INTRODUCTION
Antimicrobial-resistant microorganisms (ARMs) pose severe clinical challenges for human and animal health. Of the ARMs, extended-spectrum β-lactamase (ESBL)-producing
Enterobacteriaceae are resistant to most third- and some fourth-generation cephalosporins that are important for the treatment of human bacterial diseases (
1,
2). The prevalence of ESBL-producing
Enterobacteriaceae is increasing not only in human medicine but also in the various environmental and agricultural settings (
3–7).
Escherichia coli are major producers of ESBLs, with increasing detection of ESBL-producing
E. coli strains in livestock (
8), making it of particular concern due to the potential for transfer of resistance to human isolates through food. Although the use of certain cephalosporins in food-producing animals was banned by the Food and Drug Administration’s Center for Veterinary Medicine in 2012 (
9), high levels of ESBL-producing
E. coli strains in food-producing animals continue to occur (
10–12).
Cefotaxime, a third-generation cephalosporin, is banned for prophylactic use and treatment in food-producing animals, but the prevalence of cefotaxime-resistant bacteria (CRB) has continued to rise in beef cattle (
10,
11,
13). Due to its strong, selective antimicrobial activity, cefotaxime has been widely used to select ESBL-producing bacteria from animal and environmental samples. Resistance to cefotaxime has been attributed to the acquisition of plasmid-mediated CTX-M genes (
14). CTX-M genes are found on plasmids within the major human pathogens, such as pathogenic
E. coli and
Klebsiella pneumoniae, and have been found to originate from environmental
Kluyvera species (
15,
16). Another well-known plasmid-mediated β-lactamase gene, CMY-2 type, has also been reported to confer resistance to cefotaxime (
17). In previous studies, we reported that the presence of CRB in beef cattle arose without antibiotics on pasture (
10,
11), indicating that the emergence of ARMs in food-producing animals is caused by factors other than antibiotic use. However, the underlying mechanisms by which commensal bacteria in the gastrointestinal tract acquire cefotaxime resistance in animals grazing on pasture without antibiotics remain unclear.
In this study, we employed two research beef cattle farms to understand the occurrence of CRB on farms that not only have limited exposure to human activities but also have beef cattle raised without antibiotics, in particular, third-generation cephalosporins, including cefotaxime. By using whole-genome sequencing and comparative genomics, we explore drivers for environmental transmission of clinically relevant multidrug-resistant Escherichia coli strains in food-producing animals.
DISCUSSION
In this study, we identified and characterized ESBL- or CMY-2-producing MDR E. coli strains isolated from beef cattle grazing on pasture without a history of antibiotic treatment. MDR E. coli isolates carried genes encoding well-recognized virulence factors, in combination with a variety of antibiotic resistance genes (ARGs). Functional virulence determination revealed that these isolates have the capability to cause severe diseases in humans. Gene exchanges have driven acquisition of ARGs, and the ecological success of MDR E. coli poses a potential threat to human and animal health globally.
Natural occurrence of antibiotic resistance has recently been recognized by identifying natural resistomes of ARGs (
26) and the dissemination of bacteria that carry resistance genes (
27). In a previous study, we reported high prevalence of cefotaxime-resistant bacteria (CRB) in cattle with no known exposure to antibiotics through prophylactic or therapeutic antibiotics during their entire life span, suggesting that the occurrence of antibiotic resistance in cattle might originate in the environment or from commensal bacteria in the gastrointestinal tract of animals (
11). In this study, we characterized 36 MDR
E. coli isolates with high MICs for cefotaxime and with antibiotic resistance against various classes of drugs, including sulfonamides, aminoglycosides, tetracyclines, fluoroquinolones, chloramphenicol, penicillins, cephalosporins, and polymyxins (
Fig. 1). These isolates were resistant to most classes of antibiotics available in veterinary medicine, carrying a high level of animal health significance. By genome analysis, we revealed that these isolates carried various ARGs with high similarity to ARGs found in human clinical isolates in their chromosomal or plasmid DNA. Horizontal gene transfer by conjugative plasmids and IS elements may have driven the spread of antibiotic resistance (
Fig. 4D and
Table 1), indicating potent and wide spread of ARGs among animals and humans. This phenomenon is supported by multiple lines of evidence that have identified plasmid-mediated CMY-type and CTX-M-type β-lactamases in
Klebsiella pneumoniae,
E. coli,
Proteus mirabilis,
Enterobacter aerogenes, and
Salmonella in food animals and human clinics around the world (
28–31).
