Bacterial profile, antimicrobial susceptibility patterns, and associated factors of community-acquired pneumonia among adult patients in Gondar, Northwest Ethiopia: A cross-sectional study

Etiology of bacterial pneumonia and multi-drug resistance pattern among pneumonia suspected patients in Ethiopia: a systematic review and meta-analysis

BACKGROUND

Bacterial pneumonia can affect all age groups, but people with weakened immune systems, young children, and the elderly are at a higher risk. Streptococcus pneumoniae, Klebsiella pneumoniae, Haemophilus influenzae, and Pseudomonas aeruginosa are the most common causative agents of pneumonia, and they have developed high MDR in recent decades in Ethiopia. This systematic review and meta-analysis aimed to determine the pooled prevalence of bacterial pneumonia and multidrug resistance in Ethiopia.

METHODS

The articles were searched extensively in the electronic databases and grey literature using entry terms or phrases. Studies meeting the eligibility criteria were extracted in MS Excel and exported for statistical analysis into STATA version 14 software. The pooled prevalence of bacterial pneumonia and multidrug resistance were calculated using a random-effects model. Heterogeneity was assessed by using the I2 value. Publication bias was assessed using a funnel plot and Egger's test. A sensitivity analysis was done to assess the impact of a single study on the pooled effect size.

RESULT

Of the 651 studies identified, 87 were eligible for qualitative analysis, of which 11 were included in the meta-analysis consisting of 1154 isolates. The individual studies reported prevalence of bacterial pneumonia ranging from 6.19 to 46.3%. In this systematic review and metanalysis, the pooled prevalence of bacterial pneumonia in Ethiopia was 37.17% (95% CI 25.72-46.62), with substantial heterogeneity (I2 = 98.4%, p < 0.001) across the studies. The pooled prevalence of multidrug resistance in bacteria isolated from patients with pneumonia in Ethiopia was 67.73% (95% CI: 57.05-78.40). The most commonly isolated bacteria was Klebsiella pneumoniae, with pooled prevalence of 21.97% (95% CI 16.11-27.83), followed by Streptococcus pneumoniae, with pooled prevalence of 17.02% (95% CI 9.19-24.86), respectively.

CONCLUSION

The pooled prevalence of bacterial isolates from bacterial pneumonia and their multidrug resistance were high among Ethiopian population. The initial empirical treatment of these patients remains challenging because of the strikingly high prevalence of antimicrobial resistance.

Bacterial etiology of community-acquired pneumonia among adult patients in Ethiopia: A systematic review and meta-analysis

Background and objective

According to the Global Burden of Diseases, Injuries, and Risk Factors, lower respiratory infections cause more than 2.3 million deaths globally, with a majority occurring in sub-Saharan Africa, including Ethiopia.Community-acquired pneumonia (CAP) is a major contributor to global mortality and morbidity. Understanding the prevalence and common bacterial causes of CAP is crucial for clinicians to accurately diagnose and improve patient satisfaction. The purpose of this systematic review was to report the pooled prevalence and common bacterial etiologies of CAP among adult patients in Ethiopia.

Methods

This review was conducted based on the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. A comprehensive search of the published articles between January 2000 and October 2022 was performed using open access electronic databases such as PUBMED, Science Direct, CINAHL, HINARI, Google Scholar, and local university repositories. Cochrane Q and I2 values were used to assess heterogeneity among the studies. Publication bias was assessed using funnel plots and Egger's test. The random-effects model was used to estimate the pooled prevalence.

Results and conclusions

Of all the publications that were thoroughly searched, 9 studies with 2496 participants met the criteria for analysis. All of the studies were cross-sectionally designed and most of the studies used convenient sampling techniques. The included studies consisted of two conducted among adult patients diagnosed with CAP and living with HIV/AIDS, while the remaining seven studies were conducted among adult patients diagnosed with CAP without HIV/AIDS. The combined prevalence of bacterial causes of community-acquired pneumonia (CAP) among adult patients was found to be 39.18% (CI 36.34-42.02), with an I2 of 52.6 and a P value of 0.032. The primary bacterial cause was Klebsiella pneumoniae (9.1%), followed by Streptococcus pneumoniae (8.11%), and Staphylococcus aureus (6.8%). Therefore, it is advisable to introduce a diagnostic tool for identifying specific causative agents and drug resistance, which could lead to improved treatment and better patient outcomes by reducing the need for empirical treatments.

