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1.  Antimicrobial resistance in hospitalized surgical patients: a silently emerging public health concern in Uganda 
BMC Research Notes  2013;6:298.
Background
Surgical site infections (SSIs) are difficult to treat and are associated with substantially longer hospital stay, higher treatment cost, morbidity and mortality, particularly when the etiological agent is multidrug-resistant (MDR). To address the limited data in Uganda on SSIs, we present the spectrum of bacteria isolated from hospitalized patients, the magnitude and impact of MDR bacterial isolates among patients with SSIs.
Methods
A descriptive cross sectional study was conducted from September 2011 through April 2012 involving 314 patients with SSIs in the obstetrics & gynecology, general surgery and orthopedic wards at Mulago National Hospital in Kampala, Uganda. Wound swabs were taken and processed using standard microbiological methods. Clinico-demographic characteristics of patients were obtained using structured questionnaires and patients’ files.
Results
Of the 314 enrolled patients with SSIs (mean age 29.7 ±13.14 years), 239 (76.1%) were female. More than half of the patients were from obstetrics and gynecology (62.1%, 195/314). Of 314 wound swabs taken, 68.8% (216/314) were culture positive aerobically, yielding 304 bacterial isolates; of which 23.7% (72/304) were Escherichia coli and 21.1% (64/304) were Staphylococcus aureus. More than three quarters of Enterobacteriaceae were found to be extended spectrum beta lactamase (ESBL) producers and 37.5% of S. aureus were Methicillin resistant S. aureus (MRSA). MDR occurred in 78.3% (238/304) of the isolates; these were more among Gram-negative bacteria (78.6%, 187/238) compared to Gram-positive bacteria (21.4%, 51/238), (p-value < 0.0001, χ2 = 49.219). Amikacin and imepenem for ESBL-producing Enterobacteriacea and vancomycin for MRSA showed excellent performance except that they remain expensive drugs in Uganda.
Conclusion
Most SSIs at Mulago National Hospital are due to MDR bacteria. Isolation of MRSA and ESBL-producing Enterobacteriaceae in higher proportions than previously reported calls for laboratory guided SSIs- therapy and strengthening of infection control surveillance in this setting.
doi:10.1186/1756-0500-6-298
PMCID: PMC3729663  PMID: 23890206
Antimicrobial resistance; Surgical patients; Uganda
2.  Evaluation of in-house PCR for diagnosis of smear-negative pulmonary tuberculosis in Kampala, Uganda 
BMC Research Notes  2012;5:487.
Background
Nucleic acid amplification tests (NAATs) have offered hope for rapid diagnosis of tuberculosis (TB). However, their efficiency with smear-negative samples has not been widely studied in low income settings. Here, we evaluated in-house PCR assay for diagnosis of smear-negative TB using Lowenstein-Jensen (LJ) culture as the baseline test. Two hundred and five pulmonary TB (PTB) suspects with smear-negative sputum samples, admitted on a short stay emergency ward at Mulago Hospital in Kampala, Uganda, were enrolled. Two smear-negative sputum samples were obtained from each PTB suspect and processed simultaneously for identification of MTBC using in-house PCR and LJ culture.
Results
Seventy two PTB suspects (35%, 72/205) were LJ culture positive while 128 (62.4%, 128/205) were PCR-positive. The sensitivity and specificity of in-house PCR for diagnosis of smear-negative PTB were 75% (95% CI 62.6-85.0) and 35.9% (95% CI 27.2-45.3), respectively. The positive and negative predictive values were 39% (95% CI 30.4-48.2) and 72.4% (95% CI 59.1-83.3), respectively, while the positive and negative likelihood ratios were 1.17 (95% CI 0.96-1.42) and 0.70 (95% CI 0.43-1.14), respectively. One hundred and seventeen LJ culture-negative suspects (75 PCR-positive and 42 PCR-negative) were enrolled for follow-up at 2 months. Of the PCR-positive suspects, 45 (60%, 45/75) were still alive, of whom 29 (64.4%, 29/45) returned for the follow-up visit; 15 (20%, 15/75) suspects died while another 15 (20%, 15/75) were lost to follow-up. Of the 42 PCR-negative suspects, 22 (52.4%, 22/42) were still alive, of whom 16 (72.7%, 16/22) returned for follow-up; 11 (26.2%, 11/42) died while nine (21.4%, 9/42) were lost to follow-up. Overall, more PCR-positive suspects were diagnosed with PTB during follow-up visits but the difference was not statistically significant (27.6%, 8/29 vs. 25%, 4/16, p = 0.9239). Furthermore, mortality was higher for the PCR-negative suspects but the difference was also not statistically significant (26.2% vs. 20% p = 0.7094).
