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Fulltext Lineage-Specific Methyltransferases Define the Methylome of the Globally Disseminated Escherichia coli ST131 Clone

Forde BM, Phan MD, Gawthorne JA, Ashcroft MM, Stanton-Cook M, Sarkar S, et al.

mBio, 2015 Nov 17;6(6):e01602-15.
PMID: 26578678 DOI: 10.1128/mBio.01602-15

Escherichia coli sequence type 131 (ST131) is a clone of uropathogenic E. coli that has emerged rapidly and disseminated globally in both clinical and community settings. Members of the ST131 lineage from across the globe have been comprehensively characterized in terms of antibiotic resistance, virulence potential, and pathogenicity, but to date nothing is known about the methylome of these important human pathogens. Here we used single-molecule real-time (SMRT) PacBio sequencing to determine the methylome of E. coli EC958, the most-well-characterized completely sequenced ST131 strain. Our analysis of 52,081 methylated adenines in the genome of EC958 discovered three (m6)A methylation motifs that have not been described previously. Subsequent SMRT sequencing of isogenic knockout mutants identified the two type I methyltransferases (MTases) and one type IIG MTase responsible for (m6)A methylation of novel recognition sites. Although both type I sites were rare, the type IIG sites accounted for more than 12% of all methylated adenines in EC958. Analysis of the distribution of MTase genes across 95 ST131 genomes revealed their prevalence is highly conserved within the ST131 lineage, with most variation due to the presence or absence of mobile genetic elements on which individual MTase genes are located.
IMPORTANCE: DNA modification plays a crucial role in bacterial regulation. Despite several examples demonstrating the role of methyltransferase (MTase) enzymes in bacterial virulence, investigation of this phenomenon on a whole-genome scale has remained elusive until now. Here we used single-molecule real-time (SMRT) sequencing to determine the first complete methylome of a strain from the multidrug-resistant E. coli sequence type 131 (ST131) lineage. By interrogating the methylome computationally and with further SMRT sequencing of isogenic mutants representing previously uncharacterized MTase genes, we defined the target sequences of three novel ST131-specific MTases and determined the genomic distribution of all MTase target sequences. Using a large collection of 95 previously sequenced ST131 genomes, we identified mobile genetic elements as a major factor driving diversity in DNA methylation patterns. Overall, our analysis highlights the potential for DNA methylation to dramatically influence gene regulation at the transcriptional level within a well-defined E. coli clone.

Matched MeSH terms: Urinary Tract Infections/microbiology; Urinary Tract Infections/epidemiology
Fulltext Discovery of New Genes Involved in Curli Production by a Uropathogenic Escherichia coli Strain from the Highly Virulent O45:K1:H7 Lineage

Nhu NTK, Phan MD, Peters KM, Lo AW, Forde BM, Min Chong T, et al.

mBio, 2018 08 21;9(4).
PMID: 30131362 DOI: 10.1128/mBio.01462-18

Curli are bacterial surface-associated amyloid fibers that bind to the dye Congo red (CR) and facilitate uropathogenic Escherichia coli (UPEC) biofilm formation and protection against host innate defenses. Here we sequenced the genome of the curli-producing UPEC pyelonephritis strain MS7163 and showed it belongs to the highly virulent O45:K1:H7 neonatal meningitis-associated clone. MS7163 produced curli at human physiological temperature, and this correlated with biofilm growth, resistance of sessile cells to the human cationic peptide cathelicidin, and enhanced colonization of the mouse bladder. We devised a forward genetic screen using CR staining as a proxy for curli production and identified 41 genes that were required for optimal CR binding, of which 19 genes were essential for curli synthesis. Ten of these genes were novel or poorly characterized with respect to curli synthesis and included genes involved in purine de novo biosynthesis, a regulator that controls the Rcs phosphorelay system, and a novel repressor of curli production (referred to as rcpA). The involvement of these genes in curli production was confirmed by the construction of defined mutants and their complementation. The mutants did not express the curli major subunit CsgA and failed to produce curli based on CR binding. Mutation of purF (the first gene in the purine biosynthesis pathway) and rcpA also led to attenuated colonization of the mouse bladder. Overall, this work has provided new insight into the regulation of curli and the role of these amyloid fibers in UPEC biofilm formation and pathogenesis.IMPORTANCE Uropathogenic Escherichia coli (UPEC) strains are the most common cause of urinary tract infection, a disease increasingly associated with escalating antibiotic resistance. UPEC strains possess multiple surface-associated factors that enable their colonization of the urinary tract, including fimbriae, curli, and autotransporters. Curli are extracellular amyloid fibers that enhance UPEC virulence and promote biofilm formation. Here we examined the function and regulation of curli in a UPEC pyelonephritis strain belonging to the highly virulent O45:K1:H7 neonatal meningitis-associated clone. Curli expression at human physiological temperature led to increased biofilm formation, resistance of sessile cells to the human cationic peptide LL-37, and enhanced bladder colonization. Using a comprehensive genetic screen, we identified multiple genes involved in curli production, including several that were novel or poorly characterized with respect to curli synthesis. In total, this study demonstrates an important role for curli as a UPEC virulence factor that promotes biofilm formation, resistance, and pathogenesis.

