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.

Grant Number: 1U18FD008360-01
NIH Institute/Center: FDA
Principal Investigator: Jianfa Bai