Prevalence of phenotypic multi-drug resistant Klebsiella species recovered from different human specimens in Ethiopia: A systematic review and meta-analysis

BACKGROUND

Multidrug-resistant (MDR) Klebsiella species are among public health important bacteria that cause infections difficult to treat with available antimicrobial agents. Infections with Klebsiella lead to high morbidity and mortality in developing countries particularly in patients admitted to the intensive care unit. This systematic review and meta-analysis aimed to determine the pooled prevalence of MDR Klebsiella species from different human specimens using studies conducted in Ethiopia from 2018-2022.

METHODS

We have systematically searched online databases such as PubMed/Medline, Google Scholar, Hinari, African journals online, Web of Science, Cochrane, and grey literature (Addis Ababa University and Hawassa University) to identify studies reporting the proportion of MDR Klebsiella species in Ethiopia. Published articles were selected based on the Preferred Reporting Item of Systematic Review and Meta-analysis (PRISMA). R-Studio version 4.2.3 was used to conduct pooled prevalence, heterogeneity test, and publication bias. A binary random effect model was used to determine the pooled prevalence. Heterogeneity was checked with the inconsistency index (I2). Publication bias was checked with a funnel plot and Egger test. Sensitivity analysis was conducted with leave-one-out analysis. Joanna Briggs Institute's critical appraisal tool for prevalence studies was used to check the quality of each article.

RESULTS

In this systematic review and meta-analysis, 40 articles were included in which 12,239 human specimens were examined. Out of the total specimens examined, 721 Klebsiella species were isolated and 545 isolates were reported to be MDR Klebsiella species. The prevalence of MDR Klebsiella species ranged from 7.3%-100% whereas the pooled prevalence of MDR Klebsiella species was 72% (95% CI: 63 - 82%, I2 = 95%). Sub-group analysis based on region revealed the highest prevalence of MDR from Addis Ababa (97%) and the least from the Somali region (33%); whereas sub-group analysis based on the specimen type indicated the highest prevalence was from blood culture specimens 96% and the least was from other specimens (ear and vaginal discharge, and stool) (51%).

CONCLUSION

Our finding indicated a high prevalence of MDR Klebsiella species found in different human specimens. The prevalence of MDR Klebsiella varies across regions in Ethiopia, age, the type of specimens, source and site of infection. Therefore, integrated action should be taken to reduce the prevalence of MDR Klebsiella species in regional states and focus on clinical features. Effective infection and prevention control should be applied to reduce the transmission within and outside health care settings.

Bacterial etiology, antimicrobial resistance and factors associated with community acquired pneumonia among adult hospitalized patients in Southwest Ethiopia

Background and Objectives

Antibiotic resistance is a significant problem that restricts the options for treating bacterial pneumonia. This research aimed to determine the bacterial causes of pneumonia and antibiotic resistance among hospitalized patients in southwest Ethiopia.

Materials and Methods

We collected and analyzed 150 sputum samples from individuals with community-acquired pneumonia from April 1st to October 30th, 2019. Standard bacteriological procedures were used to identify the bacteria. Kirby Bauer's disk diffusion method was used to assess the bacteria's susceptibility patterns. Production of carbapenemase and extended-spectrum-lactamase were confirmed phenotypically. Odds ratios and the chi-square test were computed.

Results

On the whole, bacterial pathogens were verified in 50% of the sputum samples. The predominant bacterial isolates were Klebsiella species, followed by Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pneumoniae. About 77.5% of isolates were multidrug resistant. Moreover, 40.5% and 10.8% of the isolates were ESBL and carbapenemase producers, respectively. Aging, tobacco smoking, previous history of pneumonia, heart disease, and chronic respiratory disease had association with sputum culture-positivity.

Conclusion

As a result, it is important to regularly monitor the bacterial etiologies and their patterns of resistance. Additionally, sociodemographic and clinical characteristics should all be taken into account while managing patients with pneumonia empirically in this context.

Gram-negative pulmonary infections - advances in epidemiology and diagnosis

PURPOSE OF REVIEW

Pulmonary infections due to Gram-negative organisms are increasing worldwide and traditional assumptions that these are limited to hospital and ventilator-acquired pneumonia are rapidly falling away. Accordingly, empiric antibiotic guidelines have to follow suit with ever broader spectrum choices in order to remain 'safe', as the Global prevalence of extensively resistant Gram-negative organisms inexorably increases. Rapid, multiplex PCR-based detection of a wide variety of potential pathogens offers the opportunity to replace empiric antibiotic choices with targeted, evidence-based therapy in clinically actionable timeframes.

