Phenotypic characterization of carbapenem non-susceptible gram-negative bacilli isolated from clinical specimens

The magnitude of MDR carbapenemase-producing Enterobacteriaceae isolates and associated factors among hospitalized patients of Northeast Ethiopia

Background

Currently, carbapenemase-producing Enterobacteriaceae (CPE) are becoming a global public health threat. Infections caused by these bacteria limit treatment options and are associated with high morbidity and mortality. This study aimed to assess the prevalence of CPE and identify associated risk factors.

Methods

A hospital-based cross-sectional study was conducted from June to August 2023. Clinical samples were cultured, and species identification was performed using standard biochemical tests. Antimicrobial susceptibility testing was done, and a modified carbapenem inactivation method was employed to confirm carbapenemase production. Data were entered using Epi Data and analysed with SPSS.

Results

From a total of 143 isolates, the most commonly identified species were Escherichia coli (62 isolates, 43.4%) and Klebsiella pneumoniae (39 isolates, 27.3%). The highest level of resistance was against ampicillin (138 isolates, 96.5%), whereas the lowest was observed with meropenem (19 isolates, 13.3%). Overall, 123 isolates (86.0%) were classified as MDR. The prevalence of CPE and carbapenem-resistant Enterobacteriaceae (CRE) was 5.7% and 8.1%, respectively. K. pneumoniae and E. coli were the most common carbapenemase producers. Chronic underlying disease, consuming raw vegetables, and lack of regular hand-washing habits before meals showed adjusted odds ratios of 7.9 (95% CI 1.9-31.5), 11 (95% CI 3.4-40) and 8.0 (95% CI 1.7-85), respectively, showing a significant association.

Conclusions

The high prevalence of CPE underscores the need for urgent infection control measures. Implementing antimicrobial stewardship, strengthening infection control measures, and further molecular studies are vital to combating this problem.

Prevalence of phenotypic drug resistance profiles and multi-drug-resistant Pseudomonas and Acinetobacter species recovered from clinical specimens in Ethiopia: a systematic review and meta-analysis

BACKGROUND

Antimicrobial-resistant Pseudomonas and Acinetobacter species are emerging as serious public health risks, both globally and in resource-limited countries such as Ethiopia. These microorganisms cause serious, life-threatening infections and are becoming increasingly resistant to commonly prescribed antibiotics. The high prevalence and resistance patterns of these bacteria need immediate action to inform treatment guidelines, increase infection control measure, and develop effective public health policies. This systematic review and meta-analysis aimed to assess the prevalence of phenotypic drug resistance profiles and multi-drug-resistant Pseudomonas and Acinetobacter species recovered from clinical specimens in Ethiopia.

METHODS

This systematic review and meta-analysis, which followed PRISMA principles, analyzed data from PubMed, Scopus, and Google Scholar to determine the prevalence and antibiotic resistance trends of Pseudomonas and Acinetobacter species in Ethiopia. Eligible studies were extracted by using Microsoft Excel and exported to STATA version 17 for analysis. The pooled prevalence was estimated using a random-effects model, and heterogeneity was examined using the I2 statistic. Publication bias was investigated using funnel plot analysis and Egger's test, and sensitivity analysis was used to assess the impact of individual studies on the total pooled findings.

RESULT

Of the 1,375 studies identified, 187 were eligible for qualitative analysis, leading to the inclusion of 65 studies in the meta-analysis. This analysis encompassed a total of 1,264 isolates, with 364 identified as Pseudomonas and Acinetobacter species. The systematic review revealed a pooled prevalence of 19.12% (95% CI: 14.86-23.38) for Pseudomonas species and 12.46% (95% CI: 5.82-19.10) for Acinetobacter species. The combined prevalence of both pathogens was 25.31 (95% CI: 18.61-32.00) with substantial heterogeneity (I2 = 93.6%, p < 0.001). across the studies. Pseudomonas exhibited high resistance rates to amoxicillin-clavulanic Acid (83.73%) and tetracycline (89.15%), while Acinetobacter showed 87.21% resistance to tetracycline and 79.72% to ceftriaxone. The overall pooled prevalence of MDR Pseudomonas species was 72.73% (95% CI: 67.02-78.44), and for Acinetobacter species, it reached 84.69% (95% CI: 78.78-90.59), respectively. Moreover, the pooled prevalence of MDR for both species isolated from clinical samples in Ethiopia was 74.79% (95% CI: 70.14-79.43), with significant heterogeneity (I2 = 99.7%, p < 0.001) across the studies.

CONCLUSION

The pooled prevalence of Pseudomonas and Acinetobacter species and their antibiotic resistance were alarmingly high in clinical samples in Ethiopia. These findings highlight the crucial need for more antimicrobial surveillance, stronger stewardship programs, and targeted research to combat the growing threat of resistance. Strategic public health policies are required to decrease these pathogens.

Prevalence of genes encoding carbapenem-resistance in Klebsiella pneumoniae recovered from clinical samples in Africa: systematic review and meta-analysis

BACKGROUND

The potential of Klebsiella pneumoniae (K. pneumoniae) to acquire and spread carbapenem-resistant genes is the most concerning characteristic of the bacteria. In hospitals and other healthcare settings, multidrug-resistant K. pneumoniae can be prevalent and cause severe infections, posing significant challenges to patient management. Studying genetic variants and drug-resistant mutations in pathogenic bacteria of public health importance is essential. Therefore, this study aimed to assess the overall prevalence of carbapenemase-encoding genes in K. pneumoniae across Africa.

METHODS

All studies published between January 2010, and December 2023, were retrieved from the electronic databases PubMed, Science Direct, and Scopus, as well as through the Google Scholar search engine. This systematic review and meta-analysis adhered strictly to the PRISMA guidelines. Data analysis was performed using STATA version 17. The quality of the included studies was critically evaluated using the "Joanna Briggs Institute" criteria. To evaluate heterogeneity among the studies, inverse variance (I2) tests were utilized. Subgroup analysis was conducted when heterogeneity exists among studies. To assess publication bias, we used a funnel plot and Egger's regression test. A random effects model was used to calculate the weighted pooled prevalence of genetic variants associated with carbapenem resistance in K. pneumoniae.

