin/clavulanic acid, cephalosparins of the III and IV generation (ceftazidim, cefotaxime, cefepim). 86.7 % of isolates are resistant to the aminoglycoside group — amikacin, and 100 % are resistant to gentamicin. Meropenem was the most active of the carbapenem group — 26.6 %, about 7 % are sensitive to ertapenem. From the group of fluoroquinolones, the sensitivity varied from 20 to 30 %. The greatest activity of all drugs was shown by ticarcillin / clavulanate — 33.3 %. A high proportion of strains of Kl. pneumoniae with a phenotype of multiple resistance has been established. The identification of resistance genes made it possible to establish their diversity in antibiotic-resistant isolates, a high proportion (26.6 %) of multi-resistant strains with the absence of the studied genes, and the combination of VIM + NDM + OXA-48 genes, identified in every second studied strain, prevails. Thus, the analysis of the prevalence of antibiotic resistance genes of carbopenemases of the metallo- β-lactamase group in enterobacteria strains isolated from patients of a multidisciplinary hospital in a region with a developed petrochemical industry showed the predominance of isolates (53.9 %) with the production of a combination of three antibiotic resistance genes (VIM + NDM + OXA-48). Isolates containing two genes simultaneously (NDM + OXA-48 and VIM + OXA-48) identified in 7.8 and 6.3 %. Isolates containing a single gene (carbapenemase Kl. Pneumoniae) amounted to 5.4 %.

ISOLATION AND IDENTIFICATION OF BIOFILM PRODUCING ENTEROCOCCUS FAECALIS FROM ROOT CANAL

This study was aimed to one of the most prevalent causes for endodontic treatment failure is the presence of Enterococcus faecalis bacterium within teeth root canals. To achieve successful treatment, it is so important to study E. faecalis behavior. The aim of study was to investigate biofilm production and antibiotic sensitivity of E. faecalis isolated from root canals. Results showed isolation of E. feacalis (65%) of samples, identified by specific gene by PCR technique. Most isolates were sensitive to Imipenem and resistant to Erythromycin, Clindamycin, Tetracycline and Trimethoprim. Strong biofilm production was detected among 29.5% of highest antibiotic resistant isolates. The results may indicate that infected root canals with E. feacalis may lead to serious complication for patients.

Bacteriological assessment of kunu-zaki sold in selected communities in Port Harcourt, Nigeria

Kunu-zaki is a fermented beverage sold in Nigeria; often prepared under unsafe conditions, predisposing it to pathogen contaminations. The bacteria associated with Kunu-zaki sold in the different area of Port Harcourt and an antibiogram of the pathogens was determined using standard methods involving nutrient agar, Salmonella-Shigella agar, Thiosulphate citrate bile salt sucrose agar, MacConkey agar, Mannitol salt agar, Eosin-Methylene blue agar and Mueller Hinton agar. The counts for kunu-zaki obtained from Choba, Mile 1, Rumuodara and Rumuokoro ranged from 2.87±0.11 to 5.39±0.19, 4.50±0.27 to 5.46±0.38, 4.02±0.54 to 5.96±0.27 and 4.24±1.13 to 5.94±0.22 log10cfu/ml, respectively. The confirmation of the isolates as: Staphylococcus spp. (27%), Lactobacillus spp. (20%), Streptococcus spp. (17%), Bacillus spp. (17%), E. coli (10%), and Shigella at (10%) was based on cultural and biochemical characteristics. The Gram-negative bacteria were 100% susceptible to pefloxacin, gentamycin, ciprofloxacin and tarivid while the Gram-positive bacteria isolates showed varying resistance to the antibiotics with Staphylococcus being the most susceptible. The occurrence of the antibiotic resistance isolates possess danger for potential consumers, hence the need to improve the production process.

