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Abstract Background Coagulase-negative staphylococci (CoNS) have been linked to severe conditions such as bloodstream infection, with biofilm formation regarded as the major virulence mechanism. This study determined virulence genes (VGs) (icaA, icaB, icaC, and icaD) responsible for biofilm formation and antibiotic resistance genes (ARGs) (blaZ, mecA, and aac(6’)-Ie-aph(2’’)-Ia) in CoNS isolated from blood samples of 70 neonates with sepsis in Dar es Salaam, Tanzania. We used VITEK®MS (BioMérieux, France) for speciation and phenotypically detected biofilm production using the Congo red agar. Polymerase chain reaction was performed for ARGs and VGs detection; principal component analysis was used to ascertain their relationship. Results Out of 70 CoNS, Staphylococcus epidermidis, 27 (36.8%) was the most commonly isolate, subsequently to Staphylococcus haemolyticus, 24 (34.3%). The intercellular adhesion genes (ica) were detected in all isolates, with IcaD found in 70 (100.0%), followed by icaB 69 (98.6%), icaC 69 (98.6%), and icaA 65 (92.9%). Four virulence gene combinations (icaADBC, icaBCD, icaACD, and icaABD) were detected, predominantly icaADBC 63 (90.0%). Sixty-one (87.1%) isolates harbored three ARGs, mostly the mecA gene 69 (98.6%), followed by blaZ 67 (95.7%) and aac (6’)-Ie-aph (2’’)-Ia, 65 (92.7%). We observed a moderate positive correlation between mecA and icaA genes (r = 0.4341). Sixty-five (97.0%) isolates resistant to penicillin harbored blaZ genes, and all 62 (100%) resistant to oxacillin harbored mecA genes. Of the 66 isolates resistant to gentamycin, 62 (93.9%) harbored the aac (6’)-Ie-aph (2’’)-Ia gene. The mecA gene contributed most of the resistance, followed by aac(6’)-Ie-aph(2’’)-Ia genes. However, the icaA and icaD genes significantly influenced the virulence of CoNS. Conclusions Most CoNS isolated from blood samples of neonates with sepsis harbor a variety of clinically relevant virulence and resistance genes, indicating their ability to cause severe infections that are difficult to treat. Significantly, 59 (84.3%) isolates were phenotypically penicillin, gentamycin, and oxacillin resistant; the antibiotics recommended in the national guidelines for empiric treatment of neonatal sepsis.

Escherichia coli is one of the critical One Health pathogens due to its vast array of virulence and antimicrobial resistance genes. This study used multiplex PCR to determine the occurrence of virulence genes bfp, ompA, traT, eaeA, and stx1 among 50 multidrug-resistant (MDR) E. coli isolates from humans (n = 15), animals (n = 29), and the environment (n = 6) in Dar es Salaam, Tanzania. Their association with antimicrobial-resistant genes (ARGs) was determined using Principal Component Analysis (PCA). All 50/50 (100%) MDR E. coli isolates carried at least one virulence gene, with 19/50 (38%) carrying four genes, bfp + traT + eaeA + ompA. The findings showed a high occurrence of virulence genes bfp (82%), traT (82%), eaeA (78%), and ompA (72%); the study detected no stx1 in any of the isolates. In humans, the most detected virulence genes were bfp and traT 14/15 (93.3%); for poultry, it was eaeA 13/14 (92.9%); for pigs, was bfp and traT 13/15 (86.7%); while for river water, it was eaeA 6/6 (100%). The study observed no significant association between virulence genes and ARGs. PCA results show the genes ompA, traT, eaeA, and bfp contributed to the virulence of the isolates, and blaTEM, blaCTX-M, and qnrs contributed to ARGs. The PCA ellipses show that isolates from pigs had more virulence genes than those isolated from poultry, river water, and humans. The high frequency of numerous virulence genes in MDR E. coli isolates from humans, animals, and the environment indicates that these isolates have a very high potential to cause diseases that are difficult to treat because they are MDR.

Abstract Background Whole-genome sequencing (WGS)-based prediction of drug resistance in Mycobacterium tuberculosis has the potential to guide clinical decisions in the design of optimal treatment regimens. Methods We utilized WGS to investigate drug resistance mutations in a 32-year-old Tanzanian male admitted to Kibong’oto Infectious Diseases Hospital with a history of interrupted multidrug-resistant tuberculosis treatment for more than three years. Before admission, he received various all-oral bedaquiline-based multidrug-resistant tuberculosis treatment regimens with unfavourable outcomes. Results Drug susceptibility testing of serial M. tuberculosis isolates using Mycobacterium Growth Incubator Tubes culture and WGS revealed resistance to first-line anti-TB drugs, bedaquiline, and fluoroquinolones but susceptibility to linezolid, clofazimine, and delamanid. WGS of serial cultured isolates revealed that the Beijing (Lineage 2.2.2) strain was resistant to bedaquiline, with mutations in the mmpR5 gene (Rv0678. This study also revealed the emergence of two distinct subpopulations of bedaquiline-resistant tuberculosis strains with Asp47f and Glu49fs frameshift mutations in the mmpR5 gene, which might be the underlying cause of prolonged resistance. An individualized regimen comprising bedaquiline, delamanid, pyrazinamide, ethionamide, and para-aminosalicylic acid was designed. The patient was discharged home at month 8 and is currently in the ninth month of treatment. He reported no cough, chest pain, fever, or chest tightness but still experienced numbness in his lower limbs. Conclusion We propose the incorporation of WGS in the diagnostic framework for the optimal management of patients with drug-resistant and extensively drug-resistant tuberculosis.

