Chromosomal and plasmid-encoded virulence and multidrug resistance of Escherichia coli ST58/24 infecting a 2-year-old sickle cell patient with sepsis in Kampala Uganda, East Africa.

Sepsis and drug resistance represent a complex of the most common global causes of mortality in intensive care units (ICUs) especially among patients with comorbidities. Extraintestinal pathogenic Escherichia coli (ExPEC) strains are highly implicated in systemic infections, with multidrug resistance exacerbating the risk of chronic conditions and patient mortality. The diversity of virulence and evolution of multidrug resistance are yet to be fully deciphered. In this work, we aimed at unveiling the pathogens and their genomic determinants of virulence and drug resistance relevant to increased sepsis in a sickle cell child admitted to ICU. From a rectal swab, we isolated a strain of E. coli from the patient and phenotypically tested it against a panel of selected beta lactams, fluoroquinolones, macrolides, aminoglycosides and colistin. We then sequenced the entire genome and integrated multiple bioinformatic pipelines to divulge the virulence and multidrug resistance profiles of the isolate. Our results revealed that the isolate belongs to the sequence type (ST) 58/24, which (ST58), is a known ExPEC. With the use of PathogenFinder, we were able to confirm that this isolate is a human pathogen (p = 0.936). The assembled chromosome and two plasmids encode virulence factors related to capsule (antiphagocytosis), serum survival and resistance, type 6 secretion system (T6SS), multiple siderophores (iron acquisition), and biosynthetic gene clusters for polyketides and nonribosomal peptides exhibiting host cell damaging activity in silico. The genome also harbors multidrug resistance genotypes including extended spectrum beta lactamase (ESBL) genes such as blaTEM-1A/B, sulfonamide resistance genes sul1/2, fluoroquinolone resistance genes dfrA5 and nonsynonymous mutations of the gene pmrB, conferring intrinsic colistin resistance. Conclusively, this pathogen holds the potential to cause systemic infection and might exacerbate sickle cell anemia in the patient. The virulence and multidrug resistance profiles are encoded by both the chromosome and plasmids. Genomic surveillance of pathogens with multidrug resistance among patients with commodities is crucial for effective disease management.

A sophisticated virulence repertoire and colistin resistance of Citrobacter freundii ST150 from a patient with sepsis admitted to ICU in a tertiary care hospital in Uganda, East Africa: Insight from genomic and molecular docking analyses.

Sepsis and multidrug resistance comprise a complex of factors attributable to mortality among intensive care unit (ICU) patients globally. Pathogens implicated in sepsis are diverse, and their virulence and drug resistance remain elusive. From a tertiary care hospital ICU in Uganda, we isolated a Citrobacter freundii strain RSM030 from a patient with sepsis and phenotypically tested it against a panel of 16 antibiotics including imipenem levofloxacin, cotrimoxazole and colistin, among others. We sequenced the organism's genome and integrated multilocus sequencing (MLST), PathogenFinder with Virulence Factor analyzer (VFanalyzer) to establish its pathogenic relevance. Thereafter, we combined antiSMASH and PRISM genome mining with molecular docking to predict biosynthetic gene clusters (BGCs), pathways, toxin structures and their potential targets in-silico. Finally, we coupled ResFinder with comprehensive antibiotic resistance database (CARD) to scrutinize the genomic antimicrobial resistance profile of the isolate. From PathogenFinder and MLST, this organism was confirmed to be a human pathogen (p = 0.843), sequence type (ST)150, whose virulence is determined by chromosomal type III secretion system (T3SS) (the injectosome) and plasmid-encoded type IV secretion system (T4SS), the enterobactin biosynthetic gene cluster and biofilm formation through the pgaABCD operon. Pathway and molecular docking analyses revealed that the shikimate pathway can generate a toxin targeting multiple host proteins including spectrin, detector of cytokinesis protein 2 (Dock2) and plasmalemma vesicle-associated protein (PLVAP), potentially distorting the host cell integrity. From phenotypic antibiotic testing, we found indeterminate results for amoxicillin/clavulanate and levofloxacin, with resistance to cotrimoxazole and colistin. Detailed genome analysis revealed chromosomal beta lactam resistance genes, i.e. blaCMY-79, blaCMY-116 and blaTEM-1B, along with multiple mutations of the lipopolysaccharide modifying operon genes PmrA/PmrB, pmrD, mgrA/mgrB and PhoP/PhoQ, conferring colistin resistance. From these findings, we infer that Citrobacter freundii strain RSM030 is implicated in sepsis and resistance to standard antibiotics, including colistin, the last resort.

A Systematic Review of the Microbial Landscape of Diabetic Foot Ulcers in Uganda.

