Genomic Characterization of Arcobacter butzleri Strains Isolated from Various Sources in Lithuania

Abstract

Arcobacter (A.) butzleri, the most widespread species within the genus Arcobacter, is considered as an emerging pathogen causing gastroenteritis in humans. Here, we performed a comparative genome-wide analysis of 40 A. butzleri strains from Lithuania to determine the genetic relationship, pangenome structure, putative virulence, and potential antimicrobial- and heavy-metal-resistance genes. Core genome single nucleotide polymorphism (cgSNP) analysis revealed low within-group variability (≤4 SNPs) between three milk strains (RCM42, RCM65, RCM80) and one human strain (H19). Regardless of the type of input (i.e., cgSNPs, accessory genome, virulome, resistome), these strains showed a recurrent phylogenetic and hierarchical grouping pattern. A. butzleri demonstrated a relatively large and highly variable accessory genome (comprising of 6284 genes with around 50% of them identified as singletons) that only partially correlated to the isolation source. Downstream analysis of the genomes resulted in the detection of 115 putative antimicrobial- and heavy-metal-resistance genes and 136 potential virulence factors that are associated with the induction of infection in host (e.g., cadF, degP, iamA), survival and environmental adaptation (e.g., flagellar genes, CheA-CheY chemotaxis system, urease cluster). This study provides additional knowledge for a better A. butzleri-related risk assessment and highlights the need for further genomic epidemiology studies in Lithuania and other countries.

Virulence genotype and phenotype of two clinical isolates of Arcobacter butzleri obtained from patients with different pathologies

“…However, in the same assumption, EP3 and EP10 could confer resistance in both strains against erythromycin, which was not reflected in our antimicrobial susceptibility testing (AST). This discrepancy between genotype and phenotype has previously been reported for an A. butzleri isolate (Jehanne et al 2022 ; Müller et al 2020a , b ; Uljanovas et al 2023 ).…”

“…Here, in line with what has been reported so far, EP18 was not detected in any strain; only three of the genes that compose EP1 were detected in HC-1; and EP7and EP19 were only detected in HC-2. Additionally, of the two strains HC-2 was the only in which EP12 was detected, a system for which 100% prevalence has been reported to date (Isidro et al 2020 ; Müller et al 2020b ; Uljanovas et al 2023 ). Among the genes that make up the three EP systems only detected in HC-2 were mdtA and mdtB2, which could contribute to the formation of the MdtABC-TolC complex, a multidrug efflux system of Gram-negative bacteria, including E. coli and Salmonella, that confers resistance to novobiocin, deoxycholate and β-lactam antibiotics (Pletzer et al 2014 ); and mdtE , implicated in the formation of the MdtEF complex that could provide resistance to β-lactams and erythromycin in E. coli (Nishino et al 2008 ).…”

“…bla2 , hcpC, mrdA , pbpB , pbpF ) were present in both isolates. Previous studies point to a 100% prevalence for all of them (Fanelli et al 2020 ; Müller et al 2020a , b ; Uljanovas et al 2023 ) except for tetO , which is less frequently detected. Although three of the most recent studies carried out with A. butzleri did not detect it in any of the strains tested (Jehanne et al 2022 ; Müller et al 2020b ; Uljanovas et al 2023 ), those conducted by Sciortino et al ( 2021 ) and Lameei et al ( 2022 ) detected it in all tetracycline resistant strains examined.…”

“…Previous studies point to a 100% prevalence for all of them (Fanelli et al 2020 ; Müller et al 2020a , b ; Uljanovas et al 2023 ) except for tetO , which is less frequently detected. Although three of the most recent studies carried out with A. butzleri did not detect it in any of the strains tested (Jehanne et al 2022 ; Müller et al 2020b ; Uljanovas et al 2023 ), those conducted by Sciortino et al ( 2021 ) and Lameei et al ( 2022 ) detected it in all tetracycline resistant strains examined. Here, the presence of the tetO gene in both genomes is probably the reason for resistance to tetracycline, as this genotype–phenotype correlation has previously been reported (Lameei et al 2022 ; Sciortino et al 2021 ; Zambri et al 2019 ).…”

“…Those most frequently reported were detected in both, and were: (1) EP2, comprising only yajR and which being overexpressed can confer multidrug resistance in E. coli (Nishino et al 2001 ); (2) EP3, consisting of four genes including macA1 and macB2 , which encode macrolide export proteins in A. butzleri (Fanelli et al 2019 ); (3) EP4, composed of four genes that include bepD and bepE , responsible for multidrug resistance in Brucella suis (Martin et al 2009 ); (4) EP5 or msbA , coding for a protein that is related to the family of multidrug resistance proteins (Karow et al 1993 ); (5) EP6 or uup , involved in the formation of a soluble ATP-binding cassette (ABC) ATPase that has been implicated in several processes different from transmembrane transport of molecules, such as excision of transposable elements and the deletion of single copies of tandem chromosomal repeats in E. coli (Burgos Zepeda et al 2010 ); (6) EP8 or sugE , encoding a transporter from the small multidrug resistance (SMR) family that also provides resistance to narrow quaternary ammonium compounds in E. coli and Enterobacter cloacae (Chung et al 2002 ; He et al 2011 ); (7) EP9 or fsr, conferring resistance to fosmidomycin in A. butzleri (Fanelli et al 2020 ); (8) EP10, made up of five genes including the macrolide export protein coding macA3 (Fanelli et al 2019 ); (9) EP11; (10) EP15; and (11) EP16, all of which comprise several genes including mexB1 (EP11), mexA1 , mexB2 (EP15), and mexA2 (EP16), allegedly involved in the formation of the MexAB–OprM system responsible for resistance to quinolones, macrolides, novobiocin, chloramphenicol, tetracycline, lincomycin and β-lactams in Pseudomonas aeruginosa (Li et al 1995 ; Masuda et al 2000 ); (12) EP13 or ydhP , that encodes an inner membrane transport protein; and (13) EP14 or bcr1 and (14) EP17 or bcr2 , involved in the resistance to sulphonamides and bicyclomycin in E. coli (Nichols et al 1989 ) and, as far as we know, only to bicyclomycin in A. butzleri (Chieffi et al 2020 ). Studies that have investigated the prevalence of these EP systems in collections of at least 40 strains (Isidro et al 2020 ; Müller et al 2020b ; Uljanovas et al 2023 ) show that their prevalence is generally close to or above 90%, except for EP16 and EP17, which in two studies were detected at rates of less than 70% (Isidro et al 2020 ; Uljanovas et al 2023 ). Based on the three studies cited, the least prevalent systems are EP18 and EP19 (around 2%), followed by EP1 (12–38.8%) and EP7 (21.3–53.1%).…”