Assessing correlation between antimicrobial resistance genes and susceptibility phenotypes for Enterobacter cloacae complex isolates from the Vet-LIRN AMR monitoring program and clinical samples

Project Summary Enterobacter cloacae complex (ECC) are a natural component of mammalian gastrointestinal microbiota (Davin-Regli and Pagès, 2015; Ramirez and Giron, 2020), but also found in a wide range of foods and can potentially serve as foodborne pathogens (Healy et al., 2010; Shaker et al., 2007;Capita et al., 2020;

Gwida et al., 2014; Kilonzo-Nthenge et al., 2013). A recent study has identified multi-drug resistant ECC in raw tomatoes, lettuce, carrots and other fresh vegetables that were intended for direct human consumption in Spain (Pintor-Cora et al., 2023). ECC and E. aerogenes are recognized as the most predominant nosocomial clinical pathogens within

the Enterobacter genus, often linked to infection outbreaks (Davin-Regli and Pagès, 2015; Mezzatesta et al., 2012). Over the past three decades, they emerged as highly significant opportunistic, and multi-drug resistant pathogens in hospital settings (Gaston, 1988). These infections, ranging from urinary tract infections,

pneumonia, bacteremia, and sepsis, pose significant risks particularly for immunocompromised individuals (Annavajhala et al., 2019; Girlich et al., 2021; Intra et al., 2023). Antimicrobial resistance (AMR) in Enterobacteriaceae represents a global public health concern (John Jr et al., 1982; Ramirez and Giron, 2020).

Klebsiella species and Enterobacter species, including ECC isolates, are recognized as the most prevalent carbapenem-resistant Enterobacteriaceae (CRE) in the United States (Annavajhala et al., 2019; Lutgring, 2019; Mezzatesta et al., 2012). In recent years, many antibiotics commonly used to treat Enterobacter infections, including ECC-

associated diseases, have been alarmingly less effective(Sanders Jr and Sanders, 1997). This trend is attributed to the intrinsic β-lactam resistance observed in ECC species, primarily due to expression of low levels of ampC genes encoding for an inducible AmpC-type cephalosporinase (Annavajhala et al., 2019;

Seeberg et al., 1983). This unique chromosomal β-lactam mechanism enables ECC species to resist the bactericidal effect of Penicillins and first- and second-generation Cephalosporins. In cases of prolonged exposure to β-lactam drugs, ECC species may even exhibit resistance to third generation Cephalosporins

(Seeberg et al., 1983). The Vet-LIRN AMR monitoring program has collected and sequenced approximately 200 ECC strains, and determined their corresponding AMR phenotypes. KSVDL routinely receives ECC-positive diagnostic samples. The objectives of this project are to isolate ~20 ECC isolates from KSVDL submitted specimens,

obtain genome sequences and determine AMR phenotypes, then perform a comparative analysis of AMR phenotypes of these ECC genome sequences alongside the 200 ECC strains from the Vet-LIRN AMR monitoring program.