Matched MeSH terms: Urinary Tract Infections/microbiology
Urinary tract infection and non-ruptured acute appendicitis association: Uro-pathogens findings

Al Fraijat B, Al-Tawarah NM, Khlaifat AM, Qaralleh H, Khleifat KM, M A, et al.

Trop Biomed, 2019 Sep 01;36(3):620-629.
PMID: 33597484

Urinary Tract Infections (UTIs) consider as the most common infections worldwide, with higher risk in patients experienced Acute Appendicitis (AA). The purpose of this study was, to investigate the bacterial profile of UTIs in patients with non-ruptured AA postsurgically, and to assess age- and gender-related links of all AA cases in Karak region, Jordan. Urine samples obtained from 46 cases (32 male and 14 female) aged between 16-70 years were diagnosed as non-ruptured AA, following with isolation and characterization of isolated bacteria. Out of 46 AA cases, uropathogens isolated from 25 (54.3%) UTI cases. Out of these isolates; 42 (73.7%) were gram-negative isolates and 15 (26.3%) were gram-positive bacteria. The percentage of isolates were E. coli (26.3%), Enterobacter species (21%), Enterococcus faecalis and Klebsiella pneumoniea (10.5%) for each, Streptococcus saprophytics and Pseudomonas aeruginosa (7%) for each, Yersinia spp. and S. milleri (8.8%). Out of UTI cases, 20 cases (80%) possessed mixed culture, each of them had at least one of Enterobacterial species. i.e. Enterobacter spp. or E. coli or both. More precisely, out of all these positivecases, 2 cases had pure gram positive-bacterial infection (8%), while pure gram negative bacterial infection comprised 48% of them and the rest (44%) were mixed (gram-negative and gram-positive) bacterial infection. Moreover, study revealed a high prevalence rate of AA cases 24 (52.2%) in the ages of 16-22 years, then declining the rate with increasing the age, reaching the lowest rate (4.3%) in ages of 60-70. In addition to age factor, the males significantly more susceptible to AA cases than females by 2.2-fold. Antibiotic sensitivity test revealed high resistance capability of E. coli to the most used antibiotics except for nitrofurantoin. Bacterial isolates showing sensitivity against ciprofloxacin, trimethoprim/sulfamethoxazole, amoxicillin-Clavulanic acid and nitrofurantoin, with a superiority for the first two. Results demonstrate high prevalence rate of UTIs in patients with AA. For avoiding, the needless use of antibiotics through sticking to our accountability as healthcare provisioner to pursuit the antimicrobial management.

Matched MeSH terms: Urinary Tract Infections/microbiology; Urinary Tract Infections/epidemiology*
Radiology and disease patterns in Malaysia

Wastie ML

Trop Geogr Med, 1975 Mar;27(1):17-24.
PMID: 1138449

The organisation of the radiological services in Malaysia is described and those diseases in which radiology plays an important part in diagnosis are discussed. As radiology embraces all specialities a pattern of diseases emerges which is different from that seen in the West. The control of infectious diseases, the general improvement in health care and the more sophisticated radiological investigations now available mean that in future radiology will play a much more important part in diagnosis and management of patients.