Abstract Background Hospital sewage is a significant reservoir of antimicrobial-resistant pathogens and genes that pose a huge public health threat. In this study, we determined the occurrence of multidrug-resistant Escherichia coli and Klebsiella pneumoniae in sewage flowing from a referral hospital through the urban sewage system to the point of discharge in the Indian Ocean. Results A total of 400 sewage samples were collected, yielding 517 isolates. Of these, 32.3% (167/517) were from hospital sewage, while 67.7% (350/517) were from the community. E. coli was the most common isolate (44.5% (230/517)), followed by K. pneumoniae at 27.3% (141/517), and other gram-negative bacteria constituted 28.2% (146/517) of the isolates. Multidrug resistance (MDR) was seen in 80.9% (186/230) E. coli and 71.6% (101/141) K. pneumoniae. Of the MDR isolates, 27.2% (78/287) were resistant to four different classes of antibiotics, while 6.9% (20/287) exhibited resistance to eight classes. The most frequent MDR pattern was PEN/CEP/TET/QNL/SUL, seen in 14.2% (38/287) of the isolates. The isolation frequency of MDR E. coli and K. pneumoniae at different sampling sites was high, being 47.6% in hospital chambers, 62.0% in hospital ponds, 58.1% in the treated hospital wastewater, and 55.6% in the community stream draining into the Indian Ocean. Extended spectrum beta-lactamase production was observed in 40% (92/230) of E. coli and 36.2% (51/141) of K. pneumoniae isolates. Resistance to quinolones among E. coli was 54.8% (126/230) and was 39.7% in K. pneumoniae (56/141). Carbapenem resistance in E. coli was 39.6% (91/230), while among K. pneumoniae isolates was 32.6% (46/141). Conclusions We found high proportions of multidrug-resistant E. coli and K. pneumoniae in the wastewater flowing from the hospital through the community sewage system to the point where it enters the Indian Ocean. Biological treatment did not significantly reduce the proportion of resistant bacteria, posing a very serious public health threat. The release of these highly resistant pathogens into the Indian Ocean is of international concern.

Abstract Background Previous studies have shown significant differences and lack clarity on whether resistance to either isoniazid or rifampicin can predict multidrug resistance tuberculosis (MDR-TB). Some consider rifampicin resistance to be a surrogate for MDR-TB. We, therefore, conducted this study to determine resistance to either isoniazid or rifampicin can predict MDR-TB. Results A total of 315 Mycobacteria tuberculosis isolates were tested for resistance against isoniazid, rifampicin, ethambutol and streptomycin using the phenotypic proportion method on Lowenstein–Jensen media. Results showed most isolates (88.9%, 280/315) were not resistant to any anti-TB tested, 5.7% (18/315) were resistant to both isoniazid and rifampicin, 2.5% (8/315) were resistant to rifampicin only and 1.3% (4/315) were resistant to all four first-line anti-tuberculosis. Prediction of MDR TB basing on rifampicin results showed sensitivity of 100.0%, specificity of 96.3%, diagnostic accuracy of 96.5%, and positive and negative predictive values of 62.1% and 100.0%, respectively. Isoniazid had sensitivity of 100.0%, specificity of 98.3%, diagnostic accuracy of 98.4%, and positive and negative predictive values of 78.3% and 100.0%, respectively. Prediction of rifampicin resistance based on isoniazid results had sensitivity of 62.1%, specificity of 98.3%, diagnostic accuracy of 94.9%, a positive predictive value of 78.3% and a negative predictive value of 96.2%. Conclusions Resistance to either rifampicin or isoniazid sub-optimally predicts MDR-TB. Despite having high sensitivity and specificity, the positive predictive value of rifampicin was only 62.1% and for isoniazid was 78.3%, suggesting that if either is tested in isolation both could result in false positives MDR-TB cases, resulting into patients being unnecessarily subjected to the more toxic and expensive second-line anti-TB drugs, which are less effective compared to first-line anti-TB drugs.

