The Rising Tide of Antibiotic Resistance: A Study on Extended-Spectrum Beta-Lactamase and Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae.

BACKGROUND: The global spread of extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant Enterobacterales (CRE) poses a significant concern. Acquisition of antimicrobial resistance genes leads to resistance against several antibiotics, limiting treatment options. We aimed to study ESBL-producing and CRE transmission in clinical settings. METHODS: From clinical samples, 227 ESBL-producing and CRE isolates were obtained. The isolates were cultured on bacterial media and confirmed by VITEK 2. Antibiograms were tested against several antibiotics using VITEK 2. The acquired resistance genes were identified by PCR. RESULTS: Of the 227 clinical isolates, 145 (63.8%) were Klebsiella pneumoniae and 82 (36.1%) were Escherichia coli; 76 (33.4%) isolates were detected in urine, 57 (25.1%) in pus swabs, and 53 (23.3%) in blood samples. A total of 58 (70.7%) ESBL-producing E. coli were resistant to beta-lactams, except for carbapenems, and 17.2% were amikacin-resistant; 29.2% of E. coli isolates were resistant to carbapenems. A total of 106 (73.1%) ESBL-producing K. pneumoniae were resistant to all beta-lactams, except for carbapenems, and 66.9% to ciprofloxacin; 38 (26.2%) K. pneumoniae were resistant to carbapenems. Colistin emerged as the most effective antibiotic against both bacterial types. Twelve (20.6%) E. coli isolates were positive for blaCTX-M, 11 (18.9%) for blaTEM, and 8 (33.3%) for blaNDM. Forty-six (52.3%) K. pneumoniae isolates had blaCTX-M, 27 (18.6%) blaTEM, and 26 (68.4%) blaNDM. CONCLUSION: This study found a high prevalence of drug-resistant ESBL-producing and CRE, highlighting the need for targeted antibiotic use to combat resistance.

Long-Term Epidemiology and Evolution of Swine Influenza Viruses, Vietnam.

Influenza A viruses are a One Health threat because they can spill over between host populations, including among humans, swine, and birds. Surveillance of swine influenza virus in Hanoi, Vietnam, during 2013-2019 revealed gene pool enrichment from imported swine from Asia and North America and showed long-term maintenance, persistence, and reassortment of virus lineages. Genome sequencing showed continuous enrichment of H1 and H3 diversity through repeat introduction of human virus variants and swine influenza viruses endemic in other countries. In particular, the North American H1-δ1a strain, which has a triple-reassortant backbone that potentially results in increased human adaptation, emerged as a virus that could pose a zoonotic threat. Co-circulation of H1-δ1a viruses with other swine influenza virus genotypes raises concerns for both human and animal health.

Covid-19 Pandemic: Through the Lens of Science, a Painstaking Review.

BACKGROUND: Coronavirus disease 2019 (COVID-19) has imperiled human lives and global infrastructure since the emergence of SARS-CoV-2 in China. The current review meticulously summarizes the COVID-19 pandemic situation through the lens of science from the inception of the outbreak to the current progression, which is valuable to mitigate the current pandemic situation. METHODS: We reviewed all the relevant literature available on PubMed, Web of Sciences, Google Scholar, and World Health Organization (WHO) website related to COVID-19 from the inception of the outbreak to 18 June 2020. We selected ninety different scientific studies and reports to compile the current review. RESULTS: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a betacoronavirus with four major structural proteins encoded by S, M, E, and N genes and distinct in morphology. The potential provenance of SARS-Cov-2 is zoonotic, and it binds to the host cell receptors by spike protein. The SARS-CoV-2 infectious cycle carries on through direct contact, air, inanimate objects, and contaminated surfaces. The reproductive number (R0) of SARS-CoV-2 is 2 to 3.5, representing that one infected patient can spread this virus to two to three people. An expeditious laboratory diagnosis has a pivotal role in patient management and prevention. Due to the lack of definitive treatment, symptomatic medication regimen and supportive organ therapies are adapted for debilitated patients. CONCLUSIONS: Nucleoside analogs and protease-inhibitors have approved to attenuate the viral infection until the discovery of a specific drug. The other treatment strategies comprise antimalarial drugs, monoclonal antibodies, and glucocorticoids. The use of alcoholic scrubs, sodium hypochlorite, masks, social distancing, and quarantine the affected individual is inevitable to eradicate the infection vector and to break the transmission path.

