Clonal diversity and spatial dissemination of multi-antibiotics resistant Staphylococcus aureus pathotypes in Southwest Nigeria

Pathogenomic profile and clonal diversity of potential zoonotic MRSA-CC7-ST789-t091-SCCmecV from human skin and soft tissue infections

The whole genome sequence (WGS) of prevalent MRSA strains harboring mecA gene obtained from skin and soft tissue infections (SSTIs) in Nigerian hospitals were profiled for pathogenomic structure and evaluated for clonal diversity. The two MRSA strains identified among 66 isolated multi-drug resistant S. aureus from a collection of 256 clinical samples were phenotyped for antibiotic resistance and genotyped for mecA, SCCmec, and spa types. The mecA positive MRSA was analysed using whole-genome sequencing for resistomes, virulomes, phylogenomic profiles and clonal diversity. The identified MRSA-CC7-ST789-t091-SCCmecV strains from a female child (aged 1 year) with severe otorrhea and an adult male (aged 23) with purulent wound abscess showed high-level resistance to streptomycin, vancomycin, kanamycin, sulfamethoxazole and ciprofloxacin. Both strains harbored abundant resistomes, inherent plasmids, chromosomal replicons and typical seven housekeeping genes (arc3, aroE4, glpF1, gmk4, pta4, tpi6, yqiL3). The most abundant putative virulomes were pathogenesis-associated proteins (included hemolysin gamma, leucocidins, proteases, staphylococcal superantigen/enterotoxin-like genes (Set/Ssl), capsule- and biofilm-associated genes, and hyaluronate lyase). Comparative phylogenomic analysis revealed the relatedness of the two clonal strains with prevalent MRSA-CC7 pathotypes observed in Italy (2013 and 2014), Denmark (2014), Thailand (2015 and 2016), USA (2018), and Nigeria (2016 and 2020); and share high genetic similarities with livestock strains from cow milk and cattle. Identified MRSA-CC7-ST789-t091-SCCmecV pathotypes implicated in SSTIs from Nigeria harboring repertoires of antibiotic resistance and virulence genes, and genetic relatedness with livestock strains; show the possibility of gene transfer between animal and human. Adequate hospital MRSA infection control and geno-epidemiological surveillance for animal and human transfer is required.

Loop-Mediated Isothermal Amplification of DNA (LAMP) as an Alternative Method for Determining Bacteria in Wound Infections

The increasing number of patients with chronic wounds requires the development of quick and accurate diagnostics methods. One of the key and challenging aspects of treating ulcers is to control wound infection. Early detection of infection is essential for the application of suitable treatment methods, such as systemic antibiotics or other antimicrobial agents. Clinically, the most frequently used method for detecting microorganisms in wounds is through a swab and culture on appropriate media. This test has major limitations, such as the long bacterial growth time and the selectivity of bacterial growth. This article presents an overview of molecular methods for detecting bacteria in wounds, including real-time polymerase chain reaction (rtPCR), quantitative polymerase chain reaction (qPCR), genotyping, next-generation sequencing (NGS), and loop-mediated isothermal amplification (LAMP). We focus on the LAMP method, which has not yet been widely used to detect bacteria in wounds, but it is an interesting alternative to conventional detection methods. LAMP does not require additional complicated equipment and provides the fastest detection time for microorganisms (approx. 30 min reaction). It also allows the use of many pairs of primers in one reaction and determination of up to 15 organisms in one sample. Isothermal amplification of DNA is currently the easiest and most economical method for microbial detection in wound infection. Direct visualization of the reaction with dyes, along with omitting DNA isolation, has increased the potential use of this method.

A meta-analysis on the prevalence of resistance of Staphylococcus aureus to different antibiotics in Nigeria

BACKGROUND

Rapid emergence of multidrug resistant Staphylococcus aureus has resulted to difficulty in treatment of infections caused by such strains. The aim of this meta-analysis study was to determine the pooled prevalence of resistance of S. aureus to different antibiotics in Nigeria.

METHODS

Literature search for studies was done using Google scholar, PubMed, Science direct, and African Journal Online. The prevalence of S. aureus resistance to different antibiotics was evaluated using the meta-analysis proportion command in MedCalc software version 20.0 adopting a rand effect model. I² statistic and Egger test in MedCalc was used to evaluate the heterogeneity and the presence of publication bias among studies respectively.