Campylobacter jejuni is one of the major aetiologies of diarrhoea. Understanding the processes and virulence factors contributing to C. jejuni fitness is a cornerstone for developing mitigation strategies. Two-component signal transduction systems, known as two-component systems (TCSs), along with single regulators with no obvious cognate histidine kinase, help pathogens in interacting with their environments, but the available literature on C. jejuni is limited. A typical TCS possesses histidine kinase and response regulator proteins. The objective of this review was to provide insights into the virulence of C. jejuni associated with TCSs and single regulators. Despite limited research, TCSs are important contributors to the pathogenicity of C. jejuni by influencing motility (FlgSR), colonisation (DccRS), nutrient acquisition (PhosSR and BumSR), and stress response (RacRS). Of the single regulators, CbrR and CosR are involved in bile resistance and oxidative stress response, respectively. Cross-talks among TCSs complicate the full elucidation of their molecular mechanisms. Although progress has been made in characterising C. jejuni TCSs, shortfalls such as triggering signals, inability to induce mutations in some genes, or developing suitable in vivo models are still being encountered. Further research is expected to shed light on the unexplored sides of the C. jejuni TCSs, which may allow new drug discoveries and better control strategies.

Abstract Background The emergence and spread of antimicrobial resistance (AMR) present a challenge to disease control in East Africa. Resistance to beta-lactams, which are by far the most used antibiotics worldwide and include the penicillins, cephalosporins, monobactams and carbapenems, is reducing options for effective control of both Gram-positive and Gram-negative bacteria. The World Health Organization, Food and Agricultural Organization and the World Organization for Animal Health have all advocated surveillance of AMR using an integrated One Health approach. Regional consortia also have strengthened collaboration to address the AMR problem through surveillance, training and research in a holistic and multisectoral approach. This review paper contains collective information on risk factors for transmission, clinical relevance and diversity of resistance genes relating to extended-spectrum beta-lactamase-producing (ESBL) and carbapenemase-producing Enterobacteriaceae, and Methicillin-resistant Staphylococcus aureus (MRSA) across the human, animal and environmental compartments in East Africa. Main body The review of the AMR literature (years 2001 to 2019) was performed using search engines such as PubMed, Scopus, Science Direct, Google and Web of Science. The search terms included ‘antimicrobial resistance and human-animal-environment’, ‘antimicrobial resistance, risk factors, genetic diversity, and human-animal-environment’ combined with respective countries of East Africa. In general, the risk factors identified were associated with the transmission of AMR. The marked genetic diversity due to multiple sequence types among drug-resistant bacteria and their replicon plasmid types sourced from the animal, human and environment were reported. The main ESBL, MRSA and carbapenem related genes/plasmids were the bla CTX-Ms (45.7%), SCCmec type III (27.3%) and IMP types (23.8%), respectively. Conclusion The high diversity of the AMR genes suggests there may be multiple sources of resistance bacteria, or the possible exchange of strains or a flow of genes amongst different strains due to transfer by mobile genetic elements. Therefore, there should be harmonized One Health guidelines for the use of antibiotics, as well as regulations governing their importation and sale. Moreover, the trend of ESBLs, MRSA and carbapenem resistant (CAR) carriage rates is dynamic and are on rise over time period, posing a public health concern in East Africa. Collaborative surveillance of AMR in partnership with regional and external institutions using an integrated One Health approach is required for expert knowledge and technology transfer to facilitate information sharing for informed decision-making.

Abstract Background Tanzania has witnessed a significant decrease in the prevalence of human immunodeficiency virus (HIV) and viral hepatitis in the general population attributed to several interventional measures. It is uncertain whether this decline has also occurred among people who inject drugs (PWID). This study aimed to determine the seroprevalence of HIV, Hepatitis B and C viruses infection among PWID recruited from their hotspot sites in Dar es Salaam, Tanzania. Methods A cross-sectional study conducted between June and September 2017 recruited PWID from pre-identified hotspot sites using a snowball referral sampling technique. A structured questionnaire was used to obtain information regarding socio-demographic characteristics, behaviour and drug use. Blood was tested for the presence of IgG antibodies against HIV and Hepatitis C virus (HCV) and hepatitis B surface antigen (HBsAg). Data were entered in the computer using excel software and analysed using Statistical Package for Social Sciences version 20. Results A total of 219 PWID were recruited, the majority of whom were males (74.9%), unmarried (60.7%), had low education (62.6%) and low income (57.1%). The median age was 39 years, with an inter-quartile range of 35–43. Approximately 32.0% had a history of drug injection for more than 3 years, 79.9% were injecting drugs more than 3 times per day and 47.5% were sharing needles. The overall prevalence of HIV, HBsAg, and HCV was 33.8, 7.8, and 50.2%, respectively. There was serologic evidence of at least one infection for 68.9%, while 22.4% had two or more infections. HIV infection was independently associated with being married, while HCV was associated with injecting drugs for more than 3 years and unprotected sex. Conclusion Over two-third of PWID had serologic evidence of infection with at least one virus while 22.4% having at least two infections. The high prevalence of HIV and viral hepatitis infections among PWID may hamper initiatives of ending HIV and viral hepatitis epidemics in Tanzania.

