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Nicholaus Peter Mnyambwa,1,2 Esther S Ngadaya,2 Godfather Kimaro,2 Dong-Jin Kim,1 Rudovick Kazwala,3 Pammla Petrucka,1,4 Sayoki G Mfinanga2 1School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania; 2National Institute for Medical Research, Muhimbili Medical Research Center, Dar es Salaam, Tanzania; 3Department of Veterinary Medicine, Sokoine University of Agriculture, Morogoro, Tanzania; 4College of Nursing, University of Saskatchewan, Saskatoon, Canada Abstract: Diagnosis of pulmonary tuberculosis (TB) in technology-limited countries is widely achieved by smear microscopy, which has limited sensitivity and specificity. The frequency and clinical implication of smear-positive but culture-negative among presumptive TB patients remains unclear. A cross-sectional substudy was conducted which aimed to identify the proportion of nontuberculous mycobacteria (NTM) infections among 94 “smear-positive culture-negative” patients diagnosed between January 2013 and June 2016 in selected health facilities in Tanzania. Out of 94 sputa, 25 (26.60%) were GeneXpert® mycobacteria TB positive and 11/94 (11.70%) repeat-culture positive; 5 were Capilia TB-Neo positive and confirmed by GenoType MTBC to be Mycobacterium tuberculosis/Mycobacterium canettii. The remaining 6 Capilia TB-Neo negative samples were genotyped by GenoType® CM/AS, identifying 3 (3.19%) NTM, 2 Gram positive bacteria, and 1 isolate testing negative, together, making a total of 6/94 (6.38%) confirmed false smear-positives. Twenty-eight (29.79%) were confirmed TB cases, while 60 (63.83%) remained unconfirmed cases. Out of 6 (6.38%) patients who were HIV positive, 2 patients were possibly coinfected with mycobacteria. The isolation of NTM and other bacteria among smear-positive culture-negative samples and the presence of over two third of unconfirmed TB cases emphasize the need of both advanced differential TB diagnostic techniques and good clinical laboratory practices to avoid unnecessary administration of anti-TB drugs. Keywords: nontuberculous mycobacteria, pulmonary TB, smear-positive, culture-negative, tuberculosis diagnosis

Abstract Background Bovine tuberculosis is a zoonotic problem in pastoral cattle and communities in Uganda. Tuberculin tests in pastoral cattle had shown a high herd but low animal prevalence, with a high proportion of avian reactors. No work had been done to identify the mycobacterial species involved. The objective of the study was to isolate and characterise Mycobacterial species causing tuberculous lesions in slaughtered animals. Lesioned organs compatible with bovine tuberculosis in slaughtered cattle from pastoral areas in Uganda were collected and cultured to isolate mycobacteria. AccuProbe culture identification kits for the Mycobacterium tuberculosis complex, M. avium complex and M. avium were used to identify the isolates. Spoligotyping and Insertion Sequence (IS) 1311 and IS1245 Restriction Fragment Length Polymorphism analysis (RFLP) were used to further characterise the isolates. Results Of the 61 lesioned organs and tissues cultured, 19 isolates were identified as M. bovis, 3 as M. avium subsp.hominissuis, 1 as M. intracellulare, 1 as a mixed culture of M. bovis and M. avium sp. and 1 as M. avium sp. and unidentified mycobacteria. Eleven other mycobacteria outside the tuberculosis and avium complex groups were also isolated. Ten new spoligopatterns grouped into three clusters were identified from M. bovis isolates. Two of the three M. avium subsp.hominissuis isolates showed similar patterns on the IS1311 RFLP but all were different on the IS1245 RFLP. Conclusion The isolation of M. bovis confirms the ongoing infection with spoligotypes unique to Uganda. Isolation of environmental mycobacteria could explain the high avian or non specific tuberculin reactor patterns commonly observed in pastoral cattle and suggests their pathogenic or opportunistic role in the infection of cattle with disseminated bovine tuberculous lesions.

