Sudan is a moderately tuberculosis (TB) burdened country. In 2014 the prevalence was 159/100,000; it is higher among adults, in urban settings, and in the male population, although 11–13% of all notified cases are children. In 2017, the estimated TB incidence was 77/100,000, for a total of 31,000 cases and a mortality rate of 12/100,000. Comparatively, TB case notifications remained steady for the last decade in a range of (19,817–22,097). In 2016, the total notification was 21,091 cases. Among them, 19,305 (91.5%) were new, while 1,786 (8.5%) were retreatment cases. Of the new cases, 6,520 (30.9%) were smear-positive, 6,167 (29.2%) were smear-negative, 4,951 (23.5%) were extra-pulmonary, and in 1,667 (7.9%) sputum was not done. Last year there were three presumptive cases of extensively drug resistant tuberculosis (XDR-TB); only one of them was confirmed and the notified multi drug resistant tuberculosis (MDR-TB) cases were 220 (CNCDCD et al., 2018).

In Sudan, the GeneXpert network was designed and consists of three levels; it was managed and supervised centrally by the National Tuberculosis Reference Laboratory (NTRL), connected with 18 state laboratories located in capital cities, equipped with one machine or more. Based on MDR notifications, it was expanded to serve 72 sites in localities. An external quality assessment (EQA) system was planned but not yet implemented. The GeneXpert network was employed as the earliest diagnostic tool in the diagnostic algorithm which prioritizes screening and early identification of rifampicin resistant cases among TB suspect and MDR-TB high-risk groups, such as TB retreatment cases, MDR-TB contact, HIV patients, and prisoners. To scale up the programmatic management of drug resistant tuberculosis; sputum smear microscopy was only dedicated for the monitoring of treatment of first-line anti TB drugs (FLDs). So far, culture is the gold standard diagnostic method in the mycobacteriology laboratory.

Several types of culture systems have been developed, however, Löwenstein–Jensen medium (LJ) is considered the reference mycobacterial growth medium (Rageade et al., 2014). Solid egg-based cultures are cheaper and safer, more specific, and allow better visibility of colonial morphology compared to liquid systems (Kidenya et al., 2013; Ahmad et al., 2017). Cultures are more sensitive and significantly increase the number of notified cases (Asmar and Drancourt, 2015). However, they are time-consuming when compared to molecular techniques and sputum smear microscopy. Additionally, cultures provide the necessary isolates for conventional drug susceptibility testing (DST) to provide a definitive diagnosis, therefore, molecular techniques and sputum smear microscopy are not replacing the culture of M. tuberculosis (World Health Organization, 1998; Chihota et al., 2010). Cultivation of mycobacteria is the only method that enables differentiation between viable and dead bacterial cells. This characteristic was frequently recruited to monitor treatment response, to confirm patient sterility and sputum conversion, as well as to ensure the breaking of transmission cycles and to document cure of patients (Su et al., 2011; World Health Organization, 2014; Lawn and Nicol, 2015; Wong et al., 2016).

The accuracy of technical manipulation of analytical and pre-analytical processes either negatively or positively impacts the prone of mycobacterial culture contamination. Soft decontamination procedures due to the constraints of less time or lower concentration might increase the possibility of contamination occurrence. In addition, poor quality of specimens, delay in transportation to the laboratory, as well as poor quality of culture media and incubation conditions might be addressed as possible causes of contamination (World Health Organization, 2011). In this study, we aimed to explore other factors that might contribute to raised contamination rates in the Sudan National Tuberculosis Reference Laboratory.

The WHO laboratory quality management system LQMS document recommends management reviews of all information gathered in the laboratory records regularly (World Health Organization, 2011); the typical period for conducting a management review is annually to provide useful information about areas for improvement (International Organization for Standardization, 2005, 2012).

The accepted culture contamination rate in Löwenstein–Jensen (LJ) solid medium is 3–5% (European Centre for Disease Prevention Control, 2016). In this report culture contamination rates were higher, up to 28.2%. Inaccuracy of analytical processes are the most likely proposed cause of high contamination rates; however, several other factors are thought to contribute to increasing the contamination rate. High contamination rate in solid egg-based culture media is frequently seen in different settings, such as Kenya (Okumu et al., 2017) and India (Sharma et al., 2017). Further, as in other low-income countries, the laboratories infrastructure was fragile, and this could contribute to additional causes of high contamination rates (Engel et al., 2016). In this study, the team conducting the experiment was significantly associated with single tube high contamination rate; similar findings were perceived in other reports (Reddy et al., 2014). Sudan National Tuberculosis Reference Laboratory was fully staffed with experienced qualified technical personnel; however, this association might be attributed to the uneven level of proficiency or other socioeconomic factors.

Major limitations of this study were due to the missing, not recorded, or not transcribed data; this could increase the uncertainty of generated information rather than the appropriate interpretation of the study findings (Dilraj et al., 2015), as in this study approximately only one-half of data regarding age and gender was completed. However, TB epidemiology of the laboratory attendees was similar to international status (Dodd et al., 2016; Marcoa et al., 2018). Secondly, it could decrease the ability of extracting and assessing other key performance indicators in the TB culture laboratory which could be measured routinely. These indicators were highlighted in several studies. Cultures can increase TB detection by 30–50% (Demers et al., 2012; Kassaza et al., 2014). In this study, due to the negative impact of not recorded data, it was not possible to measure the recovery rate indicator. Other indicators, such as turnaround time, was also reported to affect the quality of the laboratory service (Stapleton and Sammond, 2012). The effect of delay between the collection, dispatching, and processing was seen in Burkina Faso (Kaboré et al., 2014; Reddy et al., 2014). To date, Sudan National Tuberculosis Reference Laboratory relies upon a paper-based recording system, which increases the chances of error. These limitations can partially be fixed by the development of a Laboratory information management system (LIMS); it is an important tool for the management of laboratory data on samples, instruments, results, and quality indicators. The LIMS can also support laboratory performance to acquire accreditation (Parsons et al., 2011).

The study concludes that high culture contamination is the greatest risk to the quality of laboratory service and can end in either the loss of specimens or delay in the decisions of initiating patients’ treatment. In addition, the low quality of data increases the uncertainty and undermines the measurement of key performance indicators. Furthermore, the team conducting the experiment was found to be associated with high culture contamination rate. Therefore, the study recommends that all culture laboratory staff should be on the same level of knowledge and proficiency according to their role and should be under regular restricted supervision; in addition, laboratory management should have to use regular assessment tools for internal audits.

The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author.

MM wrote the preliminary draft. RE contributed to data entry and data cleaning. SB critically reviewed the manuscript. All authors contributed to the article and approved the submitted version.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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