Abstract Background Tuberculosis (TB), particularly multi- and or extensive drug resistant TB, is still a global medical emergency. Whole genome sequencing (WGS) is a current alternative to the WHO-approved probe-based methods for TB diagnosis and detection of drug resistance, genetic diversity and transmission dynamics of Mycobacterium tuberculosis complex (MTBC). This study compared WGS and clinical data in participants with TB. Results This cohort study performed WGS on 87 from MTBC DNA isolates, 57 (66%) and 30 (34%) patients with drug resistant and susceptible TB, respectively. Drug resistance was determined by Xpert® MTB/RIF assay and phenotypic culture-based drug-susceptibility-testing (DST). WGS and bioinformatics data that predict phenotypic resistance to anti-TB drugs were compared with participant’s clinical outcomes. They were 47 female participants (54%) and the median age was 35 years (IQR): 29–44). Twenty (23%) and 26 (30%) of participants had TB/HIV co-infection BMI

Abstract Background One Health (OH) is an integrated approach, formed inclusive of using multiple disciplines to attain optimal health for humans, animals, and the environment. The increasing proximity between humans, livestock, and wildlife, and its role in the transmission dynamics of mycobacterial infections, necessitates an OH approach in the surveillance of zoonotic diseases. The challenge remains as humans, livestock, and wildlife share resources and interact at various interfaces. Therefore, this review explores the potential of the OH approach to understand the impact of mycobacterial infections in Tanzania in terms of lessons learnt and future perspectives. Materials and methods Available literature on OH and mycobacterial infections in Tanzania was searched in PubMed, Google Scholar, and Web of Science. Articles on mycobacterial infections in Tanzania, published between 1997 to 2017, were retrieved to explore the information on OH and mycobacterial infections. Main body The studies conducted in Tanzania had have reported a wide diversity of mycobacterial species in humans and animals, which necessitates an OH approach in surveillance of diseases for better control of infectious agents and to safeguard the health of humans and animals. The close proximity between humans and animals increases the chances of inter-specific transmission of infectious pathogens, including drug-resistant mycobacteria. In an era where HIV co-infection is also the case, opportunistic infection by environmental non-tuberculous mycobacteria (NTM), commonly known as mycobacteria other than tuberculosis (MOTT) may further exacerbate the impact of drug resistance. NTM from various sources have greatest potential for diverse strains among which are resistant strains due to continued evolutional changes. Conclusion A collaborative interdisciplinary approach among professionals could help in solving the threats posed by mycobacterial infections to public health, particularly by the spread of drug-resistant strains.

Rapid, accurate and reliable assays are required for timely detection of drug-resistant tuberculosis and early initiation of second-line TB treatment as well as to minimize transmission of resistant strains. This study assessed diagnostic performance characteristics of two rapid molecular assays, line probe assay (LPA) and GeneXpert (MTB/RIF), in the detection rifampicin monoresistance using the phenotypic proportion method on Lowenstein–Jensen media as the gold standard. This study involved a total of 357 isolates, 74 rifampicin-resistant and 283 rifampicin-susceptible, collected at the Central Tuberculosis Reference Laboratory (CTRL) in Dar es Salaam, Tanzania, between 2016 and 2019. Sensitivity, specificity and positive and negative predictive values were used to assess the performance characteristics of the two assays while kappa coefficient was used to determine agreement of test results. The receiver operating curve (ROC) was used to determine the discriminatory ability of the test in distinguishing resistant and susceptible TB isolates. Our results showed that GeneXpert had sensitivity, specificity and positive and negative predictive values of 93.2, 82.7, 58.5 and 97.9%, respectively; the corresponding performance for LPA was 86.5, 97.5, 90.1 and 96.5%, respectively. Compared with conventional phenotypic DST results, GeneXpert had a moderate agreement (kappa 0.621, p < 0.001), while LPA had high agreement (0.853, p < 0.001). LPA showed an accuracy of 95.2% compared to GeneXpert’s 84.9%. ROC curve depicted the ability of the tests to distinguish rifampicin-sensitive and rifampicin-resistant strains to be 87.9% for GeneXpert and 92.0% for LPA. Our results indicate the superiority of LPA over GeneXpert regarding detection of rifampicin monoresistance. However, logistic challenges such as longer turnaround time and need for skilled laboratory personnel may limit its use.