Molecular Analysis of the Antibiotic Resistant NDM-1 Gene in Clinical Isolates of Enterobacteriaceae.

BACKGROUND: The emergence of the New Dehli metallo-beta-lactamase (NDM) gene in Enterobacteriaceae is responsible for multidrug resistance responsible for severe infections and serious morbidity in patients. Our study aimed to define the molecular characteristics and antibiogram of the NDM-1 producing Enterobacteriaceae. METHODS: We isolated 370 individual enterobacteria from the clinical specimens collected from the two tertiary hospitals in Sakaka, Saudi Arabia. Bacterial isolation was performed using standard microbiological techniques and the Phoenix and Microscan WalkAway Plus automated analyzers. Bacterial strains were characterized by phenotypic methods and PCR, and DNA sequencing was used for the molecular characterization of NDM genes. RESULTS: The blaNDM gene was detected among the 68 members of the Enterobacteriaceae including a single case of rarely reported Cedecea lapagei. Of these 68, 43 isolates (63.2%) were blaNDM-1 and 25 (36.8%) were blaNDM variants. A statistically significant relationship between the NDM-1 and Klebsiella pneumoniae (p = 0.004) was seen, and the relationship between the NDM variants was significantly associated with Citrobacter freundii (p = 0.02) and Escherichia coli (p = 0.03). The in vitro minimum inhibitory concentrations (MICs) of NDM-producing Enterobacteriaceae revealed a very high rate of antibiotic resistance against several groups of antibiotics. These bacterial strains were less resistant to two aminoglycosides, gentamicin (39; 57.3%) and amikacin (27; 39.7%), and showed minimum resistance to tigecycline (25; 36.8%). CONCLUSIONS: The emergence of a large number of NDM-1 enterobacteria in our study identifies a substantial public concern, both within hospitals and the wider community, and leaves us a narrow choice of therapeutic options: the aminoglycosides, co-trimoxazole, and tigecycline.

Molecular Detection of blaIMP Genes in Metallo-Beta-Lactamase Producing Clinical Gram-Negative Isolates.

BACKGROUND: The use of carbapenem antibiotics in the treatment of serious Gram-negative bacterial infections is under threat due to the emergence of the blaIMP gene amongst the bacterial pathogens. METHODS: The present descriptive cross-sectional study aimed to determine the occurrence of the blaIMP gene and minimum inhibitory concentrations (MICs) of the bacterial pathogens. The carbapenem-resistant isolates were screened out for the detection of MBLs by using the modified Hodge test and disk potentiation method. MBL producing strains were tested for the presence of the blaIMP gene by using PCR technique. The MICs of the blaIMP gene positive bacterial isolates were detected on the Vitek 2 system (bioMerieux). RESULTS: The primary source of MBLs and blaIPM gene carrying bacterial pathogens was blood (38.5%). We isolated 104 bacterial isolates in the initial screening of carbapenem resistance. Metallo-beta-lactamases (MBLs) were detected in 76 (73%) of the isolates which predominantly included 27 (26%) Klebsiella pneumoniae, 20 (19.2%) Acinetobacter baumannii, 16 (15.4%) Pseudomonas aeruginosa, and 11 (10.6%) E. coli while the other Gram-nega-tive MBL producing bacteria were few in number. The blaIPM gene was detected in 1 (1.3%) case of Acinetobacter baumannii and 1 (1.3%) case of Stenotrophomonas maltophilia. These strains were found to be multi-drug resistant with high MICs (≥ 8 to ≥ 256 µg/mL) against the majority of the drugs. CONCLUSIONS: The emergence of the blaIPM gene is a matter of serious concern as it left us with limited treatment options of minocycline, tigecycline, and levofloxacin. The horizontal transfer of blaIPM gene in other Gram-negative isolates can lead the epidemics of multidrug resistance.