RECENT FINDINGS

Here, we describe the data underpinning both the increasing global prevalence of Gram-negative pulmonary infections and their increasing antibiotic resistance. We also describe the performance, characteristics and early emerging clinical impact of already available rapid molecular diagnostic platforms and how they might best be deployed.

SUMMARY

It seems will likely be advantageous to replace the current trend for empiric prescription of increasingly broad-spectrum antibiotics with 'same day' evidence-based, targeted therapy using high performance, rapid molecular diagnostic solutions. Several challenges remain be overcome, however, to fully realize their clear potential for better, focussed deployment of antibiotics, improved patient outcomes and antibiotic stewardship.

Nasopharyngeal Carriage Rate of Streptococcus pneumoniae, Related Risk Factors, and Antibiotic Susceptibility Among Inmates in Hawassa Central Prison Institute: Hawassa, Sidama National Region, Ethiopia

Background

The bacterium Streptococcus pneumoniae commonly causes severe bacterial illnesses in both children and adults. S. pneumoniae is the most fatal bacterial pathogen, causing 50% of the deaths from lower respiratory infections in people of all ages.

Objectives

This study was aimed to determine a nasopharyngeal carriage rate of S. pneumoniae, related risk factors, and antibiotic susceptibility among prisoners in Hawassa Central Prison Institute Hawassa, Ethiopia.

Methods

From July to August 2021, a cross-sectional investigation was carried out in Hawassa prison. All randomly chosen adult volunteers were a part of the study. In this study, about 330 different people were included. Within 3 h of collection, the swab specimen was inoculated onto 5% sheep blood agar; the inoculated medium was then incubated for 18-24 h at 35-37 °C in a CO2-enriched environment. Following incubation, the S. pneumoniae colonies were suspected, but the usual colony shape, alpha-hemolysis, Gram staining, optochin susceptibility, and bile solubility test allowed for confirmation. Antimicrobial susceptibility testing was carried out in accordance with the Clinical and Laboratory Standards Institute's guidelines.

Results

Overall carriage rate of S. pneumoniae among adult individuals were 41 (12.7%). The carriage rate of S. pneumoniae was affected by age classes that 39-48 years (OR = 4.82, 95%CI = 1.49-15.56, p = .009), 49-58 years (OR = 5.27, 95%CI = 1.27-21.89, p = .022), and greater than 58 years (OR = 4.36, 95%CI = 1.13-16.90, p = .033); cigarette smoking (OR = 3.41, 95%CI = 1.16-10.01, p = .026); and sharing beds (OR = 3.91, 95%CI = 1.27-12.07, p = .018). The majority of the isolates are susceptible for clindamycin (87.8%) and resistant for chloramphenicol (56%). Multidrug resistance was observed in 36.7%.

Conclusions

The overall carriage rate of S. pneumoniae was 12.7%. Age, cigarette smoking, and sharing beds in the same prison room had a substantial impact on this nasopharyngeal carriage rate. Chloramphenicol (56%), erythromycin (41.5%), tetracycline (39%), and co-trimoxazole (34.1%) resistance were seen in the majority of S. pneumoniae isolates. Early detection, hygiene maintenance, and appropriate treatment are necessary.

Exploration of Streptococcus core genome to reveal druggable targets and novel therapeutics against S. pneumoniae

Streptococcus pneumoniae (S. pneumoniae), the major etiological agent of community-acquired pneumonia (CAP) contributes significantly to the global burden of infectious diseases which is getting resistant day by day. Nearly 30% of the S. pneumoniae genomes encode hypothetical proteins (HPs), and better understandings of these HPs in virulence and pathogenicity plausibly decipher new treatments. Some of the HPs are present across many Streptococcus species, systematic assessment of these unexplored HPs will disclose prospective drug targets. In this study, through a stringent bioinformatics analysis of the core genome and proteome of S. pneumoniae PCS8235, we identified and analyzed 28 HPs that are common in many Streptococcus species and might have a potential role in the virulence or pathogenesis of the bacteria. Functional annotations of the proteins were conducted based on the physicochemical properties, subcellular localization, virulence prediction, protein-protein interactions, and identification of essential genes, to find potentially druggable proteins among 28 HPs. The majority of the HPs are involved in bacterial transcription and translation. Besides, some of them were homologs of enzymes, binding proteins, transporters, and regulators. Protein-protein interactions revealed HP PCS8235_RS05845 made the highest interactions with other HPs and also has TRP structural motif along with virulent and pathogenic properties indicating it has critical cellular functions and might go under unconventional protein secretions. The second highest interacting protein HP PCS8235_RS02595 interacts with the Regulator of chromosomal segregation (RocS) which participates in chromosome segregation and nucleoid protection in S. pneumoniae. In this interacting network, 54% of protein members have virulent properties and 40% contain pathogenic properties. Among them, most of these proteins circulate in the cytoplasmic area and have hydrophilic properties. Finally, molecular docking and dynamics simulation demonstrated that the antimalarial drug Artenimol can act as a drug repurposing candidate against HP PCS8235_RS 04650 of S. pneumoniae. Hence, the present study could aid in drugs against S. pneumoniae.