RESULTS

A total of 49 potential studies were included in this systematic review and meta-analysis, encompassing 8,021 K. pneumoniae isolates. Among these isolates, 2,254 (28.1%) carbapenems-resistance-conferring genes were identified. The overall pooled prevalence of carbapenemase-encoding genes in K. pneumoniae isolated from clinical specimens across Africa was found to be 34.0% (95% CI: 26.01-41.98%). Furthermore, the pooled prevalence of the carbapenemase genes blaOXA-48 and blaNDM-1 was 16.96% (95% CI: 12.17-21.76%) and 15.08% (95% CI: 9.79-20.37%), respectively. The pooled prevalence of carbapenemase genes in K. pneumoniae isolates from clinical samples across Africa increased over time, reported as 20.4%(-0.7-41.4%) for 2010-2015, 34.5% (20.2-48.8%) for 2016-2020, and 35.2% (24.8-45.5%) for 2021-2023, with heterogeneity (I2) values of 36.5%, 96.7%, and 99.3%, respectively.

CONCLUSIONS

The emergence and spread of carbapenemase-encoding genes in K. pneumoniae pose a major threat to public health. Knowledge on the genetic mechanisms of carbapenem resistance is crucial for developing effective strategies to combat these multidrug-resistant infections and reduce their impact on healthcare systems. The carbapenemase genes blaOXA-48 and blaNDM-1 were the most prevalent and showed an increasing trend over time.

Antimicrobial resistance pattern of Acinetobacter baumannii clinical isolate in Ethiopia. A systematic review and meta-analysis

BACKGROUND

Antimicrobial resistance (AMR) is a growing global health threat. Acinetobacter baumannii (A. baumannii) emerged as one of the most concerning critical priority pathogens due to its ability to develop resistance to multiple antimicrobial agents. In Ethiopia, the public health impact of AMR is increasingly significant, with A. baumannii responsible for a variety of infections. Although A. baumannii causes a range of infections in Ethiopian patients, the drug resistance status of the clinical isolates has not been thoroughly assessed. Therefore, this systematic review and meta-analysis aimed to determine the country-wide AMR of A. baumannii.

METHODS

This systematic review and meta-analysis followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We conducted a search of articles on PubMed, Web of Science, Science Direct, Scopes electronic databases, Google Scholar search engine, and institutional repositories/libraries for studies published between 2015 and 2024. Eligible studies on A. baumannii-related infections and AMR in Ethiopia were assessed for quality using the Joanna Briggs Institute (JBI) criteria. Data on study characteristics were extracted, and statistical analyses, including heterogeneity (Invers of variance), publication bias (Eggers test), and subgroup analyses, were performed using STATA 17.0. A random effect model was used to compute the pooled prevalence of AMR.

RESULTS

This systematic review and meta-analysis of 26 Ethiopian studies (26,539 participants) found an A. baumannii prevalence of 3.99% (95% CI: 3.01-4.98%) and 9.13% of all bacterial infections (95% CI: 6.73-11.54%). The most common infections were surgical site infections, urinary tract infections, pneumonia, and sepsis. Pooled resistance to antibiotics varied, with amikacin showing the lowest resistance (20.27%) (95% CI: 11.51-29.03) and cefotaxime the highest (83.18) (95% CI: 71.87-94.48). A pooled multi-drug resistant (MDR) A. baumannii was found in 88.22% (95% CI: 82.28-94.15) of isolates, with regional and infection-type variations, particularly in higher prevalence in Oromia and Amhara regions and sepsis cases.

CONCLUSION

This systematic review underscores the alarming rise of antimicrobial resistance in A. baumannii, particularly against carbapenems. The findings highlight a high prevalence of MDR A. baumannii and widespread extended-spectrum beta-lactamase production, with notable regional variations in resistance patterns. These high resistance rates reinforce A. baumannii as a critical global health threat, necessitating urgent interventions such as enhanced antimicrobial stewardship programs, improved infection control measures, and the development of alternative treatment strategies. Healthcare professionals, policymakers, and researchers must collaborate to mitigate the clinical and public health impact of this pathogen.

PROTOCOL REGISTRATION

This systematic review and meta-analysis was registered on PROSPERO (Registration ID: CRD42024623927).

Evaluating the Performance of Two Rapid Immunochromatographic Techniques for Detecting Carbapenemase in Carbapenem-Resistant Enterobacterales Clinical Isolates

Introduction

The rapid and accurate identification of carbapenemases in Enterobacterales isolates is of paramount importance for the selection of effective antibiotics and the control of hospital-acquired infections.

Methods

This study aimed to evaluate the performance of two immunochromatographic methods, NG-Test Carba 5 (Carba 5) and Goldstream Carbapenem-resistant K.N.I.V.O. Detection K-Set (K-Set) for detecting five major carbapenemase (KPC, NDM, IMP, OXA-48-like, and VIM). Carbapenemase genes were confirmed by PCR.

Results

In this study, a total of 245 carbapenem-resistant Enterobacterales (CRE) isolates were encompassed, with an overwhelming 96.7% of these strains exhibiting the ability to produce carbapenemase. A total of 58.2% of Klebsiella pneumoniae strains that produce KPC carbapenemase were the most prevalent among carbapenem-resistant Enterobacteriaceae (CRE). NDM-producing Klebsiella pneumoniae accounted for 30.4%. Importantly, NDM-type carbapenemase emerges as the predominant form in Escherichia coli and Enterobacter cloacae strains, accounting for 46 (93.9%) and 20 (83.3%) cases, respectively. The performance of the two methods in carbapenemase detection has demonstrated remarkable outcomes, exhibiting overall specificity and sensitivity exceeding 99%. Specifically, the K-Set accurately detected a unique KPC-carbapenemase in K. pneumoniae, whereas Carba 5 was unable to identify it. This was due to the presence of a novel bla KPC gene, which harbored a specific point mutation (A to G) at nucleotide position 787, differentiating it from the bla KPC-33 gene.

Conclusion

These two methods, characterized by their simplicity, rapidity, and accuracy, are ideally suited for detecting carbapenemases in routine microbiology laboratories. They serve as a vital foundation for the rational selection of antibiotics in clinical practice.

