Febrile illness of bacterial etiology in a public fever hospital in Egypt: High burden of multidrug resistance and WHO priority Gram negative pathogens

Prevalence, trends, and molecular insights into colistin resistance among gram-negative bacteria in Egypt: a systematic review and meta-analysis

BACKGROUND

This study examines colistin resistance in Gram-negative bacteria in Egypt, analyzing prevalence, trends, geographic variations, colistin-carbapenem resistance correlation, and mcr-mediated plasmid resistance.

METHODS

We conducted a systematic search of articles published between 2014 and 2024 that reported on colistin or mcr-mediated resistance in Gram-negative bacteria isolated from human infections in Egypt, with clearly defined susceptibility testing methods. A random-effects meta-analysis was conducted to estimate colistin resistance prevalence based on broth microdilution (BMD) findings, the gold standard method. To explore the influence of study-level factors-including alternative susceptibility testing methods-a multivariate meta-regression analysis was performed. The results of the meta-regression are reported as regression coefficients (β), representing the difference in colistin resistance, expressed in percentage points. All statistical analyses were conducted using R software.

RESULTS

This analysis included 55 studies. Based on BMD susceptibility testing, colistin resistance was observed in 9% of all recovered Gram-negative isolates (95% CI: 6-14%) and was significantly higher among carbapenem-resistant isolates (31%, 95% CI: 25-38%), with p < 0.001. Multivariate meta-regression analysis further confirmed that colistin resistance was significantly higher in carbapenem-resistant isolates compared to the total recovered isolates (β = 9.8% points, p = 0.001). Additionally, colistin resistance has significantly increased over time, with a β = 1.8% points per year (p = 0.001). The use of the VITEK 2 system was associated with lower detected colistin resistance compared to BMD (β = -7.0, p = 0.02). Geographically, resistance rates were higher in Upper Egypt (β = 9.3, p = 0.04). Regarding mcr plasmid-mediated resistance, mcr-1 was the most prevalent resistance gene, particularly in E. coli. In contrast, mcr-2 was rare, detected sporadically in K. pneumoniae and P. aeruginosa.

CONCLUSION

In Egypt, BMD testing identified colistin resistance in 9% of Gram-negative bacteria, increasing to 31% in carbapenem-resistant isolates. This higher resistance in carbapenem-resistant strains suggests stronger selective pressure from frequent colistin use. Additionally, colistin resistance has shown a rising trend over time, likely driven by increased usage and the spread of plasmid-mediated resistance. These findings underscore the urgent need for strict antimicrobial stewardship and alternative therapies to curb resistance evolution.

Deciphering hygromycin B biosynthetic pathway and D-optimal design for production optimization

Hygromycin B (HYG-B) is a 5-glycosylated 2-dexoystreptamine- aminoglycoside antibiotic-(2DOS-AGA) produced by Streptomyces hygroscopicus subspecies hygroscopicus NRRL ISP-5578 with broad-spectrum activity against many pathogenic bacteria, fungi and helminths. In the literature, limited studies are concerned with the biosynthetic pathway and different cultural conditions affecting the production of HYG-B. This study aimed to optimize key environmental conditions influencing its production as one-factor-at-a-time (OFAT) and as a statistical model of response surface D-optimal design (DOD). Moreover, the biosynthetic pathway of HYG-B in light of the identified genes/proteins of the HYG-B gene cluster was proposed and elucidated. The effect of culture media composition and incubation time were studied OFAT, and the results showed that both culture media 6 (CM6) and CM4 gave the highest specific productivity, 5.88 and 3.99 µg/mg, respectively, and 7 days as incubation time. So, using CM6 and 7 days incubation resulted in a sevenfold increase (190 µg/mL) compared to the original unoptimized condition (CM1 and 6 days incubation; 26.9 µg/mL). Three important factors-initial pH, incubation temperature, and agitation-were tested using a DOD quadratic model generating 20 experimental runs. An initial pH of 6.4, an incubation temperature, of 28 ℃, and agitation. of 295 rpm were predicted and experimentally verified, resulting in a 13-fold increase (371.5 µg/mL) compared to the unoptimized condition and a sevenfold increase compared to that obtained as OFAT. In conclusion, DOD design is an efficient tool for optimizing HYG-B. However, the optimized conditions should be scaled up in a bioreactor for industrial production of HYG-B by S. hygroscopicus NRRL ISP-5578.

