Detection of invA and blaCTM-genes in Salmonella spp isolated from febrile patients in Lagos hospitals, Nigeria

Salmonella infections remain a global challenge. The culture method is the gold standard for the detection of genus Salmonella. Application of Polymerase Chain Reaction (PCR) has become an effective tool for the detection of virulence and antimicrobial resistance genes. This study investigated the prevalence of Salmonella by culture and detection of invA gene and blaCTX-M and blaCTX-M-3 gene markers by PCR. A total of 612 blood samples were collected from hospitalized febrile patients between March 2020 and April 2021. The samples were cultured, isolates identified by standard method with Analytical Profile Index (API 20-E) kits and were subjected to in-vitro antimicrobial susceptibility test (AST) using disk diffusion method. Extended-spectrum beta-lactamase (ESBL) detection was carried out by double-disc synergy test. Detection of invA gene and antibiotic-resistant genes makers was done by qPCR. A total of 24 Salmonella isolates were identified given a prevalence of 3.9% Salmonella-associated bacteraemia. Children within 1-10 years with persistent pyrexia of unknown origin (PUO) accounted for 50% of the Salmonella isolated with a mean age of 5.299 years. Specifically, 75% (18/24) Salmonella isolates and their corresponding samples of positive Salmonella culture were positive for the invA gene. The AST results indicated 100% Salmonella isolates developed resistance to ceftazidime, cefotaxime , augmentin, ampicillin, ertapenem, and doripenem. None of drug resistant-Salmonella isolates expressed ESBL enzyme phenotypically. Seven resistance patterns were observed, and the pattern CAZ-CTX-OFL-AUG-NIT-AMP-ETR-DOR was the most encountered pattern. Twelve (50%) Salmonella isolates harbored the blaCTX-M and blaCTX-M-3 genes and were mostly from children. The study has added to the growing knowledge on the suitability of the invA gene primer set as a PCR target for the detection of Salmonella. It also revealed a paradigm shift in the occurrence of invasive Salmonella harboring blaCTX-M and blaCTX-M-3 genes in PUO cases. There is a need for judicious use of cephalosporin and carbapenem antibiotics to preserve their efficacies.

Emerging carbapenem resistance in ESKAPE organisms in sub-Saharan Africa and the way forward

The epidemiology of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species (ESKAPE) and their role in the development and spread of multidrug resistance (MDR) is not well characterized in sub-Saharan Africa (SSA). Carbapenems possess a broad spectrum of activity and are often reserved for the treatment of MDR infections in developed countries. However, the emergence of carbapenem resistance is increasingly being reported and therefore presents a significant public health threat. Although carbapenems are generally unavailable in African hospitals due to high cost, a small number of studies have reported the occurrence of carbapenem-resistant bacteria (CRB) in SSA. This, therefore, shows that carbapenem resistance (CR) is emerging in Africa. Thus, there is a critical need for deploying robust national and regional multidisciplinary, collaborative, and regulatory approaches aiming at elucidating the epidemiology of CR, its burden on the health care system, and strategies for compacting the development and spread of CR. This report hopes to highlight the epidemiology of carbapenem resistance and the main drivers of antibiotic resistance in SSA and proposes future strategies that can be used to combat the emergence of carbapenem resistance in the region

The German Journal of Microbiology; towards dissemination and globalization of microbiology research

The emergence and re-emergence of diseases pose serious challenges to the global community, giving a wake-up call for the entire scientific community to collaborate to understand the nature of microorganisms and control pathogens that threaten humans, animals, and the ecosystem. Dissemination and globalization of scientific research in microbiology contribute to scientific community development and subsequently to scientific progress. Therefore, it is a privilege to announce the birth of the "German Journal of Microbiology, an open-access journal to publish different research articles pertained to microbiology. To empower the disclosure of scientific information, the payment capability will not be a barrier for the publication of excellent works; therefore, a complete or partial waiver may be provided upon request

Klebsiella pneumoniae in Germany: An overview on spatiotemporal distribution and resistance development in humans