AmpC beta-lactamases in Klebsiella pneumoniae: An emerging threat to the paediatric patients.

OBJECTIVE: To determine the burden of AmpC beta-lactamase producing Klebsiella pneumoniae and its antimicrobial profile among paediatric patients. METHODS: This cross-sectional study was conducted at the Microbiology Department of The Children's Hospital and the Institute of Child Health in Lahore, Pakistan, from May 2014 to April 2015, in which isolates of Klebsiella pneumoniae were screened by using the cefoxitin disc. Confirmation was done by inhibitor-based method using 400 micro grams of boronic acid dispensed on the cefoxitin discs. The zone sizes of cefoxitin with and without the boronic acid were compared. The antimicrobial susceptibility testing was performed using Kirby Bauer disc diffusion method. RESULTS: Positive cultures yielded 585 Klebsiella pneumoniae out of which 220(37.6%) strains were AmpC beta-lactamase-positive on the basis of cefoxitin screening and 126(21.53%) were positive on the basis of inhibitor-based confirmatory method. Most of the infected patients 73(57.9%) were neonates. All AmpC beta-lactamase-producing strains were resistant to cephalosporins. They also exhibited resistance to ciprofloxacin 109(86.5%), amikacin 98(77.8%), levofloxacin 8(77.8%), cefoperazone-sulbactam 81(64.3%), piperacillin-tazobactam 82(65.1%), meropenem, 56(44.4%) and imipenem 32(25.4%). CONCLUSIONS: Prompt identification of AmpC beta-lactamases using inhibitor-based confirmatory test can help reduce the burden of these pathogens.

Phenotypic characterization of extended-spectrum-beta-lactamase producing E. coli from healthy individuals, patients, sewage sludge, cattle, chickens and raw meat.

OBJECTIVE: The present study aimed to determine the frequency and antimicrobial profile of ESBL-producing isolates of E. coli in different environments. METHODS: This cross-sectional study was conducted at The Children's Hospital and The Institute of Child Health, Lahore from July to December 2015. The faecal specimens from healthy individuals, patients, sewage sludge, cattle, chickens and raw meat (n = 122) were processed for microbiological analysis using MacConkey agar supplemented with cefotaxime. The identification of organisms was confirmed by API 10S and antimicrobial resistance profile was recorded by Kirby-Bauer disc diffusion method. RESULTS: On the basis of screening, 77 (63.0%) specimens were found to be positive for ESBL production. The confirmation of 74 (60.0%) ESBL producing E. coli was done using double disc synergy test (DDST). The frequency of ESBL producing E. coli was found to be 17 (57.0%) in healthy individuals, 15 (53.0%) in patients, 10 (66.0%) in cattle faeces, 5 (71.0%) in sewage sludge, 14 (70.0%) in raw meat and 13 (59.0%) in chicken faeces. All of these isolates were resistant to cephalosporins and some of these were resistant to fluoroquinolones and meropenem. None of the isolates showed resistance to cefoperazone-sulbactam, imipenem, piperacillin-tazobactam and amikacin. CONCLUSION: The prevalence of ESBL-producing E. coli was recorded in all the environments, suggesting a global expansion of these enzymes.

Antibacterial efficacy of indigenous Pakistani honey against extensively drug-resistant clinical isolates of Salmonella enterica serovar Typhi: an alternative option to combat antimicrobial resistance.