Matched MeSH terms: Urinary Tract Infections/radiography
Screening for urinary tract infection in women with hyperemesis gravidarum

Tan PC, King AS, Omar SZ

J Obstet Gynaecol Res, 2012 Jan;38(1):145-53.
PMID: 21955280 DOI: 10.1111/j.1447-0756.2011.01652.x

AIM: The aim of this study was to evaluate urine microscopy, dipstick analysis and urinary symptoms in screening for urinary tract infection (UTI) in hyperemesis gravidarum (HG).
MATERIALS AND METHODS: A prospective cross-sectional study was performed on women at first hospitalization for HG. A clean-catch mid-stream urine sample from each recruit was sent for microscopy (for bacteria, leucocytes and erythrocytes), dipstick analysis (for leukocyte esterase, nitrites, protein and hemoglobin) and microbiological culture. The presence of current urinary symptoms was elicited by questionnaire. UTI is defined as at least 10(5) colony-forming units/mL of a single uropathogen on culture. Screening test parameters were analyzed against UTI.
RESULTS: UTI was diagnosed in 15/292 subjects (5.1%). Receiver-operator characteristic curve analysis of microscopic urine leucocytes revealed area under the curve=0.64, 95% confidence interval (CI) 0.5-0.79, P=0.063 and erythrocytes area under the curve=0.53, 95%CI 0.39-0.67, P=0.67 for UTI indicating the limited screening utility of these parameters. Microscopic bacteriuria (likelihood ratio [LR] 1.1, 95%CI 0.7-1.5) and urine dipstick leukocyte esterase (LR 1.4, 95%CI 1.1-1.8), nitrites (LR 2.3, 95%CI 0.3-17.2), protein (LR 1.0, 95%CI 0.7-1.6) and hemoglobin (LR 0.8, 95%CI 0.4-1.5) were not useful screening tests for UTI in HG. Elicited symptoms were also not predictive of UTI.
CONCLUSION: Urine microscopy, dipstick analysis and urinary symptoms were not useful in screening for UTI in HG. UTI should be established by urine culture in HG before starting antibiotic treatment.

Matched MeSH terms: Urinary Tract Infections/complications; Urinary Tract Infections/diagnosis*; Urinary Tract Infections/microbiology; Urinary Tract Infections/urine
Late onset group b beta-hemolytic streptococcus infection in a neonate manifesting as a urinary tract infection: a rare clinical presentation

Zurina Z, Rohani A, Neela V, Norlijah O

Southeast Asian J. Trop. Med. Public Health, 2012 Nov;43(6):1470-3.
PMID: 23413711

Group B beta-hemolytic streptococcus (GBS) sepsis is a serious bacterial infection in neonates, with significant morbidity and mortality. We report here a neonate with late onset GBS infection manifesting as a urinary tract infection (UTI) in an infant presenting with prolonged neonatal jaundice. The pathogenesis of this late onset is postulated.

Matched MeSH terms: Urinary Tract Infections/diagnosis*; Urinary Tract Infections/drug therapy; Urinary Tract Infections/microbiology
Fulltext The value of positive nitrites in screening asymptomatic bacteriuria amongst Malaysian school children

Zainal D, Baba A

Southeast Asian J. Trop. Med. Public Health, 1996 Mar;27(1):184-8.
PMID: 9031425

It is important to diagnose and treat urinary tract infection in children before renal damage has taken place. Hence a new screening procedure will be of interest. This study was conducted to evaluate the efficacy of urinary nitrite in screening for asymptomatic bacteriuria among school children compared to a more traditional method. Of the 44,816 school children investigated 240 (0.54%) students were judged to have bacteriuria ie 82 (0.19%) in boys and 158 (0.35%) in girls. Escherichia coli was the commonest organism isolated (28.75%). Urine dipstick testing for nitrite was found to have a low sensitivity and positive predictive value. While urinalysis for pyuria was noted to have a sensitivity of 77.9%, a specificity of 95.8% and a negative predictive value of 99.9%.

Matched MeSH terms: Urinary Tract Infections
Fulltext Co-morbid medical conditions and medical complications of prostate cancer in Southern Nigeria

Sapira MK, Onwuchekwa AC, Onwuchekwa CR

Med J Malaysia, 2012 Aug;67(4):412-6.
PMID: 23082452

BACKGROUND:
Prostate cancer often co-exists with other diseases. It accounts for 11% of all cancers in Nigerian men, and it is the commonest cause of mortality due to cancer in elderly males in Nigeria.