Current trends in the epidemiology of multidrug-resistant and beta-lactamase-producing Pseudomonas aeruginosa in Asia and Africa: a systematic review and meta-analysis

Pseudomonas aeruginosa continues to be a significant contributor to high morbidity and mortality rates worldwide, particularly due to its role in severe infections such as hospital-acquired conditions, including ventilator-associated pneumonia and various sepsis syndromes. The global increase in antimicrobial-resistant (AMR) P. aeruginosa strains has made these infections more difficult to treat, by limiting the effective drug options available. This systematic review and meta-analysis aim to provide an updated summary of the prevalence of AMR P. aeruginosa over the past 5 years. A systematic search was performed across three major electronic databases-PubMed, ScienceDirect, and Web of Science-yielding 40 eligible studies published between 2018 and 2023. Using a random-effects model, our meta-analysis estimated that the overall prevalence of P. aeruginosa in Asia and Africa over the past 5 years was 22.9% (95% CI [14.4-31.4]). The prevalence rates for multidrug-resistant (MDR) and extensively drug-resistant (XDR) P. aeruginosa strains were found to be 46.0% (95% CI [37.1-55.0]) and 19.6% (95% CI [4.3-34.9]), respectively. Furthermore, the prevalence rates of extended-spectrum β-lactamase- and metallo-β-lactamase-producing P. aeruginosa were 33.4% (95% CI [23.6-43.2]) and 16.0% (95% CI [9.8-22.3]), respectively. Notably, resistance rates to β-lactams used for treating pseudomonal infections were alarmingly high, with rates between 84.4% and 100.0% for cephalosporins, and over 40% of P. aeruginosa isolates showed resistance to penicillins. Our analysis identified the lowest resistance rates for last-resort antimicrobials, with 0.3% (95% CI [0.0-1.3]) resistance to polymyxin B and 5.8% (95% CI [1.5-10.2]) to colistin/polymyxin E. The low resistance rates to polymyxins suggest that these antibiotics remain effective against MDR P. aeruginosa. However, the findings also highlight the critical public health threat posed by antimicrobial-resistant P. aeruginosa, particularly concerning β-lactam antibiotics. This underscores the need for effective and carefully planned intervention strategies, including the development of new antibiotics to address the growing challenge of resistance. Developing robust antibiotic treatment protocols is essential for better management and control of pseudomonal infections globally. Therefore, continued research and international collaboration is vital to tackle this escalating public health challenge. This study protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO), under registration number CRD42023412839.

Phenotypic identification of Metallo-ß- lactamase resistance Gram negative bacteria from a clinical specimen in Sidama, Ethiopia

BACKGROUND

Metallo-beta lactamase resistance is one of the carbapenem resistances that worsen the world nowadays. A new variant of carbapenem-resistant has only limited reports from Africa including Ethiopia. This study aimed to determine Metallo -ß- lactamase resistance Gram-negative bacteria in Hawassa University Comprehensive Specialized Hospital January-June 2023.

METHOD

A cross-sectional study was conducted in which consecutive patients infected with Gram-negative bacteria were included in the study. A structured questionnaire was used to collect the data with oriented nurses if the patients/or caregivers gave consent to participate in the study. Clinical specimens are processed based on the standard operating procedure of the Microbiology laboratory and Clinical laboratory standard institute guidelines. Culture and sensitivity testing was used to isolate the bacteria. Gram staining and biochemical tests was used to identify the bacteria to genus and species. Kirby disc diffusion technique was used to determine the susceptibility of antibiotics. Statistical Software for Social Science (SPSS) version 21 is used for data entry and analysis. Descriptive statistics and logistic regression were used to interpret the data. The odds ratio at 95% confidence interval (CI) and p-value < 0.05 were taken as a statistically significant association.

RESULT

Our study included 153 isolates from different specimens, 83 (54.2%) were from male patients and 70 (45.8%) were from females. Klebsiella pneumonia was the predominant 43, followed by Escherichia coli 32, Acinetobacter spp 25, Pseudomonas spp 15, Enterobacter agglomerus 9, Klebsiella ozaenae 6, Enterobacter cloacae 5, Klebsiella oxytoca 4, (Klebsiella rhinoscleromatis, Proteus mirabilis and Morganella morganii) 3, Providencia stuartii 2 and (Citrobacter spp & Proteus vulgaris) 1. The rates of multi, extensive and pan-drug resistance bacteria accounted for 128/153 (83.7%), 77 /153(50.3%), and 26/153 (17.0%), respectively. Carbapenem resistance was 21 (13.7%), of this 7.2% were Enterobacteriaceae, 5.2% were Acetinobacter spp. and 1.3% Pseudomonas spp. Metallo-beta-lactamase was 17 (11.1%), of this, Enterobacteriaceae were 9(5.9%), Acetinobacter spp. 7(4.6%), and Pseudomonas spp. 1(0.7%). There were no variables statistically significantly associated with metallo-beta-lactamase-resistant.

CONCLUSION

Our study revealed that Metallo-beta-lactamase resistance was circulating in the study area. There was a high rate of carbapenem resistance, multi, extensive and pan-drug resistance. Therefore, a measure should be taken to alleviate the emerging threat that leaves the patients without the option of treatment.

Antimicrobial resistance profile, biofilm forming capacity and associated factors of multidrug resistance in Pseudomonas aeruginosa among patients admitted at Tikur Anbessa Specialized Hospital and Yekatit 12 Hospital Medical College in Addis Ababa, Ethiopia

BACKGROUND

Pseudomonas aeruginosa is one of the leading causes of nosocomial infections and the most common multidrug-resistant pathogen. This study aimed to determine antimicrobial resistance patterns, biofilm-forming capacity, and associated factors of multidrug resistance in P. aeruginosa isolates at two hospitals in Addis Ababa, Ethiopia.