Virulence gene profiles and functional analyses of MDR
E. coli strains showed that these strains have evolved in a manner which supports having severe pathogenic capacities (
Fig. 5). Notably, JEONG5446, serotype O84, carried genes encoding T3SS, effectors, and Shiga toxin 1 with versatile adherence. Although there is no evidence that JEONG5446 is associated with any human outbreaks, it may have the potential to cause disease outbreaks which could lead to hemolytic uremic syndrome (HUS) once infected within the human GI tract, since this strain encodes robust virulence factors necessary for adherence, chemotaxis, invasion, and iron uptake. In fact, serotype O84 has been associated with isolates causing outbreaks in New Zealand among humans, cattle, and sheep (
32). Previously, it has been shown that an enteroaggregative
E. coli O104:H4 strain acquired Shiga toxin-encoding genes and ARGs (CTX-M-15 and TEM-1) that led to a large number of HUS cases in Germany during 2011 (
33). Moreover, MDR
E. coli isolates showed virulence gene profiles similar to those of clinically relevant human and swine isolates, suggesting that these strains may cause outbreaks in humans and animals. Since these isolates are resistant to medically important antibiotics, treatment options would be limited.
Antibiotic-resistant bacteria are widespread through multiple routes, including human travel, precipitation, and migratory birds (
34). Phylogenetic analyses have been widely used to determine the relatedness of isolates and trace the sources of potential reservoirs of pathogens (
24,
25,
35). In this study, having less than 10 SNPs in the core genome, we could not identify clonal variants among the strains isolated from two farms (
Fig. 2), suggesting that MDR
E. coli isolates in these farms were independently introduced or divergently evolved. Interestingly, JEONG5776 had very close phylogenetic relatedness with swine pathogen PCN033 (isolated from China), indicating that continental transmissions of MDR
E. coli might have occurred via unknown routes or vehicles. In addition, phylogenetic analysis of STs (973, 117, 5727, 5731, 5728, 10, 5204, 306, 155, and 5730) in GenomeTrakr showed genetic relatedness of MDR
E. coli strains with other strains isolated from different regions and hosts (
Fig. 7 and Fig. S2 in the supplemental material). Previous studies have shown that migratory birds were responsible for the dissemination of antibiotic-resistant
E. coli found in the Arctic, an environment where no selective pressures for antibiotic resistance exist (
36). Furthermore, some studies have shown that up to 30% of migratory Franklin’s gulls in Chile and up to 17% of wild gulls in Canada were carriers of ESBL-producing
E. coli strains (
37,
38). Wild gull species have also been found to acquire antibiotic-resistant organisms in their countries of origin and to spread the bacteria throughout their migration (
39). Moreover, potential spread to farms is possible, as migratory birds often interact with cattle during migration periods. There are several species of migratory birds which have large breeding distributions and often frequent animal farms in order to feed on animal waste (
40), suggesting migratory birds could be one of the routes that have transmitted MDR
E. coli into beef cattle farms. However, many questions regarding transmission routes remain unanswered.
The findings of our study have critical ramifications for animal and human medical practice. Not only do potentially clinically relevant pathogens acquire multidrug resistance mechanisms, but these mechanisms appear to disseminate globally. There is also a strong possibility that pathogens with MDR profiles have evolved to adapt within new hosts by acquisition of genes conferring traits like virulence factors that are critically necessary for survival. More detailed analyses of MDR E. coli strains in wildlife, livestock, and the environment could provide information regarding pathogen transmission. In addition, we were unable to generate complete genome sequences due to the constraints inherent in using short-read Illumina sequencing data and the repetitive sequences like phage genomes and mobile elements that might have limited specificity and sensitivity for comparative bioinformatic analyses. For example, we used the PlasmidFinder database to identify plasmid replicons based on sequence homologies, which might have provided false-positive data. Therefore, further analyses using long-read sequencing technology, such as PacBio sequencing, along with functional analyses, may be helpful to validate the conclusions drawn in this study.
MATERIALS AND METHODS
Statement of ethics.
Standard practices of animal husbandry were applied to all animals in this study. Research protocols were approved by the University of Florida Institutional Animal Care and Use Committee (IACUC number 2015-68003-22971).
Fecal sample collection.
A total of 1,535 fecal samples were collected from beef calves belonging to two different herds housed at two different farms in North Central Florida. The herds were located at the Beef Research Unit (BRU) in Waldo, FL, and the North Florida Research and Education Center (NFREC) in Marianna, FL. The animals were grazing on pasture. None of the animals in this study had been previously exposed to antibiotics for treatment purpose. Sterile cotton swabs were used to collect fecal samples directly from the recto-anal junction (RAJ) of each animal. Following sample collection, fecal swabs were placed in sterile 15-ml centrifuge tubes, transported on ice to the Emerging Pathogens Institute at the University of Florida, and immediately processed.
