Whole-Genome Sequencing Identifies In Vivo Acquisition of a bla _CTX-M-27 -Carrying IncFII Transmissible Plasmid as the Cause of Ceftriaxone Treatment Failure for an Invasive Salmonella enterica Serovar Typhimurium Infection

Abstract

bWe report a case of ceftriaxone treatment failure for bacteremia caused by Salmonella enterica subsp. enterica serovar Typhimurium, due to the in vivo acquisition of a bla CTX-M-27 -encoding IncFII group transmissible plasmid. The original ␤-lactamasesusceptible isolate ST882S was replaced by the resistant isolate ST931R during ceftriaxone treatment. After relapse, treatment was changed to ciprofloxacin, and the patient recovered. Isolate ST931R could transfer resistance to Escherichia coli at 37°C. We used whole-genome sequencing of ST882S and ST931R, the E. coli transconjugant, and isolated plasmid DNA to unequivocally show that ST882S and ST931R had identical chromosomes, both having 206 identical single-nucleotide polymorphisms (SNPs) versus S. Typhimurium 14028s. We assembled a complete circular genome for ST931R, to which ST882S reads mapped with no SNPs. ST882S and ST931R were isogenic except for the presence of three additional plasmids in ST931R. ST931R and the E. coli transconjugant were ceftriaxone resistant due to the presence of a 60.5-kb IS26-flanked, bla CTX-M-27 -encoding IncFII plasmid. Compared to 14082s, ST931R has almost identical Gifsy-1, Gifsy-2, and ST64B prophages, lacks Gifsy-3, and instead carries a unique Fels-2 prophage related to that found in LT2. ST882S and ST931R both had a 94-kb virulence plasmid showing >99% identity with pSLT14028s and a cryptic 3,904-bp replicon; ST931R also has cryptic 93-kb IncI1 and 62-kb IncI2 group plasmids. To the best of our knowledge, in vivo acquisition of extended-spectrum ␤-lactamase resistance by S. Typhimurium and bla CTX-M-27 genes in U.S. isolates of Salmonella have not previously been reported. G reater than 1.4 million cases of nontyphoidal salmonellosis are estimated to occur each year in the United States, with approximately 95% of cases resulting from foodborne transmission (1). Although most infections result in mild to moderate gastroenteritis that usually resolves with or without treatment, concurrent bacteremia is observed in approximately 6% of patients and can be associated with serious disease, especially in infants aged Ͻ1 year, the elderly, and those with immunocompromised states such as HIV infection (2-5). Although routine use of antimicrobial therapy is not generally recommended for the treatment of most Salmonella infections, such therapy may be lifesaving in persons with invasive disease.Treatment of invasive salmonellosis has been compromised in recent years due to the emergence of Salmonella isolates with single or multidrug resistance to a number of first-line agents (6, 7). Antimicrobial resistance in strains of nontyphoidal Salmonella (NTS) has been linked to the use of antimicrobial agents in livestock (8-11). Consequently, agents such as fluoroquinolones and third generation cephalosporins, such as ceftriaxone, have become treatment modalities of choice for therapy against severe Salmonella infections. In the United States before 1996, all reported cases of infection with ceftriaxone-resistant NTS isolates were known o...

Antimicrobial Resistant Salmonella enterica Typhimurium Colonizing Chickens: The Impact of Plasmids, Genotype, Bacterial Communities, and Antibiotic Administration on Resistance

“…These plasmids often contain other resistances including chloramphenicol, florfenicol, streptomycin, and tetracycline (Winokur et al, 2000;Doublet et al, 2004;Fernández-Alarcón et al, 2011). In nature, Salmonella acquires MDR plasmids from commensals that inhabit the same environment (Winokur et al, 2001;Fricke et al, 2009;McCollister et al, 2016) and its acquisition of antimicrobial resistance is dependent on an abundant, antimicrobial-resistant donor population (Smith, 1975;Schjørring et al, 2008;Faure et al, 2009;Card et al, 2017). How quickly Salmonella acquires plasmids and associated antimicrobial resistances are dependent on the presence and abundance of the plasmid in the intestinal microbiome, rate of plasmid transmission, plasmid stability and fitness cost (Stewart and Levin, 1977;Ponciano et al, 2007).…”

Zinc Blockade of SOS Response Inhibits Horizontal Transfer of Antibiotic Resistance Genes in Enteric Bacteria

“…Classically, conjugation proceeds via transfer of ssDNA via a conjugation pilus to the recipient strain, whereas transformation (such as by electroporation) is usually more efficient with double-stranded plasmid DNA. McCollister et al recently described in vivo acquisition of the CTX-M27 plasmid by a Salmonella enterica strain in a relapsed infection (McCollister et al, 2016 ). In that case, the patient's Salmonella strain was initially susceptible to the 3 rd -generation cephalosporins and the patient was treated with ceftriaxone.…”

“…Although we have not conducted the detailed DNA sequencing done by McCollister et al, we believe that our results may reflect a similar process, but with gene transfer between E. cloacae and E. coli . Notably, beta-lactam antibiotics such as ceftriaxone do induce the SOS response (Drago et al, 2004 ; Maiques et al, 2006 ), and so SOS induction could have played a role in the in vivo transfer of the resistance gene in the GI tract of the patient described by McCollister et al It is also notable that the work of McCollister et al ( 2016 ) and Beaber et al ( 2003 ), and the work in this study all used wild-type enteric pathogens in their studies of DNA transfer between species. Over-reliance on highly passaged laboratory strains of E. coli in the past may have prevented earlier recognition of these phenomena.…”

Whole-Genome Sequence Analysis of CTX-M ContainingEscherichia coliIsolates from Retail Meats and Cattle in the United States

“…A recent report has documented a case of ceftriaxone treatment failure caused by Salmonella Typhimurium due to the in vivo acquisition of a bla CTX-M-27 -encoding IncFII group transmissible plasmid. 47 …”