Draft genome sequence of Staphylococcus urealyticus strain MUWRP0921, isolated from the urine of an adult female Ugandan.

Staphylococcus urealyticus bacteria are pathogenic among immune-compromised individuals. A strain (MUWRP0921) of Staphylococcus urealyticus with a genome of 2,708,354 bp was isolated from Uganda and carries genes that are associated with antibiotic resistance, including resistance to macrolides (erm(C) and mph(C')), aminoglycosides (aac(6")-aph(2")), tetracyclines (tet(K)), and trimethoprim (dfrG).

Genome Analysis of Klebsiella pneumoniae Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda.

Klebsiella pneumoniae is a threat to public health due to its continued evolution. In this study, we investigated the evolution, convergence, and transmission of hypervirulent and multi-drug resistant (MDR) clones of K. pneumoniae within healthcare facilities in Uganda. There was high resistance to piperacillin (90.91%), cefuroxime (86.96%), ceftazidime (84.62%), cefotaxime (84.00%), amoxicillin/clavulanate (75%), nalidixic acid (73.68%), and nitrofurantoin (71.43%) antibiotics among K. pneumoniae isolates. The isolates were genetically diverse, consisting of 20 different sequence types (STs) and 34 K-serotype groups. Chromosomal fosA (for fosfomycin) and oqxAB efflux pump genes were detected in all isolates. Two carbapenem resistance genes, blaNDM-5 and blaOXA-181 plus extended-spectrum beta-lactamase (blaCTX-M-15) gene (68.12%), quinolone-resistant genes qnrS1 (28.99%), qnrB1 (13.04%), and qnrB6 (13.04%) and others were found. All, except three of the isolates, harbored plasmids. While the isolates carried a repertoire of virulence genes, only two isolates carried hypervirulent genes demonstrating a low prevalence (2.90%) of hypervirulent strains. Our study demonstrated genetically diverse populations of K. pneumoniae, low levels of carbapenem resistance among the isolates, and no convergence of MDR and hypervirulence. Emerging high-risk international pandemic clones (ST11, ST14, ST147, ST 86 and ST307) were detected in these healthcare settings which are difficult to treat.

Resistome and virulome of high-risk pandemic clones of multidrug-resistant extra-intestinal pathogenic Escherichia coli (ExPEC) isolated from tertiary healthcare settings in Uganda.

Multi-drug resistant (MDR) globally disseminated extraintestinal pathogenic high-risk Escherichia coli (ExPEC) clones are threatening the gains in bacterial disease management. In this study, we evaluated the genomic structure including the resistome and virulome of the E. coli isolates from extraintestinal infections using whole genome sequencing (WGS). The results highlight that isolates were highly resistant (≥ 90.0%) to commonly used antibiotics (Ampicillin, Trimethoprim-Sulfamethoxazole, Nalidixic acid, and Piperacillin) and were less (<14%) resistant to last resort antibiotics; Imipenem (10.94%) and Meropenem (10.20%). A greater proportion of the E. coli isolates belonged to phylogroup B2 (30.52%) and phylogroup A (27.37%). The sequence types ST131 of phylogroup B2 (21.05%) and ST648 of phylogroup F (9.3%) were the dominant pandemic high-risk clones identified in addition to the ST1193, ST410, ST69, ST38, ST405, and ST10. Many of the isolates were MDR and most (64.58%) carried the blaCTX-M-15 gene for extended-spectrum ß-lactamases. There was a high correlation between phylogroups and the occurrence of both antimicrobial resistance and virulence genes. The cephalosporin-resistance gene blaEC-5 was only found in phylogroup B2 while blaEC-8 and blaEC-19, were only found within phylogroup D and phylogroup F respectively. Aminoglycoside gene (aadA1) was only associated with phylogroups D and C. The isolates were armed with a broad range of virulence genes including adhesins, toxins, secreted proteases, iron uptake genes, and others. The yfcv, chuA, and kpsE genes preferentially occurred among isolates of phylogroup B2. The study underlines the predominance of MDR internationally disseminated high-risk ExPEC clones with a broad range of virulence genes known to be highly transmissible in healthcare and community settings.

