SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis

BACKGROUND

SARS-CoV-2 continues to be a major issue in resource-limited settings, particularly owing to the limited supply of vaccinescaused by inequitable distribution.

OBJECTIVE

To monitor diagnostic gene targets to identify potential test failures caused by mutations, which is important for public health.

METHODS

Here we analysed the genome sequence of SARS-CoV-2 from the second wave in Zimbabwe. A total of 377 samples weresequenced at Quadram Institute Bioscience. After quality control, 192 sequences passed and were analysed.

RESULTS

The Beta variant was dominant during this period, contributing 77.6% (149) of the genomes sequenced and having a total of 2994mutations in diagnostic polymerase chain reaction target genes. Many single nucleotide polymorphism mutations resulted in amino acidsubstitution that had the potential to impact viral fitness by increasing the rate of transmission or evading the immune response to previousinfection or vaccination.

CONCLUSION

There were nine lineages circulating in Zimbabwe during the second wave. The B.1.351 was dominant, accounting for >75%.There were over 3 000 mutations on the diagnostic genes and lineage B.1.351, contributing almost two-thirds of the mutations. The S-genehad the most mutations and the E-gene was the least mutated.

Coronavirus Disease 2019 (COVID-19) Pandemic across Africa: Current Status of Vaccinations and Implications for the Future

The introduction of effective vaccines in December 2020 marked a significant step forward in the global response to COVID-19. Given concerns with access, acceptability, and hesitancy across Africa, there is a need to describe the current status of vaccine uptake in the continent. An exploratory study was undertaken to investigate these aspects, current challenges, and lessons learnt across Africa to provide future direction. Senior personnel across 14 African countries completed a self-administered questionnaire, with a descriptive analysis of the data. Vaccine roll-out commenced in March 2021 in most countries. COVID-19 vaccination coverage varied from low in Cameroon and Tanzania and up to 39.85% full coverage in Botswana at the end of 2021; that is, all doses advocated by initial protocols versus the total population, with rates increasing to 58.4% in Botswana by the end of June 2022. The greatest increase in people being fully vaccinated was observed in Uganda (20.4% increase), Botswana (18.5% increase), and Zambia (17.9% increase). Most vaccines were obtained through WHO-COVAX agreements. Initially, vaccination was prioritised for healthcare workers (HCWs), the elderly, adults with co-morbidities, and other at-risk groups, with countries now commencing vaccination among children and administering booster doses. Challenges included irregular supply and considerable hesitancy arising from misinformation fuelled by social media activities. Overall, there was fair to reasonable access to vaccination across countries, enhanced by government initiatives. Vaccine hesitancy must be addressed with context-specific interventions, including proactive programmes among HCWs, medical journalists, and the public.

Analysis of virulence factors and antibiotic resistance genes in group B streptococcus from clinical samples

BACKGROUND

Streptococcus agalacticae (Group B Streptococcus, GBS) is one of the most important causative agents of serious infections among neonates. This study was carried out to identify antibiotic resistance and virulence genes associated with GBS isolated from pregnant women.

METHODS

A total of 43 GBS isolates were obtained from 420 vaginal samples collected from HIV positive and negative women who were 13-35 weeks pregnant attending Antenatal Care at Chitungwiza and Harare Central Hospitals in Zimbabwe. Identification tests of GBS isolates was done using standard bacteriological methods and molecular identification testing. Antibiotic susceptibility testing was done using the modified Kirby-Bauer method and E-test strips. The boiling method was used to extract DNA and Polymerase Chain Reaction (PCR) was used to screen for 13 genes. Data was fed into SPSS 24.0.

RESULTS

Nine distinct virulence gene profiles were identified and hly-scpB-bca-rib 37.2% (16/43) was common. The virulence genes identified were namely hly 97.8% (42/43), scpB 90.1% (39/43), bca 86.0% (37/43), rib 69.8% (30/43) and bac 11.6% (5/43). High resistance to tetracycline 97.7% (42/43) was reported followed by 72.1% (31/43) cefazolin, 69.8% (30/43) penicillin G, 58.1% (25/43) ampicillin, 55.8% (24/43) clindamycin, 46.5% (20/43) ceftriaxone, 34.9% (15/43) chloramphenicol, and 30.2% (13/43) for both erythromycin and vancomycin using disk diffusion. Antibiotic resistance genes among the resistant and intermediate-resistant isolates showed high frequencies for tetM 97.6% (41/42) and low frequencies for ermB 34.5% (10/29), ermTR 10.3% (3/29), mefA 3.4% (1/29), tetO 2.4% (1/42) and linB 0% (0/35). The atr housekeeping gene yielded 100% (43/43) positive results, whilst the mobile genetic element IS1548 yielded 9.3% (4/43).