BACKGROUND: Extensively drug-resistant (XDR) Salmonella enterica serovar Typhi (S. Typhi) poses a grave threat to public health due to increased mortality and morbidity caused by typhoid fever. Honey is a promising antibacterial agent, and we aimed to determine the antibacterial activity of honey against XDR S. Typhi. METHODS: We isolated 20 clinical isolates of XDR S. Typhi from pediatric septicemic patients and determined the minimum inhibitory concentrations (MICs) of different antibiotics against the pathogens using the VITEK 2 Compact system. Antimicrobial-resistant genes carried by the isolates were identified using PCR. The antibacterial efficacy of five Pakistani honeys was examined using agar well diffusion assay, and their MICs and minimum bactericidal concentrations (MBCs) were determined with the broth microdilution method. RESULTS: All 20 isolates were confirmed as S. Typhi. The antibiogram phenotype was confirmed as XDR S. Typhi with resistance to ampicillin (≥ 32 µg/mL), ciprofloxacin (≥ 4 µg/mL), and ceftriaxone (≥ 4 µg/mL) and sensitivity to azithromycin (≤ 16 µg/mL) and carbapenems (≤ 1 µg/mL). Molecular conformation revealed the presence of blaTM-1, Sul1, qnrS, gyrA, gyrB, and blaCTX-M-15 genes in all isolates. Among the five honeys, beri honey had the highest zone of inhibition of 7-15 mm and neem honey had a zone of inhibition of 7-12 mm. The MIC and MBC of beri honey against 3/20 (15%) XDR S. Typhi isolates were 3.125 and 6.25%, respectively, while the MIC and MBC of neem were 3.125 and 6.25%, respectively, against 3/20 (15%) isolates and 6.25 and 12.5%, respectively, against 7/20 (35%) isolates. CONCLUSION: Indigenous honeys have an effective role in combating XDR S. Typhi. They are potential candidates for clinical trials as alternative therapeutic options against XDR S. Typhi isolates.

Detection of Klebsiella pneumoniae antibiotic-resistant genes: An impending source of multidrug resistance dissemination through raw food.

This study aimed to find out the prevalence and antimicrobial resistance profile of Klebsiella pneumoniae in raw food items. A total of 261 raw food items, including vegetables, fruits, meat, and milk samples, were collected and processed for isolation of K. pneumoniae. Further antimicrobial susceptibility testing and molecular analysis was done to analyze the drug resistance encoding genes. The prevalence rate of K. pneumoniae was found to be high (38%), and the raw milk samples were predominantly contaminated (19/51), followed by fruits (12/51), meat (11/51), and vegetables (9/51). However, no significant association was observed for the isolation of K. pneumoniae and any particular specimen. Among the isolates, 43% were extended-spectrum ß-lactamase producers, 24% were AmpC, and 20% were carbapenemase producers. The highest rates of ESBLs and AmpC were observed in vegetables (cabbage, bell pepper, and spinach) and carbapenemases in raw chicken, fish, and raw meat samples. Notably, bla CTX-M was the most prevalent, followed by bla SHV and bla TEM. Six K. pneumoniae possessed bla MOX, and five possessed bla FOX genes. Numerous carbapenemases were identified with a higher proportion of bla NDM. This study indicates that raw vegetables, fruits, meat, and milk are exposed to contaminants. These findings imply a potential threat that drug-resistant K. pneumoniae pathogens could transmit to humans through raw vegetables, fruits, and meat.

Bibliometric Analysis of Publications on the Omicron Variant from 2020 to 2022 in the Scopus Database Using R and VOSviewer.

Human respiratory infections caused by coronaviruses can range from mild to deadly. Although there are numerous studies on coronavirus disease 2019 (COVID-19), few have been published on its Omicron variant. In order to remedy this deficiency, this study undertook a bibliometric analysis of the publishing patterns of studies on the Omicron variant and identified hotspots. Automated transportation, environmental protection, improved healthcare, innovation in banking, and smart homes are just a few areas where machine learning has found use in tackling complicated problems. The sophisticated Scopus database was queried for papers with the term "Omicron" in the title published between January 2020 and June 2022. Microsoft Excel 365, VOSviewer, Bibliometrix, and Biblioshiny from R were used for a statistical analysis of the publications. Over the study period, 1917 relevant publications were found in the Scopus database. Viruses was the most popular in publications for Omicron variant research, with 150 papers published, while Cell was the most cited source. The bibliometric analysis determined the most productive nations, with USA leading the list with the highest number of publications (344) and the highest level of international collaboration on the Omicron variant. This study highlights scientific advances and scholarly collaboration trends and serves as a model for demonstrating global trends in Omicron variant research. It can aid policymakers and medical researchers to fully grasp the current status of research on the Omicron variant. It also provides normative data on the Omicron variant for visualization, study, and application.