Whole Genome Sequencing Reveals High Genetic Diversity, Diverse Repertoire of Virulence-Associated Genes and Limited Antibiotic Resistance Genes among Commensal Escherichia coli from Food Animals in Uganda.

Commensal Escherichia coli with broad repertoire of virulence and antimicrobial resistance (AMR) genes pose serious public health risks as reservoirs of AMR and virulence. This study undertook whole genome characterization of commensal E. coli from food-producing animals in Uganda to investigate their genome variability (resistome and virulome). We established that the E. coli had high genomic diversity with 38 sequence types, 24 FimH types, and 33 O-antigen serotypes randomly distributed within three phylogroups (A, B1, and E). A greater proportion (≥93.65%) of the E. coli were resistant to amoxicillin/clavulanate and ampicillin antibiotics. The isolates were AmpC beta-lactamase producers dominated by blaEC-15 (71.88%) and tet(A) (20.31%) antimicrobial resistant genes besides a diverse armory of virulence-associated genes in the class of exotoxin, adhesins, iron uptake, and serine protease autotransporters which varied by host species. Cattle were found to be the major source of E. coli carrying Shiga toxin genes, whereas swine was the main source of E. coli carrying colicin-like Usp toxin gene. The study underscores the importance of livestock as the carrier of E. coli with antimicrobial resistance and a large repertoire of virulence traits with a potential of causing disease in animals and humans by acquiring more genetic traits.

Colonization of patients hospitalized at orthopedic department of tertiary hospital in Uganda with extended-spectrum beta-lactamase-producing enterobacterales.

BACKGROUND: Beta-lactamase production remains the most contributing factor to beta-lactam resistance. Extended-Spectrum Beta-Lactamase-Producing Enterobacterales (ESBL-PE) are associated with risk factors both in hospital and community settings. OBJECTIVES: To assess the incidence and risk factors for intestinal carriage of ESBL-PE among patients admitted to orthopedic ward of Mulago National Referral Hospital, and to analyze the acquisition of ESBL-PE during hospital stay and associated factors. METHODS: We screened 172 patients aged 18 years old and above who got admitted to the orthopedic ward of Mulago National Referral Hospital between May to July 2017. Stool samples or rectal swabs were collected at admission, every 3 days until fourteen days and screened for ESBL-PE. Data on demographic status, antibiotic use, admission and travel, length of hospital stay, hygiene practices and drinking boiled water were analyzed by logistic regression and cox regression model. RESULTS: At admission, 61% of patients showed intestinal ESBL-PE carriage. Co- resistance was common but no Carbapenem resistance was detected. Of the ESBL-PE negative, 49% were colonized during hospitalization. On admission, prior antibiotic use was significantly associated with carriage, but none was associated with acquisition during hospitalization at p-value < 0.05. CONCLUSION: Carriage of ESBL-PE on admissions and acquisition at orthopedic ward of Mulago Hospital were high, and dissemination into the community are of substantial concern. We suggested refinement of empirical treatment based on risk stratification, and enhanced infection control measures that target health care workers, patients and attendants.

Genome Sequence Analysis of a Wohlfahrtiimonas chitiniclastica Strain Isolated from a Septic Wound of a Hospitalized Patient in Uganda.

We report a genome sequence of Wohlfahrtiimonas chitiniclastica strain MUWRP0946, isolated from a hospitalized patient in Uganda. The genome size was 2.08 million bases, and the genome completeness was 94.22%. The strain carries tetracycline, folate pathway antagonist, ß-lactam, and aminoglycoside antibiotic resistance genes.

Anti-bacterial activity of Corchorus olitorius L. and Acmella caulirhiza Del. on Streptococcus mutans, a cariogenic bacterium.

