Abstract:

Background: Urinary tract infection (UTI) is mainly caused by Escherichia coli, but there is a growing body of evidence on potential involvement of Coagulase Negative Staphylococci spp. (CoNS). Here were report CoNS spp. associated with UTIs that will help to understand the species distribution, their virulence and phenotypic antimicrobial resistance patterns. This will be of great value in justifying routine identifications of CoNS in clinical microbiology laboratories and development of therapeutic strategies for the prevention and effective treatment of CoNS causing UTIs.

Objective: To determine phenotypic and genotypic characterization of Coagulase-Negative Staphylococci Causing Urinary Tract Infection in Tanzania.

Methods: A cross-sectional analytical laboratory based study was conducted from February to August 2021. Previously identified CoNS from patients who were clinically and microbiologically confirmed to have UTIs were retrieved, sub-cultured and whole genome sequenced. The de-novo assembled sequences were analyzed to identify species, STs, virulence genes, antimicrobial resistance genes. Moreover phenotypic antimicrobial susceptibility profile among CoNS was determined.

Results: A total of 65 CoNS isolates were WG sequenced and 8 different species identified were predominated by Staphylococcus haemolyticus 27 (41.5%), and Staphylococcus epidermidis 24 (36.9%). Staphylococcus haemolyticus was assigned to 6 different ST [ST30 (8), ST56 (2), ST49 (2), ST38 (1) and ST66 (1); while Staphylococcus epidermidis were assigned 3 different STs [ST490 (4), ST329 (1) and ST150 (1)]. Total of 61 (93.8%) isolates had either one or multiple antimicrobial resistance genes. Of the 248 antimicrobial resistance genes identified, the most predominant genes were dfrG 53 (21.4%), blaZ 32(12.9%) and mecA 26 (10.5%). The most prevalent virulence genes that may be implicated for UTI pathogenesis were icaC 46.5% (47/101), and icaA 13.9% (14/101). The majority of CoNS were susceptible to Linezolid 65 (100%), Nitrofurantoin 59 (90.8%), and Clindamycin 55 (84.6%). High resistance was exhibited by Trimethoprim/Sulphamethaxazole 59 (90.8) and Erythromycin 46 (70.8%).

Conclusion: The most predominant CoNS species identified were Staphylococcus haemolyticus and Staphylococcus epidermidis, and were harboring virulence genes implicated in UTI like icaC and icaA and antimicrobial resistance genes like dfrG and blaZ. The CoNS identified were mainly susceptible to Linezolid, Nitrofurantoin, and Clindamycin and highly resistant to Trimethoprim/Sulfamethoxazole and Erythromycin. Further studies to explore the treatment outcome of patient with UTI due CoNS is recommended.