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Background  Strong laboratory capacity is essential for detecting and responding to emerging and re-emerging global health threats. We conducted a quantitative laboratory assessment during 2014–2015 in two resource-limited provinces in southern China, Guangxi and Guizhou in order to guide strategies for strengthening core capacities as required by the International Health Regulations (IHR 2005).    Methods  We selected 28 public health and clinical laboratories from the provincial, prefecture and county levels through a quasi-random sampling approach. The 11-module World Health Organization (WHO) laboratory assessment tool was adapted to the local context in China. At each laboratory, modules were scored 0–100% through a combination of paper surveys, in-person interviews, and visual inspections. We defined module scores as strong (> = 85%), good (70–84%), weak (50–69%), and very weak (< 50%). We estimated overall capacity and compared module scores across the provincial, prefecture, and county levels.    Results  Overall, laboratories in both provinces received strong or good scores for 10 of the 11 modules. These findings were primarily driven by strong and good scores from the two provincial level laboratories; prefecture and county laboratories were strong or good for only 8 and 6 modules, respectively. County laboratories received weak scores in 4 modules. The module, ‘Public Health Functions’ (e.g., surveillance and reporting practices) lagged far behind all other modules (mean score = 46%) across all three administrative levels. Findings across the two provinces were similar.    Conclusions  Laboratories in Guangxi and Guizhou are generally performing well in laboratory capacity as required by IHR. However, we recommend targeted interventions particularly for county-level laboratories, where we identified a number of gaps. Given the importance of surveillance and reporting, addressing gaps in public health functions is likely to have the greatest positive impact for IHR requirements. The quantitative WHO laboratory assessment tool was useful in identifying both comparative strengths and weaknesses. However, prior to future assessments, the tool may need to be aligned with the new WHO IHR monitoring and evaluation framework.    Electronic supplementary material  The online version of this article (10.1186/s12889-019-6777-2) contains supplementary material, which is available to authorized users.

Capacity assessment of the health laboratory system in two resource-limited provinces in China