Background: Diabetes is a growing health concern globally. Poorly managed diabetes may result in diabetic foot ulcers (DFU), which can become a source of chronic infection known as diabetic foot infections. The increasing trend of diabetes in Uganda speaks to the potential for diabetic foot ulcers which may eventually become infected and their attendant impact on the quality of life of diabetic patients. This review assesses the microbial diversity of DFUs in Uganda, aiming to guide treatment and identify research gaps. Main Body of the Abstract: We searched PubMed, Scopus and Embase for studies conducted in Uganda that reported isolating microorganisms from diabetic foot ulcers. Following the preferred reporting items for systematic reviews and meta-analysis (PRISMA), we included two eligible studies that reported isolating 122 bacteria spread across eleven (11) species using swab samples and conventional culture methods. Significant isolates included World Health Organization priority pathogens including: Enterobacter specie, Staphylococcus aureus, Klebsiella pneumoniae, and Acinetobacter specie. Methicillin resistant Staphylococcus aureus (MRSA) constituted 33.3% of Staphylococci species and 26% of all bacterial isolates while extended-spectrum beta-lactamase producing Escherichia coli and Klebsiella specie constituted 14.29% of total microbial isolates. Most bacteria showed susceptibility to Imipenem, Vancomycin, Ciprofloxacin, and Clindamycin, but resistance to Cotrimoxazole and Ampicillin was noted. Short Conclusion: We conclude that data on the microbiology of DFUs in Uganda is scarce; however, the bioburden of DFUs in the country is similar to those in other parts of the world, and MRSA poses a challenge to antibiotic therapy. Consequently, the continued use of swab samples and conventional culture and sensitivity methods may limit the isolation, identification, and presentation of other important isolates. We recommend characterization of bacterial isolates to better understand their genetic makeup, and the development of a national guideline for managing diabetic foot infections.

Fluoroquinolone resistant bacterial isolates from the urinary tract among patients attending hospitals in Bushenyi District, Uganda.

INTRODUCTION: bacterial resistance to fluoroquinolones is on the rise globally, bacteria causing urinary tract infections (UTIs) are no exception to this fact. Judicious use of the current antibiotics by clinicians is therefore deemed necessary to combat development of resistance. This study determined fluoroquinolone resistant profiles, multiple antibiotic resistance indices (MARI), factors associated with fluoroquinolone resistance and their strength among patients attending hospitals in Bushenyi District, Uganda. METHODS: this was a cross-sectional study in which a total of 86 bacterial uropathogens isolated previously by standard microbiological methods were subjected to antibiotic susceptibility testing using Kirby Bauer disk diffusion method. Data for factors suspected to be associated with fluoroquinolone resistant UTI were obtained by use of questionnaires. RESULTS: the most resisted fluoroquinolone was ofloxacin with 29/83 (34.9%), followed by moxifloxacin 27/83 (32.5%), levofloxacin 24/86 (27.9%) and ciprofloxacin 23/86 (26.7%). The bacterial uropathogens that exhibited the highest frequency of fluoroquinolone resistant strains were P. mirabilis with 2/3 (66.7%) and E. faecalis with 2/3 (66.7%), followed by E. coli 19/36 (52.8%), S. aureus 13/27 (48.1%), K. oxytoca 2/6 (33.3%), K. pneumoniae 2/10 (20.0%) and P. vulgaris 0/1 (0.0%). All the bacterial uropathogens tested showed MARI of ≥ 0.2. Hospitalization, history of fluoroquinolones use in the last 12 months and wrong prescription of antibiotics were found to bear statistically significant relationships (p < 0.05) with fluoroquinolone resistant UTI. CONCLUSION: antibiotic susceptibility testing of the first generation quinolones such as nalidixic acid in hospitalized patients, patients with history of fluoroquinolones' use in the last 12 months and wrong prescription of antibiotics should be adopted to avoid fluoroquinolone abuse. For empiric treatment of UTIs in Bushenyi District, ciprofloxacin still remains the first line of choice among the fluoroquinolone class of antibiotics.

Prevalence of Dermatophytosis and Antifungal Activity of Ethanolic Crude Leaf Extract of Tetradenia riparia against Dermatophytes Isolated from Patients Attending Kampala International University Teaching Hospital, Uganda.

Dermatophyte infections are a global health problem but neglected in Uganda. This work aimed at determining prevalence of dermatophytosis and antifungal activity of ethanolic crude leaf extract of Tetradenia riparia against dermatophytes isolated from patients attending Kampala International University Teaching Hospital (KIU-TH), Uganda. A total of 100 samples of skin and nail scrapings were collected and processed using standard microscopy (KOH) and cultural methods. T. riparia leaves were collected and processed with 95% ethanol using standard extraction method. The crude leaves ethanolic extract was tested against three dermatophytes: Trichophyton tonsurans, T. mentagrophyte, and Microsporum audouinii using modified agar well diffusion method. Minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) of the ethanolic leaves crude extract were also determined using broth tube dilution and culture, respectively. Out of 100 samples collected, 49 (49%, 95%CI: 0.3930-0.5876) were found positive for microscopy. The prevalence of dermatophytosis was significantly (p=0.001) associated with age groups of participants with higher infection among those aged 11-20 and 21-30 years with 75.0% each. Out of the 49 that were positive by microscopy, 28 (57.15%, 95% CI: 0.1987-0.3739) were positive by culture. Thirty-one (31) fungal isolates were obtained which included both dermatophyte and non-dermatophyte fungi. T. verrucosum had highest distribution 6 (19.35%) among dermatophytes species while Aspergillus spp. were found to have highest distribution 7 (22.58%) among non-dermatophyte species. The result of the antidermatophytic test showed that T. riparia ethanolic crude leaves extract had activity against tested dermatophytes at 1 g/ml. MIC and MFC of the crude extract of T. riparia against tested dermatophytes ranged from 62.5 to 250 mg/ml and 125 to 500 mg/ml, respectively. The findings of this study reported the presence of dermatophytes causing dermatophytosis among patients attending KIU-TH. The results of the current study showed that T. riparia leaves ethanolic crude extract has antidermatophytic activity against tested dermatophytes.