Conclusion
In-house PCR correlates poorly with LJ culture for diagnosis of smear-negative PTB. Therefore, in-house PCR may not be adopted as an alternative to LJ culture.
doi:10.1186/1756-0500-5-487
PMCID: PMC3497582  PMID: 22947399
Pulmonary tuberculosis; Smear-negative TB; HIV-infected; HIV-TB co-infection; CD4 cell counts; Nucleic acid amplification tests; In-house PCR; Lowenstein-Jensen culture; Sensitivity; Specificity; Resource limited settings
3.  Evaluation of Capilia TB assay for rapid identification of Mycobacterium tuberculosis complex in BACTEC MGIT 960 and BACTEC 9120 blood cultures 
BMC Research Notes  2012;5:44.
Background
Capilia TB is a simple immunochromatographic assay based on the detection of MPB64 antigen specifically secreted by the Mycobacterium tuberculosis complex (MTC). Capilia TB was evaluated for rapid identification of MTC from BACTEC MGIT 960 and BACTEC 9120 systems in Kampala, Uganda. Since most studies have mainly dealt with respiratory samples, the performance of Capilia TB on blood culture samples was also evaluated.
Methods
One thousand samples from pulmonary and disseminated tuberculosis (TB) suspects admitted to the JCRC clinic and the TB wards at Old Mulago hospital in Kampala, Uganda, were cultured in automated BACTEC MGIT 960 and BACTEC 9120 blood culture systems. BACTEC-positive samples were screened for purity by sub-culturing on blood agar plates. Two hundred and fifty three (253) samples with Acid fast bacilli (AFB, 174 BACTEC MGIT 960 and 79 BACTEC 9120 blood cultures) were analyzed for presence of MTC using Capilia TB and in-house PCR assays.
Results
The overall Sensitivity, Specificity, Positive and Negative Predictive values, and Kappa statistic for Capilia TB assay for identification of MTC were 98.4%, 97.6%, 97.7%, 98.4% and 0.96, respectively. Initially, the performance of in-house PCR on BACTEC 9120 blood cultures was poor (Sensitivity, Specificity, PPV, NPV and Kappa statistic of 100%, 29.3%,7%, 100% and 0.04, respectively) but improved upon sub-culturing on solid medium (Middlebrook 7H10) to 100%, 95.6%, 98.2%, 100% and 0.98, respectively. In contrast, the Sensitivity and Specificity of Capilia TB assay was 98.4% and 97.9%, respectively, both with BACTEC blood cultures and Middlebrook 7H10 cultured samples, revealing that Capilia was better than in-house PCR for identification of MTC in blood cultures. Additionally, Capilia TB was cheaper than in-house PCR for individual samples ($2.03 vs. $12.59, respectively), and was easier to perform with a shorter turnaround time (20 min vs. 480 min, respectively).
Conclusion
Capilia TB assay is faster and cheaper than in-house PCR for rapid identification of MTC from BACTEC MGIT 960 and BACTEC 9120 culture systems in real-time testing of AFB positive cultures.
doi:10.1186/1756-0500-5-44
PMCID: PMC3282630  PMID: 22260090
4.  Nasopharyngeal carriage rate of Streptococcus pneumoniae in Ugandan children with sickle cell disease 
BMC Research Notes  2012;5:28.