CONCLUSION

The study showed high prevalence of hly, scpB, bca and rib virulence genes in S. agalactiae strains isolated from pregnant women. Tetracycline resistance was predominantly caused by the tetM gene, whilst macrolide resistance was predominantly due to the presence of erm methylase, with the ermB gene being more prevalent. Multi-drug resistance coupled with the recovery of resistant isolates to antimicrobial agents such as penicillins indicates the importance of GBS surveillance and susceptibility tests. It was also observed that in vitro phenotypic resistance is not always accurately predicted by resistance genotypes.

Human Immunodeficiency Virus Infection Is Associated With Preterm Delivery Independent of Vaginal Microbiota in Pregnant African Women

BACKGROUND

During pregnancy, the vaginal microbiota is relatively stable. However, African women have more diverse vaginal microbiota than their European counterparts, in addition to high human immunodeficiency virus (HIV) prevalence and risk of adverse birth outcomes. Although HIV is associated with alterations in vaginal microbiota and inflammation in nonpregnant women, these relationships are underexplored in pregnant women.

METHODS

In this study, we characterize the vaginal microbiota and immune factors in pregnant African women who were HIV-uninfected (n = 314) versus HIV-infected (n = 42). Mucosal samples were collected once at the enrollment visit (between 15 and 35 weeks of gestation) and women were followed until delivery.

RESULTS

Vaginal microbial communities of pregnant women with HIV were significantly more diverse than women without HIV (P = .004), with community structure also differing by HIV status (P = .002, R2 = 0.02). Human immunodeficiency virus infection was also associated with increased risk of preterm birth (PTB) (31% versus 15.3%; P = .066). In a multivariate analysis, HIV infection was independently associated with diverse vaginal community state type (CST)-IVA (P = .005) and CST-IVB (P = .018) as well as PTB (P = .049). No association between HIV status and cytokine concentrations was found.

CONCLUSIONS

Longitudinal studies with accurate gestational age assessment would be important to confirm these relationships.

Sepsis in cancer patients residing in Zimbabwe: spectrum of bacterial and fungal aetiologies and their antimicrobial susceptibility patterns

Background

Cancer and sepsis comorbidity is a major public health problem in most parts of the world including Zimbabwe. The microbial aetiologies of sepsis and their antibiograms vary with time and locations. Knowledge on local microbial aetiologies of sepsis and their susceptibility patterns is critical in guiding empirical antimicrobial treatment choices.

Methods

This was a descriptive cross-sectional study which determined the microbial aetiologies of sepsis from blood cultures of paediatric and adult cancer patients obtained between July 2016 and June 2017. The TDR-X120 blood culture system and TDR 300B auto identification machine were used for incubation of blood culture bottles and identification plus antimicrobial susceptibility testing, respectively.

Results

A total of 142 participants were enrolled; 50 (35.2%) had positive blood cultures, with 56.0% Gram positive, 42.0% Gram-negative bacteria and 2.0% yeast isolated. Common species isolated included coagulase negative Staphylococcus spp. (CoNS) (22.0%), E. coli (16.0%), K. pneumoniae (14.0%), E. faecalis (14.0%) and S. aureus (8.0%). Gram-negative isolates exhibited high resistance to gentamicin (61.9%) and ceftriaxone (71.4%) which are the empiric antimicrobial agents used in our setting. Amikacin and meropenem showed 85.7 and 95.2% activity respectively against all Gram-negative isolates, whilst vancomycin and linezolid were effective against 96.2 and 100.0% of all Gram-positive isolates respectively. We isolated 10 (66.7%) extended spectrum β-lactamase (ESBL) amongst the E. coli and K. pneumoniae isolates. Ten (66.7%) of the Staphylococcus spp. were methicillin resistant.