In Tanzania, the increased demand for animal-derived foods, particularly eggs, meat, and milk, has resulted in the intensification of farming systems with the use of antimicrobials, particularly sulphonamides and tetracyclines. According to the FAO/WHO Codex Alimentarius commission, concentrations of antimicrobial residues in food exceeding the acceptable daily intake (ADI) and maximum residual limit (MRL) pose a health risk to consumers. This cross-sectional study determined the concentrations of sulphonamide and tetracycline residues in the liver tissues of commercial broiler chicken sold in Dar es Salaam, Tanzania, to find out whether the amounts of residues were within the legally permitted and acceptable limits in food. We conveniently sampled eighty-four liver tissue samples from broiler chicken sold in two out of six large markets in Dar es Salaam. The amounts of tetracycline and sulphonamide residues were determined using an ELISA kit (Shenzhen Lvshiyuan Biotechnology Company, Shenzhen, China). The results showed that all 100% (n = 84) samples contained tetracycline residues and 21.4% (n = 18) samples contained sulphonamide residues, while 21.4% (n = 18) contained both sulphonamide and tetracycline residues. The concentrations of sulphonamide residues were within the maximum residual limit (MRL). However, 90.5% (n = 76) of the samples had tetracycline levels that exceeded the acceptable daily intake (ADI) range 0–3 µg/kg and 13.1% (n = 11) of the samples had tetracycline levels that exceeded the maximum residue limit of 300 µg/kg. The observed presence of antibiotic residues in the poultry tissues poses a health risk to consumers, and may lead to antimicrobial resistance micro-organisms, which may spread to humans and animals via the environment. Vigorous surveillance and observation of the withdrawal periods should be advocated to ensure that the food from animals is safe with regard to the residues of veterinary medicines.

Thermophilic Campylobacter species are among the major etiologies of bacterial enteritis globally. This study aimed at assessing the antimicrobial resistance (AMR) profiles, virulence genes, and genetic diversity of thermophilic Campylobacter species isolated from a layer poultry farm in South Korea. One hundred fifty-three chicken feces were collected from two layer poultry farms in Gangneung, South Korea. The Campylobacter species were isolated by cultural techniques, while PCR and sequencing were used for species confirmation. Antimicrobial susceptibility testing for six antimicrobials [ciprofloxacin (CIP), nalidixic acid (NAL), sitafloxacin (SIT), erythromycin (ERY), tetracycline (TET), and gentamicin (GEN)] was carried out by broth microdilution. Three AMR and nine virulence genes were screened by PCR. Genotyping was performed by flaA-restriction fragment length polymorphism (RFLP) and multilocus sequence typing (MLST). Of the 153 samples, Campylobacter spp. were detected in 55 (35.9%), with Campylobacter jejuni and Campylobacter coli being 49 (89.1%) and six (10.9%), respectively. High-level resistance was observed for CIP (100%), NAL (100%), and TET (C. jejuni, 93.9%; C. coli: 83.3%). No resistance was observed for SIT. The missense mutation (C257T) in gyrA gene was confirmed by sequencing, while the tet(O) gene was similar to known sequences in GenBank. The rate of multidrug-resistant (MDR) strains was 8.2%, and they all belonged to C. jejuni. All Campylobacter isolates possessed five virulence genes (cdtB, cstII, flaA, cadF, and dnaJ), but none possessed ggt, while the rates for other genes (csrA, ciaB, and pldA) ranged between 33.3 and 95.9%. The flaA-RFLP yielded 26 flaA types (C. jejuni: 21 and C. coli: five), while the MLST showed 10 sequence types (STs) for C. jejuni and three STs for C. coli, with CC-607 (STs 3611) and CC-460 (ST-460) being predominant. Among the 10 STs of C. jejuni, three were newly assigned. The findings of this study highlight the increased resistance to quinolones and TET, the virulence potential, and the diverse genotypes among Campylobacter strains isolated from the layer poultry farm.

In Tanzania, information on antimicrobial resistance in small-scale dairy cattle is scarce. This cross-sectional study was conducted to determine the different levels and pattern of antimicrobial resistance (AMR), in 121 Escherichia coli isolated from rectal swab of 201 apparently healthy small-scale dairy cattle in Dar es Salaam, Tanzania. Isolation and identification of E. coli were carried out using enrichment media, selective media, and biochemical tests. Antimicrobial susceptibility testing was carried out using the Kirby–Bauer disk diffusion method on Mueller-Hinton agar (Merck), according to the recommendations of Clinical and Laboratory Standards Institute (CLSI). Resistance was tested against ampicillin, gentamicin, chloramphenicol, trimethoprim-sulfamethoxazole, tetracycline, nalidixic acid, ciprofloxacin and cefotaxime. Resistance to almost all antimicrobial agents was observed. The agents to which resistance was demonstrated most frequently were ampicillin (96.7%), cefotaxime (95.0%), tetracycline (50.4%), trimethoprim-sulfamethoxazole (42.1%) and nalidixic acid (33.1%). In this case, 20 extended-spectrum beta-lactamases (ESBLs) producing E. coli were identified. 74.4% (90/121) of the isolates were Multidrug resistant (MDR), ranging from a combination of three to 8 different classes. The most frequently observed phenotypes were AMP-SXT-CTX with a prevalence of 12.4%, followed by the combination AMP-CTX with 10.7% and TE-AMP-CTX and NA + TE + AMP + CTX with 8.3% each. The high prevalence and wide range of AMR calls for prudent antimicrobial use.

