A multiplex PCR assay for the differentiation of Mycobacterium tuberculosis complex reveals high rates of mixed-lineage tuberculosis infections among patients in Ghana

In low-resource settings with high tuberculosis (TB) burdens, lack of rapid diagnostic methods for detection and differentiation of Mycobacterium tuberculosis complex (MTBC) is a major challenge affecting TB management. This study utilized comparative genomic analyses of MTBC lineages; M. tuberculosis, M. africanum Lineages 5/6 and M. bovis to identify lineage-specific genes. Primers were designed for the development of a Multiplex PCR assay which was successful in differentiating the MTBC lineages. There was no cross-reaction with other respiratory pathogens tested. Validation of the assay using clinical samples was performed with sputum DNA extracts from 341 clinically confirmed active TB patients. It was observed that 24.9% of cases were caused by M. tuberculosis, while M. africanum L5 & L6 reported 9.0% and 14.4%, respectively. M. bovis infection was the least frequently detected lineage with 1.8%. Also, 27.0% and 17.0% of the cases were PCR negative and unspeciated, respectively. However, mixed-lineage TB infections were recorded at a surprising 5.9%. This multiplex PCR assay will allow speciation of MTBC lineages in low-resource regions, providing rapid differentiation of TB infections to select appropriate medication at the earliest possible time point. It will also be useful in epidemiological surveillance studies providing reliable information on the prevalence of TB lineages as well as identifying difficult to treat cases of mixed-lineage tuberculosis infections

The burden of drug resistance tuberculosis in Ghana; results of the First National Survey.

Resistance to Tuberculosis drugs has become a major threat to the control of tuberculosis (TB) globally. We conducted the first nation-wide drug resistance survey to investigate the level and pattern of resistance to first-line TB drugs among newly and previously treated sputum smear-positive TB cases. We also evaluated associations between potential risk factors and TB drug resistance. Using the World Health Organization (WHO) guidelines on conducting national TB surveys, we selected study participants from 33 health facilities from across the country, grouped into 29 clusters, and included them into the survey. Between April 2016 and June 2017, a total of 927 patients (859 new and 68 previously treated) were enrolled in the survey. Mycobacterium tuberculosis complex (MTBC) isolates were successfully cultured from 598 (65.5%) patient samples and underwent DST, 550 from newly diagnosed and 48 from previously treated patients. The proportion of patients who showed resistance to any of the TB drugs tested was 25.2% (95% CI; 21.8-28.9). The most frequent resistance was to Streptomycin (STR) (12.3%), followed by Isoniazid (INH) (10.4%), with Rifampicin (RIF), showing the least resistance of 2.4%. Resistance to Isoniazid and Rifampicin (multi-drug resistance) was found in 19 (3.2%; 95% CI: 1.9-4.9) isolates. Prevalence of multidrug resistance was 7 (1.3%; 95% CI: 0.5-2.6) among newly diagnosed and 12 (25.0%; 95% CI: 13.6-39.6) among previously treated patients. At both univariate and multivariate analysis, MDR-TB was positively associated with previous history of TB treatment (OR = 5.09, 95% CI: 1.75-14.75, p = 0.003); (OR = 5.41, 95% CI: 1.69-17.30, p = 0.004). The higher levels of MDR-TB and overall resistance to any TB drug among previously treated patients raises concerns about adherence to treatment. This calls for strengthening existing TB programme measures to ensure a system for adequately testing and monitoring TB drug resistance

Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa.

The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection

Retraction.

This is a retraction of 'Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa' 10.1126/science.add873

Antimicrobial activities of Hibiscus sabdariffa and Aspilia africana against clinical isolates of Salmonella typhi