METHODS

A cross-sectional study was conducted from August 2022 to August 2023 at Tikur Anbessa Specialized Hospital and Yekatit 12 Hospital Medical College. Culture and identification of P. aeruginosa were done using standard microbiological methods. An antimicrobial susceptibility test was done by Kirby-Bauer disk diffusion according to CLSI recommendations. The microtiter plate assay method was used to determine biofilm-forming capacity. SPSS version 25 was used for data analysis. Bivariate and multivariable logistic regression were used to assess factors associated with multidrug resistance in P. aeruginosa. The Spearman correlation coefficient (rs = 0.266)) was performed to evaluate the relationship between biofilm formation and drug resistance.

RESULTS

The overall prevalence of P. aeruginosa was 19.6%. High levels of resistance were observed for ciprofloxacin (51.8%), ceftazidime (50.6%), and cefepime (48.2%). The level of multidrug-resistance was 56.6%. The isolates showed better susceptibility to ceftazidime-avibactam (95.2%) and imipenem (79.5%). Overall, 95.2% of P. aeruginosa were biofilm-producing isolates, and 27.7% and 39.8% of isolates were strong and moderate biofilm producers, respectively. A positive correlation and statistically significant relationship was observed between resistance to multiple drugs and the level of biofilm formation (rs = 0.266; p-value = 0.015). Previous history of exposure to ciprofloxacin (OR, 5.1; CI, 1.12-24.7, p-value, 0.032) was identified as an independent associated factor for multidrug resistance in P. aeruginosa.

CONCLUSION

The present study indicates an association between multidrug resistance in P. aeruginosa and its biofilm formation capabilities. Additionally, over half of the isolates were resistant to multiple drugs, with prior use of ciprofloxacin linked to the development of multidrug-resistance. These findings suggest that antibiotic stewardship programs in hospital settings may be beneficial in addressing resistance.

Carbapenemase producing Gram negative bacteria: Review of resistance and detection methods

Gram negative bacilli that are carbapenem resistant have emerged and are spreading worldwide. Infections caused by carbapenem resistant isolates posses a significant threat due to their high morbidity and mortality rates. Carbapenemases production by multi-drug resistant pathogens severely restricts treatment choices for illnesses caused by bacteria that are resistant to both carbapenems and majority of β-lactam antibiotics. Various phenotypic and genotypic methods for identification can distinguish between different classes of carbapenemase and identify pathogens that are resistant to carbapenems. The establishment of a quick, accurate and reliable test for identifying the clinical strains that produce the carbapenemase enzyme is essential for optimum diagnosis of microbial pathogens and management of the global rise in the prevalence of carbapenemase producing bacterial strains. The aim of this review was to summarize the mechanisms of carbapenem resistance and to provide an overview of different carbapenemase detection methods for carbapenem resistant Gram negative bacilli.

Cell morphology as biomarker of carbapenem exposure

Characterizing the physiological response of bacterial cells to antibiotics is crucial for designing diagnostic techniques, treatment choices, and drug development. While bacterial cells at sublethal doses of antibiotics are commonly characterized, the impact of exposure to high concentrations of antibiotics on bacteria after long-term serial exposure and their effect on withdrawal need attention for further characterization. This study investigated the effect of increasing imipenem concentrations on carbapenem-susceptible (S) and carbapenem-resistant (R) E. coli on their growth adaptation and cell surface structure. We exposed the bacterial population to increasing imipenem concentrations through 30 exposure cycles. Cell morphology was observed using a 3D laser scanning confocal microscope (LSCM) and transmission electron microscope (TEM). Results showed that the exposure resulted in significant morphological changes in E. coli (S) cells, while minor changes were seen in E. coli (R) cells. The rod-shaped E. coli (S) gradually transformed into round shapes. Further, the exposed E. coli (S) cells' surface area-to-volume ratio (SA/V) was also significantly different from the control, which is non-exposed E. coli (S). Then, the exposed E. coli (S) cells were re-grown in antibiotic-free environment for 100 growth cycles to determine if the changes in cells were reversible. The results showed that their cell morphology remained round, showing that the cell morphology was not reversible. The morphological response of these cells to imipenem can assist in understanding the resistance mechanism in the context of diagnostics and antibacterial therapies.

Prevalence of multidrug resistance Salmonella species isolated from clinical specimens at University of Gondar comprehensive specialized hospital Northwest Ethiopia: A retrospective study

BACKGROUND

Multidrug resistance Salmonellosis remains an important public health problem globally. The disease is among the leading causes of morbidity and mortality in developing countries, but there have been limited recent studies about the prevalence, antimicrobial resistance, and multidrug resistance patterns of Salmonella isolates from various clinical specimens.

OBJECTIVE

Aimed to assess the prevalence, antimicrobial resistance, and multidrug resistance patterns of Salmonella isolates from clinical specimens at the University of Gondar Comprehensive Specialised Hospital, northwestern Ethiopia.

METHOD

A retrospective hospital-based cross-sectional study was conducted to determine the prevalence, antimicrobial resistance, and multidrug resistance patterns of isolated from all clinical specimens at the University of Gondar Salmonella Comprehensive Specialised Hospital from June 1st, 2017 to June 3rd, 2022. A total of 26,154 data points were collected using a checklist of records of laboratory registration. Clinical specimens were collected, inoculated, and incubated for about a week with visual inspection for growth and gram staining. The isolates were grown on MacConkey agar and Xylose Lysine Deoxycholate agar. Pure colonies were identified with a conventional biochemical test, and those unidentified at the species level were further identified by the analytical profile index-20E. Then, antimicrobial susceptibility was determined by the Kirby-Bauer disc diffusion technique. The multidrug resistance Salmonella isolates was identified using the criteria set by Magiorakos. Finally, the data was cleaned and checked for completeness and then entered into SPSS version 26 for analysis. Then the results were displayed using tables and figures.

RESULTS

Of the total 26,154 Salmonella suspected clinical samples, 41 (0.16%) Salmonella species were isolated. Most of the Salmonella isolates, 19 (46.3%), were in the age group of less than 18 years, followed by the age group of 19-44 years, 11 (26.8%). In this study, S. enterica subsp. arizonae accounts for the highest 21 (51%), followed by S. paratyphi A 9 (22%). Of the Salmonella isolates, S. typhi were highly resistant to ampicillin (100%), followed by tetracycline and trimethoprim-sulfamethoxazole, each accounting for 83.3%. Furthermore, S. paratyphi A was resistant to ampicillin (100%), tetracycline (88.9%), and chloramphenicol (88.9%). The overall multi-drug resistance prevalence was 22 (53.7%; 95% CI: 39.7-61). Accordingly, S. paratyphi A was 100% multidrug-resistant, followed by S. typhi (66.6%).