Conclusions

CoNS, E. coli, K. pneumoniae, E. faecalis and S. aureus were the major microbial drivers of sepsis amongst cancer patients in Zimbabwe. Most isolates were found to be resistant to commonly used empirical antibiotics, with isolates exhibiting high levels of ESBL and methicillin resistance carriage. A nationwide survey on microbial aetiologies of sepsis and their susceptibility patterns would assist in the guidance of effective sepsis empiric antimicrobial treatment among patients with cancer.

Evaluation of the Xpert® MTB/RIF assay and microscopy for the diagnosis of Mycobacterium tuberculosis in Namibia

BACKGROUND

Tuberculosis (TB) kills approximately two million people and infects around nine million worldwide annually. Its proper management, especially in resource-limited settings, has been hindered by the lack of rapid and easy-to-use diagnostic tests. Sputum smear microscopy remains the cheapest, readily available diagnostic method but it only identifies less than half of the patients with a HIV/TB co-infection because the bacilli would have disseminated from the lungs to other areas of the body. The fully automated Xpert® MTB/RIF assay is a promising innovation for diagnosing TB and detecting resistance to rifampicin. This study aimed to evaluate the use of Xpert® MTB/RIF assay and microscopy in the diagnosis of Mycobacterium tuberculosis in Namibia, by determining the disease's epidemiology and calculating the proportion of cases infected just with TB and those with a resistance to rifampicin among the total suspected cases of TB in the country.

METHODS

This retrospective study analysed TB cases that were diagnosed using both the Xpert® MTB/RIF assay and microscopy. Data were collected from patient records from the Meditech laboratory information system of the Namibia Institute of Pathology for the time period of July 2012-April 2013. Data from 13 regions were collected.

RESULTS

The total number of specimens collected from patients with symptoms of pulmonary TB was 1 842. Of these, 594 (32.20%) were found to be positive for MTB by Xpert® MTB/RIF assay, out of which 443 (24.05%) were also found to be positive by microscopy. The remainder was negative. The male patients were more resistant to rifampicin when compared to the female patients.

CONCLUSIONS

Tuberculosis is widely distributed throughout Namibia, with slightly more males infected than females. Most TB patients are also co-infected with HIV. Both microscopy and Xpert® MTB/RIF assay are crucial for the diagnosis of TB in the country. Screening diagnostic efforts should focus on the sexually active HIV positive male population who could be the source of more RIF-resistant TB than females to prevent its spread.

Antibiotic resistance of Streptococcus agalactiae isolated from pregnant women in Garankuwa, South Africa

Background

This study was undertaken to determine the susceptibility profile and the mechanism of antibiotic resistance in Group B streptococcus (GBS) isolates detected in vaginal and rectal swabs from pregnant women attending Dr George Mukhari Academic Hospital, a University Teaching Hospital in Pretoria, South Africa.

Methods

The samples were collected over an 11-month period, cultured on selective media (colistin and nalidixic acid agar and Todd-Hewitt broth), and GBS positively identified by using different morphological and biochemical tests. The susceptibility testing was done using the Kirby–Bauer and E test methods according to CLSI guidelines 2012. The D test method was used for the detection of inducible clindamycin resistance. Multiplex PCR with specific primers was used to detect different genes coding for resistance.

Results

Out of 413 samples collected, 128 (30.9 %) were positive with GBS. The susceptibility testing revealed that 100 % of isolates were sensitive to penicillin, ampicillin, vancomycin and high level gentamicin. Erythromycin and clindamycin resistance was 21.1 and 17.2 %, respectively, in which 69 % had harboured constitutive macrolide, lincosamide and streptogramin B (MLS_B), 17.4 % had inducible MLS_B. The M and L phenotypes were present in 6.8 % each. The methylation of target encoded by ermB genes was the commonest mechanism of resistance observed in 55 % of isolates, 38 % of isolates had both ermB and linB genes and efflux pump mediated by mefA genes was also distributed among the isolates.

Conclusions

The study reaffirmed the appropriateness of penicillin as the antibiotic of choice for treating GBS infection. However it identified the challenges of resistance to macrolides and lincosamides used as alternative drugs for individuals allergic to penicillin. More GBS treatment options for penicillin allergic patients need to be researched on.