Emergence and dissemination of monkeypox, an intimidating global public health problem.

The monkeypox virus (MPXV) is the cause of a zoonotic infection similar to smallpox. Although it is endemic to Africa, it has recently begun to circulate in other parts of the world. In July 2022, the World Health Organization declared monkeypox an international public health emergency. This review aims to provide an overview of this neglected zoonotic pathogen. MPXV circulates as two distinct clades, the Central African and West African, with case fatality rates of 10.6% and 3.6%, respectively. The risk of infection is greater for those who work with animals or infected individuals. The virus' entry into the human body provokes both natural and acquired immunity. Although natural killer cells, CD4 + T cells, and CD8 + T cells play an essential role in eradicating MPXV, there is still a gap in the understanding of the host immune response to the virus. Currently, there are no specific therapeutic guidelines for treating monkeypox; however, some antiviral drugs such as tecovirimat and cidofovir may help to abate the severity of the disease. The use of nonpharmaceutical interventions and immunization can reduce the risk of infection. Increased surveillance and identification of monkeypox cases are crucial to understand the constantly shifting epidemiology of this resurging and intimidating disease. The present review provides a detailed perspective on the emergence and circulation of MPXV in human populations, infection risks, human immune response, disease diagnosis and prevention strategies, and future implications, and highlights the importance of the research community engaging more with this disease for an effective global response.

Rubella Virus Infections: A Bibliometric Analysis of the Scientific Literature from 2000 to 2021.

Rubella virus (RuV) generally causes a mild infection, but it can sometimes lead to systemic abnormalities. This study aimed to conduct a bibliometric analysis of over two decades of RuV research. Medical studies published from 2000 to 2021 were analyzed to gain insights into and identify research trends and outputs in RuV. R and VOSviewer were used to conduct a bibliometric investigation to determine the globally indexed RuV research output. The Dimensions database was searched with RuV selected as the subject, and 2500 published documents from the preceding two decades were reviewed. The number of publications on RuV has increased since 2003, reaching its peak in 2020. There were 12,072 authors and 16,769 author appearances; 88 publications were single-authored and 11,984 were multi-authored. The United States was the most influential contributor to RuV research, in terms of publications and author numbers. The number of RuV-related articles has continued to increase over the past few years due to the significant rubella burden in low-income nations. This study will aid in formulating plans and policies to control and prevent RuV infections.

The Molecular Detection of Class B and Class D Carbapenemases in Clinical Strains of Acinetobacter calcoaceticus-baumannii Complex: The High Burden of Antibiotic Resistance and the Co-Existence of Carbapenemase Genes.

The emergence of carbapenem-resistant Acinetobacter calcoaceticus-baumannii complex (CRACB) in clinical environments is a significant global concern. These critical pathogens have shown resistance to a broad spectrum of antibacterial drugs, including carbapenems, mostly due to the acquisition of various ß-lactamase genes. Clinical samples (n = 1985) were collected aseptically from multiple sources and grown on blood and MacConkey agar. Isolates and antimicrobial susceptibility were confirmed with the VITEK-2 system. The modified Hodge test confirmed the CRACB phenotype, and specific PCR primers were used for the molecular identification of blaOXA and blaNDM genes. Of the 1985 samples, 1250 (62.9%) were culture-positive and 200 (43.9%) were CRACB isolates. Of these isolates, 35.4% were recovered from pus samples and 23.5% from tracheal secretions obtained from patients in intensive care units (49.3%) and medical wards (20.2%). An antibiogram indicated that 100% of the CRACB isolates were resistant to ß-lactam antibiotics and ß-lactam inhibitors, 86.5% to ciprofloxacin, and 83.5% to amikacin, while the most effective antibiotics were tigecycline and colistin. The CRACB isolates displayed resistance to eight different AWaRe classes of antibiotics. All isolates exhibited the blaOXA-51 gene, while blaOXA-23 was present in 94.5%, blaVIM in 37%, and blaNDM in 14% of the isolates. The blaOXA-51, blaOXA-23, and blaOXA-24 genes co-existed in 13 (6.5%) isolates. CRACB isolates with co-existing blaOXA-23, blaOXA-24, blaNDM, blaOXA-51 and blaVIM genes were highly prevalent in clinical samples from Pakistan. CRACB strains were highly critical pathogens and presented resistance to virtually all antibacterial drugs, except tigecycline and colistin.