Antimicrobial resistance is a serious and escalating threat to global health. This study established a baseline antimicrobial resistance profile and prevalence for cloacal Escherichia coli in chickens in central Tanzania. Animal husbandry practices, flock size, and chicken breed were recorded for risk factor evaluation to elucidate potential drivers of resistance across populations. Cloacal samples were collected from poultry in Iringa, Tanzania, and E. coli isolates cultured were then tested for susceptibility to seven medically important antimicrobial drugs: ampicillin, amoxicillin-clavulanate, cefoxitin, enrofloxacin, gentamicin, sulfamethoxazole-trimethoprim, and tetracycline using the Kirby-Bauer disk diffusion method. Over 94% of the 59 E. coli isolates tested were resistant to at least one antimicrobial drug, and over 61% of isolates were resistant to three or more classes of antimicrobial drugs. The highest prevalence of resistance found was to tetracycline and sulfamethoxazole-trimethoprim (88% and 86%, respectively), which were used regularly on many sampled chickens. Previous antimicrobial usage emerged as the only significant risk factor associated with increased detection of multi-drug resistant E. coli. Further surveillance and educational outreach about antimicrobial resistance and stewardship is recommended to reduce antimicrobial drug use and to limit the potential spread of resistance to antimicrobial drugs in Tanzania. [ABSTRACT FROM AUTHOR]

The aim of this study was to characterize the role of biocide interventions in the emergence of biocide-tolerant Salmonella, its co-selective association with multidrug-resistant Salmonella and the association with carriage of specific efflux gene markers. Salmonella isolates were detected in 13.9% (208/1,497) and 6.7% (98/1,468) of swine barn drag swab samples at pre- and postdisinfection with biocide, whereas, Salmonella isolates were detected in 17.2% (1,180/6,842) and 7.1% (431/6,093) of the early and late finishing pigs, respectively. Barn-level prevalence of antimicrobial resistance among Salmonella isolates recovered from the floor swab samples was 92.3% (1,503 of 1,628), whereas, the barn-level prevalence of antimicrobial resistance among Salmonella isolates recovered from the fecal samples was 98.02% (4,415 of 4,504). A total of 348 Salmonella isolates from swine barns formerly disinfected with Biosentry and 428 from swine barns disinfected with Synergize were subjected to minimum inhibitory concentration (MIC) testing for Biosentry and Synergize, respectively. In addition, selected Salmonella isolates were also genotyped to identify the carriage of quaternary ammonium compound (qac) tolerance genes. Interestingly, 22.9% (98 of 428) of Salmonella isolates from swine barns disinfected with Synergize carried the qac gene and the 86% of isolates that carried the qac gene also carried attenuated qacE-1. Nearly 31% (109 of 348) of Salmonella isolates from swine barns disinfected with Biosentry carried the qac gene. Furthermore, out of 109 Salmonella isolates that carried qac genes, 94.5% of the isolates contained attenuated qacE-1 gene, whereas 72.5% of the isolates carrying qacE-1 gene also carried class 1 integrons which is associated with both antibiotic and quaternary ammonium compound resistance. Although biocides are effective in limiting the growth, load and the colonization of bacterial pathogens, this study underscores the contribution of biocides in selective pressure towards antibiotic resistant in Salmonella. [ABSTRACT FROM AUTHOR]

Mycobacterium bovis, the causative agent of bovine tuberculosis ( bTB), is a multihost pathogen of public health and veterinary importance. We characterized the M. bovis isolated at the human-livestock-wildlife interface of the Serengeti ecosystem to determine the epidemiology and risk of cross-species transmission between interacting hosts species. DNA was extracted from mycobacterial cultures obtained from sputum samples of 472 tuberculosis ( TB) suspected patients and tissue samples from 606 livestock and wild animal species. M. bovis isolates were characterized using spoligotyping and Mycobacterial Interspersed Repetitive Units-Variable Tandem Repeats ( MIRU- VNTR) on 24 loci. Only 5 M. bovis were isolated from the cultured samples. Spoligotyping results revealed that three M. bovis isolates from two buffaloes ( Syncerus caffer) and 1 African civet ( Civettictis civetta) belonged to SB0133 spoligotype. The two novel strains ( AR1 and AR2) assigned as spoligotype SB2290 and SB2289, respectively, were identified from indigenous cattle ( Bos indicus). No M. bovis was detected from patients with clinical signs consistent with TB. Of the 606 animal tissue specimens and sputa of 472 TB-suspected patients 43 (7.09%) and 12 (2.9%), respectively, yielded non-tuberculous mycobacteria ( NTM), of which 20 isolates were M. intracellulare. No M. avium was identified. M. bovis isolates from wildlife had 45.2% and 96.8% spoligotype pattern agreement with AR1 and AR2 strains, respectively. This finding indicates that bTB infections in wild animals and cattle were epidemiologically related. Of the 24 MIRU- VNTR loci, QUB 11b showed the highest discrimination among the M. bovis strains. The novel strains obtained in this study have not been previously reported in the area, but no clear evidence for recent cross-species transmission of M. bovis was found between human, livestock and wild animals. [ABSTRACT FROM AUTHOR]