Fecal Microbiome Features Associated with Extended-Spectrum β-Lactamase-Producing Enterobacterales Carriage in Dairy Heifers
Adar Cohen,
Liat Poupko,
Hillary A. Craddock,
Yair Motro,
Boris Khalfin,
Amit Zelinger,
Sharon Tirosh-Levy,
Shlomo E. Blum,
Amir Steinman,
Jacob Moran-Gilad
Affiliations
Adar Cohen
Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Rehovot 76273, Israel
Liat Poupko
Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
Hillary A. Craddock
Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
Yair Motro
Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
Boris Khalfin
Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
Amit Zelinger
Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Rehovot 76273, Israel
Sharon Tirosh-Levy
Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Rehovot 76273, Israel
Shlomo E. Blum
Division of Bacteriology and Mycology, Kimron Veterinary Institute, Bet Dagan 50200, Israel
Amir Steinman
Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Rehovot 76273, Israel
Jacob Moran-Gilad
Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
Extended-spectrum β-lactamases (ESBLs) are a growing public health threat, and one key human exposure point is through livestock and the food supply. Understanding microbiome factors associated with fecal ESBL carriage can help detect and ideally assist with controlling and preventing ESBL dissemination among livestock. The objective of this study was to investigate the diversity and composition of the heifer fecal microbiota in ESBL-producing Enterobacterales (ESBL-PE) carriers and noncarriers. A total of 59 fecal samples were collected from replacement heifers between 12 and 18 months old from eight dairy farms in central Israel. Genomic DNA was extracted, and 16S rRNA amplicon sequencing was performed (Illumina short reads), focusing on a comparison between 33 ESBL-PE carriers (55.9%) and 26 (44.1%) noncarriers. Samples were analyzed and compared using QIIME2 (DADA2 pipeline and taxonomic assignment with SILVA database) and associated R packages for alpha and beta diversity and taxonomic abundances. Alpha diversity (Shannon diversity) and beta diversity (unweighted UniFrac) showed no significant difference between ESBL-PE carriers and noncarriers. Heifers from farms feeding calves with pooled colostrum had higher ESBL-PE carriage rates than heifers from farms feeding with individual mother colostrum (p Bacteroides, Rikenellaceae, and uncultured Bacteroidales were more abundant in ESBL carriers than noncarriers. Some aspects of microbiota composition differ between ESBL carriers and noncarriers in dairy heifers, specifically the abundance of certain genera. Feeding with pooled colostrum may play a role in that assembly. These could potentially serve as markers of ESBL-PE carriage. However, further research is needed to determine whether these observed differences have a significant impact on colonization with ESBL-PE.