Multiple Antimicrobial Resistance and Heavy Metal Tolerance of Biofilm-Producing Bacteria Isolated from Dairy and Non-Dairy Food Products.

Foodborne pathogens have acquired the ability to produce biofilms to survive in hostile environments. This study evaluated biofilm formation, antimicrobial resistance (AMR), and heavy metal tolerance of bacteria isolated from dairy and non-dairy food products. We aseptically collected and processed 200 dairy and non-dairy food specimens in peptone broth, incubated them overnight at 37 °C, and sub-cultured them on various culture media. Bacterial growth was identified with biochemical tests and API 20E and 20NE strips. The AMR of the isolates was observed against different antibacterial drug classes. Biofilm formation was detected with the crystal violet tube method. Heavy metal salts were used at concentrations of 250−1500 µg/100 mL to observe heavy metal tolerance. We isolated 180 (50.4%) bacteria from dairy and 177 (49.6%) from non-dairy food samples. The average colony-forming unit (CFU) count for dairy and non-dairy samples was 2.9 ± 0.9 log CFU/mL and 5.1 ± 0.3 log CFU/mL, respectively. Corynebacterium kutscheri (n = 74), lactobacilli (n = 73), and Staphylococcus aureus (n = 56) were the predominant Gram-positive and Shigella (n = 10) the predominant Gram-negative bacteria isolated. The correlation between biofilm formation and AMR was significant (p < 0.05) for most cephalosporins, aminoglycosides, and fluoroquinolones. Heavy metal tolerance tended to be higher in biofilm producers at different metal concentrations. The pathogens isolated from dairy and non-dairy food showed a high burden of AMR, high propensity for biofilm formation, and heavy metal tolerance, and pose an imminent threat to public health.

Phylogenetic diversity and mutational analysis of New Delhi Metallo-ß-lactamase (NDM) producing E. coli strains from pediatric patients in Pakistan.

The evolution of NDM genes (bla NDM) in E. coli is accounted for expansive multidrug resistance (MDR), causing severe infections and morbidities in the pediatric population. This study aimed to analyze the phylogeny and mutations in NDM variants of E. coli recovered from the pediatric population. Carbapenem-resistant clinical strains of E. coli were identified using microbiological phenotypic techniques. PCR technique used to amplify the bla NDM genes, identified on agarose gel, and analyzed by DNA sequencing. The amino acid substitutions were examined for mutations after aligning with wild types. Mutational and phylogenetic analysis was performed using Lasergene, NCBI blastn, Clustal Omega, and MEGA software, whereas PHYRE2 software was used for the protein structure predictions. PCR amplification of the bla NDM genes detected 113 clinical strains of E. coli with the contribution of bla NDM-1 (46%), bla NDM-4 (3.5%), and bla NDM-5 (50%) variants. DNA sequencing of bla NDM variants showed homology to the previously described bla NDM-1, bla NDM-4, and bla NDM-5 genes available at GenBank and NCBI database. In addition, the mutational analysis revealed in frame substitutions of Pro60Ala and Pro59Ala in bla NDM-4 and bla NDM-5, respectively. The bla NDM-1 was ortholog with related sequences of E. coli available at GenBank. The phylogenetic analysis indicated that the NDM gene variants resemble other microbes reported globally with some new mutational sites.

Diagnostic approach to elucidate the efficacy and side effects of direct-acting antivirals in HCV infected patients.