Prevalence of bacterial contamination in blood and blood products at the National Blood Service Zimbabwe

Introduction: Advances in screening for infections improve the safety of donated blood. Transfusion-related bacterial sepsis, although not established in Zimbabwe, stills makes bacterial contamination of blood clinically relevant. Methodology: This cross-sectional study was conducted in Harare. Bacteriological and antibiotic susceptibility testing were done using standard methods. Results: Of the 196 samples analyzed, 6 (3.1%) were contaminated with bacteria. Platelets had a significantly high contamination rate compared to other blood products. Bacteria showed varying patterns of susceptibility to the antibiotics tested. Conclusions: The prevalence of bacterial contamination in blood products suggests that patients who receive blood products are at risk of developing infection.

Prevalence of human immunodeficiency virus, syphilis, hepatitis B and C in blood donations in Namibia

BACKGROUND

Transfusion Transmissible Infections (TTIs) such as Human Immunodeficiency Virus (HIV), syphilis, hepatitis B virus (HBV) and hepatitis C virus (HCV) are infections which are common in some communities in Southern Africa. It is important to screen blood donations for these infections.

METHODS

This is a retrospective study which involved reviewing of previous blood donation records for the year 2012 in Namibia. The records were analyzed to determine the prevalence of HIV, syphilis, Hepatitis B and C among blood donations with regard to gender, age and geographical region of the donors.

RESULTS

The findings indicated a significantly low prevalence of HIV, syphilis, HBsAg and anti-Hepatitis C among the blood donations. A low infection rate of 1.3% by any of the four tested TTIs was found among the blood donations given by the donor population in Namibia in 2012.

CONCLUSION

The blood donations given by the donor population in Namibia has a low infection rate with the HIV, syphilis, HBsAg and anti-HCV. A strict screening regime must continue to be used as the infections are still present albeit in small numbers.

Streptococcus agalactiae (group B streptococcus (GBS)) colonisation and persistence, in pregnancy; a comparison of two diverse communities (rural and urban)

OBJECTIVE

To establish the extent of GBS colonisation, persistence of colonisation in pregnancy and influence of obstetric history in two diverse communities (rural and urban) in Zimbabwe.

DESIGN

Cross sectional survey.

SETTING

Rutsanana Clinic in Highfield, Harare (representing the urban area) and Chitsungo Mission Hospital in Lower Guruve, (representing the rural area).

SUBJECTS

300 and 100 pregnant women from the urban and rural areas respectively.

MAIN OUTCOME MEASURES

GBS colonisation and persistence rates for both urban and rural areas were established, together with pregnancy outcome.

RESULTS

Mother colonisation rate was significantly higher in the rural areas (60%) as compared to the urban areas (46%). GBS colonisation persistence was evidently more in rural (48%) that in urban women (12%). Baby colonisation was also more in the rural (23%) that in urban area (5%). In both the rural and urban areas, flu-like illness was a common feature and was equally reported by the subjects. Vaginal discharge requiring treatment, previous stillbirths and previous miscarriages were equally reported in both communities.

Use of culture methods for recovery of atypical mycobacteria from stools of AIDS patients

OBJECTIVE

To establish recovery rates of atypical mycobateria from stools of suspected AIDS patients using culture media.

DESIGN

Laboratory evaluation of recovery rates, contamination rates, optimum exposure time and optimum concentration of alkali used for decontamination.

SETTING

The study was conducted in Harare, Zimbabwe at two medical institutions: Beatrice Road Infectious Diseases Hospital (BRIDH) (a tuberculosis referral hospital) and Mashambanzou Care Unit (MCU) (a home-based care centre).

SUBJECTS

A total of 386 stool specimens from suspected AIDS patients from the two health institutions plus 81 stool specimens from clinically healthy patients were collected. The number of patients from MCU was 144 (49 females, 95 males) and 242 from BRIDH (119 males, 123 females).

MAIN OUTCOME MEASURE

The main goals were to determine optimum exposure time and optimum concentration of alkali used in decontamination and to identify the culture medium with the best recovery rates of atypical mycobacteria.

RESULTS

Optimum recovery of atypical mycobacteria was achieved on Peizer TB medium after treating stool specimens with 4% sodium hydroxide for 35 minutes. In addition, the use of Kirchner's medium improved isolation rates, although with a slight increase in contamination at levels of 2.9%.

CONCLUSION

A stool specimen can be used to recover atypical mycobacteria in suspected AIDS patients. Recovery is achieved using Peizer TB medium at a concentration of 4%. Varying the exposure time of the stool specimen to the decontaminating alkali and incorporating antifungal agents and antibiotics into the medium, improves recovery of atypical mycobacteria.