Providencia pseudovermicola sp. nov.: redefining Providencia vermicola and unveiling multidrug-resistant strains from diabetic foot ulcers in Egypt

BACKGROUND

Providencia species are concerning due to their intrinsic resistance to colistin and tigecycline, complicating the treatment of multidrug-resistant (MDR) infections.

METHODS

In the current study, two MDR isolates, DFU6 and DFU52T, were recovered from infected diabetic foot ulcers in Egypt in 2024. Following their initial identification as Providencia stuartii using VITEK® 2 and MALDI-TOF-MS, the isolates were subjected to whole-genome sequencing via DNBseq.

RESULTS

While the 16S rRNA gene showed 100% similarity to that of Providencia vermicola, phylogenomic analysis against the type strains in the TYGS database, including P. vermicola DSM 17385T confirmed that these isolates represent a distinct species within the genus, further supported by overall genome-relatedness indices (ORGIs). This discrepancy prompted us to revise the taxonomy of all published genomes of P. vermicola strains (n = 59) which revealed misidentification of at least 56 strains that are unrelated to the type strain of this species. DFU6 and DFU52T carried novel sequence types (ST29 and ST41, submitted to PubMLST) and harbored multiple resistance genes. Both strains contained the qnrD1 gene on a small, non-mobilizable plasmid. DFU52T possessed a conjugative plasmid encoding blaCMY-6, blaNDM-1, rmtC, aac(6')-Ib10, sul1, aph(3')-Ia, and qacEΔ1. DFU6 carried an ISEcp1-associated blaCTX-M-14, along with aadA, dfrA1, lnuF in a class 2 integron, and armA, msrE, and mphE on a resistance plasmid. Both isolates also featured a pathogenicity island (PAI) integrated into the pheV gene with fimbriae-encoding genes.

CONCLUSION

Following our reassessment of the taxonomic classification of all P. vermicola strains with published genomes, we propose reclassifying certain strains, including DFU6 and DFU52T, into distinct species for which we propose the name Providencia pseudovermicola sp. nov. We recommend DFU52T (= CCASU-2024-72) as the type strain for the novel species. We also shed light on the public health threat of this novel species as a human pathogen that harbours carbapenem and aminoglycoside resistance genes on mobile genetic elements.

Response Surface D-Optimal Design for Optimizing Fortimicins Production by Micromonospora olivasterospora and New Synergistic Fortimicin-A-Antibiotic Combinations

Fortimicins (FTMs) are fortamine-containing aminoglycoside antibiotics (AGAs) produced by M. olivasterospora DSM 43868 with excellent bactericidal activities against a wide range of Enterobacteriaceae and synergistic activity against multidrug-resistant (MDR) pathogens. Fortimicin-A (FTM-A), the most active member of FTMs, has the lowest susceptibility to inactivation by the aminoglycoside modifying enzymes (AMEs). Therefore, this study aimed to evaluate the antibacterial activity of FTM-A alone or in combination with other antibiotics against 18 non-clonal clinically relevant MDR Gram-positive and Gram-negative pathogens. This study also aimed to statistically optimize various environmental factors affecting its production using the response surface D-optimal design. Results showed that FTM-A/meropenem combination showed the highest synergistic bactericidal activity (61.1%) followed by its combination with cefotaxime and cefepime (38.8% each). However, FTM-A/gentamicin and FTM-A/doxycycline combinations showed mostly additive effects in 66.6% and 50% of the tested isolates, respectively. For FTM-A production optimization, maximum specific activity (µg/mg) to cell growth was achieved using aminoglycoside production medium followed by yeast extract-malt extract and M65 production medium. A D-optimal quadratic model consisting of 27 different media composition variations was used to predict an optimal composition for FTM-A production and verified experimentally. Lab verification of the model was carried out using HPLC analysis, resulting in a 10.5-fold increase in their production compared to the un-optimized conditions. The model revealed that the initial pH, incubation temperature, and incubation time significantly affected FTMs production (P-value < 0.05), however, the tested range of calcium carbonate 2-7 gL-1 and agitation rate (100-300 rpm) showed no significant effect (P-value > 0.05). In conclusion, the D-optimal design resulted in an effective model and optimized FTMs production on the shake flask level. FTM-A combinations with meropenem, cefotaxime, cefepime, and gentamicin showed mostly synergistic/additive effects and are advised for clinical evaluation.