Background: Plants hold prospects for novel drugs discovery against Salmonella typhi and its swift antibiotics resistance. This study aimed to determine the antimicrobial activities of Hibiscus sabdariffa and Aspilia africana extracts against clinical isolates of S. typhi. Methods: Active ingredients of plants were extracted using ethanol and constituted into Extracts I, II and III. Extract I is A. africana, Extract II is H. sabdariffa and Extract III is a combination of extracts of A. africana and H. sabdariffa. Phytochemical screening, antimicrobial sensitivity test (Agar Well Diffusion), Minimum Inhibitory Concentration (MIC), Minimum Bactericidal Concentration (MBC) tests were conducted during this study. Results: Results on phytochemicals of H. sabdariffa and A. africana extracts showed phenols, saponins, tannins, reducing sugars, triterpenoids, coumarins, alkaloids and steroids. Antimicrobial sensitivity test showed that S. typhi was sensitive to all extracts indicating zones of inhibition of 29.0, 19.0 and 18.5 mm for Extract I, II and III respectively while resistant to lower concentrations of Extract I at 100, 50 and 25 mg/ml. Resistant S. typhi was sensitive to Extract I, II, and III (21.0, 19.0 and 19.0 mm) respectively at 200 mg/ml while resistant to both Extract I and II at (100, 50 and 25 mg/ml) and (50 and 25 mg/ml) respectively. MIC experiments showed 3.125, 6.25 and 3.125 mg/ml against sensitive S. typhi and 25, 12.5 and 12.5 mg/ml against resistant S. typhi for Extract I, II and III respectively. MBC values were 25, 12.5 and 12.5 mg/ml against sensitive S. typhi and 50, 25 and 25 mg/ml against resistant S. typhi for Extract I, II and III respectively. Plant extracts, when combined with ciprofloxacin (concentration), indicated MBCs of 0.19, 0.19, and 0.39 mg/ml against sensitive S. typhi compared with 0.19, 0.097 and 0.19 mg/ml against resistant S. typhi for Extract I, II and III respectively. Conclusion: These plant extracts showed great antimicrobial activities and therefore could be exploited and harnessed for future antibiotic drug discovery

No evidence for yaws infection in a small‐scale cross‐sectional serosurvey in Ghanaian monkeys

Abstract Background Treponema pallidum (TP) is a spirochaete bacterium with subspecies that in humans cause syphilis (subsp. pallidum), bejel (subsp. endemicum) and yaws (subsp. pertenue; TPE). The latter is target for eradication which requires detailed information on yaws epidemiology. It has been shown that African nonhuman primates (NHPs) are infected with TPE strains that are closely related to the human infecting yaws bacterium. While human yaws infection is known to be endemic in Ghana, there is a paucity of information regarding TPE infection of Ghana's native NHPs. Objectives The objective was to perform a small‐scale cross‐sectional serological screening for antibodies against TPE in Ghanaian monkeys. Due to the reports of TPE‐infected NHPs from neighbouring Côte d'Ivore, we hypothesised that monkeys in Ghana are infected with TPE and, therefore, are seropositive for antibodies against‐Treponema. Methods We sampled blood from 37 NHPs representing four species: Erythrocebus patas (16/37) 43.2%, Papio anubis (15/37) 40.5%, Chlorocebus sabaeus (3/37) 8.1% and Cercopithecus mona (3/37) 8.1%. Samples were tested using the NHP validated treponemal test ESPLINE TP. Results All 37 animals were seronegative for yaws infection. Conclusions We cannot exclude yaws infection in NHPs in Ghana at this point. Our study, in combination with the absence of reports of clinically infected NHPs in a yaws endemic country is, however, supportive for the current thinking that interspecies infection with TPE is extremely rare. This is an important finding for the current ongoing yaws eradication campaign

Antimicrobial Resistance of Escherichia coli from Broilers, Pigs, and Cattle in the Greater Kumasi Metropolis, Ghana

Globally, resistance to antimicrobial drugs in food animals is on the rise. Escherichia coli of livestock, though commensal in nature, serves as reservoir for antimicrobial resistance genes with the potential of disseminating them. This study sought to examine the antimicrobial resistance profiles of Escherichia coli in broilers, pigs, and cattle in the Kumasi Metropolis and undertake molecular characterisation of the resistances. Faecal E. coli isolates (n = 48) were obtained from 10 broiler farms, (n = 43) from 15 pig farms, and (n = 42) from cattle from the Kumasi Abattoir using standard bacteriological techniques. The Kirby–Bauer disc diffusion method was employed in testing the sensitivities of 133 E. coli isolates to 15 antimicrobials. All 48 isolates from broilers presented no resistance to amoxicillin/clavulanic acid and ceftiofur. A 100% resistance to meropenem was observed in pig and cattle isolates. Multidrug resistance (MDR) across animal groups was 95.8% (n = 46), 95.3% (n = 41), and 64.3% (n = 27) for broilers, pigs, and cattle, respectively. Twenty-eight isolates presenting phenotypic resistance to aminopenicillins and cephalosporins were screened for the presence of extended-spectrum beta-lactamase (ESBL) genes by PCR. One isolate from poultry and another from cattle tested positive for the blaCTX-M ESBL gene. There were no positives for the blaTEM and blaSHV ESBL genes. Commensal E. coli of food animal origin represents an important reservoir of antimicrobial resistance that transfers resistance to pathogenic and nonpathogenic microbes affecting humans and animals. There is an urgent need to institute routine surveillance for the establishment of the mechanisms and molecular orientation of resistance in these organisms

