Extrahuman epidemiology of Acinetobacter baumannii in Lebanon

Abstract

The presence of Acinetobacter baumannii outside hospitals is still a controversial issue. The objective of our study was to explore the extrahospital epidemiology of A. baumannii in Lebanon. From February 2012 to October 2013, a total of 73 water samples, 51 soil samples, 37 raw cow milk samples, 50 cow meat samples, 7 raw cheese samples, and 379 animal samples were analyzed by cultural methods for the presence of A. baumannii. Species identification was performed by rpoB gene sequencing. Antibiotic susceptibility was investigated, and the A. baumannii population was studied by two genotyping approaches: multilocus sequence typing (MLST) and blaOXA-51 sequence-based typing (SBT). A. baumannii was detected in 6.9% of water samples, 2.7% of milk samples, 8.0% of meat samples, 14.3% of cheese samples, and 7.7% of animal samples. All isolates showed a susceptible phenotype against most of the antibiotics tested and lacked carbapenemase-encoding genes, except one that harbored a blaOXA-143 gene. MLST analysis revealed the presence of 36 sequence types (STs), among which 24 were novel STs reported for the first time in this study. blaOXA-51 SBT showed the presence of 34 variants, among which 21 were novel and all were isolated from animal origins. Finally, 30 isolates had new partial rpoB sequences and were considered putative new Acinetobacter species. In conclusion, animals can be a potential reservoir for A. baumannii and the dissemination of new emerging carbapenemases. The roles of the novel animal clones identified in community-acquired infections should be investigated.

FIG 1

Map of Lebanon showing the distribution of epidemiological samples between districts. E, environmental samples (soil and water); A, animal samples; F, food samples (meat, milk, and cheese).

FIG 2

Population snapshot determined by eBURST analysis of 587 sequences present in the MLST Pasteur database (last update, 8 July 2014). The dots represent STs. The STs identified in this study are shown next to their corresponding dots. Boldface indicates a new ST described in this study. The large circles indicate that our identified ST belonged to a clonal complex, whose name is shown next to the circle.

FIG 3

Maximum-likelihood nucleotide tree of 35 bla_OXA-51-like genes. These 35 genes correspond to 34 bla_OXA-51 variants identified in this study and the bla_OXA-66 gene (the blaOXA-51 representative of clonal complex 2). MEGA 6 was used to build the phylogenetic tree. Bootstrap values are shown at the nodes. One thousand replicates were used to calculate the bootstrap values.

FIG 4

Amino acid sequence alignment of the 16 new OXA-51-like proteins detected in this study and of OXA-51 (the founding member of OXA-51-like beta-lactamases), OXA-66 (an OXA-51 representative variant of CC2), OXA-69 (an OXA-51 representative variant of CC1), and OXA-71 (an OXA-51 representative variant of CC3) (52). Protein accession numbers: OXA-51, WP_002033109.1; OXA-66, YP_001846219.1; OXA-69, YP_001713983.1; and OXA-71, WP_001021785.1.