Acinetobacter baumannii complex, national laboratory-based surveillance in South Africa, 2017 to 2019.

OBJECTIVE: We aimed to provide an analysis of A. baumannii complex (ABC) isolated from blood cultures in South Africa. MATERIALS AND METHODS: ABC surveillance was conducted from 1 April 2017 to 30 September 2019 at 19 hospital sites from blood cultures of any age and sex. Organism identification was performed using the MALDI-TOF MS and antimicrobial susceptibility testing (AST), MicroScan Walkaway System. We confirmed colistin resistance with Sensititre, FRCOL panel, and selected for whole-genome sequencing. RESULTS: During the study period, we identified 4822 cases of ABC, of which 2152 cases were from 19 enhanced surveillance sites were reported during the enhanced surveillance period (1 August 2018 to 30 September 2019). Males accounted for 54% (2611/4822). Of the cases with known age, 41% (1968/4822) were infants (< 1-year-old). Seventy-eight percent (1688/2152) of cases had a known hospital outcome, of which 36% (602/1688) died. HIV status was known for 69% (1168/1688) of cases, and 14% (238/1688) were positive. Eighty-two percent (1389/1688) received antimicrobial treatment in admission. Three percent (35/1389) of cases received single colistin. Four percent (75/2033) were resistant to colistin. At least 75% of the isolates (1530/2033) can be classified as extensively drug-resistant (XDR), with resistance to most antibiotics except for colistin. The majority, 83% (20/24), of the colistin-resistant isolates were of the sequence type (ST) 1. Resistance genes, both plasmid- and chromosomal- mediated were not observed. Although all isolates had, nine efflux pump genes related to antimicrobial resistance. CONCLUSION: Our surveillance data contributed to a better understanding of the natural course of A. baumannii disease, the patient characteristics among infants, and the level of resistance. At least two-thirds of the isolates were extensively drug-resistant, and four percent of isolates were resistant to colistin.

The role of color histograms in predicting the prognosis of patients with digestive tract adenocarcinoma.

OBJECTIVES: To establish the correlation between the degree of vascularisation detected using power Doppler ultrasonography in digestive tract adenocarcinoma and the prognosis of these patients. MATERIAL AND METHOD: Ultrasonography was performed in 45 patients diagnosed with digestive tract adenocarcinoma (16 stomach-35.6%, 6 cecum and ascending colon-13.3%, 2 transverse colon-4.4%, 5 descending colon 11.1%, 13 sigmoid colon-28.9%, and 3 rectum-6.7%). The degree of maximum tumor vascularization was determined using the highest percentage of colored pixels obtained in the histogram- maximum color pixels density (MCPD). The hepatic Doppler perfusion index (HDPI) was also calculated. The presence and development of liver metastases was evaluated by ultrasonography and computed tomography. The patients were monitored for a period of 18 months. The results of each method in detecting and predicting the development of liver metastases were compared. RESULTS: MCPD and HDPI had fairly similar results (p>0.05) in establishing the positive and negative predicting values for the entire group of patients with liver metastasis (55.9% compared to 66.7%, p>0.05, and 53.3%, compared to 54.6%, p>0.05) and the group that developed liver metastases during follow-up (80.0% compared to 90.0%, p>0.05, and 61.5%, compared to 75.0%, p>0.05). When comparing MCPD and HDPI for the group of patients who had or developed metastases, MCPD had an equal sensitivity (86.4%, compared to 90.9%, p >0.05), a higher specificity (65.0% compared to 46.5%, p<0.05), but a lower accuracy (60.0% compared to 73.3%, p<0.05). In detecting patients who developed metastases during the 18 months follow-up, MCPD had a superior sensitivity (85.7% compared to 64.3%, p<0.05), a lower specificity (66.7% compared to 88.9%, p<0.05) and an equal accuracy (78.3% vs. 73.9%, p >0.05.). CONCLUSIONS: The calculation of MCPD using color histograms can be a simple and quick method in the evaluation and prognosis of patients with digestive tract adenocarcinoma.

Comparison of Xpert MTB/RIF with other nucleic acid technologies for diagnosing pulmonary tuberculosis in a high HIV prevalence setting: a prospective study.