Susceptibility patterns of Escherichia coli and streptococcal isolates from bovine mastitis cases to antibiotics and selected South African plant extracts with known antibacterial activities

Bovine mastitis, an inflammatory condition affecting the mammary glands of dairy cattle, poses a significant economic burden on the dairy industry. Staphylococcus species, Streptococcus species and Escherichia coli are common pathogens. Managing mastitis typically involves antibiotics, but antimicrobial resistance (AMR) is a growing concern, promoting further research exploring alternative treatments including plant extracts. This study aimed to determine the antibiotic resistance of E. coli and streptococcal isolates from mastitis cases, and to investigate four indigenous South African plants for their selective antibacterial activities against these pathogens. The antimicrobial susceptibility of the bacterial strains was determined using a standard disc diffusion method. Minimum inhibitory concentration (MIC) values of acetone and ethanol extracts of Searsia lancea, Indigofera frutescens, Erythrina caffra and Antidesma venosum were determined against the bacterial isolates using a serial microdilution assay, and cytotoxicity was also investigated. The results showed that 82.14% of the clinical isolates tested were resistant to at least one antimicrobial agent used, and 52.17% of the antibiotic resistant isolates were multidrug resistant. All plant extracts had antibacterial activity against all the bacterial isolates, but S. lancea demonstrated higher efficacy compared to other plants. The MIC values ranged from 0.01 to 2.50 mg/mL, with the lowest range obtained with the acetone extract of S. lancea (0.01 to 0.57 mg/mL). Furthermore, the extracts were relatively non-cytotoxic to bovine dermis and Vero cells, with the highest mean selectivity index value of 25.70 recorded with S. lancea. This study highlights the growing concern of AMR in livestock management, and demonstrates the promising therapeutic potential of the selected plant species, particularly S. lancea, in treating bovine mastitis. Further exploration of S. lancea is recommended to develop novel alternative or complementary formulations for mastitis management.

Heterogeneity of Antibiotic-Resistant Isolates of Listeria Monocytogenes Isolated from Food Products in Moscow

Relevance. Listeria monocytogenes is a ubiquitous bacterium that causes listeriosis, which represents a widespread infectious disease currently inflicting great damage to livestock production and posing a serious threat to human health.Aim. To analyze the population structure and assess the pathogenic potential of Listeria monocytogenes isolates isolated on the territory of the Russian Federation.Materials and methods. A total of 79 listeria isolates were isolated from food products. Species identification and phenotypic analysis for antibiotic resistance were performed using VITEK MS system (bioMerieux, Marcyl’toile, France). Thirty-five antibiotic-resistant isolates were characterized by analysis of whole-genome sequencing data.Results. Whole genome sequences of thirty-five antibiotic-resistant Listeria monocytogenes isolates of food origin were analyzed. We determined clonal structure of this population and revealed a small number of antibiotic resistance determinants (fosX, tetM и сlpL), extensive set of virulence factors, as well as the presence of CRISPR/Cas systems. Most of the isolates belonged to phylogenetic line II and were divided into nine clonal complexes with the prevalence of CC121, which was one of the epidemiologically significant genetic clones. Two CC2 isolates belonging to the most pathogenic phylogenetic lineage I were also found. Thirteen isolates were characterized by the presence of putative CRISPR/Cas systems of IB and IIA types. All ST 121 isolates contained two types of identified adaptive immunity systems simultaneously in their genomes. Correlation analysis confirmed their functionality.Conclusion. We believe that the whole genome data obtained for the foodborne Listeria monocytogenes isolates will facilitate and complement further epidemiological studies of this pathogen, as well as the investigations of its genome variability in terms of the acquisition of various genetic elements associated with adaptation, antimicrobial resistance, and virulence. Moreover, the results of such studies will help to develop preventive measures to effectively solve problems associated with the bacterial contamination of animal products and ensure food safety in production conditions and the «farm-to-table» chain.

Inhibition of the type IV secretion system from antibiotic-resistant Helicobacter pylori clinical isolates supports the potential of Cagα as an anti-virulence target.