OBJECTIVE:
To present co-morbid medical conditions and medical complications of prostate cancer in patients with the disease in Southern Nigeria.

PATIENTS AND METHODS:
The study was carried out prospectively (2002 to 2003) at University of Port Harcourt Teaching Hospital (UPTH), and Nnamdi Azikiwe University Teaching Hospital (NAUTH) Nnewi- both in Southern Nigeria. Using common proforma, patients who presented to the urology units of the two teaching hospitals were evaluated clinically and with relevant investigations for prostate cancer and other diseases. Those with histologically confirmed prostate cancer were included in this study. Data was also collected retrospectively by using the same proforma to obtain information from case files of 37 patients diagnosed with prostate cancer at UPTH. Data from the two institutions were collated and analysed.

RESULTS:
Of 189 cases analysed, 73.4% had significant medical co-morbid diseases/complications. These included anaemia (69.8%), urinary tract infection (56.1%), chronic renal failure (33.9%), hypertension (41.8%), diabetes mellitus (9.5%), paraplegia (9.5%), congestive cardiac failure (9.0%) and cerebrovascular disease (5.3%).

CONCLUSION/RECOMMENDATIONS:
These patients had high disease burden. Improved health education and well coordinated interdisciplinary team work are suggested in managing this malignancy.

Matched MeSH terms: Urinary Tract Infections/complications
Fulltext Purple urine bag syndrome: Case report from a nursing home resident with a false alarm of urosepsis

Mohamed Faisal AH, Shathiskumar G, Nurul Izah A

Med J Malaysia, 2015 Aug;70(4):265-6.
PMID: 26358028 MyJurnal

Purple urine bag syndrome (PUBS), as the name implies produces purplish discoloration of the urine. It is commonly observed among elderly women with constipation, and individuals with long term catheter in the setting of urinary tract infection (UTI). From the literature research, there were no publications on PUBS in Malaysia; however we believe that it is underreported. We present a unique case of this rare condition occurring in a 68-year-old man, a nursing home resident on long term urinary catheter. The urine cleared after hydration, antibiotic therapy and replacement of the catheter.

Matched MeSH terms: Urinary Tract Infections
Fulltext Bacterial pathogens and antibiotic resistance patterns in children with urinary tract infection in a Malaysian tertiary hospital

Noor Shafina MN, Nor Azizah A, Mohammad AR, Faisal MF, Mohamad Ikhsan S, Hafizah Z, et al.

Med J Malaysia, 2015 Jun;70(3):153-7.
PMID: 26248777 MyJurnal

INTRODUCTION: Urinary tract infection (UTI) is a common bacterial infection affecting children and therefore, prompt recognition and accurate antimicrobial management are vital to prevent kidney damage. This study aims to determine the bacterial pathogens and their patterns of antimicrobial resistance in children presenting with UTI.
METHODS: A retrospective study of 721 cases, involving children between the ages of 1-day old to 13 years old with culture-proven UTI in Selayang Hospital, Malaysia between January 2007 and December 2011. The bacterial pathogens and antibiotic resistance patterns in the total population, prophylaxis and no prophylaxis groups were studied.
RESULTS: The 3 most common organisms isolated in the total population were E.Coli (41.6%), Klebsiella spp. (21.2%) and Enterococcus spp. (11.0%). With regards to the antibiotic resistance, E.Coli resistance rates to ampicillin, cefuroxime and gentamicin were 67.7%, 15.3% and 7.3% respectively. Ampicillin-resistance was also highest in Klebsiella spp. (84.3%), Enterococcus spp. (15.5%) and Proteus spp. (55.5%).
CONCLUSION: E.coli remains to be the leading bacterial pathogen causing UTI in children, with ampicillin-resistance occurring in more than half of these cases. Therefore, accurate choice of antibiotics is important to ensure optimal outcome. In our study, cefuroxime and gentamicin have lower antibiotic resistance rates and can be used in the treatment of UTI in children.

Matched MeSH terms: Urinary Tract Infections*
Fulltext Urogenital melioidosis: a review of clinical presentations, characteristic and outcomes

Chong Vh VH, Sharif F, Bickle I

Med J Malaysia, 2014 Dec;69(6):257-60.
PMID: 25934955 MyJurnal

INTRODUCTION: Melioidosis is endemic to the tropical regions, in particular Thailand and Northern Australia. Any organ can be affected by melioidosis. Involvement of the urogenital system is common in Northern Australia, but is less common in other regions. This study assesses the characteristics of melioidosis affecting the urogenital system treated in a tertiary referral centre in Brunei Darussalam.