RESULTS

A total of 40, 682 studies were retrieved through the database search of which 98 studies met the study inclusion criteria. Prevalence of resistance of S. aureus to different antibiotics ranges from 13 to 82%. Results showed a very high degree of resistance to penicillin G (82% [95% confidence interval (CI) 61%, 0.96%]), cloxacillin (77% [95% CI 64%, 88%]), amoxacillin (74% [95% CI 66%, 81%]), cefuroxime (69% [95% CI 51%, 85%]), ampicillin (68% [95% CI 53%, 81%]). Moderately resistance to erythromycin (47% [95% CI 40%, 53%]), chloramphenicol (47% [95% CI 37%, 56%]), methicillin (46% [95% CI 37%, 56%]), ofloxacin (24% [95% CI 18%, 31%]) and rifampicin 24% [95% CI 6%, 48%]). Low resistance was observed in vancomycin 13% (95% CI 7%, 21%). For each individual meta-analysis, high heterogeneity was observed with I² range (79.36-98.60%) at p-values ≤ 0.01). Egger's tests for regression intercept in funnel plots indicated no evidence of publication bias.

CONCLUSION

This meta-analysis study established that S. aureus in Nigeria has developed resistance to commonly used antibiotics such as the beta-lactam class antibiotics, sulphonamides, tetracyclines, chloramphenicol, and vancomycin. Hence it is imperative to develop programs to promote rational use of antimicrobial agents, infection prevention and control to reduce the incidence of antimicrobial resistance.

Evaluation of Efflux-Mediated Resistance and Biofilm formation in Virulent Pseudomonas aeruginosa Associated with Healthcare Infections

Pseudomonas aeruginosa is a significant pathogen identified with healthcare-associated infections. The present study evaluates the role of biofilm and efflux pump activities in influencing high-level resistance in virulent P. aeruginosa strains in clinical infection. Phenotypic resistance in biotyped Pseudomonas aeruginosa (n = 147) from diagnosed disease conditions was classified based on multiple antibiotic resistance (MAR) indices and analysed with logistic regression for risk factors. Efflux pump activity, biofilm formation, and virulence factors were analysed for optimal association in Pseudomonas infection using receiver operation characteristics (ROC). Age-specificity (OR [CI] = 0.986 [0.946-1.027]), gender (OR [CI] = 1.44 [0.211-9.827]) and infection sources (OR [CI] = 0.860 [0.438-1.688]) were risk variables for multidrug resistance (MDR)-P. aeruginosa infection (p < 0.05). Biofilm formers caused 48.2% and 18.5% otorrhea and wound infections (95% CI = 0.820-1.032; p = 0.001) respectively and more than 30% multidrug resistance (MDR) strains demonstrated high-level efflux pump activity (95% CI = 0.762-1.016; p = 0.001), protease (95% CI = 0.112-0.480; p = 0.003), lipase (95% CI = 0.143-0.523; p = 0.001), and hemolysin (95% CI = 1.109-1.780; p = 0.001). Resistance relatedness of more than 80% and 60% to cell wall biosynthesis inhibitors (ceftazidime, ceffproxil, augumentin, ampicillin) and, DNA translational and transcriptional inhibitors (gentamicin, ciprofloxacin, ofloxacin, nitrofurantoin) were observed (p < 0.05). Strong efflux correlation (r = 0.85, p = 0.034) with MDR strains, with high predictive performances in efflux pump activity (ROC-AUC 0.78), biofilm formation (ROC-AUC 0.520), and virulence hierarchical-clustering. Combine activities of the expressed efflux pump and biofilm formation in MDR-P. aeruginosa pose risk to clinical management and infection control.

Nasal Carriage of Staphylococcus aureus and Associated Risk Factors among Food Handlers in a Nigerian University

Staphylococcal foodborne illness, caused by the ingestion of contaminated foods by induced Staphylococcus aureus enterotoxins, is one of the most recurrent foodborne diseases worldwide. Food handlers working in food-service establishments who carry enterotoxigenic isolates represent a reservoir for potential contamination leading to staphylococcal food intoxication. The aim of this research was to investigate the prevalence of nasal transmission of S. aureus among food handlers in a University community. A total of 100 nasal swab specimens were obtained from the food handlers and analyzed by standard laboratory techniques for isolation and identification. Questionnaires were administered to ascertain the risk determinants associated with nasal carriage of S. aureus. Antibiotic susceptibility testing of the isolates was done by disk diffusion method. Thirty-two food handlers were found to be carriers of S. aureus. Majority were females (63%), and 30% had been certified for food safety and handling. There were however no significant association between the nasal distribution of S. aureus together with established risk factors. Among the isolates, 93.75% were found to be resistant to penicillin, 50% to gentamicin and 50% to oxacillin. These findings indicate the need for training of food handlers on food safety, as well as the knowledge of antibiotic resistance.

Emerging vancomycin-non susceptible coagulase negative Staphylococci associated with skin and soft tissue infections

Backgrounds

Observable emergence of Vancomycin-Non susceptible Coagulase-negative Staphylococci (VNS-CoNS) associated with skin and soft tissue infections spreading among the urban and rural populace is gradually intensifying severe complications. The isolated VNS-CoNS were evaluated with Matrix-assisted Laser Desorption/ionization Time of Flight Mass Spectrometry (MALDI ToF MS) for species characterization and pan-antimicrobial resistance pattern.