Abstract Background The introduction of Xpert MTB/RIF assay (Xpert) has significantly improved diagnosis of Tuberculosis (TB) in resource limited human immunodeficiency virus (HIV) endemic settings. We aimed to modify the Xpert protocol to improve the detection of Mycobacterium tuberculosis (MTB). Methods This cross sectional study was conducted among presumptive pulmonary tuberculosis (PTB) patients at Kibong’oto Infectious Diseases Hospital between August and November 2015. Each patient consented to provide 2 samples of raw sputa. One-sputum sample was sedimented using the Petroff’s method and divided into two portions. One portion of sediment was inoculated on Lowenstein-Jensen culture media and observed for any growth for up to 8 weeks. Both, raw sputum and the portions of sediments were tested separately using Xpert with a sample reagent ratio of 1:2. Mean age of patients, prevalence of MTB, Xpert sensitivity, specificity, positive and negative predictive value were calculated. An incremental sensitivity was determined. Pearson chi-square and either an independent T or Mann-Whitney U-test were used to compared categorical and continuous variables respectively. A p- value of ≤0.05 was considered significant. Results Of the 270 presumptive PTB cases, 262 were eligible for analysis. Eight (3%) were excluded due to contaminated culture. Patients’ mean age was 42.9 (±SD 15.1) years of which 173 (66%) were female. The overall prevalence of PTB was 112 (43%), of which the Xpert detected 105 (40%) in sediments and 98 (37%) in raw sputa as compared to culture which detected 85 (32%) cases of PTB. Sensitivity, specificity, positive and negative predictive values of Xpert on sputum sediments were 92%, 85%, 74% and 96% respectively. Overall, the incremental sensitivity of Xpert on sediment over raw sputum was 6%. In HIV infected Presumptive PTB, the incremental sensitivity was 12%. Conclusion Lowering the sample reagent to sediment dilution ratio increases sensitivity of Xpert on MTB detection among presumptive PTB cases, especially in HIV infected individuals.

OBJECTIVE: Nine out of ten tuberculosis deaths occur in tuberculosis-burdened countries, particularly Sub Saharan Africa. In these setting mortality has not been fully described. We describe the magnitude and pattern of TB mortality in Tanzania. METHODS: A multicenter prospective cohort study was conducted among HIV infected and uninfected pulmonary tuberculosis patients from time of anti-TB treatment initiation to completion. Patients were censored at the time of treatment completion, or at their last visit for those who did not complete TB treatment. Kaplan-Meier curves were used to estimate time to death; cox proportional hazards model was used to examine risk factors for mortality. RESULTS: A total of 58 deaths out of 1696 patients (3.4%) occurred, two thirds (n = 39) during the first two months of treatment. Compared to HIV un-infected TB patients, mortality risk for TB/HIV co-infected patients was least when antiretroviral therapy (ART) was initiated after 14 days of anti-TB (RR = 3.55; 95% CI: 1.44, 8.73 p

Thermophilic Campylobacter species are clinically important aetiologies of gastroenteritis in humans throughout the world. The colonization of different animal reservoirs by Campylobacter poses an important risk for humans through shedding of the pathogen in livestock waste and contamination of water sources, environment, and food. A review of published articles was conducted to obtain information on the prevalence and antimicrobial resistance (AMR) profiles of thermophilic Campylobacter species in humans and animals in sub-Saharan Africa (SSA). Electronic databases, namely, PubMed, Google Scholar, Research4life-HINARI Health, and Researchgate.net, were searched using the following search terms “thermophilic Campylobacter,” “Campylobacter jejuni,” “Campylobacter coli,” “diarrhea/diarrhoea,” “antimicrobial resistance,” “antibiotic resistance,” “humans,” “animals,” “Sub-Saharan Africa,” and “a specific country name.” Initially, a total of 614 articles were identified, and the lists of references were screened in which 22 more articles were identified. After screening, 33 articles on humans and 34 on animals and animal products were included in this review. In humans, Nigeria reported the highest prevalence (62.7%), followed by Malawi (21%) and South Africa (20.3%). For Campylobacter infections in under-five children, Kenya reported 16.4%, followed by Rwanda (15.5%) and Ethiopia (14.5%). The country-level mean prevalence in all ages and under-five children was 18.6% and 9.4%, respectively. The prevalence ranged from 1.7%–62.7% in humans and 1.2%–80% in animals. The most reported species were C. jejuni and C. coli. The AMR to commonly used antimicrobials ranged from 0–100% in both humans and animals. Poultry consumption and drinking surface water were the main risk factors for campylobacteriosis. The present review provides evidence of thermophilic Campylobacter occurrence in humans and animals and high levels of AMR in SSA, emphasizing the need for strengthening both national and regional multisectoral antimicrobial resistance standard surveillance protocols to curb both the campylobacteriosis burden and increase of antimicrobial resistance in the region.