Multi-drug resistant gram-negative bacterial pneumonia: etiology, risk factors, and drug resistance patterns

Bacterial pneumonia is one of the most serious public health issues owing to its medical and economic costs, which result in increased morbidity and mortality in people of all ages around the world. Furthermore, antimicrobial resistance has risen over time, and the advent of multi-drug resistance in GNB complicates therapy and has a detrimental impact on patient outcomes. The current review aimed to summarize bacterial pneumonia with an emphasis on gram-negative etiology, pathogenesis, risk factors, resistance mechanisms, treatment updates, and vaccine concerns to tackle the problem before it causes a serious consequence. In conclusion, the global prevalence of GNB in CAP was reported 49.7% to 83.1%, whereas in VAP patients ranged between 76.13% to 95.3%. The most commonly reported MDR-GNB causes of pneumonia were A. baumannii, K. pneumoniae, and P. aeruginosa, with A. baumannii isolated particularly in VAP patients and the elderly. In most studies, ampicillin, tetracyclines, amoxicillin-clavulanic acid, cephalosporins, and carbapenems were shown to be highly resistant. Prior MDR-GNB infection, older age, previous use of broad-spectrum antibiotics, high frequency of local antibiotic resistance, prolonged hospital stays, ICU admission, mechanical ventilation, and immunosuppression are associated with the MDR-GNB colonization. S. maltophilia was reported as a severe cause of HAP/VAP in patients with mechanically ventilated and having hematologic malignancy due to its ability of biofilm formation, site adhesion in respiratory devices, and its intrinsic and acquired drug resistance mechanisms. Effective combination therapies targeting PDR strains and drug-resistant genes, antibiofilm agents, gene-based vaccinations, and pathogen-specific lymphocytes should be developed in the future.

Inducible Clindamycin-Resistant Staphylococcus aureus Strains in Africa: A Systematic Review

Introduction

Excessive use of clindamycin enhances the acquisition of inducible clindamycin-resistant S. aureus strains, which is a significant health problem in Africa. The main objective of this review study was to determine the prevalence of inducible clindamycin resistance and related genes among S. aureus isolates in Africa.

Methods

A qualitative systematic review was conducted on inducible clindamycin resistance among S. aureus isolates in Africa using electronic databases such as Google Scholar and PubMed. Articles published in English before 2021 were selected, and relevant data were extracted, collected, and analyzed.

Results

In our search, 22 articles met the eligibility criteria for this review study. Of 3064 total S. aureus isolates, 605 had iMLSB phenotype. The overall prevalence of inducible clindamycin resistance in S. aureus isolates was 19.8% with a range of 2.9% to 44.0%. A high number of iMLSB phenotypes were observed in MRSA isolates (3.6–77.8%) than MSSA (0–58.8%). The overall prevalence of the iMLSB phenotype in MRSA strains was 26.8% (279/1041). The maximum peak prevalence of inducible clindamycin resistance among S. aureus isolates recorded in the continent was 44.0% in Egypt, followed by 35.8% in Libya and 33.3% in Uganda in 2017, 2007, and 2013, respectively. The highest prevalence of iMLSB phenotype in MRSA strains was reported in Egypt, 77.8%, followed by Nigeria, 75.0%, and Libya, 66.2%. Among the recovered drug-resistance genes, ermA, ermC, and msrA genes were commonly detected in Egypt with 67.9%, 70.0%, and 70.0% prevalence, respectively.

Conclusion

This review highlights a higher inducible resistance of S. aureus, including MRSA strains to clindamycin in the continent. Regular screening of these strains, wise use of clindamycin, and molecular detection and genotyping of resistant genes are urgent.