Isolation and identification of ESBL-producing E. coli strains.
Samples were serially diluted (up to 10
−4) with Luria Bertani (LB) broth and then plated on MacConkey agar (BD, USA) containing cefotaxime (4 μg/ml). Plates were incubated at 37°C and examined after 24 h to enumerate bacterial colonies. Resistance to cefotaxime due to the production of extended-spectrum β-lactamase was identified by streaking cefotaxime-resistant isolates on ChromAgar ESBL (CHROMagar, France) as previously described (
41,
42). Up to four colonies from each fecal sample with the presence of cefotaxime-resistant bacteria were purified and stored at −80°C in 15% glycerol for future use. Frozen cefotaxime-resistant isolates (
n = 2,769) were revived on MacConkey agar plates containing 4 μg/ml cefotaxime and screened by PCR for the presence of the CTX-M gene using primers KCP 685 (5′-TTTGCGATGTGCAGTACCAGTAA-3′) and KCP 686 (5′-CGATATCGTTGGTGGTGCCATA-3′) (544 bp) as described previously (
43). In addition, we confirmed the presence of the CMY-2 and MCR-1 genes using primers KCP556 (5′-ATGATGAAAAAATCGTTATGC-3′) and KCP557 (5′-TTGCAGCTTTTCAAGAATGCGC-3′) (1,200 bp) for the CMY-2 gene (
44) and primers KCP830 (5′-CGGTCAGTCCGTTTGTTC-3′) and KCP831 (5′-CTTGGTCGGTCTGTAGGG-3′) (305 bp) for the MCR-1 gene (
45). Taxonomic identification was conducted at the species level to identify cefotaxime-resistant
E. coli. Genomic DNA was extracted with a Qiagen DNA minikit (Qiagen, Valencia, CA) and used as a template for PCR to amplify the 16S rRNA gene using primers KCP 812 (5′-CAGGCCTAACACATGCAAGTC-3′) and KCP 813 (5′-GGGCGGWGTGTACAAGGC-3′) (∼1,300 bp) (
46). The PCR products were purified using the QIAquick PCR purification kit and sequenced by the Sanger sequencing method at the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida. The resulting sequences were analyzed using the NCBI nucleotide BLAST program to compare the homology of the sequences to the 16S rRNA gene sequences of other organisms.
Characterization of cefotaxime-resistant E. coli strains.
A total of 36 cefotaxime-resistant
E. coli isolates, as identified by the 16S rRNA gene sequencing, were further subjected to MIC testing against cefotaxime using the broth microdilution method (
47). Isolates were further tested for susceptibility to 13 different antimicrobial compounds according to the Clinical and Laboratory Standards Institute guidelines (
18). Briefly, the isolates were tested using the standard Kirby-Bauer disk diffusion method on Mueller-Hinton agar to generate antibiograms of the cefotaxime-resistant isolates. The control strains used for the antibiotic susceptibility testing were
Escherichia coli (ATCC 35401),
Staphylococcus aureus (ATCC 25923), and
Pseudomonas aeruginosa (ATCC 27853). The following antimicrobial-disk concentrations were used: amikacin (30 μg), ampicillin (10 μg), amoxicillin-clavulanic acid (30 μg), ceftiofur (30 μg), cephalothin (30 μg), chloramphenicol (30 μg), colistin (10 μg), gentamicin (10 μg), nalidixic acid (30 μg), streptomycin (10 μg), sulfamethoxazole-trimethoprim (23.75 μg/1.25 μg), sulfisoxazole (250 μg), and tetracycline (30 μg) (BD, USA).
Whole-genome sequencing and phylogenetic-tree analysis.