Geographical mapping and temporal trends of Acinetobacter baumannii carbapenem resistance: A comprehensive meta-analysis

BACKGROUND

Carbapenem-resistant Acinetobacter baumannii (CRAB) is of critical concern in healthcare settings, leading to limited treatment options. In this study, we conducted a comprehensive meta-analysis to assess the prevalence of CRAB by examining temporal, geographic, and bias-related variations.

METHODS

We systematically searched prominent databases, including Scopus, PubMed, Web of Science, and EMBASE. Quality assessment was performed using the JBI checklist. Subgroup analyses were performed based on the COVID-19 timeframes, years, countries, continents, and bias levels, antimicrobial susceptivity test method and guidelines.

RESULTS

Our comprehensive meta-analysis, which included 795 studies across 80 countries from 1995 to 2023, revealed a surge in carbapenem resistance among A. baumannii, imipenem (76.1%), meropenem (73.5%), doripenem (73.0%), ertapenem (83.7%), and carbapenems (74.3%). Temporally, 2020-2023 witnessed significant peaks, particularly in carbapenems (81.0%) and meropenem (80.7%), as confirmed by meta-regression, indicating a steady upward trend.

CONCLUSION

This meta-analysis revealed an alarmingly high resistance rate to CRAB as a global challenge, emphasizing the urgent need for tailored interventions. Transparency, standardized methodologies, and collaboration are crucial for the accurate assessment and maintenance of carbapenem efficacy.

Tracking Multidrug Resistance in Gram-Negative Bacteria in Alexandria, Egypt (2020-2023): An Integrated Analysis of Patient Data and Diagnostic Tools

BACKGROUND

The rise in carbapenem-resistant Enterobacteriaceae (CRE) in Egypt, particularly in hospital settings, poses a significant public health challenge. This study aims to develop a combined epidemiological surveillance tool utilizing the Microreact online platform (version 269) and molecular microarray technology to track and analyze carbapenem-resistant Escherichia coli strains in Egypt. The objective is to integrate molecular diagnostics and real-time data visualization to better understand the spread and evolution of multidrug-resistant (MDR) bacteria.

METHODS

The study analyzed 43 E. coli isolates collected from Egyptian hospitals between 2020 and 2023. Nanopore sequencing and microarray analysis were used to identify carbapenemase genes and other resistance markers, whereas the VITEK2 system was employed for phenotypic antibiotic susceptibility testing. Microreact was used to visualize epidemiological data, mapping the geographic and temporal distribution of resistant strains.

RESULTS

We found that 72.09% of the isolates, predominantly from pediatric patients, carried the blaNDM-5 gene, while other carbapenemase genes, including blaOXA-48 and blaVIM, were also detected. The microarray method demonstrated 92.9% diagnostic sensitivity and 87.7% diagnostic specificity compared to whole-genome sequencing. Phenotypic resistance correlated strongly with next-generation sequencing (NGS) genotypic data, achieving 95.6% sensitivity and 95.2% specificity.

CONCLUSIONS

This method establishes the utility of combining microarray technology, NGS and real-time data visualization for the surveillance of carbapenem-resistant Enterobacteriaceae, especially E. coli. The high concordance between genotypic and phenotypic data underscores the potential of DNA microarrays as a cost-effective alternative to whole-genome sequencing, especially in resource-limited settings. This integrated approach can enhance public health responses to MDR bacteria in Egypt.

Multiplex PCR assays developed for neglected pathogen detection in undifferentiated acute febrile illness cases in tropical regions

BACKGROUND

Undifferentiated acute febrile illness (UAFI) cause by several pathogens poses a diagnostic challenge due to the similarity on the clinical manifestations across these diseases. Precise pathogen detection is vital for appropriate medical intervention, early treatment, and timely outbreak alerts regarding emerging pathogens. In tropical regions, UAFI is predominantly linked to a wide range of viral, bacterial, and parasitic infections. Hence, confirmatory laboratory tests are essential for specific pathogen identification.

OBJECTIVES

Our primary goal was to develop two real-time multiplex polymerase chain reaction (PCR) assays for simultaneous detection of six neglected pathogens (Leptospira spp., Rickettsia spp., Borrelia spp., Anaplasma spp., Brucella spp., and Bartonella spp.), known for causing UAFI in tropical regions.