In Africa, there is dearth of information on antimicrobial use (AMU) in agriculture and food production systems and its consequential resistance in pathogens that affect animal, human and environmental health. Data published between 1980 and 2021 on the magnitude of AMU and AMR in agriculture and food productions systems in Africa were reviewed. Data from 13–27 countries in Africa indicate that 3558–4279 tonnes of antimicrobials were used in animals from 2015 to 2019. Tetracyclines and polypeptides contributed the largest proportion of antimicrobials used. Cattle and poultry production account for the largest consumption of antimicrobials in Africa. Although limited studies have reported AMR in crops, fish and beekeeping, AMR from a variety of farm animals has been substantially documented in Africa. Some countries in Africa have developed policies/plans to address AMU and AMR in agriculture and food production systems; however, their enforcement is challenged by weak regulations. In conclusion, although there is limited information on the quantities of antimicrobials used in agriculture and food production system, the levels of AMR are high. There is a need to strengthen regulatory authorities with a capacity to monitor AMU in agriculture and food production systems in Africa.

We conducted a qualitative study to explore the practices and challenges of veterinary paraprofessionals (paravets) on antimicrobial use and resistance in domestic animals. Methods: This was a qualitative study, which involved semi-structured interviews with paravets from the Ilala, Ubungo, Kigamboni, Kinondoni, and Temeke districts in Dar es Salaam, Tanzania. Results: A total of 40 paravets participated in this study. The majority (72.5%) admitted to having not undergone any formal training on antimicrobial use and/or resistance. Paravets face several challenges, including poor working conditions and having no access to laboratory services to advise on antimicrobial choice and selection. They also face challenges from livestock farmers such as the inability to afford the recommended medicines, the self-prescription of antimicrobials, and poor record keeping. The presence of sub-standard medicine and the lack of guidelines on the appropriate disposal of medicines were also identified as affecting their services. Conclusion: Paravets should be trained in the judicious use of antimicrobials, and the same training should be used to refresh their knowledge on the diagnosis and prevention of infections. The Veterinary Council of Tanzania and other regulatory agencies should assist in addressing the challenges facing paravets that are related to animal health services and the quality of medicines.

This cross-sectional study was conducted between January and June 2020, in five large poultry slaughter slabs in Dar es Salaam, Tanzania. Purposive sampling was used to select broilers and spent layers, from which meat and cloaca swabs were collected to determine the occurrence of multidrug resistant (MDR) Escherichia coli. Identification of isolates was done using API 20E, and antimicrobial susceptibility testing was performed as per CLSI (2018) guidelines. EBSL (CTX-M, TEM, SHV) and plasmid mediated quinolone (qnrA, qnrB, qnrS and aac(6′)-Ib-cr) were screened using PCR. Out of 384 samples, 212 (55.2%) were positive for E. coli, of which 147 (69.3%) were resistant to multiple drugs (MDR). Highest resistance was detected to tetracycline (91.9%), followed by sulfamethoxazole-trimethoprim (80.5%), ampicillin (70.9%), ciprofloxacin (40.2%) and 25% cefotaxime, gentamycin (10.8%) and imipenem (8.6%) (95% CI, p < 0.01). Out of the E. coli-positive samples, ten (10/212) (4.7%) were ESBL producing E. coli, of which CTX-M was detected in two isolates and quinolones resistant gene (qnrS) in eight, while TEM, SHV, qnrA, qnrB and aac(6′)-lb-cr were not detected. The high level of resistance and multidrug resistance imply these antibiotics are ineffective, add unnecessary cost to poultry farmers and certainly facilitate emergence and spread of resistance.

Campylobacter species have developed resistance to existing antibiotics. The development of alternative therapies is, therefore, a necessity. This study evaluates the susceptibility of Campylobacter strains to selected natural products (NPs) and frontline antibiotics. Two C. jejuni strains (ATCC® 33560TM and MT947450) and two C. coli strains (ATCC® 33559TM and MT947451) were used. The antimicrobial potential of the NPs, including plant extracts, essential oils, and pure phytochemicals, was evaluated by broth microdilution. The growth was measured by spectrophotometry and iodonitrotetrazolium chloride. Antibiotic resistance genes (tet(O) and gyrA) were characterized at the molecular level. The minimum inhibitory concentrations (MICs) and the minimum bactericidal concentrations (MBCs) ranged from 25 to 1600 µg/mL. Cinnamon oil, (E)-Cinnamaldehyde, clove oil, eugenol, and baicalein had the lowest MIC and MBC values (25–100 µg/mL). MT947450 and MT947451 were sensitive to erythromycin and gentamicin but resistant to quinolones and tetracycline. Mutations in gyrA and tet(O) genes from resistant strains were confirmed by sequencing. The findings show that NPs are effective against drug-sensitive and drug-resistant Campylobacter strains. The resistance to antibiotics was confirmed at phenotypic and genotypic levels. This merits further studies to decipher the action mechanisms and synergistic activities of NPs.

