Microbial Contamination in the Coffee Industry: An Occupational Menace besides a Food Safety Concern?

Abstract

Respiratory abnormalities among workers at coffee roasting and packaging facilities have already been reported; however, little is known about microbiological contamination inside coffee production facilities. This study intends to assess the microbial contamination (fungi and bacteria) in two coffee industries from Brazil with a multi-approach protocol for sampling and for subsequent analyses using four main sources of samples: filtering respiratory protection devices (FRPD) used by workers, settled dust, electrostatic dust cloths (EDC) and coffee beans. The fungal contamination in the assessed industries was also characterized through the molecular detection of toxigenic species and antifungal resistance. Total bacteria contamination presented the highest values in FRPD collected from both industries (7.45 × 104 CFU·m^-2; 1.09 × 104 CFU·m^-2). Aspergillus genera was widespread in all the environmental samples collected and sections with clinical relevance (Fumigati) and with toxigenic potential (Nigri and Circumdati) were recovered from FRPD. Circumdati section was observed in 4 mg/mL itraconazole. Sections Circumdati (EDC, coffee beans and settled dust) and Nidulantes (EDC, coffee beans and FRPD) were detected by qPCR. Some of the targeted Aspergillus sections that have been identified microscopically were not detected by qPCR and vice-versa. Overall, this study revealed that microbial contamination is a potential occupational risk in the milling stage and should be tackled when assessing exposure and performing risk assessment. In addition, a multi-sampling campaign should be the approach to follow when assessing microbial contamination and FRPD should be included in this campaign. Occupational exposure to mycotoxins should be considered due to high fungal diversity and contamination. A One Health approach should address these issues in order to prevent consumption of coffee crops and beans infected by fungi and, more specifically, to avoid widespread azole resistance.

Keywords: Aspergillus; One Health approach; azole resistance; milling stage; multi-approach for sampling and analyses.

Figure 1

Coffee production flow.

Figure 2

Bacterial (TSA; VRBA) and fungal (MEA; DG18) distribution among the sampled matrices (EDC: log [CFU·m⁻²·day⁻¹]; Grains, settled dust: log [CFU·g⁻¹]; FRPD: log [CFU·m⁻²]).Concerning fungal distribution, the highest fungal diversity was obtained from EDC samples on both coffee companies. Grain samples had the same diversity on samples isolated from both companies (MEA: 8 species; DG18: 5 species). In settled dust from industry B, five species were identified on MEA and seven species on DG18, while on industry A, three species were found on MEA and four species on DG18 in samples from the same matrix. Lower fungal diversity was associated with FRPD samples from industry A (MEA: five species; DG18: two species), whereas on industry B, two species were found on DG18.

Figure 3

Aspergillus sp. distribution in DG18 culture medium in samples from: (a) industry A and (b) industry B. (EDC: log [CFU·m⁻²·day⁻¹]; Grains, settled dust: log [CFU·g⁻¹]; FRPD: log [CFU·m⁻²]).

Figure 4

Aspergillus sections distribution in DG18 in both industries (EDC: log [CFU·m⁻² day⁻¹]; Grains, settled dust: log [CFU·g⁻¹]; FRPD: log [CFU·m⁻²]).

Figure 5

Fungal average counts, per industry and sample matrix (EDC, log CFU·m⁻²·day⁻¹; Grains, settled dust, log CFU·g⁻¹; FRPD, log CFU·m⁻²), by screening in azole-supplemented Sabouraud dextrose agar (SDA) media. ICZ, 4 mg/mL itraconazole; VCZ, 2 mg/mL voriconazole; PCZ, 0.5 mg/mL Posaconazole.

Figure 6

Fungal diversity, per industry, by screening in azole-supplemented Sabouraud dextrose agar (SDA) media. ICZ, 4 mg/mL itraconazole; VCZ, 2 mg/mL voriconazole; PCZ, 0.5 mg/mL posaconazole.