For whole-genome sequencing of 36 isolates, DNA was extracted from each isolate using the DNeasy blood and tissue kit (Qiagen, Valencia, CA) following the protocol for Gram-negative bacteria. DNA libraries were constructed using the Nextera XT sample preparation kit (Illumina, San Diego, CA) according to the manufacturer's protocol. Sequencing was performed using an Illumina MiSeq with cartridges providing 2 × 250-bp paired-end read coverage. The resulting sequence reads were trimmed for quality and length using Sickle (
48) and then assembled using SPAdes (version 3.0) (
49). The assembled genome sequences of 36 isolates were deposited in NCBI (Table S1 in the supplemental material). Next, a multiple alignment of the
de novo assemblies was performed using progressiveMauve (version 2.4.0) (
http://darlinglab.org/mauve/user-guide/progressivemauve.html) to understand genome rearrangement and compare whole-genome architecture (
50). The phylogenetic trees of 36 sequenced genomes and 88 ST306 strains were generated using Parsnp (
https://harvest.readthedocs.io/en/latest/) (
51) based on the core-genome single-nucleotide polymorphisms (SNPs). The assembled genomes were used as input files of Parsnp that used PhiPack (
52) to detect recombination and generated reliable core-genome SNPs. The set of core-genome SNPs was used to generate maximum-likelihood phylogenetic trees using 1,000 bootstrap replicates with FastTree2 (
53) embedded in the Parsnp program. The number of SNPs in each phylogenetic clade was calculated by using NCBI Pathogen Detection (
https://www.ncbi.nlm.nih.gov/pathogens/) (
54). The phylogenetic trees of each representative strain were generated using Genome Workbench (
https://www.ncbi.nlm.nih.gov/tools/gbench/) after uploading the raw reads to GenomeTrakr (
25).
Identification of virulence genes and antibiotic resistance genes.
Virulence genes were identified through PATRIC (
https://patricbrc.org/) (
55) by aligning whole-genome sequences against the Virulence Factor Database (VFDB) (
56) using BLAST. The identity of each virulence gene was defined by multiplying gene coverage times query identity with subject identity. The Comprehensive Antibiotic Resistance Database (CARD, version 2.0.1,
https://card.mcmaster.ca/analyze) (
57) was also employed for discovery of additional antibiotic resistance genes. Briefly, the whole-genome sequence of each isolate was submitted to Resistance Gene Identifier (RGI, version 4.0.3) in CARD to predict resistance genes using homology and SNP models.
Identification of MLST, plasmid replicon type, and serotype.
The multilocus sequence type (MLST), serotype, plasmid replicons, and plasmid MLST (pMLST) of each isolate were determined using MLST 1.8 (
58), SerotypeFinder (
59), PlasmidFinder and pMLST 1.4 (
60) of the Center for Genomic Epidemiology (CGE) (
http://www.genomicepidemiology.org/).
Identification of CTX-M and CMY-2 gene loci and their genetic environments.
To identify whether the CTX-M and CMY-2 genes were in the chromosome or plasmid, we employed PLACNETw (
https://castillo.dicom.unican.es/upload/) as previously described (
61). PLACNETw assembled sequence reads to generate contigs, and then the contigs were aligned to reference sequences of complete chromosomes and plasmids from NCBI. An original network was generated to illustrate the relatedness among contigs and reference sequences. Following the manual pruning of the original network, the contigs were assigned to either chromosome or plasmid. To find out the location of a CTX-M or CMY-2 gene, alignment was conducted using the sequence of the CTX-M or CMY-2 gene against the chromosomal and plasmid sequences by BLASTn. The genetic environments of CTX-M and CMY-2 genes, i.e., the genes surrounding a CTX-M or CMY-2 gene, were acquired from GenBank files of sequenced strains. Similarity of genetic environments of CTX-M or CMY-2 genes was determined by BLASTn embedded in EasyFig (
http://mjsull.github.io/Easyfig/) (
62).
Adherence assay.
An adherence assay was conducted to evaluate the adherence of the representative isolates to Caco-2 cells (human epithelial colon cancer cell). EDL933 and DH5α were used as a positive and a negative control, respectively. Caco-2 cells were maintained in Dulbecco modified Eagle medium (DMEM) (product number 10-017-CV; Corning, USA) supplemented with 20% (vol/vol) heat-inactivated fetal bovine serum at 37°C and 5% CO2. A total of 105 Caco-2 cells were seeded into each well of a 24-well polystyrene plate, followed by incubation until 90% confluence. Overnight bacterial cultures in LB broth were seeded into new tubes of LB broth (1:250) to produce the main cultures, followed by incubation at 37°C with shaking for 8 h. A total of 106 bacterial cells were washed with sterile phosphate-buffered saline (PBS) three times, resuspended in 500 μl DMEM, and added to each well with 105 Caco-2 cells (multiplicity of infection [MOI] of 10). After a 3-h incubation at 37°C with 5% CO2, the medium in each well was replaced by 500 μl of new DMEM, followed by another 3-h incubation. After the medium was removed, each well was washed with sterile PBS three times to remove the unattached bacteria. Then, 1 ml of 1% Triton X-100 was added to each well to lyse the Caco-2 cells. Finally, 100 μl of the diluted suspension was spread on LB agar and incubated at 37°C overnight, followed by the enumeration of colonies on the plates. This experiment was conducted in duplicate three times.