BACKGROUND: The Xpert MTB/RIF (Cepheid) non-laboratory-based molecular assay has potential to improve the diagnosis of tuberculosis (TB), especially in HIV-infected populations, through increased sensitivity, reduced turnaround time (2 h), and immediate identification of rifampicin (RIF) resistance. In a prospective clinical validation study we compared the performance of Xpert MTB/RIF, MTBDRplus (Hain Lifescience), LightCycler Mycobacterium Detection (LCTB) (Roche), with acid fast bacilli (AFB) smear microscopy and liquid culture on a single sputum specimen. METHODS AND FINDINGS: Consecutive adults with suspected TB attending a primary health care clinic in Johannesburg, South Africa, were prospectively enrolled and evaluated for TB according to the guidelines of the National TB Control Programme, including assessment for smear-negative TB by chest X-ray, clinical evaluation, and HIV testing. A single sputum sample underwent routine decontamination, AFB smear microscopy, liquid culture, and phenotypic drug susceptibility testing. Residual sample was batched for molecular testing. For the 311 participants, the HIV prevalence was 70% (n = 215), with 120 (38.5%) culture-positive TB cases. Compared to liquid culture, the sensitivities of all the test methodologies, determined with a limited and potentially underpowered sample size (n = 177), were 59% (47%-71%) for smear microscopy, 76% (64%-85%) for MTBDRplus, 76% (64%-85%) for LCTB, and 86% (76%-93%) for Xpert MTB/RIF, with specificities all >97%. Among HIV+ individuals, the sensitivity of the Xpert MTB/RIF test was 84% (69%-93%), while the other molecular tests had sensitivities reduced by 6%. TB detection among smear-negative, culture-positive samples was 28% (5/18) for MTBDRplus, 22% (4/18) for LCTB, and 61% (11/18) for Xpert MTB/RIF. A few (n = 5) RIF-resistant cases were detected using the phenotypic drug susceptibility testing methodology. Xpert MTB/RIF detected four of these five cases (fifth case not tested) and two additional phenotypically sensitive cases. CONCLUSIONS: The Xpert MTB/RIF test has superior performance for rapid diagnosis of Mycobacterium tuberculosis over existing AFB smear microscopy and other molecular methodologies in an HIV- and TB-endemic region. Its place in the clinical diagnostic algorithm in national health programs needs exploration. Please see later in the article for the Editors' Summary.

Staphylococcus aureus bacteraemia at two academic hospitals in Johannesburg.

OBJECTIVES AND METHODS: Staphylococcus aureus bacteraemia (SAB) remains a major problem worldwide. A retrospective study of patients with SAB seen from November 1999 to October 2002 was conducted at two academic hospitals in Johannesburg to determine mortality rates (death within 14 days of submission of blood culture) in patients bacteraemic with methicillin-sensitive (MSSA) and resistant S. aureus (MRSA) and to identify risk factors associated with mortality. RESULTS: Of 449 patients with SAB, 104 (23.2%) died within 14 days of clinically suspected SAB. Of the 204 patients who acquired SAB in hospital, 6 patients died within 2 days, 39 between 2 and 14 days, and 41 more than 14 days after onset of SAB. One hundred and five patients (23.4%) had MRSA bacteraemia, 21 (20%) originating from the community. The MRSA bacteraemia rate among patients with hospital-acquired infection was 41.1%, significantly higher (p < 0.0001) than the 10.3% community-acquired MRSA bacteraemia. Thirty-five (33.3%) of the 105 patients with MRSA bacteraemia died within 14 days, compared with 69 (20.1%) of 344 MSSA patients (p = 0.0048). Admission to the intensive care unit (ICU) was significantly associated with mortality (p < 0.001)--30 of 79 patients admitted to ICU died (38%). Among 222 patients whose HIV status was known, 117 (52.7%) were positive, and of these 32 died (27.4%), a rate not significantly higher than that among HIV-seronegative patients (18 of 105 patients, p = 0.69). CONCLUSIONS: Compared with MSSA, MRSA was shown to be significantly associated with mortality. Stay in ICU and infection with strains resistant to oxacillin, ofloxacin and rifampicin were highly significant predictors for mortality.