Background: Dental caries remains a global oral health challenge with the prevalence reported as high as 66.7% in adults. Despite the use of modern medicines, the prevalence of dental caries remains high. This has led to extensive screening of natural products particularly from plants such as Corchorus olitorius L. and Acmella caulirhiza Del. for anti-cariogenic activity. Aim: To assess the anti-bacterial activity of Corchorus olitorius L. and Acmella caulirhiza Del. on Streptococcus mutans, a cariogenic bacteria. Methods: Plant materials of C. olitorius L. and A. caulirhiza Del. were extracted using diethyl ether, methanol, distilled water by cold maceration. Agar well diffusion method was used for sensitivity and susceptibility tests on S. mutans (ATCC 6519). Results: The aqueous plant extract of C. olitorius L. and the ether plant extract of A. caulirhiza Del. had the highest zones of inhibition (16.10mm and 12.03mm respectively) at a concentration of 1000mg/ml. The lowest MIC and MBC were 62.5mg/ml and 250mg/ml respectively. Conclusion: Both C. olitorius L. and A. caulirhiza Del. as used in oral health practices have been found to have antibacterial activity against the cariogenic S. mutans. Further studies should be conducted to isolate bioactive compounds against S. mutans.

Factors associated with community-acquired urinary tract infections among adults attending assessment centre, Mulago Hospital Uganda.

BACKGROUND: Urinary tract infections (UTI) are a common medical problem affecting the general population and thus commonly encountered in medical practice, with the global burden of UTIs at about 150 million people. Because uropathogens largely originate from colonic flora, they are easy to predict, and this is the rationale for empirical treatment in Community Acquired-UTI (CA-UTIs). With the increasing prevalence of drug-resistant bacteria among adults with CA-UTI in Uganda, it is no longer adequate to manage CA-UTIs on empiric regimen without revising the susceptibility patterns of common CA-UTI causative agents. Thus in this study we set out to identify: The factors associated with CA-UTIs, the common uropathogens and the drug sensitivity patterns of the common uropathogens cultured. METHODOLOGY: This was a cross-sectional study that was conducted in adults who presented with symptoms of a UTI at Mulago Hospital, assessment center. There were 139 patients who consented to the study and were recruited, an interviewer administered questionnaire was used to collect information from the study participants as regards demographic, social and clinical characteristics and Mid Stream Urine (MSU) samples were collected for urinalysis, culture and antibiotic susceptibility testing using the Kirby-Bauer disc diffusion technique was applied to the isolates.Numeric data were summarized using measures of central tendency while the categorical data was summarized using proportions and percentages. RESULTS: Age, female sex and marital status were factors that were significantly associated with CA-UTIs. Fifty four (54) cultures were positive for UTI with 26 giving pure growths. The commonest uropathogen isolated was Escherichia coli at 50%, this was followed by Staphylococcus aureus at 15.4%. The sensitivity of Escherichia coli to Ampicillin and Nitrofurantoin were78.6%, 64.3% respectively, and the sensitivity of Staphylococcus aureus to ciprofloxacin, Nitrofurantoin and gentamycin were 100%, 66.7% and 66.7% respectively. CONCLUSION: There are known factors associated with CA-UTIs such as age, female sex. There was generally high sensitivity to nitrofurantoin and gentamycin by most of the uropathogens isolated, and high resistance to the common antibiotics such as nalidixic acid and erythromycin thus a need for a bigger study that can be used to effect the change of the current recommendations in the Uganda Clinical Guidelines as regards empirical management of CA-UTIs.

Timing and reasons for coming late for the first antenatal care visit by pregnant women at Mulago hospital, Kampala Uganda.

BACKGROUND: Mothers who attend antenatal care late miss the opportunity of early detection of HIV and STDs, malaria and anaemia prophylaxis, health education and treatment or prevention of complications. Whereas many women in Mulago hospital make their first antenatal care visit after 20 weeks of gestation, the reasons for coming late are not documented. The objectives were to determine the gestation age at which pregnant women make their first antenatal care visit and the reasons for late coming. METHOD: The study was conducted in June 2012 among women with a gestation age of more than 20 weeks on their first antenatal care visit. We collected data on gestation age (from weeks of amenorrhea or based on ultrasound scan) and reasons for coming late. RESULTS: Four hundred women participated in the study. Their mean age was 25.2 years with a standard deviation of 5.2 years. The majority of the participants were Catholics (n = 126, 31.5%), they lived in a distance of greater than five kilometers from the hospital (n = 201, 50.3%) and had attained secondary education (n = 220, 55.0%). The mean of their weeks of amenorrhea was 27.9 (± 4.6) weeks. The results showed that 291 (72.7%) of the study participants did not know the right gestation age at which a pregnant woman should start attending antenatal care. One hundred and ten (27.5%) agreed that they did not have money for transport to bring them to the hospital while 37 (9.3%) thought that they had to pay for the antenatal care services. Two hundred thirteen (53.3%) reported that they did not have any problem with their current pregnancy and so they saw no reason to come early for antenatal care, even though some of these knew the right gestation age at which they should make their first antenatal care visit. CONCLUSION: Pregnant women who come late for antenatal care in Mulago hospital, Uganda are not well-informed about the right gestation age at which they should make their first antenatal care visit and/or of the importance of early attendance at antenatal care.