The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC) genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient) collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs) were: SIT21/CAS1-Kili (n = 76; 25.94%), SIT59/LAM11-ZWE (n = 22; 7.51%), and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%). Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1). We noted that the East-African-Indian (EAI) lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS) lineage was more predominant in Dar es Salaam (p-value

Pulmonary tuberculosis and anemia are both prevalent in Tanzania. There is limited and inconsistent literature on the association between anemia and sputum conversion following tuberculosis treatment.Newly diagnosed sputum smear positive pulmonary tuberculosis patients aged ≥15 years initiating on standard anti tuberculosis therapy were recruited from 14 of 54 tuberculosis clinics in Dar es Salaam. Patients were receiving medication according to the recommended short course Directly Observed Therapy (DOT) strategy and were followed up prospectively until completion of treatment (six months). Patients were evaluated before initiation of TB treatment by performing the following; clinical history, physical examination, complete blood counts, serum biochemistry and sputum microscopy. Sputum smears were re-examined at two months of anti-tuberculosis therapy for presence of acid fast bacilli. Anemia was defined as hemoglobin

Infectious diseases account for nearly 40% of the burden of human mortality and morbidity in low-income countries, of which 7% is attributable to zoonoses and 13% to recently emerging diseases from animals. One of the strategic approaches for effective surveillance, monitoring and control of infectious diseases compromising health in both humans and animals could be through a combination of multiple disciplines. The approach can be achieved through a joint effort from stakeholders comprising health professionals (medical and veterinary), social, economic, agricultural, environmental and other interested parties. With resource scarcity in terms of number of staff, skills and facility in low-income countries, participatory multi- sectoral and multidisciplinary approaches in limiting the burden of zoonotic diseases could be worthwhile. We review challenging issues that may limit the ‘One Health’ approach for infectious diseases surveillance in Tanzania with a focus on Health Policy and how best the human and animal health systems could be complemented or linked to suit the community in need for disease control under the theme’s context.

Despite the apparent public health concern about Bovine tuberculosis (BTB) in Tanzania, little has been done regarding the zoonotic importance of the disease and raising awareness of the community to prevent the disease. Bovine tuberculosis is a potential zoonotic disease that can infect a variety of hosts, including humans. The presence of multiple hosts including wild animals, inefficient diagnostic techniques, absence of defined national controls and eradication programs could impede the control of bovine TB. In Tanzania, the diagnosis of Mycobacterium bovis in animals is mostly carried out by tuberculin skin testing, meat inspection in abattoirs and only rarely using bacteriological techniques. The estimated prevalence of BTB in animals in Tanzania varies and ranges across regions from 0.2% to 13.3%, which is likely to be an underestimate if not confirmed by bacteriology or molecular techniques. Mycobacterium bovis has been detected and isolated from different animal species and has been recovered in 10% of apparently healthy wildebeest that did not show lesions at post-mortem. The transmission of the disease from animals to humans can occur directly through the aerosol route and indirectly by consumption of raw milk. This poses an emerging disease threat in the current era of HIV confection in Tanzania and elsewhere. Mycobacterium bovis is one of the causative agents of human extra pulmonary tuberculosis. In Tanzania there was a significant increase (116.6%) of extrapulmonary cases reported between 1995 and 2009, suggesting the possibility of widespread M. bovis and Mycobacterium tuberculosis infection due to general rise of Human Immunodeficiency virus (HIV). This paper aims to review the potential health and economic impact of bovine tuberculosis and challenges to its control in order to safeguard human and animal population in Tanzania.

For centuries, tuberculosis, which is a chronic infection caused by the bacillus Mycobacterium tuberculosis has remained a global health problem. The global burden of tuberculosis has increased, particularly in the Southern African region, mainly due to HIV, and inadequate health systems which has in turn given rise to emergent drug resistant tuberculosis (TB) strains. Bovine tuberculosis (BTB) has also emerged as a significant disease with the tendency for inter-species spread. The extent of interspecies BTB transmission both in urban and rural communities has not been adequately assessed. The phenomenon is of particular importance in rural communities where people share habitats with livestock and wildlife (particularly in areas near national parks and game reserves). Aerosol and oral intake are the major routes of transmission from diseased to healthy individuals, with health care workers often contracting infection nosocomially. Although TB control has increasingly been achieved in high-income countries, the disease, like other poverty-related infections, has continued to be a disaster in countries with low income economies. Transmission of infections occurs not only amongst humans but also between animals and humans (and occasionally vice versa) necessitating assessment of the extent of transmission at their interface. This review explores tuberculosis as a disease of humans which can cross-transmit between humans, livestock and wildlife. The review also addresses issues underlying the use of molecular biology, genetic sequencing and bioinformatics as t tools to understand the extent of inter-species cross-transmission of TB in a ‘One Health’ context.