The emerging of multidrug-resistant Klebsiella pneumoniae (K. pneumoniae) is increasing worldwide. Rapid dissemination and increase of its incidence in Germany are observed and becoming a significant challenge for clinical laboratories and physicians. The current review highlights its chronological sequence of appearance and resistance development in humans in the past two decades in Germany. Emerging resistance problems of K. pneumoniae to the vast majority of available antimicrobial agents, including carbapenems and those of the ß-lactam group, were observed since the end of the last century and strains carrying diverse resistance patterns have emerged in most federal states of Germany. Still, several aspects of resistance development and pathogenesis are not fully understood. To date, hypervirulent K. pneumoniae (hvKp) isolates have been rarely isolated from German patients. The most frequent resistance genes identified are blaOXA-48, blaCTX-M-15, blaKPC-2, blaOXA-9, blaSHV-11, blaSHV-5 blaCTX-M-3, blaCTX-M-14, blaVIM-1 and the plasmid-encoded quinolone resistance (PMQR) gene. One Health genomic surveillance of K. pneumoniae strains from different reservoirs is required. This would help to understand in great detail the mechanisms leading to resistance development, spread and transmission, and developing alternative treatment regimens

An overview of the ongoing challenges in SARS-CoV-2 global control

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has caused a severe global pandemic with major public health issues. Public health sectors implemented several control strategies, such as social distancing, hygienic measures, and the development of anti-viral drugs and vaccines. However, the situation is still critical due to several challenges facing the global control strategy. SARS-CoV-2 has undergone several mutations that will drive viral evolution, which might impact the virus’s transmissibility and pathogenicity and the immune escape and development of resistance to therapeutics. Moreover, although the European Medicines Agency (EMA) and the US Food and Drug Administration (FDA) have approved several vaccines, however, some vaccines, especially vector-based vaccines, have rarely induced severe fatal side effects. These side effects led to widespread doubts about the safety of the coronavirus disease-19 (COVID-19) vaccines, which in turn dragged a certain proportion of the public from getting vaccinated. This review highlights some of the ongoing challenges in controlling the COVID-19 pandemic, including side effects of the developed vaccines, potential mechanisms for the development of thrombocytopenia, and the clinical impacts of the emerged SARS-CoV-2 variants on the pathogenesis of the virus and vaccine efficacy. Additionally, we discuss the comorbidity and the potential role of gastrointestinal microbiota in controlling SARS-CoV-2. Finally, we shed light on the substantial collateral health damage and unprecedented economic disaster caused by the lockdown.

Molecular docking study of Lens culinaris L. phytochemicals to NS3-NS2B protease of dengue virus serotype 2

Forty-three phytochemicals present in Lens culinaris were evaluated through in-silico molecular docking studies for their binding affinities to the NS2B-NS3 activator-protease complex of dengue virus serotype 2 (DENV-2). Among the various compounds tested, flavonoids (flavanols,favonols, proanthocyanidins, flavanones, flavones, and anthocyanins) demonstrated high binding affinities for the protease complex. Eriodictyol-7-O-rutinoside showed the least predicted binding energy at -9.1 kcal/mol followed by luteolin-7-O-glucoside at -8.8 kcal/mol. Glycosidic linkages appeared to enhance the binding affinities of flavonoids, aldohexoses being more potent than aldopentoses. Besides flavonoids, other classes of compounds demonstrating high binding affinities for the protease were carotenoids, phytosterols, and polyphenolic compounds like resveratrol and trans-resveratrol 3-O-b-glucoside (piceid), the latter showing predicted binding energy of -8.5 kcal/mol versus predicted binding energy of -7.2 kcal/mol for resveratrol. The 2D interactions of four high binding affinity compounds like eriodictyol, eriodictyol-7-O-rutinoside, catechin gallate, and luteolin-7-O-glucoside showed that all four compounds bound to the active site of the NS3 protease and not to the activator NS2B. Lys74 of NS3 was the common amino acid interacting with all four phytochemicals. Analysis of physicochemical properties of the compounds (Lipinski's Rule of 5) showed that the high binding affinity compounds have less than two violations, indicating that they can serve as useful lead compounds or as dengue virus serotype 2 therapeutics.