Mitomycin C treatment and phage induction.
Mitomycin C (MMC) treatment was previously described (
63). Briefly, the optical densities of bacteria were measured to determine whether the bacterial cells were lysed by phage induction. Overnight bacterial cultures were seeded to LB medium. When the OD
600 of the bacterial culture reached between 0.5 and 0.7, MMC was added to a final concentration of 0.5 μg/ml. The negative-control and positive-control strains were DH5α and EDL933, respectively. Phage induction was conducted as previously described with minor changes (
23). To collect phage particles in the bacterial cultures, 25-ml amounts of bacterial cell cultures were treated without or with MMC (final concentration of 1 μg/ml) when the OD
600 reached 0.7. After 24 h of incubation, bacterial cultures were centrifuged at 3,700 ×
g for 30 min at 4°C, followed by filtration of the supernatants through 0.22-μm-pore-size membrane filters (catalog number 09-719A; Fisher Scientific, USA). To precipitate phage particles, 25% (vol/vol) polyethylene glycol 8000 (PEG 8000) (product number 81268; Sigma-Aldrich, USA)-and-NaCl solution (20% PEG 8000 and 10% NaCl) was added to the supernatant. The mixture was incubated at 4°C overnight, followed by centrifugation at 12,000 ×
g for 1 h. The pellets acquired were resuspended using STE buffer (1 M Tris [pH 8], 0.5 M EDTA [pH 8], and 5 M NaCl), and used for immuno-dot blotting.
Immuno-dot blot assay.
To detect the expression of Shiga toxin type 1 (Stx1) and Shiga toxin type 2 (Stx2), we used an immuno-dot blot assay. Briefly, 3 μl of each phage particle sample (bacterial cell cultures of strains EDL933, JEONG5446, and DH5α treated with or without MMC) was loaded to a nitrocellulose membrane (0.2-μm pores; Bio-Rad, USA). The membranes were blocked with 5% skim milk (BD, USA) at room temperature for 1 h, followed by incubation with Stx1 antibody (sc-52726; Santa Cruz, USA) diluted 1:100 in 5% skim milk or Stx2 antibody (sc-52727; Santa Cruz, USA) diluted 1:100 in 5% skim milk for 1 h at room temperature. After washing with PBS with 0.2% Tween 20 (TPBS), the membranes were incubated at room temperature for 1 h with goat anti-mouse IgG1 secondary antibody (IRDye 800CW, product number 926-32350; LI-COR, USA) diluted 1:10,000 in 5% skim milk. After washing with TPBS, the blots were imaged with an Odyssey CLs (LI-COR, USA) to identify Stx1 and Stx2.
Statistical analysis.
The data from the adherence assay were analyzed using one-way analysis of variance (ANOVA) followed by Tukey’s multiple-comparison test.
Accession number(s).
Whole-genome sequences of 36 strains have been deposited in the NCBI database. The accession numbers of these sequenced genomes are listed in Table S1 in the supplemental material, including JEONG5084 (
NSED00000000), JEONG5114 (
NSEE00000000), JEONG5120 (
NSEF00000000), JEONG5232 (
NSEG00000000), JEONG5250 (
NSEH00000000), JEONG5298 (
NSEI00000000), JEONG5413 (
NSEJ00000000), JEONG5446 (
NSEK00000000), JEONG5453 (
NSEL00000000), JEONG5507 (
NSEM00000000), JEONG5511 (
NSEN00000000), JEONG5617 (
NSEO00000000), JEONG5650 (
NSEP00000000), JEONG5766 (
NSEQ00000000), JEONG5776 (
NSER00000000), JEONG9566 (
PKKV00000000), JEONG9567 (
PKKU00000000), JEONG9592 (
PKKW00000000), JEONG9593 (
QDJW00000000), JEONG9594 (
QDJX00000000), JEONG9596 (
QDJY00000000), JEONG9597 (
QDKF00000000), JEONG9598 (
PKKX00000000), JEONG9599 (
QDJZ00000000), JEONG9600 (
QDKA00000000), JEONG9601 (
QDKB00000000), JEONG9602 (
QDKC00000000), JEONG9603 (
QDKD00000000), JEONG9615 (
QDKE00000000), KCJ9488 (
QGNB00000000), KCJ9489 (
QGNC00000000), KCJ9491 (
QGND00000000), KCJ9492 (
QGNE00000000), KCJ9493 (
QGNF00000000), KCJ9499 (
QGNS00000000), and KCJ9511 (
QGNG00000000).