Helicobacter pylori resistance to antibiotics is a growing problem and it increasingly leads to treatment failure. While the bacterium is present worldwide, the severity of clinical outcomes is highly dependent on the geographical origin and genetic characteristics of the strains. One of the major virulence factors identified in H. pylori is the cag pathogenicity island (cagPAI), which encodes a type IV secretion system (T4SS) used to translocate effectors into human cells. Here, we investigated the genetic variability of the cagPAI among 13 antibiotic-resistant H. pylori strains that were isolated from patient biopsies in Québec. Seven of the clinical strains carried the cagPAI, but only four could be readily cultivated under laboratory conditions. We observed variability of the sequences of CagA and CagL proteins that are encoded by the cagPAI. All clinical isolates induce interleukin-8 secretion and morphological changes upon co-incubation with gastric cancer cells and two of them produce extracellular T4SS pili. Finally, we demonstrate that molecule 1G2, a small molecule inhibitor of the Cagα protein from the model strain H. pylori 26695, reduces interleukin-8 secretion in one of the clinical isolates. Co-incubation with 1G2 also inhibits the assembly of T4SS pili, suggesting a mechanism for its action on T4SS function.

In Silico and In Vitro Identification of 1,8-Dihydroxy-4,5-dinitroanthraquinone as a New Antibacterial Agent against Staphylococcus aureus and Enterococcus faecalis.

Increasing rates of bacterial resistance to antibiotics are a growing concern worldwide. The search for potential new antibiotics has included several natural products such as anthraquinones. However, comparatively less attention has been given to anthraquinones that exhibit functional groups that are uncommon in nature. In this work, 114 anthraquinones were evaluated using in silico methods to identify inhibitors of the enzyme phosphopantetheine adenylyltransferase (PPAT) of Staphylococcus aureus, Enterococcus faecalis, and Escherichia coli. Virtual screenings based on molecular docking and the pharmacophore model, molecular dynamics simulations, and free energy calculations pointed to 1,8-dihydroxy-4,5-dinitroanthraquinone (DHDNA) as the most promising inhibitor. In addition, these analyses highlighted the contribution of the nitro group to the affinity of this anthraquinone for the nucleotide-binding site of PPAT. Furthermore, DHDNA was active in vitro towards Gram-positive bacteria with minimum inhibitory concentration (MIC) values of 31.25 µg/mL for S. aureus and 62.5 µg/mL for E. faecalis against both antibiotic-resistant isolates and reference strains but was ineffective against E. coli. Experiments on kill-time kinetics indicated that, at the tested concentrations, DHDNA produced bacteriostatic effects on both Gram-positive bacteria. Overall, our results present DHDNA as a potential PPAT inhibitor, showing antibacterial activity against antibiotic-resistant isolates of S. aureus and E. faecalis, findings that point to nitro groups as key to explaining these results.

Systematic identification and repurposing of FDA-approved drugs as antibacterial agents against Streptococcus pyogenes: In silico and in vitro studies

Streptococcus pyogenes (Group A Streptococcus - GAS) is a human pathogen causing wide range of infections and toxin-mediated diseases in human beings of all age groups with fatality of 10–30 %. The limited success of antibiotics and the non-availability of vaccines makes GAS a global burden. The multi-subunit RNA polymerase (RNAP) is a validated bacterial therapeutic target as it is involved in transcription and can arrest growth. Of the five subunits of this enzyme complex, the β-subunit (RpoC) has attracted specific attention as a drug target, particularly in the switch region. Here we attempt to repurpose non-antimicrobial drugs to act as RpoC inhibitors against S. pyogenes. In this study, 1826 FDA approved drugs have been identified through high-throughput virtual screening. Free Energy Perturbation (FEP) based binding free energy calculations have been performed at the final step of the virtual screening funnel to ensure high accuracy in silico results. Three compounds identified have been tested for susceptibility of S. pyogenes MTCC 442 strain and two antibiotic-resistant clinical isolates of S. pyogenes using microdilution assay. Among the three, two drugs Amlodipine Besylate (Amd) and Ranitidine hydrochloride (Rnt) have shown inhibition against all the tested strains and its mechanism of interaction with RpoC has been studied. The docked complexes were analyzed to understand the binding mode of the drugs to the target. Classical Molecular Dynamics studies for RpoC-Rnt complex and the two stable conformations of RpoC-Amd complex was carried out. Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (RoG) and Solvent Accessible Surface Area (SASA) of the complexes were plotted and studied. The thermodynamic parameters of protein-drug were experimentally determined using Isothermal Titration Calorimetry (ITC). Infrared spectroscopic studies and Fluorescence quenching studies provided insights into the secondary structural changes in RpoC on binding to the drugs.