MATERIAL AND METHODS: All patients treated for melioidosis of the urogenital system were identified and retrospectively reviewed.

RESULTS: There were 9 patients with 11 episodes of urogenital infections treated over 13 years. The median age at diagnosis was 38 years old (range 29 - 63) with men predominantly affected. The major risk factor was underlying diabetes mellitus (n=9), including three patients diagnosed at the time of diagnosis of melioidosis. The median glycosylated haemoglobin (HbA1c) was 12.8% (range 6.4 to 16.6%). One patient's risk factor was only moderate alcohol consumption. Common symptoms included; fever, lethargy, rigor and anorexia. Dysuria was reported by two patients. The median duration of symptoms before presentation was 7 days (range 2 to 21 days) and the median number of sites involved were 3 (range of 2 to 6). Urogenital involvement included prostate (n=6), kidney (n=8), seminal vesicles (n=1) and testis (n=1). Radiological imaging showed that large prostate abscesses (>4.5cm) were common, and in some patients, the kidney abscess had the 'honeycomb' previously described as typical for melioidosis liver abscess. All patients were successfully treated for melioidosis and at a median follow up of 34 months (range 1 - 97), there was one death from complications of diabetes mellitus.

CONCLUSION: Urogenital melioidosis only accounted for a small proportion of all melioidosis involvement, with prostate and kidney most commonly affected. Concomitant involvement of other sites were common. The major risk factor was poorly controlled diabetes mellitus.

Matched MeSH terms: Urinary Tract Infections
Fulltext Sexual function outcomes following treatment for lower urinary tract symptoms. A one-year study

Quek KF, Razack AH, Chua CB, Low WY, Loh CS

Med J Malaysia, 2003 Dec;58(5):735-42.
PMID: 15190661

The aim of this study was to assess the effects of treating lower urinary tract symptoms (LUTS) on the quality of sexual function in a one-year follow up. A total of 116 patients with LUTS received alpha-blocker treatment, 111 patients underwent transurethral resection of the prostate (TURP) and 70 patients with renal stones, with no or mild symptoms served as a control group. The patients were assessed at baseline, three months, six months and twelve months using the International Index of Erectile Function (IIEF-15). The surgical group exhibited some changes in the domain of IIEF-15. Patients in the medical group showed improvement in erectile function and intercourse satisfaction, while orgasmic, overall sexual satisfaction and sexual drive were relatively unchanged. In contrast, the surgical group suffered retrograde ejaculation and overall sexual dissatisfaction after undergoing TURP. TURP has been found to be associated with retrograde ejaculation intercourse and overall sexual dissatisfaction.

Matched MeSH terms: Urinary Tract Infections/drug therapy*
Trimethoprim-sulphamethoxazole in the treatment of infections in obstetrical and gynaecological practice. A bacteriological and clinical study

Hing NK, Hai CK, Ping WW

Med J Malaysia, 1974 Jun;28(4):260-2.
PMID: 4278676
Matched MeSH terms: Urinary Tract Infections/drug therapy*
X-ray diagnosis in urinary tract infection

Devadason I

Med J Malaysia, 1975 Dec;30(2):114-20.
PMID: 1228376
Matched MeSH terms: Urinary Tract Infections/radiography*
TRENDS IN OBSTETRICS

MACAFEE CH

Med J Malaysia, 1963 Jun;17:274-81.
PMID: 14060504
Matched MeSH terms: Urinary Tract Infections*
Stewardship opportunities in the treatment of urinary tract infection using oral fosfomycin

Alias AM, Shahruniza AS, Sulaiman H

Med J Malaysia, 2019 Oct;74(5):456-458.
PMID: 31649232

Fosfomycin (FMT) was first isolated in 1969 and has gained popularity in the past few decades, specifically in the treatment of uncomplicated urinary tract infection (UTI). A retrospective study was undertaken to study the pattern of FMT use in our outpatient clinics. Subjects were divided into guideline compliant (GC) and non-guideline compliant (NGC) groups, based on available guidelines. More than half of the subjects (51, 51%) fall in the NGC group. Diabetes was an independent risk factor for inappropriate FMT prescription. This represented an opportunity for antimicrobial stewardship in treating diabetic patients with uncomplicated UTI when this agent is chosen.