Background
Nasopharyngeal carriage of Streptococcus pneumoniae is a determinant for invasive pneumococcal disease, which often complicates homozygous sickle cell disease. Here, we determined the nasopharyngeal carriage rate of S. pneumoniae in Ugandan children with homozygous sickle cell disease, who attended the outpatient Sickle Cell Clinic at Mulago National Referral hospital in Kampala, Uganda.
Results
S. pneumoniae occurred in 27 of the 81 children with homozygous sickle cell disease (giving a carriage rate of 33%, 27/81). Twenty three children were previously hospitalized of whom S. pneumoniae occurred in only two (9%, 2/23), while among the 58 who were not previously hospitalized it occurred in 25 (43%, 25/58, χ2 = 8.8, p = 0.003), meaning there is an association between high carriage rate and no hospitalization. Two children previously immunized with the pneumococcal conjugate vaccine did not carry the organism. Prior antimicrobial usage was reported in 53 children (65%, 53/81). There was high resistance of pneumococci to penicillin (100%, 27/27) and trimethoprime-sulfamethoxazole (97%, 26/27), but low resistance to other antimicrobials. Of the 70 children without sickle cell disease, S. pneumoniae occurred in 38 (54%, 38/70) of whom 43 were males and 27 females (53% males, 23/43, and 56% females, 15/27).
Conclusion
Nasopharyngeal carriage of penicillin resistant pneumococci in Ugandan children with homozygous sickle cell disease is high. While nasopharyngeal carriage of S. pneumoniae is a determinant for invasive pneumococcal disease, pneumococcal bacteremia is reportedly low in Ugandan children with sickle cell disease. Studies on the contribution of high carriage rates to invasive pneumococcal disease in these children will be helpful. This is the first report on pneumococcal carriage rate in Ugandan children with sickle cell disease.
doi:10.1186/1756-0500-5-28
PMCID: PMC3283489  PMID: 22243524
5.  High prevalence of methicillin resistant Staphylococcus aureus in the surgical units of Mulago hospital in Kampala, Uganda 
BMC Research Notes  2011;4:326.
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.
doi:10.1186/1756-0500-4-326
PMCID: PMC3184088  PMID: 21899769
6.  Determination of circulating Mycobacterium tuberculosis strains and transmission patterns among pulmonary TB patients in Kawempe municipality, Uganda, using MIRU-VNTR 
BMC Research Notes  2011;4:280.
Background
Mycobacterial interspersed repetitive units - variable number of tandem repeats (MIRU-VNTR) genotyping is a powerful tool for unraveling clonally complex Mycobacterium tuberculosis (MTB) strains and detection of transmission patterns. Using MIRU-VNTR, MTB genotypes and their transmission patterns among patients with new and active pulmonary tuberculosis (PTB) in Kawempe municipality in Kampala, Uganda was determined.
Results
MIRU-VNTR genotyping was performed by PCR-amplification of 15 MTB-MIRU loci from 113 cultured specimens from 113 PTB patients (one culture sample per patient). To determine lineages, the genotypes were entered into the MIRU-VNTRplus database [http://www.miru-vntrplus.org/] as numerical codes corresponding to the number of alleles at each locus. Ten different lineages were obtained: Uganda II (40% of specimens), Uganda I (14%), LAM (6%), Delhi/CAS (3%), Haarlem (3%), Beijing (3%), Cameroon (3%), EAI (2%), TUR (2%) and S (1%). Uganda I and Uganda II were the most predominant genotypes. Genotypes for 29 isolates (26%) did not match any strain in the database and were considered unique. There was high diversity of MIRU-VNTR genotypes, with a total of 94 distinct patterns. Thirty four isolates grouped into 15 distinct clusters each with two to four isolates. Eight households had similar MTB strains for both index and contact cases, indicating possible transmission.
Conclusion
MIRU-VNTR genotyping revealed high MTB strain diversity with low clustering in Kawempe municipality. The technique has a high discriminatory power for genotyping MTB strains in Uganda.
doi:10.1186/1756-0500-4-280
PMCID: PMC3162915  PMID: 21835016

Results 1-6 (6)