Prevalence of virulence determinants in Staphylococcus epidermidis from ICU patients in Kampala, Uganda.

INTRODUCTION: Staphylococcus epidermidis is often considered a non-pathogenic organism but it causes nosocomial infections. To distinguish invasive strains, comparative studies of patient and community isolates may offer some clues. We investigated the distribution of virulence determinants in patient isolates from Uganda. METHODOLOGY: S. epidermidis isolates were identified with the Staph API ID 32 kit. Antimicrobial susceptibility, biofilm formation and hemolysis were detected with standard procedures. Genes associated with virulence (aap, atlE, bhp, hla, hld, ica, IS256, sdrE, sea, tsst) and antimicrobial resistance (aac(6')-Ie-aph(2'')-Ia, aph(3')-IIIa, ant(4')-Ia, blaZ, mecA, vanA/vanB1) were detected by PCR. RESULTS: S. epidermidis grew in 30 (30/50, 60%) ICU samples and 20 (20/60, 33%) community samples (one isolate per sample per patient/person). All ICU isolates (30/30, 100%) were IS256 and hld positive, 22 (22/30, 73%) were biofilm/ica positive, 21 (21/30, 70%) were hemolytic on blood agar, nine (9/30, 30%) contained atlE gene, six (6/30, 20%) hla gene, five (5/30, 17%) aap gene, and three (3/30, 10%) bhp gene. A gene encoding an aminoglycoside-modifying enzyme, aph(3')-IIIa, was highly prevalent (28/30, 93%), while blaZ (2/30, 7%), mecA (3/30, 10%), vanA (3/30, 10%) and vanB1 (3/30, 10%) were less prevalent. Of the community isolates, one (1/20, 5%) was ica positive, two (2/20, 10%) formed biofilms, and three (3/20, 15%) possessed the atlE gene. bhp, aap, IS256, hld and antimicrobial resistance genes were not detected in community isolates. CONCLUSIONS: S. epidermidis from ICU patients in Mulago Hospital is potentially virulent and could be a reservoir for antimicrobial resistant genes.

Prevalence of Virulence Determinants in Staphylococcus Epidermidis from ICU Patients in Kampala; Uganda

Introduction: Staphylococcus epidermidis is often considered a non-pathogenic organism but it causes nosocomial infections. To distinguish invasive strains; comparative studies of patient and community isolates may offer some clues. We investigated the distribution of virulence determinants in patient isolates from Uganda. Methodology: S. epidermidis isolates were identified with the Staph API ID 32 kit. Antimicrobial susceptibility; biofilm formation and hemolysis were detected with standard procedures. Genes associated with virulence (aap; atlE; bhp; hla; hld; ica; IS256; sdrE; sea; tsst) and antimicrobial resistance (aac(6')-Ie-aph(2'')-Ia; aph(3')-IIIa; ant(4')-Ia; blaZ; mecA; vanA/vanB1) were detected by PCR. Results: S. epidermidis grew in 30 (30/50; 60) ICU samples and 20 (20/60; 33) community samples (one isolate per sample per patient/person). All ICU isolates (30/30; 100) were IS256 and hld positive; 22 (22/30; 73) were biofilm/ica positive; 21 (21/30; 70) were hemolytic on blood agar; nine (9/30; 30) contained atlE gene; six (6/30; 20) hla gene; five (5/30; 17) aap gene; and three (3/30; 10) bhp gene. A gene encoding an aminoglycoside-modifying enzyme; aph(3')-IIIa; was highly prevalent (28/30; 93); while blaZ (2/30; 7); mecA (3/30; 10); vanA (3/30; 10) and vanB1 (3/30; 10) were less prevalent. Of the community isolates; one (1/20; 5) was ica positive; two (2/20; 10) formed biofilms; and three (3/20; 15) possessed the atlE gene. bhp; aap; IS256; hld and antimicrobial resistance genes were not detected in community isolates. Conclusions: S. epidermidis from ICU patients in Mulago Hospital is potentially virulent and could be a reservoir for antimicrobial resistant genes

