Molecular Characterization and Antibiotic Susceptibility Profile of Acinetobacter baumannii Recovered from Hospital Wastewater Effluents.

Acinetobacter baumannii (A. baumannii) plays a significant part in nosocomial infections world over and is re-emerging as a formidable pathogen due to the wide range of antibiotic resistance factors it acquires and environmental resilience. The high attendance of patients (outpatients and inpatients) into the health care facilities formed the basis for the selection of the hospitals. Consequently, this study profiled the antibiogram and antibiotic resistance genes of A. baumannii isolated from selected hospital wastewater effluents. A total of twenty-four (24) wastewater samples from three selected hospital drainages were collected and analysed presumptively by culture-dependent methods for A. baumannii. The identity confirmation of A. baumannii was done by the amplification of recA and blaoxa-51 genes. Virulence and antibiotic resistance markers were assessed using polymerase chain reaction. A total of 53 A. baumannii isolates were confirmed and the highest antibiotic resistance profile was 93% (piperacillin). Multiple antibiotic resistance index (MARI) showed a range of 0.23 and 0.46. FimH virulence gene was detected in 29 (55%) of the isolates. Tetracycline and beta-lactam resistance markers were found; 70% and 92% of the isolates possessed tetA and ampC genes. The isolates showed high level of resistance to antibiotics. The multiple antibiotic resistance index (MARI) of ≥ 0.2 indicates that some of the isolates harbour virulence and resistance traits emerging from high-risk source thereby projecting a threat to public health.

Chemokine Coreceptor Usage Among HIV-1 Drug-Naive Patients Residing in the Rural Eastern Cape, South Africa.

Sub-Saharan region in Africa still holds the highest burden of HIV/AIDS globally. HIV-1 requires coreceptor to gain entry into permissive cells to initiate infection. Molecular analysis of the chemokine coreceptor usage is important clinically and in the effective management of AIDS virus. This study aims to determine the coreceptor usage among HIV-1 drug-naive patients residing in the rural Eastern cape, South Africa. We collected blood samples from 55 HIV-infected patients into an anticoagulant vacutainer. RNA was extracted from separated plasma, and reverse transcription-polymerase chain reaction (RT-PCR) was performed followed by nested polymerase chain reaction to amplify the partial envelope fragment spanning the C2-C3 region. Sanger sequencing was done on the amplicons using the BigDye Terminator V3.1 sequencing kit (Applied Biosystems, Foster City, CA) while sequences were manually edited using BioEdit and Geneious 10.2.6 tools. The WebPSSM and Geno2pheno online tools were also utilized to predict coreceptor tropism while the phylogenetic analysis of the isolates was determined using MEGA 7. Of the 55 blood samples collected for the study, 50 (91%) were successfully amplified and sequenced. The mean age of the patients was 32 (18-56) years while the ratio of men to women was 35% and 65% correspondingly. Phylogenetic analysis revealed that all 50 sequences clustered with HIV-1 subtype C reference strains. Viral tropism of the V3 loop revealed 47 sequences to be R5 strains, while three sequences (T1E, T10E, and T11E,) were classified as X4 strains based on the WebPSSM and the Geno2pheno algorithm. HIV-1 R5 tropic strains were the most dominant virus obtained from this study, while HIV-1 subtype C still drives the epidemic in South Africa suggesting greater in vivo and host pathogen fitness. Documented data on mapping out cellular tropism based on viral tropism are important as maraviroc and the other CCR5 antagonist could be introduced as part of the treatment regimen in South Africa.

Molecular Genetics and the Incidence of Transmitted Drug Resistance Among Pre-Treatment HIV-1 Infected Patients in the Eastern Cape, South Africa.

BACKGROUND: Transmitted drug resistance (TDR) remains a significant threat to Human immunodeficiency virus (HIV) infected patients that are not exposed to antiretroviral treatment. Although, combined antiretroviral therapy (cART) has reduced deaths among infected individuals, emergence of drug resistance is gradually on rise. OBJECTIVE: To determine the drug resistance mutations and subtypes of HIV-1 among pre-treatment patients in the Eastern Cape of South Africa. METHODS: Viral RNA was extracted from blood samples of 70 pre-treatment HIV-1 patients while partial pol gene fragment amplification was achieved with specific primers by RT-PCR followed by nested PCR and positive amplicons were sequenced utilizing ABI Prism 316 genetic sequencer. Drug resistance mutations (DRMs) analysis was performed by submitting the generated sequences to Stanford HIV drug resistance database. RESULTS: Viral DNA was successful for 66 (94.3%) samples of which 52 edited sequences were obtained from the protease and 44 reverse transcriptase sequences were also fully edited. Four major protease inhibitor (PI) related mutations (I54V, V82A/L, L76V and L90M) were observed in seven patients while several other minor and accessory PIs were also identified. A total of 11(25.0%) patients had NRTIs related mutations while NNRTIs were observed among 14(31.8%) patients. K103N/S, V106M and M184V were the most common mutations identified among the viral sequences. Phylogenetic analysis of the partial pol gene indicated all sequences clustered with subtype C. CONCLUSION: This study indicates that HIV-1 subtype C still predominates and responsible for driving the epidemic in the Eastern Cape of South Africa with slow rise in the occurrence of transmitted drug resistance.