Graduate students’ interest in immunology as a discipline

Interest and motivation significantly influence achievement; however, interest in immunology remains to be determined. Using a structured questionnaire, the current study assessed for the first time interest in immunology among biomedical graduate students in Ghana after a one-week introduction to immunology course. Our results revealed that approximately 80% of study participants expressed an interest in immunology. In addition, we showed that interest in immunology was independent of age and gender of the study participants. More interestingly, we observed that interest in immunology was primarily influenced by career choice. The findings from the present study have implications on immunology education and calls for investment in building capacity in immunology especially in developing countries

Antimicrobial susceptibility profile of oral and rectal microbiota of non‐human primate species in Ghana: A threat to human health

Abstract Background The potential for the transfer of zoonotic diseases, including bacteria between human and non‐human primates (NHPs), is expected to rise. It is posited that NHPs that live in close contact with humans serve as sentinels and reservoirs for antibiotic‐resistant bacteria. Objectives The objective was to characterize the oral and rectal bacteria in Ghanaian NHPs and profile the antimicrobial susceptibility of the isolated bacteria. Methods Oral and rectal swabs were obtained from 40 immobilized wild and captive NHPs from 7 locations in Ghana. Standard bacteriological procedures were used in the isolation, preliminary identification, automated characterization and antimicrobial susceptibility test (AST) of bacteria using the Vitek 2 Compact system. Results Gram‐negative bacteria dominated isolates from the rectal swabs (n = 76, 85.4%), whereas Gram‐positive bacteria were more common in the oral swabs (n = 41, 82%). Staphylococcus haemolyticus (n = 7, 14%) was the most occurring bacterial species isolated from the oral swabs, whereas Escherichia coli (n = 32, 36%) dominated bacteria isolates from rectal swabs. Enterobacter spp. had the highest (39%) average phenotypic resistance to antimicrobials that were used for AST, whereas a trend of high resistance was recorded against norfloxacin, Ampicillin and Tetracycline in Gram‐negative bacteria. Similarly, among Gram‐positive bacteria, Staphylococcus spp. had the highest (25%) average phenotypic resistance to antimicrobials used for AST, and a trend of high resistance was recorded against penicillin G and oxacillin. Conclusions This study has established that apparently healthy NHPs that live in anthropized environments in Ghana harbour zoonotic and antimicrobial resistant bacteria

Comparable Detection of SARS-CoV-2 in Sputum and Oropharyngeal Swab Samples of Suspected COVID-19 Patients

The accurate detection of SARS-CoV-2 through respiratory sampling is critical for the prevention of further transmission and timely initiation of treatment. There is a diverse range of SARS-CoV-2 detection rates in reported studies, with uncertainty regarding the optimal sampling method for COVID-19 diagnosis and monitoring. Oropharyngeal sampling (OPS) is one of the most commonly used methods of respiratory sampling in Ghana and other parts of the world for the detection of SARS-CoV-2 viral RNA. However, this sampling technique has a number of drawbacks, which include difficulty in obtaining high-quality swab samples, increased risk of infection to healthcare workers, and increased cost from a regular supply of swabs, transport media, and personal protective equipment (PPE). This study, therefore, sought to evaluate the diagnostic performance of sputum specimens in the diagnosis of COVID-19. This was a cross-sectional analytical study conducted in two health facilities in Kumasi, Ghana, between April and September 2021. Paired samples (an oropharyngeal swab and sputum) were taken from each recruited patient and run concurrently for the detection of SARS-CoV-2 genes (the N and ORF1ab genes) using RT-qPCR. Of the 317 patients recruited, 50.8% were males, and 60.4% were young adults aged 20–39 years. A significant proportion (65.9%) of the patients did not have any co-morbidity, and the majority were with symptoms; predominantly cough (36.3%), headache (31.5%), general weakness (24.0%), fever (20.2%), and sore throat (16.1%). Being symptomatic (p = 0.003), having comorbidity (p = 0.001), and the reporting facility (p = 0.010) were significantly associated with the COVID-19 status. The sputum samples yielded more COVID-positive, 120/317 (37.9%), as compared to OPS, 83/317 (26.2%). The sputum samples were 85.5% (95% CI, 76.4–91.5) sensitive, 79.1% (95% CI, 73.4–83.7) specific, and with positive and negative predictive values of 59.2% and 93.9%, respectively, when compared with OPS. The overall median of the SARS-CoV-2 viral loads for sputum (3.70 × 103 copies/mL) were significantly higher than in OPS (1.18 × 102 copies/mL) (p = 0.003). Findings from the study suggest self-collected sputum as a useful alternative to OPS for the diagnosis of COVID-19, providing a comparable diagnostic performance and, thereby, easing the uncomfortable process and mitigating risk of aerosol transmission to healthcare workers