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Background  The bacteria of the genus  Bartonella  are obligate parasites of vertebrates. Their distribution range covers almost the entire world from America, Europe, Asia to Africa and Australia. Some species of  Bartonella  are pathogenic for humans. Their main vectors are blood-sucking arthropods such as fleas, ticks and blood-feeding flies. One such dipteran able to transfer vector-borne pathogens is the deer ked ( Lipoptena cervi ) of the family Hippoboscidae. This species acts as a transmitter of  Bartonella  spp. in cervid hosts in Europe.    Methods  In the present study, 217 specimens of deer ked ( Lipoptena cervi ) were collected from 26 red deer ( Cervus elaphus ) hunted in January 2014. A short fragment (333 bp) of the  rpoB  gene was used as a marker to identify  Bartonella  spp. in deer ked tissue by PCR test. A longer fragment (850 bp) of the  rpoB  gene was amplified from 21 of the positive samples, sequenced and used for phylogenetic analysis.    Results  The overall prevalence of  Lipoptena cervi  infection with  Bartonella  spp. was 75.12% (163/217); 86.67% (104/120) of females and 60.82% (59/97) of males collected from red deer hunted in the Strzałowo Forest District in Poland (53°45′57.03″N, 21°25′17.79″E) were infected. The nucleotide sequences from 14 isolates ( Bartonella  sp. 1) showed close similarity to  Bartonella schoenbuchensis  isolated from moose blood from Sweden (GenBank: KB915628) and human blood from France (GenBank: HG977196);  Bartonella  sp. 2 (5 isolates) and  Bartonella  sp. 3 (one isolate) were similar to  Bartonella  sp. from Japanese sika deer (GenBank: AB703149), and  Bartonella  sp. 4 (one isolate) was almost identical to  Bartonella  sp. isolated from Japanese sika deer from Japan (GenBank: AB703146).    Conclusions  To the best of our knowledge, this is the first report to confirm the presence of  Bartonella  spp. in deer keds ( Lipoptena cervi ) in Poland by molecular methods.  Bartonella  sp. 1 isolates were most closely related to  B. schoenbuchensis  isolated from moose from Sweden and human blood from France. The rest of our isolates ( Bartonella  spp. 2–4) were similar to  Bartonella  spp. isolated from Japanese sika deer from Japan.    Electronic supplementary material  The online version of this article (10.1186/s13071-017-2413-0) contains supplementary material, which is available to authorized users.

Molecular detection of Bartonella spp. in deer ked (Lipoptena cervi) in Poland