METHODS

We rigorously assessed assays parameters including: linearity, efficiency, sensitivity, and reproducibility in both singleplex and multiplex formats.

FINDINGS

Our results demonstrated that these multiplex assays are reliable and sensitive methods. They showed good performance with low intra- and inter-variability (< 10%) and consistently high efficiencies (> 90%).

MAIN CONCLUSIONS

These assays offer the alternative of streamlining work, reducing processing costs, and minimizing sample volume use. In conclusion, we present two dependable, user-friendly, rapid, and cost-effective methods for simultaneously detecting six neglected bacteria, as a significant laboratory tool in resource-limited tropical settings.

Central composite design for optimizing istamycin production by Streptomyces tenjimariensis

Istamycins (ISMs) are 2-deoxyfortamine-containing aminoglycoside antibiotics (AGAs) produced by Streptomyces tenjimariensis ATCC 31603 with broad-spectrum bactericidal activities against most of the clinically relevant pathogens. Therefore, this study aimed to statistically optimize the environmental conditions affecting ISMs production using the central composite design (CCD). Both the effect of culture media composition and incubation time and agitation rate were studied as one factor at the time (OFAT). The results showed that both the aminoglycoside production medium and the protoplast regeneration medium gave the highest specific productivity. Results also showed that 6 days incubation time and 200 rpm agitation were optimum for their production. A CCD quadratic model of 17 runs was employed to test three key variables: initial pH, incubation temperature, and concentration of calcium carbonate. A significant statistical model was obtained including, an initial pH of 6.38, incubation temperature of 30 ˚C, and 5.3% CaCO3 concentration. This model was verified experimentally in the lab and resulted in a 31-fold increase as compared to the unoptimized conditions and a threefold increase to that generated by using the optimized culture media. To our knowledge, this is the first report about studying environmental conditions affecting ISM production as OFAT and through CCD design of the response surface methodology (RSM) employed for statistical optimization. In conclusion, the CCD design is an effective tool for optimizing ISMs at the shake flask level. However, the optimized conditions generated using the CCD model in this study should be scaled up in a fermenter for industrial production of ISMs by S. tenjimariensis ATCC 31603 considering the studied environmental conditions that significantly influence the production proces.

Fosfomycin: A potential oral option for treatment of urinary tract infections in Sri Lanka in the context of high antibiotic resistance

Introduction

Fosfomycin is an effective treatment for urinary tract infections (UTIs). It is not currently used in Sri Lanka to treat UTIs. Hence, this study was conducted to assess the fosfomycin susceptibility for E. coli in urinary isolates, with an aim to find the usability of fosfomycin in the context of high antibiotic resistance.

Methods

E. coli isolates were identified by the colony appearance and by performing biochemical tests for the urinary coliform isolates collected from two different hospitals in Western Province Sri Lanka, during the period of November 2021 to February 2022. Susceptibility to fosfomycin 200 μg disc was performed following the Clinical Laboratory Standard Institute (CLSI) disc diffusion method.

Results

A total of 101 E. coli isolates from both oncology patients (52.5%) and non-oncology patients (47.5%) were identified and included in the study. The study sample showed majority of females (63.3%). Ampicillin showed the highest resistance rate (72.2%) while fosfomycin was the only antibiotic that showed 100% in vitro susceptibility to all the tested clinical isolates. The overall presence of multidrug-resistant (MDR) and carbapenem-resistant (CR) E. coli were 47.5% and 9.9% respectively.

Conclusions

Fosfomycin is a potential antibiotic option especially for MDR and CR organisms, with 100% in vitro susceptibility. Further studies involving multiple centers, with larger sample size and clinical efficacy studies would be important to assess the potential use of fosfomycin especially for the treatment of UTI-causing MDR and CR organisms.

