Rapid diagnosis of tuberculosis and multidrug resistance by the microscopic-observation drug-susceptibility assay.

RATIONALE: Mortality is exceedingly high and rapid among patients infected with HIV and tuberculosis (TB), in part because of limited access to appropriate TB diagnostics. The microscopic observation drug-susceptibility (MODS) assay is a simple, rapid, low-cost test for TB and multidrug-resistant (MDR) TB, but data in individuals infected with HIV and in Africa are limited. OBJECTIVES: To evaluate the MODS assay in a high-HIV-prevalence setting. METHODS: We performed a prospective diagnostic accuracy study of consecutive adults suspected to have TB from outpatient and inpatient settings at a district hospital in rural South Africa. Sputum was tested by concentrated smear microscopy; agar (Middlebrook 7H11) and liquid (mycobacterial growth indicator tube) culture; and the MODS assay. Drug-susceptibility testing (DST) was by indirect 1% proportion method and MODS. Reference standard for Mycobacterium tuberculosis detection was growth on Middlebrook or mycobacterial growth indicator tube culture; 1% proportion was the reference standard for isoniazid and rifampin DST. MEASUREMENTS AND MAIN RESULTS: Among 534 adults enrolled, 388 (73%) were HIV-positive, with a median CD4 count of 161 cells/mm(3) (interquartile range [IQR]: 72-307). TB was diagnosed by the reference standard culture in 113 (21%). MODS sensitivity was 85% (95% confidence interval [CI], 78-92%), and specificity was 97% (CI, 95-99%). MODS test performance did not differ by patients' HIV status (sensitivity 88% vs. 90%, specificity 97% vs. 100% for HIV-positive versus HIV-negative, respectively). For MDR-TB diagnosis (n = 11), sensitivity was 100% (one-sided CI, 68-100%) and specificity was 94% (CI, 82-98%). Median turnaround time for MDR-TB diagnosis was 7 days (IQR: 6-9) with MODS versus 70 days (IQR: 49-96) with indirect proportion method (P < 0.001). CONCLUSIONS: Among adult TB suspects predominantly infected with HIV, MODS provided high sensitivity and specificity for rapid diagnosis of TB and MDR-TB. Given the high mortality from TB and MDR-TB and prolonged opportunity for TB transmission before diagnosis, the MODS assay warrants serious consideration for use in similar high-HIV-prevalence, resource-limited settings.

A Public Health Insight into Salmonella in Poultry in Africa: A Review of the Past Decade: 2010-2020.

Poultry is a cheap source of animal protein and constituent of diets in Africa. Poultry can serve as a reservoir for Salmonella and cause food-borne infections in humans. This review describes Salmonella contamination of food, poultry, and the farming environment, antimicrobial resistance profiles, and serotypes of Salmonella, as well as the farming systems, antimicrobial use (AMU), hygiene, and husbandry conditions used to rear poultry in Africa. Using the PRISMA (preferred reporting items for systematic reviews and meta-analysis) guidelines, PubMed, Science Direct, and Web of Science databases were searched using a set of predefined keywords. Full-length research articles in English were examined for the period 2010-2020 and relevant information extracted for the narrative synthesis. Of the articles that met the inclusion criteria, 63.1% were conducted on farms and among households, while 36.9% were undertaken at government-controlled laboratories, which quarantine imported birds, processing plants, and retail outlets. The farming systems were intensive, semi-intensive, and extensive. AMU was described in 11.5% of the studies and varied within and across countries. Multidrug-resistant (MDR) Salmonella isolates were detected in 30 studies and the prevalence ranged from 12.1% in Zimbabwe to 100% in Egypt, Ethiopia, Nigeria, Senegal, and South Africa. A total of 226 different Salmonella serotypes were reported. Twenty-four (19.7%) of the studies reported food-borne Salmonella contamination in eggs, poultry, and poultry products at retail outlets and processing plants. The apparent extensive use of antimicrobials and circulation of MDR Salmonella isolates of various serotypes in Africa is a concern. It is important to implement stricter biosecurity measures on farms, regulate the use of antimicrobials and implement surveillance systems, in addition to food safety measures to monitor the quality of poultry and poultry products for human consumption.

Molecular Epidemiology of Salmonella enterica in Poultry in South Africa Using the Farm-to-Fork Approach.