CONCLUSION

A low prevalence of Salmonella species was observed in the past six years. Moreover, most S. typhi and S. paratyphi strains in the study area were found to be resistant to routinely recommended antibiotics like ciprofloxacin and ceftriaxone, compared to what was reported earlier. In addition, all isolates of S. paratyphi A and the majority of S. typhi were multidrug resistant. Therefore, health professionals should consider antimicrobial susceptibility tests and use antibiotics with caution for Salmonellosis management.

Prevalence of meropenem-resistant Pseudomonas Aeruginosa in Ethiopia: a systematic review and meta‑analysis

INTRODUCTION

Antimicrobial resistance (AMR) is a pressing global health concern, particularly pronounced in low-resource settings. In Ethiopia, the escalating prevalence of carbapenem-resistant Pseudomonas aeruginosa (P. aeruginosa) poses a substantial threat to public health.

METHODS

A comprehensive search of databases, including PubMed, Scopus, Embase, Hinari, and Google Scholar, identified relevant studies. Inclusion criteria encompassed observational studies reporting the prevalence of meropenem-resistant P. aeruginosa in Ethiopia. Quality assessment utilized JBI checklists. A random-effects meta-analysis pooled data on study characteristics and prevalence estimates, with subsequent subgroup and sensitivity analyses. Publication bias was assessed graphically and statistically.

RESULTS

Out of 433 studies, nineteen, comprising a total sample of 11,131, met inclusion criteria. The pooled prevalence of meropenem-resistant P. aeruginosa was 15% (95% CI: 10-21%). Significant heterogeneity (I2 = 83.6%) was observed, with the number of P. aeruginosa isolates identified as the primary source of heterogeneity (p = 0.127). Subgroup analysis by infection source revealed a higher prevalence in hospital-acquired infections (28%, 95% CI: 10, 46) compared to community settings (6%, 95% CI: 2, 11). Geographic based subgroup analysis indicated the highest prevalence in the Amhara region (23%, 95% CI: 8, 38), followed by Addis Ababa (21%, 95% CI: 11, 32), and lower prevalence in the Oromia region (7%, 95% CI: 4, 19). Wound samples exhibited the highest resistance (25%, 95% CI: 25, 78), while sputum samples showed the lowest prevalence. Publication bias, identified through funnel plot examination and Egger's regression test (p < 0.001), execution of trim and fill analysis resulted in an adjusted pooled prevalence of (3.7%, 95% CI: 2.3, 9.6).

CONCLUSION

The noteworthy prevalence of meropenem resistance among P. aeruginosa isolates in Ethiopia, particularly in healthcare settings, underscores the urgency of implementing strict infection control practices and antibiotic stewardship. Further research is imperative to address and mitigate the challenges posed by antimicrobial resistance in the country.

Epidemiology, risk factors, and clinical outcomes of carbapenem-resistant Enterobacterales in Africa: A systematic review

OBJECTIVES

Carbapenem-resistant Enterobacterales (CRE) commonly cause hospital-acquired infections and hospital outbreaks worldwide, with an alarming increase in Africa, necessitating review of regional CRE epidemiological trends.

METHODS

A systematic review was conducted using PRISMA guidelines, searching PubMed, Scopus and Web of Science databases for studies describing CRE distribution, risk factors for CRE acquisition and clinical outcome of CRE infections in Africa.

RESULTS

One-hundred and sixty-nine studies were included, with the majority from North Africa (92/169, 54.4%). Most studies (136/169; 80.4%) focused only on infection, with a total of 15666 CRE isolates (97.4% clinical infection, 2.6% colonisation). The leading bacterial species included Klebsiella (72.2%), Escherichia coli (13.5%), and Enterobacter (8.3%). The most frequently detected carbapenemases were NDM (43.1%) and OXA-48-like (42.9%). Sequence types were reported in 44 studies, with ST101 and ST147 most commonly reported in K. pneumoniae, and ST410, ST167 and ST38 in E. coli. Previous antibiotic use, prior hospitalisation, surgical procedures, indwelling devices, intensive care unit admission and prolonged hospital stay, were the most frequent factors associated with CRE infection/colonisation. Crude mortality for CRE infection was 37%.

CONCLUSION

Although K. pneumoniae and E. coli remain the most frequent CRE in Africa, observed sequence types are not the commonly reported global 'high-risk' clones. The distribution of species and carbapenemases differs across African regions, while risk factors for CRE colonisation/infection, and patient outcomes are similar to those reported globally. There are limited data on CREs from parts of Africa, highlighting the need to strengthen epidemiologic surveillance programmes in the region.

Prevalence of carbapenem resistance in Acinetobacter baumannii and Pseudomonas aeruginosa in sub-Saharan Africa: A systematic review and meta-analysis