Phenotypic and Genotypic Analysis of Bacterial Pathogens Recovered from Patients Diagnosed with Fever of Unknown Origin in Egypt

Fever of unknown origin (FUO) is a medical term describing fever that lasts for at least three weeks without a diagnosis being reached after extensive diagnostic evaluation. Therefore, this study aimed to identify the common pathogens causing FUO in patients admitted to Abbasia Fever Hospital in Egypt from January 2020 to December 2022, their antimicrobial susceptibility profiles, and associated resistance genes. The study also aimed to investigate the burden of multidrug-resistant (MDR) pathogens and the priority pathogens nominated by the World Health Organization (WHO) for posing the greatest threat to human health due to antibiotic resistance. During the study period, about 726 patients were diagnosed with FUO. After extensive investigations, the cause of the FUO was found to be infectious diseases in 479/726 patients (66.0%). Of them, 257 patients had positive bacterial cultures, including 202 Gram-negative isolates that comprised Klebsiella pneumoniae (85/202; 42.1%), Escherichia coli (71/202; 35.1%), Acinetobacter baumannii (26/202; 12.9%), and Pseudomonas aeruginosa (14/202; 6.9%) and 55 Gram-positive isolates, including Staphylococcus aureus (23/55; 41.8%), Streptococcus pneumoniae (7/55; 12.7%), and Enterococcus spp. (25/55; 45.5%). The MDR phenotype was shown by 68.3% and 65.5% of the Gram-negative and Gram-positive isolates, respectively. Carbapenem resistance (CR) was shown by 43.1% of the Gram-negative isolates. Of the 23 S. aureus isolates obtained from research participants, 15 (65.2%) were methicillin-resistant S. aureus (MRSA). A high-level aminoglycoside resistance (HLAR) phenotype was found in 52.0% of the Enterococcus sp. isolates. The PCR screening of resistance genes in the MDR isolates showed that blaOXA-48 was the most prevalent (84%) among the carbapenemase-coding genes, followed by blaVIM (9%) and then blaIMP (12%). The ESBL-coding genes blaTEM, blaCTX-M,aac(6')-Ib, and blaSHV, were prevalent in 100%, 93.2%, 85,% and 53.4% of the MDR isolates, respectively. This study updates the range of bacteria that cause FUO and emphasizes the burden of multidrug resistance and priority infections in the region. The obtained data is of relevant medical importance for the implementation of evidence-based antimicrobial stewardship programs and tailoring existing empirical treatment guidelines.

Correlation of CRISPR/Cas and Antimicrobial Resistance in Klebsiella pneumoniae Clinical Isolates Recovered from Patients in Egypt Compared to Global Strains

The CRISPR/Cas system has been long known to interfere with the acquisition of foreign genetic elements and was recommended as a tool for fighting antimicrobial resistance. The current study aimed to explore the prevalence of the CRISPR/Cas system in Klebsiella pneumoniae isolates recovered from patients in Egypt in comparison to global strains and correlate the CRISPR/Cas to susceptibility to antimicrobial agents. A total of 181 clinical isolates were PCR-screened for cas and selected antimicrobial resistance genes (ARGs). In parallel, 888 complete genome sequences were retrieved from the NCBI database for in silico analysis. CRISPR/Cas was found in 46 (25.4%) isolates, comprising 18.8% type I-E and 6.6% type I-E*. Multidrug resistance (MDR) and extensive drug resistance (XDR) were found in 73.5% and 25.4% of the isolates, respectively. More than 95% of the CRISPR/Cas-bearing isolates were MDR (65.2%) or XDR (32.6%). No significant difference was found in the susceptibility to the tested antimicrobial agents among the CRISPR/Cas-positive and -negative isolates. The same finding was obtained for the majority of the screened ARGs. Among the published genomes, 23.2% carried CRISPR/Cas, with a higher share of I-E* (12.8%). They were confined to specific sequence types (STs), most commonly ST147, ST23, ST15, and ST14. More plasmids and ARGs were carried by the CRISPR/Cas-negative group than others, but their distribution in the two groups was not significantly different. The prevalence of some ARGs, such as blaKPC, blaTEM, and rmtB, was significantly higher among the genomes of the CRISPR/Cas-negative strains. A weak, nonsignificant positive correlation was found between the number of spacers and the number of resistance plasmids and ARGs. In conclusion, the correlation between CRISPR/Cas and susceptibility to antimicrobial agents or bearing resistance plasmids and ARGs was found to be nonsignificant. Plasmid-targeting spacers might not be naturally captured by CRISPR/Cas. Spacer match analysis is recommended to provide a clearer image of the exact behavior of CRISPR/Cas towards resistance plasmids.