The presence of the zoonotic pathogen Salmonella in the food supply chain poses a serious public health threat. This study describes the prevalence, susceptibility profiles, virulence patterns, and clonality of Salmonella from a poultry flock monitored over six weeks, using the farm-to-fork approach. Salmonella was isolated using selective media and confirmed to the genus and species level by real-time polymerase chain reaction (RT-PCR) of the invA and iroB genes, respectively. Antimicrobial susceptibility profiles were determined using Vitek-2 and the Kirby-Bauer disk diffusion method against a panel of 21 antibiotics recommended by the World Health Organisation Advisory Group on Integrated Surveillance of Antimicrobial Resistance (WHO-AGISAR). Selected virulence genes were identified by conventional PCR, and clonality was determined using enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Salmonella was present in 32.1% of the samples: on the farm (30.9%), at the abattoir (0.6%), and during house decontamination (0.6%). A total of 210 isolates contained the invA and iroB genes. Litter, faeces, and carcass rinsate isolates were classified as resistant to cefuroxime (45.2%), cefoxitin (1.9%), chloramphenicol (1.9%), nitrofurantoin (0.4%), pefloxacin (11.4%), and azithromycin (11%). Multidrug resistance (MDR) was observed among 3.8% of the isolates. All wastewater and 72.4% of carcass rinsate isolates were fully susceptible. All isolates harboured the misL, orfL, pipD, stn, spiC, hilA, and sopB virulence genes, while pefA, spvA, spvB, and spvC were absent. In addition, fliC was only present among the wastewater isolates. Various ERIC-PCR patterns were observed throughout the continuum with different subtypes, indicating the unrelated spread of Salmonella. This study concluded that poultry and the poultry environment serve as reservoirs for resistant and pathogenic Salmonella. However, there was no evidence of transmission along the farm-to-fork continuum.

Salmonella Yoruba: A rare serotype revealed through genomic sequencing along the farm-to-fork continuum of an intensive poultry farm in KwaZulu-Natal, South Africa.

Salmonella enterica is a zoonotic pathogen of worldwide public health importance. We characterised Salmonella isolates from poultry along the farm-to-fork continuum using whole genome sequencing (WGS) and bioinformatic analyses. Three multilocus sequence types (MLSTs), i.e., ST15 (1.9%), ST152 (5.9%) and ST1316 (92.2%) and three serotypes, i.e., S. Heidelberg (1.9%), Kentucky (5.9%) and Yoruba (92.2%) were detected. The rare serotype, S. Yoruba, was detected among the farm and abattoir isolates and contained resistance and virulence determinants. Resistome analysis revealed the presence of the aac(6')-Iaa gene associated with aminoglycoside resistance, a single point mutation in the parC gene associated with fluoroquinolone and quinolone resistance, and a single isolate contained the fosA7 gene responsible for fosfomycin resistance. No antibiotic resistance genes (ARGs) were identified for isolates phenotypically non-susceptible to azithromycin, cephalosporins, chloramphenicol and nitrofurantoin and resistance was thought to be attributable to other resistance mechanisms. The fully susceptible profiles observed for the wastewater isolates suggest that the poultry environment may receive antibiotic-resistant strains and resistance determinants from poultry with the potential of becoming a pathway of Salmonella transmission along the continuum. Six plasmids were identified and were only carried by 92.2% of the S. Yoruba isolates in varying combinations. Four plasmids were common to all S. Yoruba isolates along the continuum; isolates from the litter and feces on the farm contained two additional plasmids. Ten Salmonella pathogenicity islands (SPIs) and 177 virulence genes were identified; some were serotype-specific. Phylogenetic analysis of S. Heidelberg and Kentucky showed that isolates were related to animal and human isolates from other countries. Phylogenetic analysis among the S. Yoruba isolates revealed four clades based on the isolate sources along the farm-to-fork continuum. Although the transmission of Salmonella strains along the farm-to-fork continuum was not evident, pathogenic, resistant Salmonella present in the poultry production chain poses a food safety risk. WGS analysis can provide important information on the spread, resistance, pathogenicity, and epidemiology of isolates and new, rare or emerging Salmonella strains to develop intervention strategies to improve food safety.

Increasing drug resistance in extensively drug-resistant tuberculosis, South Africa.

We expanded second-line tuberculosis (TB) drug susceptibility testing for extensively drug-resistant Mycobacterium tuberculosis isolates from South Africa. Of 19 patients with extensively drug-resistant TB identified during February 2008-April 2009, 13 (68%) had isolates resistant to all 8 drugs tested. This resistance leaves no effective treatment with available drugs in South Africa.

Synthesis and Biological Evaluation of a Teixobactin Analogue.

The first synthesis and biological activity of a teixobactin analogue is reported. Substitution of the unusual L-allo-enduracididine residue by the naturally occurring L-arginine was achieved, and the analogue gave an activity trend similar to that of teixobactin (against Gram-postive bacteria) and meropenem, which was approved by the FDA in 1996. The synthetic route used allows for the synthesis of the natural product as well as the development of a program of medicinal chemistry.