Carbapenems are effective drugs against bacterial pathogens and resistance to them is considered a great public health threat, especially in notorious nosocomial pathogens like Acinetobacter baumannii and Pseudomonas aeruginosa. In this study, we aimed to determine the prevalence of carbapenem resistance in A. baumannii and P. aeruginosa infections in Sub-Saharan Africa. Databases (PubMed, Scopus, Web of Science, and African Journal Online) were systematically searched following the Preferred Reporting Items for Systematic review and meta-analysis protocols (PRISMA-P) 2020 statements for articles reporting carbapenem-resistant Acinetobacter baumannii (CRAB) and carbapenem-resistant Pseudomonas aeruginosa (CRPA) prevalence between 2012 and 2022. Pooled prevalence was determined with the random effect model and funnel plots were used to determine heterogeneity in R. A total of 47 articles were scanned for eligibility, among which 25 (14 for carbapenem-resistant A. baumannii and 11 for carbapenem-resistant P. aeruginosa) were included in the study after fulfilling the eligibility criteria. The pooled prevalence of CRPA in the present study was estimated at 8% (95% CI; 0.02-0.17; I2 = 98%; P <0.01). There was high heterogeneity (Q = 591.71, I2 = 98.9%; P<0.0001). In addition, this study's pooled prevalence of CRAB was estimated at 20% (95% CI; 0.04-0.43; I2 = 99%; P <0.01). There was high heterogeneity (Q = 1452.57, I2 = 99%; P<0.0001). Also, a funnel plot analysis of the studies showed high degree of heterogeneity. The carbapenemase genes commonly isolated from A. baumannii in this study include blaOXA23, blaOXA48, blaGES., blaNDM, blaVIM, blaOXA24, blaOXA58, blaOXA51, blaSIM-1, blaOXA40, blaOXA66, blaOXA69, blaOXA91, with blaOXA23 and blaVIM being the most common. On the other hand, blaNDM, blaVIM, blaIMP, blaOXA48, blaOXA51, blaSIM-1, blaOXA181, blaKPC, blaOXA23, blaOXA50 were the commonly isolated carbapenemase genes in P. aeruginosa, among which blaVIM and blaNDM genes were the most frequently isolated. Surveillance of drug-resistant pathogens in Sub-Saharan Africa is essential in reducing the region's disease burden. This study has shown that the region has significantly high multidrug-resistant pathogen prevalence. This is a wake-up call for policymakers to put in place measures to reduce the spread of these critical priority pathogens.

Drug resistance and extended-spectrum β-lactamase (ESBLs) - producing Enterobacteriaceae, Acinetobacter and Pseudomonas species from the views of one-health approach in Ethiopia: a systematic review and meta-analysis

BACKGROUND

Although antimicrobial resistance (AMR) bacteria present a significant and ongoing public health challenge, its magnitude remains poorly understood, especially in many parts of the developing countries. Hence, this review was conducted to describe the current pooled prevalence of drug resistance, multidrug- resistance (MDR), and Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, Acinetobacter, and Pseudomonas species in humans, the environment, and animals or food of animal origin in Ethiopia.

METHODS

PubMed, Google Scholar, and other sources were searched for relevant articles as per the preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines. A critical appraisal for screening, eligibility, and inclusion in the meta-analysis was made based on the Joanna Briggs Institute's (JBI) essential appraisal tools. The meta-analysis was done on Statistical Software Package (STATA) version 17.0.

RESULTS

A total of 33 research articles were included in this systematic review and meta-analysis. Escherichia coli, Klebsiella species, Acinetobacter, and Pseudomonas species were the most frequently reported bacteria from two or more sources. More than 50% of Klebsiella species and 25% to 89% of Escherichia coli from two or more sources were resistant to all analysed antibiotics, except carbapenems. Fifty-five percent (55%) to 84% of Acinetobacter species and 33% to 79% of Pseudomonas species from human and environmental sources were resistant to all analyzed antibiotics. Carbapenem resistance was common in Acinetobacter and Pseudomonas species (38% to 64%) but uncommon in Enterobacteriaceae (19% to 44%). Acinetobacter species (92%), Klebsiella species (86%), and Pseudomonas species (79%) from human sources, and Proteus species (92%), and Acinetobacter species (83%), from environmental sources, were the common multidrug-resistant isolates. About 45% to 67% of E. coli, Klebsiella, Acinetobacter, and Pseudomonas species from human and environmental sources were ESBL producers.

CONCLUSION

Our review report concluded that there was a significant pooled prevalence of drug resistance, MDR, and ESBL-producing Enterobacteriaceae, Acinetobacter, and Pseudomonas species from two or more sources. Hence, our finding underlines the need for the implementation of integrated intervention approaches to address the gaps in reducing the emergence and spread of antibiotic- resistant bacteria.

A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia

Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.

Prevalence of carbapenemase-producing Enterobacteriaceae from human clinical samples in Ethiopia: a systematic review and meta-analysis

INTRODUCTION

Carbapenemase-producing Enterobacteriaceae are by far the most public health and urgent clinical problems with antibiotic resistance. They cause longer hospital stays, more expensive medical care, and greater mortality rates. This systematic review and meta-analysis aimed to indicate the prevalence of carbapenemase-producing Enterobacteriaceae in Ethiopia.

METHODS

This systematic review and meta-analysis was conducted based on Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. Electronic databases like PubMed, Google Scholar, CINAHL, Wiley Online Library, African Journal Online, Science Direct, Embase, ResearchGate, Scopus, and the Web of Sciences were used to find relevant articles. In addition, the Joanna Briggs Institute quality appraisal tool was used to assess the quality of the included studies. Stata 14.0 was used for statistical analysis. Heterogeneity was assessed by using Cochran's Q test and I² statistics. In addition, publication bias was assessed using a funnel plot and Egger's test. A random effect model was used to estimate the pooled prevalence. Sub-group and sensitivity analysis were also done.

RESULTS

The overall pooled prevalence of carbapenemase-producing Enterobacteriaceae in Ethiopia was 5.44% (95% CI 3.97, 6.92). The prevalence was highest [6.45% (95% CI 3.88, 9.02)] in Central Ethiopia, and lowest [(1.65% (95% CI 0.66, 2.65)] in the Southern Nations and Nationalities People Region. In terms of publication year, 2017-2018 had the highest pooled prevalence [17.44 (95% CI 8.56, 26.32)] and 2015-2016 had the lowest [2.24% (95% CI 0.87, 3.60)].

CONCLUSION

This systematic review and meta-analysis showed a high prevalence of carbapenemase-producing Enterobacteriaceae. So, to alter the routine use of antibiotics, regular drug susceptibility testing, strengthening the infection prevention approach, and additional national surveillance on the profile of carbapenem resistance and their determining genes among Enterobacteriaceae clinical isolates are required.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO (2022: CRD42022340181).

A spectrum of non-spore-forming fermentative and non-fermentative Gram-negative bacteria: multi-drug resistance, extended-spectrum beta-lactamase, and carbapenemase production

Background

In developing countries, the co-existence of a high burden of infectious diseases caused by Gram-negative bacteria and the rapid increase and spread of multidrug-resistant bacteria have become a serious health threat.

Objective

Profiling of Gram-negative bacteria and determining the magnitude of their antimicrobial resistance among patients.

