Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States

Abstract

Fluoroquinolones and cephalosporins are critically important antimicrobial classes for both human and veterinary medicine. We previously found a drastic increase in enrofloxacin resistance in clinical Escherichia coli isolates collected from diseased pigs from the United States over 10 years (2006 to 2016). However, the genetic determinants responsible for this increase have yet to be determined. The aim of the present study was to identify and characterize the genetic basis of resistance against fluoroquinolones (enrofloxacin) and extended-spectrum cephalosporins (ceftiofur) in swine E. coli isolates using whole-genome sequencing (WGS). blaCMY-2 (carried by IncA/C2, IncI1, and IncI2 plasmids), blaCTX-M (carried by IncF, IncHI2, and IncN plasmids), and blaSHV-12 (carried by IncHI2 plasmids) genes were present in 87 (82.1%), 19 (17.9%), and 3 (2.83%) of the 106 ceftiofur-resistant isolates, respectively. Of the 110 enrofloxacin-resistant isolates, 90 (81.8%) had chromosomal mutations in gyrA, gyrB, parA, and parC genes. Plasmid-mediated quinolone resistance genes [qnrB77, qnrB2, qnrS1, qnrS2, and aac-(6)-lb′-cr] borne on ColE, IncQ2, IncN, IncF, and IncHI2 plasmids were present in 24 (21.8%) of the enrofloxacin-resistant isolates. Virulent IncF plasmids present in swine E. coli isolates were highly similar to epidemic plasmids identified globally. High-risk E. coli clones, such as ST744, ST457, ST131, ST69, ST10, ST73, ST410, ST12, ST127, ST167, ST58, ST88, ST617, ST23, etc., were also found in the U.S. swine population. Additionally, the colistin resistance gene (mcr-9) was present in several isolates. This study adds valuable information regarding resistance to critical antimicrobials with implications for both animal and human health. IMPORTANCE Understanding the genetic mechanisms conferring resistance is critical to design informed control and preventive measures, particularly when involving critically important antimicrobial classes such as extended-spectrum cephalosporins and fluoroquinolones. The genetic determinants of extended-spectrum cephalosporin and fluoroquinolone resistance were highly diverse, with multiple plasmids, insertion sequences, and genes playing key roles in mediating resistance in swine Escherichia coli. Plasmids assembled in this study are known to be disseminated globally in both human and animal populations and environmental samples, and E. coli in pigs might be part of a global reservoir of key antimicrobial resistance (AMR) elements. Virulent plasmids found in this study have been shown to confer fitness advantages to pathogenic E. coli strains. The presence of international, high-risk zoonotic clones provides worrisome evidence that resistance in swine isolates may have indirect public health implications, and the swine population as a reservoir for these high-risk clones should be continuously monitored.

Silent spread of mobile colistin resistance gene mcr-9.1 on IncHI2 ‘superplasmids’ in clinical carbapenem-resistant Enterobacterales

“…This study confirms their broad host range and ongoing ability to acquire novel resistance determinants, such as carbapenemase genes and mcr-9.1. There appears to be a close association between mcr-9.1 and IncHI2 plasmids, first noted in the initial reports of mcr-9.1 [4,5] and subsequently confirmed in multiple publications on mcr-9.1 [7,8,10,25,26,[28][29][30][34][35][36][37][38][39][40][41][42][43].…”

“…For E. hormaechei ST93 and ST190 median pairwise single nucleotide variant (SNV) distance was 8 SNVs (IQR 2-16) and 2 SNVs (IQR 1-2), respectively (Figure S1). In contrast, E. hormaechei ST114 had a median pairwise SNV distance of 28 SNVs (IQR [23][24][25][26][27][28][29][30][31][32][33][34][35][36]. For all clones, the low SNV distances are suggestive of intra-institutional spread.…”

Multi-Drug Resistant Plasmids with ESBL/AmpC and mcr-5.1 in Paraguayan Poultry Farms: The Linkage of Antibiotic Resistance and Hatcheries

“…Moreover, a recent study focused on antibiotic resistance in Italian poultry detected ST457 as the most prevalent ST, despite carrying different ARGs than our Paraguayan collection [ 6 ]. A recent study on diseased pigs in the USA described ST457 as one of the most prevalent ST with closely related isolates found in diverse sources including humans [ 40 ].…”

High Risk Clone: A Proposal of Criteria Adapted to the One Health Context with Application to Enterotoxigenic Escherichia coli in the Pig Population

“…We demonstrated that the clone A-I appeared in 2013 and became predominant in 2015 (data from this study and [ 16 ]), consequently meeting the emergence criteria (cf Table 1 ). The clonality of ETEC isolates from various states of the USA and belonging to clonal lineage A had already been demonstrated [ 20 ]. In addition, we demonstrated the international distribution of the clone A-I, as it is also present in Canada, at least in Quebec.…”

“…In addition, fluoroquinolone non-susceptibility in E. coli isolated from diseased pigs has been observed in other countries [ 17 , 18 ] and has been associated with enrofloxacin treatment previously in herds [ 19 ]. Moreover, clonality has been demonstrated among ETEC isolates causing disease in pigs in the USA [ 20 ]. Our hypothesis is that a high risk fluoroquinolone non-susceptible pathogenic ETEC clone has emerged in pigs in various countries, thus representing a threat for swine and public health.…”