INTRODUCTION: The conventional interferon therapy of hepatitis C virus has been substituted substantially with sofosbuvir and daclatasvir due to constraints in efficacy and tolerability. This study aimed diagnostically to monitor the effectiveness and side effects of direct-acting antivirals in the management of HCV infections. METHODOLOGY: This prospective study was conducted on HCV-infected patients treated with sofosbuvir and daclatasvir. Different serological, biochemical, hematological, and molecular techniques were used for the assessment of patients. Only treatment-naive patients aged ≥ 18 to 75 years received 12 weeks of treatment. The primary endpoint was a sustained virologic response with undetectable HCV RNA in the patients' serum at the end of the treatment. RESULTS: We identified 229 cases of confirmed HCV infections by PCR, 94.3% of which had genotype 3. The study population comprised 66% females and 34% males with a median age of 42.2 ± 10.6 SD. Ninety-three percent of the patients accomplished SVR at week 12. The combined therapy of SOF/DAC achieved the highest efficacy rate (92.6%) among the different HCV genotype 3 patients. A statistically significant relationship was observed between low baseline viral load (p < 0.001; 95% CI = 1.2-3.1) and HCV genotype 3 with minor side effects, including lethargy, headache, nausea, insomnia, diarrhea, and fever. CONCLUSIONS: HCV-infected patients can be treated well with an interferon-free SOF/DAC regimen, tolerated with generally mild adverse effects with a higher SVR.

Molecular analysis of blaSHV, blaTEM, and blaCTX-M in extended-spectrum ß-lactamase producing Enterobacteriaceae recovered from fecal specimens of animals.

Colonization of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae as animal gut microbiota is a substantial global threat. This study aimed to determine the molecular characterization of blaSHV, blaTEM, and blaCTX-M variants in animals, as well as to evaluate the antimicrobial resistance conferred by these genes. We prospectively analyzed 1273 fecal specimens of farm and domestic animals for the isolation of enterobacteria that had the ESBL phenotype by using biochemical methods. The extracted genes were amplified by polymerase chain reaction and sequenced for the characterization of blaSHV, blaTEM, and blaCTX-M variants. The drug-resistance spectrum and hierarchical clusters were analyzed against 19 antibacterial agents. Out of 245 (19.2%) ESBL enterobacteria, 180 (75.5%) Escherichia coli and 34 (13.9%) Klebsiella pneumoniae were prevalent species. A total of 73.9% blaCTX-M, 26.1% blaTEM, and 14.2% blaSHV were found among the enterobacteria; however, their association with farm or domestic animals was not statistically significant. The distribution of bla gene variants showed the highest number of blaCTX-M-1 (133; 54.3%), followed by blaCTX-M-15 (28; 11.4%), blaTEM-52 (40; 16.3%), and blaSHV-12 (22; 9%). In addition, 84.5% of the enterobacteria had the integrons intI1. We observed ±100% enterobacteria resistant to cephalosporin, 7 (2.9%) to colistin (minimum inhibitory concentration breakpoint ≥4 µg/mL), 9 (3.7%) to piperacillin-tazobactam, 11 (4.5%) to imipenem, 14 (5.7%) to meropenem, and 18 (7.3%) to cefoperazone-sulbactam, without statistically significant association. Animal gut microbiota contain a considerable number of blaCTX-M, blaTEM, blaSHV, and integrons, which are a potential source of acquired extensive drug resistance in human strains and leaves fewer therapeutic substitutes.

Molecular Epidemiology of Extensively-Drug Resistant Acinetobacter baumannii Sequence Type 2 Co-Harboring bla NDM and bla OXA From Clinical Origin.