Results

A total of 175 non-spore-forming Gram-negative bacteria were isolated from 873 different clinical samples. Of a total of 175 bacteria, 154 (88%) were fermentative Gram-negative bacteria, while 21 (12%) were non-fermentative Gram-negative bacteria. E. coli with a frequency of 58.3% and K. pneumoniae with a frequency of 18.3% were the predominant fermentative Gram-negative bacteria, while P. aeruginosa 9 (5.1%) and A. baumannii 6 (3.4%) were the predominant non-fermentative Gram-negative bacteria. The highest percentage level of antibiotic resistance was seen against ampicillin (86%), and the lowest against meropenem (9.8). About 49 (28%) Gram-negative bacilli were positive for ESBLase. The overall prevalence rate of MDR bacteria was 80.5%, of which 100% of A. baumannii, 90.6% of K. pneumonia. Sixteen isolates were resistant to meropenem, out of which 11 tested for carbapenemase production. Five of the nine were metallo-lactamase producers, with the remaining four being serine carbapenemase producers.

Conclusion

The prevalence of Gram-negative bacterial infection was found to be 20%, with a significant proportion (80.0%) due to fermentative Gram-negative bacteria and the remaining 20% due to non-fermentative Gram-negative bacteria. The study has also demonstrated a high prevalence rate of MDR, ESBLase, and carbapenemase-producing Gram-negative bacteria. Antimicrobial resistance of Gram-negative bacteria should be monitored on a regular basis, and an effective infection control program should be implemented.

Bacteriological spectrum, extended-spectrum β-lactamase production and antimicrobial resistance pattern among patients with bloodstream infection in Addis Ababa

Bloodstream infection coupled with drug resistance in bloodborne bacteria is a major health problem globally. The current study sought to identify the bacterial spectrum, extended-spectrum -lactamase production, and antimicrobial resistance pattern in patients with bloodstream infection. This prospective cross-sectional study was conducted at Arsho Advanced Medical Laboratory, Addis Ababa, Ethiopia from January 2019- until July 2020. Blood collected from patients was inoculated into blood culture bottles and incubated appropriately. Identification, antimicrobial susceptibility testing, and extended-spectrum β-lactamase-production were determined with the VITEK 2 compact system. Of the samples collected, 156 (18.5%) were culture-positive. Klebsiella pneumoniae and Staphylococcus epidermidis were the dominant isolates. In Gram-negative bacteria, the prevalence of drug resistance was the highest against ampicillin (80.8%) and the lowest against imipenem (5.2%). While in Gram-positive bacteria it was the highest against clindamycin and the lowest against vancomycin and daptomycin. The prevalence of multi-drug resistance and extended-spectrum β-lactamase production of Gram-negative bacteria were 41.6% and 34.2%, respectively. The prevalence of bloodstream infection was 18.5%. Serious life-threatening pathogens including S. aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and Enterobacter spp was predominant. The prevalence of multi-drug resistance to both Gram-positive and Gram-negative bacteria and extended-spectrum β-lactamase-production were high but prevalence of carbapenem resistance was low. All these situations call for the establishment of strong infection control strategies, a drug regulatory system, and established antibiotic stewardship in healthcare settings.

Combating the menace of antimicrobial resistance in Africa: a review on stewardship, surveillance and diagnostic strategies

The emergence of antibiotic-resistant pathogens has threatened not only our ability to deal with common infectious diseases but also the management of life-threatening complications. Antimicrobial resistance (AMR) remains a significant threat in both industrialized and developing countries alike. In Africa, though, poor clinical care, indiscriminate antibiotic use, lack of robust AMR surveillance programs, lack of proper regulations and the burden of communicable diseases are factors aggravating the problem of AMR. In order to effectively address the challenge of AMR, antimicrobial stewardship programs, solid AMR surveillance systems to monitor the trend of resistance, as well as robust, affordable and rapid diagnostic tools which generate data that informs decision-making, have been demonstrated to be effective. However, we have identified a significant knowledge gap in the area of the application of fast and affordable diagnostic tools, surveillance, and stewardship programs in Africa. Therefore, we set out to provide up-to-date information in these areas. We discussed available hospital-based stewardship initiatives in addition to the role of governmental and non-governmental organizations. Finally, we have reviewed the application of various phenotypic and molecular AMR detection tools in both research and routine laboratory settings in Africa, deployment challenges and the efficiency of these methods.

Carbapenem-Resistant Gram-Negative Bacilli Causing Ventilator Associated Pneumonia: Study of MASTDISCS Combi Carba Plus for Detection of Carbapenemase Producing Enterobacterales

Background

Ventilator-associated pneumonia (VAP) caused by carbapenem-resistant gram-negative bacteria has been proven to be an escalating public health challenge in Egypt owing to its high mortality rate and raised health care costs.

Purpose

Detection of carbapenem-resistant gram-negative bacilli among VAP patients, genotypic identification of carbapenemase genes in the isolated strains with evaluation of their impact on patient outcome and detection of carbapenemase-producing enterobacterales by MASTDISCS combi Carba plus disc system.

Methods

Broncho-alveolar lavage fluid (BALF) and endotracheal aspirate were collected aseptically from clinically suspected VAP patients. Pathogen identification and antibiotic sensitivity testing were done. Carbapenemase-encoding genes (bla_KPC, bla_NDM, and bla_OXA-48) were tested by PCR in all carbapenem-resistant gram-negative isolates. Performance of MASTDISCS combi Carba plus in isolated Enterobacterales was assessed in relation to the PCR results.

Results

Eighty-three carbapenem-resistant gram-negative isolates were detected. The most frequent pathogens were Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa representing 34.9%, 20.5% and 18.1%, respectively. bla_KPC was the predominant gene. Patients with persistent mechanical ventilation less than 15 days and Pseudomonas aeruginosa infection were significantly associated with a higher death rate. MAST-Carba plus had the highest sensitivity, specificity, positive and negative predictive values for detecting OXA-48 carbapenemases representing 81.8%, 92.5%, 75% and 94.9%, respectively.

Conclusion

Worse outcome in VAP patients was associated with carbapenem-resistant gram-negative bacilli. MASTDISCS combi Carba plus is an efficient simple method for identification of different carbapenemases among enterobacterales.