Evaluation of Antibiotic Resistance of Klebsiella Pneumoniae Isolated from Patients in Hospitals in Iraq

The emergence of Multidrug-Resistant (MDR) Klebsiella pneumoniae is a significant health concern, given its severe impact on human health, mainly among young and elderly citizens. Understanding the need to explore the potential risk of K. pneumoniae infections, this study aimed to evaluate the presence and transmission of K. pneumoniae among hospital patients and determine the sensitivity and resistance of K. pneumoniae to multiple types of commonly used antibiotics. Primarily, clinical samples, including sputum, urine, blood, and wound, were taken from 120 patients aged 3–65 who visited the hospital for follow-up treatment in Ramadi, Iraq. Based on the result, 29 K. pneumoniae isolates were obtained, with a higher prev¬alence among patients aged 50–65 (45%). In addition, the isolates mainly originated from sputum (51.5%). Meanwhile, the antibiotic susceptibility test showed that most of the isolates were resistant to almost all of the 11 currently used antibiotics (piperacillin, azithromycin, ceftriaxone, cefepime, cefotaxime, ciproflox¬acine, ceftazidime, imipenem, levofloxacin, tetracyclin, and rifampin). Remarkably, the isolates recorded 100% resistance to rifampin, while most isolates showed the least resistance to imipenem at only 27.6%. Furthermore, the Minimum Inhibitory Concentration (MIC) of eight antibiotics at a concentration range of 16–256 μg/mL was tested against high antibiotic-resistant isolates, and the MIC for each isolate showed varying resistance strength.

Molecular epidemiology, phenotypic and genomic characterization of antibiotic-resistant enterococcal isolates from diverse farm animals in Xinjiang, China

Multidrug-resistant (MDR) bacteria in farm environments can be transferred to humans through the food chain and occupational exposure. Enterococcus infections caused by linezolid resistant enterococci (LRE) are becoming more challenging to treat as their resistance to antibiotics intensifies. Therefore, this study investigated the molecular epidemiology, phenotypic and genomic characterization of enterococci in seven species of farm animals (sheep, chicken, swine, camel, cattle, equine, pigeon) anal swab from Xinjiang, China by agar dilution method, polymerase chain reaction (PCR), whole-genome sequencing (WGS) and bioinformatics analysis. A total of 771 samples were collected, 599 (78 %) were contaminated with Enterococcus spp., among which Enterococcus faecalis (350/599) was dominant. Antimicrobial susceptibility testing showed that high resistance was observed in rifampicin (80 %), tetracycline (71 %), doxycycline (71 %), and erythromycin (69 %). The results of PCR showed the highest prevalent antibiotic resistance genes (ARGs) were aac(6′)-aph(2″) (85 %), followed by tet(M) (73 %), erm(B) (62 %), and aph(3′)-IIIa (61 %). Besides, 29 optrA-carrying E. faecalis isolates belonging to 13 STs (including 3 new alleles) were detected, with ST714 (31 %, 9/29) being the dominant ST type. The phylogenetic tree showed that optrA-carrying E. faecalis prevalent in the intensive swine farm is mainly caused by clonal transmission. Notably, optrA gene in Enterococcus spp. isolate from camel was first characterized here. WGS of E. faecalis F109 isolate from camel confirmed the colocalization of optrA with other five ARGs in the same plasmid (pAFL-109F). The optrA-harboring genetic context is IS1216E-fexA-optrA-erm(A)-IS1216E. This study highlights the prevalence of MDR Enterococcus (≥88 %) and four ARGs (≥75 %) in swine (intensive farming), cattle (commercial farming), and chickens (backyard farming) are high and also highlights that optrA-carrying E. faecalis of farm animals incur a transmission risk to humans through environment, food consumption and others. Therefore, antibiotic-resistant bacteria (ARB) monitoring and effective control measures should be strengthened and implemented in diverse animals.