BACKGROUND: The therapeutic management of carbapenem-resistant Acinetobacter baumannii (CR-AB) represents a serious challenge to the public health sector because these pathogens are resistant to a wide range of antibiotics, resulting in limited treatment options. The present study was planned to investigate the clonal spread of CR-AB in a clinical setting. METHODOLOGY: A total of 174 A. baumannii clinical isolates were collected from a tertiary care hospitals in Lahore, Pakistan. The isolates were confirmed by VITEK 2 compact system and molecular identification of recA and bla OXA-51. Antimicrobial profile and the screening of carbapenem-resistant genes were carried out using VITEK 2 system and PCR, respectively. The molecular typing of the isolates was performed according to the Pasteur scheme. RESULTS: Of the 174 A. baumannii isolates collected, the majority were isolated from sputum samples (46.5%) and in the intensive care unit (ICU, 75%). Among these, 113/174 (64.9%) were identified as CR-AB, and 49.5% and 24.7% harbored bla OXA-23 and bla NDM-1, respectively. A total of 11 (9.7%) isolates co-harbored bla OXA-51, bla NDM-1, and bla OXA-23. Interestingly, 46.9% of the CR-AB belonged to sequence type 2 (ST2; CC1), whereas 15.9% belonged to ST1 (CC1). All of the CR-AB isolates showed extensive resistance to clinically relevant antibiotics, except colistin. CONCLUSION: The study concluded CR-AB ST2 clone harboring bla OXA-23 and bla NDM-1 are widely distributed in Pakistan's clinical settings, which could result in increased mortality. Strict compliance with the National Action Plan on Antimicrobial Resistance is necessary to reduce the impacts of these strains.

Association of IL28 B and IL10 Polymorphism with HCV Infection and Direct Antiviral Treatment.

OBJECTIVE: Single nucleotide polymorphisms (SNPs) in IL28B and IL10 regions are important in predicting the antiviral response in hepatitis C virus (HCV) patients. In this study, the association of IL28B and IL10 genetic polymorphisms and other clinical factors was assessed as a predictive marker for the sustained virological response (SVR) of HCV patients taking direct-acting antivirals (DAAs). METHODS: We processed 384 serum specimens of HCV serology positive cases for qualitative and quantitative polymerase chain reaction (PCR). Patients were followed up for 12 weeks after the start of antiviral therapy, and the viral load was monitored at each time point. IL28B and IL10 polymorphisms (rs8103142 and rs12980275, rs1800872 and rs3021094, respectively) were detected by real-time PCR, followed by melt curve analysis for genotyping. RESULTS: This study's findings indicate an independent association of SVR with high basal viral load (P=0.005) and an HCV genotype other than 3 (P=0.001). Patients with viral load log10 >6.5 IU/mL required more days to reach an undetectable viral RNA load. The results of the genetic analysis showed a significant association of rs8103142 genotype CC (P<0.01) and rs12980275 genotype AA (P=0.01) with non-SVR. Both SNPs showed an independent association in the multivariate analysis. CONCLUSION: High basal viral load, HCV genotype, and host polymorphisms of rs8103142 and rs12980275 have an independent association in predicting the therapeutic response of HCV patients. The preliminary identification of polymorphisms prior to treatment will help in predicting the outcome of therapy.

Insight into the emerging role of SARS-CoV-2 nonstructural and accessory proteins in modulation of multiple mechanisms of host innate defense.

Coronavirus disease-19 (COVID-19) is an extremely infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has become a major global health concern. The induction of a coordinated immune response is crucial to the elimination of any pathogenic infection. However, SARS-CoV-2 can modulate the host immune system to favor viral adaptation and persistence within the host. The virus can counteract type I interferon (IFN-I) production, attenuating IFN-I signaling pathway activation and disrupting antigen presentation. Simultaneously, SARS-CoV-2 infection can enhance apoptosis and the production of inflammatory mediators, which ultimately results in increased disease severity. SARS-CoV-2 produces an array of effector molecules, including nonstructural proteins (NSPs) and open-reading frames (ORFs) accessory proteins. We describe the complex molecular interplay of SARS-CoV-2 NSPs and accessory proteins with the host's signaling mediating immune evasion in the current review. In addition, the crucial role played by immunomodulation therapy to address immune evasion is discussed. Thus, the current review can provide new directions for the development of vaccines and specific therapies.