One-Pot Isothermal LAMP-CRISPR-Based Assay for Klebsiella pneumoniae Detection

Klebsiella pneumoniae (K. pneumoniae) is one of the most common pathogens causing nosocomial infection. A rapid, accurate, and convenient detection method is required for early diagnosis and directed therapy of K. pneumoniae infection. CRISPR-top (CRISPR-mediated testing in one pot) is a LAMP-CRISPR-based nucleic acid detection platform, which integrates target preamplification with CRISPR/Cas12b-based detection into a one-pot reaction mixture, performed at a constant temperature. In this study, we established the K. pneumoniae CRISPR-top assay to precisely identify K. pneumoniae at 56°C within 60 min. The reaction mixture with 0.53 μM (each) FIP and BIP, 0.27 μM LF, 0.13 μM (each) F3 and B3, and 2 μM ssDNA fluorescence probe was determined as the optimal reaction system of our assay. The limit of detection of this assay is 1 pg genomic DNA (equivalent to 160 K. pneumoniae cells and 1.6 × 10⁵ CFU/mL for samples) per reaction, which is 10-fold more sensitive than LAMP. Up to 105 strains composed of K. pneumoniae clinical isolates and non-K. pneumoniae strains were correctly identified by our assay. A total of 58 sputum samples collected from patients with respiratory symptoms were used to evaluate the diagnostic performance of the K. pneumoniae CRISPR-top assay. As a result, the K. pneumoniae CRISPR-top assay yielded 100% (33/33) specificity and 96% (24/25) sensitivity, as well as a positive predictive value of 100% (24/24) and a negative predictive value of 97.1% (33/34), which were all higher than LAMP detection. In conclusion, the K. pneumoniae CRISPR-top assay developed in this study is a simple, rapid and ultra-specific method to detect K. pneumoniae.

IMPORTANCEKlebsiella pneumoniae is a significant threat to global health. At present, the methods of K. pneumoniae detection are culture-based and instrument-dependent and are not suitable for rapid diagnostic. This study reports K. pneumoniae CRISPR-top assay, which can precisely identify K. pneumoniae using nucleic acids of pure cultures or clinical samples in one pot with one fluid-handling step. The K. pneumoniae CRISPR-top reaction can be completed within 60 min at a constant temperature, thus specific instruments are not required. Our results show that CRISPR-top assay yields enormous advantages compared with LAMP detection. The K. pneumoniae CRISPR-top assay can be a high-efficiency alternative tool for rapid and accurate diagnosis of K. pneumoniae infection, especially in resource-limited settings.

What Doesn’t Kill Them Makes Them Stronger: The Impact of the Resistance Patterns of Urinary Enterobacterales Isolates in Patients from a Tertiary Hospital in Eastern Europe

(1) Background: The evolution of bacterial resistance to antibiotics is one of the factors that make infectious pathology an extremely dynamic field, also inducing a significant burden on public health systems; therefore, continuous updates on the bacterial resistance to antibiotics and their particular regional patterns is crucial for the adequate approach of various infectious diseases. (2) Methods: We retrospectively analyzed 354 patients with Enterobacterales urinary tract infections (UTIs), determined their antibiotic resistance pattern, thus aiming to correlate them with the outcome and other specific markers of poor prognosis. (3) Results: The most frequent causative agent was Escherichia coli, representing 64.6% of all UTIs. We identified 154 patients resistant to multiple antibiotic classes, of which 126 were multidrug-resistant (MDR), 17 were extensive drug-resistant (XDR) and 11 were pandrug-resistant (PDR). Moreover, 25 isolates were resistant to carbapenems (CRE), 25 were difficult-to-treat (DTR), and 84 were extended-spectrum cephalosporin-resistant (ESC), with only 95 isolates susceptible to all tested antibiotics. Mortality ranged from 1% for UTIs caused by isolates susceptible to all tested antibiotics, to 24% for the ones caused by DTR or CRE isolates. Other significant risk factors associated with mortality were: prolonged hospital stay (p = 0.0001), Charlson comorbidity index ≥ 3 (p = 0.02), urinary catheterization (p = 0.001), associated respiratory pathologies (p = 0.004), obesity (p = 0.047), a history of previous hospitalizations (p = 0.007), inappropriate empiric antibiotic regimen (p = 0.001), or hyper inflammatory status (p = 0.006). Basically, we observed that a multiple regression model comprising urinary catheterization, inappropriate empiric anti-biotherapy, obesity, and respiratory comorbidities exhibits the best correlation with mortality rate in patients with UTI (R = 0.347, R² = 0.12). (4) Conclusions: By focusing on the novel resistance patterns, our study provides complementary evidence concerning the resistance profiles found in an Eastern European region, as well as their prognostic implications in patients with UTI.

The Evaluation of Eazyplex® SuperBug CRE Assay Usefulness for the Detection of ESBLs and Carbapenemases Genes Directly from Urine Samples and Positive Blood Cultures

Increasing antimicrobial resistance of Gram-negative rods is an important diagnostic, clinical and epidemiological problem of modern medicine. Therefore, it is important to detect multi-drug resistant strains as early on as possible. This study aimed to evaluate Eazyplex^® SuperBug CRE assay usefulness for beta-lactamase gene detection among Gram-negative rods, directly from urine samples and positive blood cultures. The Eazyplex^® SuperBug CRE assay is based on a loop-mediated isothermal amplification of genetic material and allows for the detection of a selection of genes encoding carbapenemases, KPC, NDM, VIM, OXA-48, OXA-181 and extended-spectrum beta-lactamases from the CTX-M-1 and CTX-M-9 groups. A total of 120 clinical specimens were included in the study. The test gave valid results for 58 (96.7%) urine samples and 57 (95.0%) positive blood cultures. ESBL and/or carbapenemase enzymes genes were detected in 56 (93.3%) urine and 55 (91.7%) blood samples, respectively. The Eazyplex^® SuperBug CRE assay can be used for a rapid detection of the genes encoding the most important resistance mechanisms to beta-lactams in Gram-negative rods also without the necessity of bacterial culture.