Methods

Out of 256 clinical samples collected including pus, abscess, ear swabs, eye swabs, and aspirates, 91 CoNS isolates were biotyped and further characterized with MALDI-TOF MS. Staphylococci marker genes, Vancomycin susceptibility, and biofilm assays were performed.

Results

Of 91 CoNS isolates, S.cohnii (2.3%), S.condimentii (3.4%), S. saprophyticus (6.7%), and S.scuri (21.1%) were characterized with MALDI-TOF with significant detection rate (99.4%; CI 95, 0.775–0.997, positive predictive values, 90.2%) compared to lower biotyping detection rate (p = 0.001). Hemolytic VNS-CoNS lacked nuc, pvl and spa genes from wound, ear, and aspirates of more 0.83 MARI clustered into a separate phylo-diverse group and were widely distributed in urban and peri-urban locations. MALDI TOF–MS yielded a high discriminatory potential of AUC-ROC score of 0.963 with true-positivity prediction. VNS-CoNS of MIC ≥ 16 µg/mL were observed among all the ages with significant resistance at 25th and 75th quartiles. More than 10.5% of CoNS expressed multi-antibiotic resistance with more than 8 µg/mL vancomycin cut-off values (p < 0.05).

Conclusion

Antibiotic resistant CoNS should be considered significant pathogens rather than contaminant. Biofilm producing VNS-S. sciuri and S. condimentii are potential strains with high pathological tropism for skin, soft tissues and wound infections, and these strains require urgent surveillance in peri-urban and rural communities.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-022-00516-4.

Antibacterial activities of plant leaf extracts against multi-antibiotic resistant Staphylococcus aureus associated with skin and soft tissue infections

Background

The antibacterial activities of aqueous leaf extracts of Moringa oleifera, Vernonia amygdalina, Azadirachta indica and Acalypha wilkesiana against multidrug resistance (MDR) Staphylococcus aureus associated with skin and soft tissue infections were investigated.

Methods

Staphylococcus aureus (n = 183) from the skin and soft tissue infections with evidence of purulent pus, effusions from aspirates, wounds, and otorrhea were biotyped, and evaluated for biofilm production. The phenotypic antibiotic resistance and MDR strains susceptibility to plant leaves extract were determined using disc diffusion and micro-broth dilution assays respectively. The correlation of plant extract bioactive components with inhibitory activities was determined.

Results

High occurrence rate of S. aureus were recorded among infant and adult age groups and 13.2% mild biofilm producers from the wound (p < 0.05). Of 60.2% MDR strains with overall significant MARI of more than 0.85 (p < 0.05), high resistant rates to linozidine (92.7%; 95% CI:7.27–10.52), ofloxacin (94.2%; 95% CI:6.09–8.15), chloramphenicol (91.2%; 95% CI:6.11–8.32), gentamicin (97.3%; 95% CI:6.20–8.22), ciprofloxacin (92.7%; 95% CI: 5.28–7.99) and vancomycin (86.6%; 95% CI:6.81–9.59) were observed. Vernonia amygdalina and Azadirachta indica showed significant antimicrobial activity at 100 mg/ml and 75 mg/ml, with low susceptibility of less than 10% to 25 mg/ml, 50 mg/ml, and 75 mg/ml Moringa oleifera. Alkaloids, saponin and terpenoids were significant in Moringa oleifera, Acalypha wilkesiana, Azadirachta indica and Vernonia amygdalina leaves extracts (p < 0.05). High inhibitory concentrations at IC50; 3.23, 3.75 and 4.80 mg/ml (p = 0.02, CI: − 0.08 – 11.52) and IC90; 12.9, 7.5, and 9.6 mg/ml (p = 0.028, CI: 2.72–23.38) were shown by Acalypha wilkesiana, Vernonia amygdalina and Moringa oleifera respectively. Comparative outcome of the plant extracts showed Acalypha wilkesiana, Vernonia amygdalina and Moringa oleifera to exhibit significant inhibition activities (p < 0.05) compared to other extracts. Significant median inhibitory concentration (15.3 mg/ml) of Azadirachta indica were observed (p < 0.01) and strong associations of phytochemical compounds of Azadirachta indica (eta = 0.527,p = 0.017), Vernonia amygdalina (eta = 0.123,p = 0.032) and Acalypha wilkesiana (eta = 0.492,p = 0.012) with their respective inhibitory values.

Conclusion

Observed high occurrence rate of skin and soft tissue infections caused by biofilm-producing MDR S. aureus requires alternative novel herbal formulations with rich bioactive compounds from Moringa oleifera, Acalypha wilkesiana, Azadirachta indica and Vernonia amygdalina as skin therapeutic agents.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12906-022-03527-y.