Study of heavy metal resistance genes in Escherichia coli isolates from a marine ecosystem with a history of environmental pollution (arsenic, cadmium, copper, and mercury).

We analyzed whole genome sequences of 308 Escherichia coli isolates from a marine ecosystem to determine the prevalence and relationships of heavy metal resistance genes (HMRGs) and antibiotic resistance genes (ARGs), as well as the presence of plasmid sequences. We screened all genomes for presence of 18 functional HMRGs conferring resistance to arsenic, cadmium, copper, or cadmium/mercury. In subset analyses, we examined geographic variations of HMRG carriage patterns in 224 isolates from water sources, and sought genetic linkages between HMRGs and ARGs in 25 genomes of isolates resistant to antibiotics. We found high carriage rates of HMRGs in all genomes, with 100% carrying at least one copy of 11 out of 18 HMRGs. A total of 173 (56%) of the isolates carried both HMRGs and plasmid sequences. In the 25 genomes of antibiotic-resistant isolates, 80% (n = 20) carried HMRGs, ARGs, and plasmid sequences, while 40% (n = 10) had linked HMRGs and ARGs on their assembled genomes. We found no evidence of geographic variation in HMRG frequency, nor any association between locational proximity to Superfund sites and co-carriage of HMRGs and ARGs. Our study findings indicate that HMRGs are common among E. coli in marine ecosystems, suggesting widespread heavy metal presence in water sources of a region with history of environmental pollution. Further research is needed to determine the role HMRGs play in driving antimicrobial resistance in human pathogens through genetic linkage and the value their detection in environmental bacterial genomes may offer as an indicator of environmental heavy metal pollution.

Profiling toxin genes and antibiotic resistance in Bacillus cereus isolated from pre-launch spacecraft.

Characterization of the microbiomes of pre-launch spacecraft in spacecraft assembly facilities is an important step in keeping crews healthy during journeys that can last several hundred days in small artificial environments in space. Bacillus cereus, a foodborne pathogenic bacterium, has the potential to be a significant source of food contamination in such environments. This bacterium is a spore-forming bacteria that resists different antimicrobial treatments in cleanrooms where spacecraft are assembled. This study evaluated 41 B. cereus isolates from four pre-launch spacecraft in spacecraft assembly facilities for their toxin gene profile and antibiotic resistance. Four enterotoxin genes (hlbC, cytK, nheA, and entFM) and two emetic toxin genes (ces and CER) were targeted for chromosomal DNA and plasmid DNA. Results showed 31.7, 7.3, 85, and 41.5% of isolates contained hblC, cytK, nheA, and entFM, respectively, in chromosomal or plasmid DNA. Overall, 37 isolates (90.2%) showed at least one enterotoxin gene. The emetic toxin gene, ces, was detected in the plasmid DNA of three isolates (7.3%). The antibiotic resistance of isolates was evaluated by the Kirby-Bauer disk diffusion procedure. All the isolates exhibited 100% susceptibility to gentamicin, 97% were susceptible to clindamycin, and 95% to chloramphenicol, imipenem, tetracycline, and vancomycin. The overall susceptibility average is 51%. However, 98% of the isolates were resistant to β-lactam antibiotics, 97.5% were resistant to sulfamethoxazole/trimethoprim, and 80% were resistant to rifampin. This study provides important information on B. cereus isolates from spacecraft assembly facilities for use in microbial monitoring programs of spacecraft.