Matched MeSH terms: Urinary Tract Infections
Prophylactic antibiotics in children

Sinniah D

Med J Malaya, 1971 Dec;26(2):84-9.
PMID: 4260865
Matched MeSH terms: Urinary Tract Infections/prevention & control
The antibiogram and the distribution of Proteus organisms isolated from urinary tracts

Chai KH, Soo-Hoo TS

Med J Malaya, 1970 Sep;25(1):43-5.
PMID: 4249494
Matched MeSH terms: Urinary Tract Infections/microbiology*
Fulltext High Genetic Diversity among Stenotrophomonas maltophilia Isolates from Single Hospital: Nosocomial Outbreaks or Genotypic Profile Changes during Subcultures

Güvenir M, Otlu B, Tunc E, Aktas E, Suer K

Malays J Med Sci, 2018 Mar;25(2):40-49.
PMID: 30918454 DOI: 10.21315/mjms2018.25.2.5

Background: Stenotrophomonas maltophilia is a non-fermentative gram-negative bacillus which is widely recognised as an important nosocomial pathogen causing pneumonia, blood-stream, wound and urinary tract infections, particularly in immunosuppressed patients. The aim of this study was to evaluate a nosocomial outbreak of by S. maltophilia in an intensive care unit of a tertiary hospital and evaluate unexpected multiclonality.
Methods: A total of 11 isolates from respiratory cultures in intensive care unit of a 24 bed tertiary hospital obtained over a one months period and one isolate obtained from the nebuliser during environmental screening were investigated. The bacteria were identified by Phoenix 100 system. The clonal relatedness was evaluated by PFGE and semi-automated repetitive sequence-based PCR. Genotyping tests were repeated for 10 serial subcultures.
Results: PFGE and DiversiLab yielded 10 genotypic profiles for 12 isolates. Four to eight different genotypes were observed from 10 subcultures of the same isolate.
Conclusion: We conclude that, high genetic diversity and supposed multiclonal appearance of the outbreak isolates may be due to changing profiles during subcultures most probably depending on hypermutation.

Matched MeSH terms: Urinary Tract Infections
Midstream urine culture and sensitivity test is a poor predictor of infected urine proximal to the obstructing ureteral stone or infected stones: a prospective clinical study

Mariappan P, Loong CW

J Urol, 2004 Jun;171(6 Pt 1):2142-5.
PMID: 15126773

PURPOSE: This prospective study was performed to determine if midstream urine (MSU) culture and sensitivity (C&S) alone could adequately predict infected urine proximal to the obstructing ureteral stone or the infected stones. Can pelvic urine C&S predict infected stones?
MATERIALS AND METHODS: A prospective clinical study was performed on all patients undergoing ureterorenoscopy and lithotripsy for ureteral stones with obstruction between December 1, 2000 and January 31, 2002. We obtained MSU, renal pelvic urine and fragmented stones for culture and sensitivity. An analysis of the data was performed to assess statistical association.
RESULTS: A total of 73 patients who fulfilled the criteria were recruited. Of these patients 25 (34.3%) had positive stone culture, 43 (58.9%) had positive pelvic urine and 21 (28.8%) patients had positive MSU C&S. Stone and pelvic C&S were positive simultaneously in 17 (23.3%) cases, MSU and stone C&S were positive in 8 (10.9%) cases, whereas pelvic and MSU C&S were positive in 13 (16.4%) cases (p = 0.03). MSU C&S had a sensitivity of 30.2% and specificity of 73% to detect pelvic urine C&S positivity. MSU C&S had a low positive predictive value and negative predictive value (NPV) in relation to infected pelvic urine (positive predictive value = 0.62, NPV = 0.42). Pelvic urine C&S had a NPV of 0.73 in detecting noninfected stones.
CONCLUSIONS: The results of this study suggest that in obstructive uropathy secondary to a stone MSU C&S is a poor predictor of infected urine proximal to the obstruction and infected stones.

Matched MeSH terms: Urinary Tract Infections/etiology; Urinary Tract Infections/microbiology*

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