Dynamics of the Human Nasal Microbiota and Staphylococcus aureus CC398 Carriage in Pig Truck Drivers across One Workweek

• Published in: Applied and environmental microbiology Vol. 87; no. 18; pp. 1 - 16
• Main Authors: Ingham, Anna Cäcilia, Urth, Tinna Ravnholt, Sieber, Raphael Niklaus, Stegger, Marc, Edslev, Sofie Marie, Angen, Øystein, Larsen, Anders Rhod
• Format: Journal Article
• Language: English
• Published: 1752 N St., N.W., Washington, DC American Society for Microbiology 26.08.2021
• Subjects: Clustering; Drug resistance; Genomes; Health care facilities; Human Microbiome; Livestock; Methicillin; Microbiota; Psychrobacter; Public and Environmental Health Microbiology; Staphylococcus aureus; Staphylococcus infections; Swine; Switches; Truck drivers; Trucks; Workweeks; pig transport; nasal microbiota; LA-MRSA CC398; swine lorry; MRSA transmission; microbiome; Staphylococcus aureus
• ISSN: 0099-2240; 1098-5336; 1098-5336
• DOI: 10.1128/AEM.01225-21

In Denmark, the number of human methicillin-resistant Staphylococcus aureus (MRSA) cases has increased dramatically since the early 2000s, starting from imported cases and spreading in the community. However, today, approximately one-third of all new cases are attributed to livestock-associated MRSA clonal complex 398 (LA-MRSA CC398). Drivers of pig trucks constitute a potential route of human transmission of livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398 (LA-MRSA CC398). In this study, we determined MRSA prevalence in pig truck drivers ( n  = 47) and monitored the nasal microbiota of 9 drivers 3 times daily throughout 1 workweek ( n  = 113 samples) and compared it to that of their spouses ( n  = 25 samples from 6 spouses) and 89 nonexposed subjects. S. aureus isolates ( n  = 232) derived from a subset of nasal and truck samples were whole-genome sequenced. The nasal alpha diversity of drivers in the beginning of the workday was lower than that of nonexposed subjects. During the workday, it increased significantly. Similarly, the drivers’ nasal composition shifted during the workday, becoming increasingly different from that of their spouses and nonexposed individuals. Clustering into community state types (CSTs) revealed frequent switches from either S. aureus - or Corynebacterium -dominated CSTs in the mornings to a Psychrobacter- dominated CST during the workday. Six intermittent MRSA carriers were mostly MRSA negative in the mornings, and their nasal microbiota resembled that of nonexposed subjects. When acquiring MRSA during the workday, they switched to the Psychrobacter- dominated CST. In contrast, the nasal microbiota of two persistent MRSA carriers was dominated by staphylococci. In conclusion, we show that the nasal microbiota of pig truck drivers is very dynamic, undergoes drastic changes during workdays, and differs from that of nonexposed subjects even before pig contact. MRSA-carrying drivers may eventually introduce MRSA into the community and health care facilities. Carriage dynamics, however, showed that for most drivers, CC398 MRSA is rapidly lost and only rarely causes transmission to spouses. IMPORTANCE In Denmark, the number of human methicillin-resistant Staphylococcus aureus (MRSA) cases has increased dramatically since the early 2000s, starting from imported cases and spreading in the community. However, today, approximately one-third of all new cases are attributed to livestock-associated MRSA clonal complex 398 (LA-MRSA CC398). This mirrors the increase in pig farms, of which 95% are now positive for LA-MRSA, and this has been caused mainly by three dominant lineages enriched for a number of key antimicrobial resistance genes. Although most human LA-MRSA CC398 infections in Denmark are linked to livestock contact, still up to one-third are not. Pig truck drivers constitute a previously understudied occupation group which may transmit LA-MRSA CC398 to household members, the community, and hospitals. In this study, we demonstrate dramatic work-related changes in the nasal microbiota of pig truck drivers, as well as in their carriage of LA-MRSA CC398. However, they likely do not constitute an important reservoir for LA-MRSA CC398 dissemination.