A rapid method for the detection of motility in Acinetobacter baumannii and its association to the existence of the virulence-associated genes pilA and algW

Acinetobacter (A.) baumannii is one of the major nosocomial pathogens worldwide. It is associated with bloodstream infection, pneumonia, meningitis, urinary tract, soft tissue, and wound infections. Several factors contribute to its survival and spread as a nosocomial pathogen, and motility is often associated with the virulence, fitness, and tenacity of A. baumannii on surfaces. In the present study, the correlation between the presence of genes encoding for fimbrial protein PilA and periplasmic protease AlgW and motility was investigated in 87 clinical and non-clinical A. baumannii isolates from Germany. A. baumannii exhibited robust swimming, swarming, and twitching movement based on the percentage of agar in the medium, as well as the time and temperature of incubation. The swarm motility medium utilizing 2% agar with tetrazolium salts provided an efficient assay for the phenotypic characterization of A. baumannii and it was more efficient than the classical motility assays in terms of time, visibility, and biosafety. The presence of the pilA gene increased motility of A. baumannii but was not required for motility. The algW gene was found in 18 strains obtained from milk, all of them with proven phenotypic motility. The rapid detection of motility is essential to evaluate the virulence and fitness of A. baumannii. Further studies on the level of genome, transcriptome and proteome are needed to investigate the secrets behind different movement paths in each strain.

COVID-19: Risk assessment and mitigation measures in healthcare and non-healthcare workplaces

The coronavirus disease-2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is the third emerging human coronavirus, leading to fatal respiratory distress and pneumonia. The disease originated in December 2019 in Wuhan City, Hubei province, China. As of 23 November 2021, over 258 million cases and 5.1 million deaths have been reported in more than 222 countries and territories worldwide. The COVID-19 is under biological hazards group 4 of high risk of spreading to the community with the potential to overwhelm the health system, especially in resource limited countries. Transmission of COVID-19 within healthcare and non-healthcare facilities has been recorded. Therefore, several authorities such as the World Health Organization (WHO), the Centers for Disease Control and Prevention (CDC), and other global partners issued guidance to mitigate the COVID-19 pandemic in these facilities. A global emergency due to the COVID-19 pandemic requires various studies of mitigation measures and risk assessment. The Failure Mode and Effects Analysis (FMEA) was used as a tool for risk assessment in healthcare and clinical fields that assigns a numerical value to each risk associated with failure. Therefore, in this review, the FMEA procedure was used to evaluate the COVID-19 risks and risk groups in health care and non-healthcare workplaces. Proposed mitigation measures and risk ranking tools were also summarized. The COVID-19 transmission risk should be theoretically and practically reduced by applying the best hygienic practices. However, providing safe work practices must be improved for infection control measures in healthcare and non-healthcare workplaces. Additionally, it is recommended to reassess the risk of COVID-19 infection from time to time, especially after vaccines availability.

Susceptibility of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae to Roundup

Bacteria and other microorganisms have several mechanisms to react to stress in the environment. Exposure of bacteria to antibiotics, biocides, or selective pressure may favor the emergence of antimicrobial resistance by several mechanisms as an evolution principle. Bacteria may possess cross-tolerance or cross-resistance to other environmental toxic substances present in soil, water, foods, and feeds. Glyphosate (N-phosphonomethylglycine), one of these substances used in modern agriculture might change the susceptibility of bacteria to antibiotics. The present study aimed to investigate the tolerance of extended-spectrum ß-lactamases (ESBL)-producing Enterobacteriaceae isolated from patients with nosocomial infections to glyphosate. Therefore, the minimum inhibitory concentrations of glyphosate-based herbicides (Roundup) of ESBL-positive and ESBL-negative Enterobacteriaceae were determined. Results showed that ESBL-producing Enterobacteriaceae exhibited a higher tolerance to Roundup compared with non-ESBL. To investigate the putative link between ESBL-producing Enterobacteriaceae and the resistance to glyphosate, a non-ESBL E. coil strain was used for development of glyphosate-resistant mutants using high concentrations of Roundup. Nine Roundup-resistant mutants were developed and characterized using Matrix-Assisted Laser Desorption/Ionization-Time of Flight. One Roundup-resistant mutant (Mut-A) exhibited different antibiotic susceptibility profiles compared with wild type strain. The Mut-A developed resistance to ampicillin/sulbactam, piperacillin, and streptomycin. Overall herbicides resistant Enterobacteriaceae might render resistant to β-lactam antibiotics as well. Further studies are urgently needed to investigate the mechanism of the putative link between antibiotic resistance and the herbicide-based glyphosate