High prevalence of methicillin resistant Staphylococcus aureus in the surgical units of Mulago hospital in Kampala, Uganda.

BACKGROUND: There is limited data on Methicillin resistant Staphylococcus aureus (MRSA) in Uganda where, as in most low income countries, the routine use of chromogenic agar for MRSA detection is not affordable. We aimed to determine MRSA prevalence among patients, healthcare workers (HCW) and the environment in the burns units at Mulago hospital, and compare the performance of CHROMagar with oxacillin for detection of MRSA. RESULTS: One hundred samples (from 25 patients; 36 HCW; and 39 from the environment, one sample per person/item) were cultured for the isolation of Staphylococcus aureus. Forty one S. aureus isolates were recovered from 13 patients, 13 HCW and 15 from the environment, all of which were oxacillin resistant and mecA/femA/nuc-positive. MRSA prevalence was 46% (41/89) among patients, HCW and the environment, and 100% (41/41) among the isolates. For CHROMagar, MRSA prevalence was 29% (26/89) among patients, HCW and the environment, and 63% (26/41) among the isolates. There was high prevalence of multidrug resistant isolates, which concomitantly possessed virulence and antimicrobial resistance determinants, notably biofilms, hemolysins, toxin and ica genes. One isolate positive for all determinants possessed the bhp homologue which encodes the biofilm associated protein (BAP), a rare finding in human isolates. SCCmec type I was the most common at 54% prevalence (22/41), followed by SCCmec type V (15%, 6/41) and SCCmec type IV (7%, 3/41). SCCmec types II and III were not detected and 10 isolates (24%) were non-typeable. CONCLUSIONS: Hyper-virulent methicillin resistant Staphylococcus aureus is prevalent in the burns unit of Mulago hospital.

Identification of Staphylococcus aureus: DNase and Mannitol salt agar improve the efficiency of the tube coagulase test.

BACKGROUND: The ideal identification of Staphylococcus aureus clinical isolates requires a battery of tests and this is costly in resource limited settings. In many developing countries, the tube coagulase test is usually confirmatory for S. aureus and is routinely done using either human or sheep plasma. This study evaluated Mannitol salt agar and the deoxyribonuclease (DNase) test for improving the efficiency of the tube coagulase test in resource limited settings. The efficiency of human and sheep plasma with tube coagulase tests was also evaluated. METHODS: One hundred and eighty Gram positive, Catalase positive cocci occurring in pairs, short chains or clusters were subjected to growth on Mannitol salt agar, deoxyribonuclease and tube coagulase tests. Of these, isolates that were positive for at least two of the three tests (n = 60) were used to evaluate the performance of the tube coagulase test for identification of S. aureus, using PCR-amplification of the nuc gene as a gold standard. RESULTS: Human plasma was more sensitive than sheep plasma for the tube coagulase test (sensitivity of 91% vs. 81% respectively), but both plasmas had very low specificity (11% and 7% respectively). The sensitivity and specificity of the tube coagulase test (human plasma) was markedly improved when Mannitol salt agar and DNase were introduced as a tri-combination test for routine identification of Staphylococcus aureus (100% specificity and 75% sensitivity). The specificity and sensitivity of Mannitol salt agar/DNase/tube coagulase (sheep plasma) combination was 100% and 67%, respectively. CONCLUSION: The efficiency of the tube coagulase test can be markedly improved by sequel testing of the isolates with Mannitol salt agar, DNase and Tube coagulase. There is no single phenotypic test (including tube coagulase) that can guarantee reliable results in the identification of Staphylococcus aureus.