ABSTRACT
The incidence of drug-resistant community-acquired urinary tract infections (CA-UTI) continues to increase worldwide. In 1999 to 2000, a single lineage of uropathogenic Escherichia coli (UPEC) sequence type 69 (ST69) caused 51% of trimethoprim-sulfamethoxazole-resistant UTI in a Northern California university community. We compared the clonal distributions of UPEC and its impact on antimicrobial resistance prevalence in the same community during two periods separated by 17 years. We analyzed E. coli isolates from urine samples from patients with symptoms of UTI who visited a health service between September 2016 and May 2017 and compared them to UPEC isolates collected similarly between October 1999 and March 2000. Isolates were tested for antimicrobial drug susceptibility and genotyped by multilocus sequence typing. In 1999 to 2000, strains belonging to ST95, ST127, ST73, ST69, ST131, and ST10 caused 125 (56%) of 225 UTI cases, while the same STs caused 148 (64%) of 233 UTI cases in 2016 to 2017. The frequencies of ampicillin resistance and ciprofloxacin resistance rose from 24.4% to 41.6% (P < 0.001) and from 0.9% to 5.1% (P < 0.003), respectively. The six STs accounted for 78.6% and 72.7% of these increases, respectively. Prevalence of drug-resistant UTI in this community appears to be largely influenced by a small set of dominant UPEC STs circulating in the same community 17 years apart. Further research to determine the origin and reasons for persistence of these dominant genotypes is necessary to combat antimicrobial-resistant CA-UTI.
KEYWORDS: Escherichia coli, molecular epidemiology, multilocus sequence typing, urinary tract infection, uropathogenic E. coli
INTRODUCTION
Community-acquired urinary tract infection (CA-UTI) is one of the most common bacterial infectious diseases for women worldwide (1, 2). It accounts for a considerable number of outpatient health care visits and a considerable proportion of health care costs, and it negatively affects the quality of life of affected individuals (1, 2). In 1995, it was estimated that 11% of women aged 18 years and older had experienced at least one presumed UTI episode during the previous 12-month period and the annual cost of UTI was estimated at 11.6 billion dollars (2).
The most common causative agent of CA-UTI is uropathogenic Escherichia coli (UPEC) (3). Infectious Diseases Society of America (IDSA) recommends nitrofurantoin and fosfomycin as empirical treatment regimens for uncomplicated cystitis and pyelonephritis (4), but trimethoprim-sulfamethoxazole (TMP-SMZ) and fluoroquinolones are still widely used (5), and resistance to these drugs is increasing (6–9).
It is often believed that clinical use of antimicrobial agents contributes to the selection of drug-resistant strains of UPEC causing resistant CA-UTI. In a study of patients with symptoms of UTI at a Northern California university in 1999 to 2000, Manges et al. demonstrated that a single strain of UPEC, referred to as clonal group A (CgA), on the basis of enterobacterial repeat intergenic consensus 2 (ERIC2)-PCR typing (6), later classified as ST69 by multilocus sequence typing (MLST), accounted for 11% of 255 UPEC isolates and 51% of 55 TMP-SMZ-resistant isolates (6, 10). Another study conducted in the same community between 1999 and 2005 demonstrated that all initially pan-susceptible clonal groups remained pan-susceptible and that only four lineages accounted for 52% of multidrug-resistant (MDR) UPEC isolates over the 6-year study period (11).
Globally, E. coli genotypes ST10, ST69, ST73, ST95, ST127, and ST131 defined by MLST account for more than 50% of extraintestinal pathogenic E. coli (ExPEC) infections (12–14). These have come to be referred to as pandemic ExPEC lineages (15). Given the selective pressure exerted on bacteria by heavy antimicrobial use in human medical practices and animal husbandry, it is unclear why a large proportion of drug-resistant ExPEC infections are caused by a small set of genotypes. We used MLST to determine the distribution of UPEC genotypes and the prevalence of drug-resistant CA-UTI during two study periods separated by 17 years at one Northern California university community.
MATERIALS AND METHODS
Sample collection.
E. coli was isolated from urine samples collected consecutively between 19 September 2016 and 4 May 2017 from the patients with symptoms of UTI seen at a university health service. All urine samples were collected as part of routine clinical care at the health service. We collected them before they were discarded without personal identifiers or clinical information. All urine samples were first tested at the health service by dipstick, and those specimens found to test positive for leukocytes, nitrates, protein, blood, or glucose were collected for this study and subjected to further microbiologic examination. A case of urinary tract infection was defined as a patient with a clean-catch urine specimen that contained more than 102 CFU of E. coli per milliliter (16).
Microbiologic examinations.
A 10-μl aliquot of urine sample was cultured on a MacConkey agar plate to isolate Gram-negative bacteria. Lactose-positive and indole-positive colonies were presumptively identified as E. coli and further analyzed. All E. coli isolates were screened for susceptibility to ampicillin, trimethoprim-sulfamethoxazole (TMP-SMZ), and ciprofloxacin (CIP) by the standard disc diffusion assay, according to the standard interpretive criteria of the Clinical and Laboratory Standards Institute (M100-S25; Clinical and Laboratory Standards Institute, 2015). E. coli 25922 from the American Type Culture Collection was used as a reference strain. Susceptibility to cephalosporin (cefotaxime [CTX], cefoxitin [FOX], and ceftazidime [CAZ]), nitrofurantoin (NIT), fosfomycin (FOS), and gentamicin (GEN) was also assessed for isolates belonging to major lineages by the disc diffusion method. Isolates with intermediate susceptibility were classified as resistant. Isolates with multidrug resistance were defined as isolates with resistance to three or more classes of antimicrobial agents (17).
Strain typing.
Five colonies recovered from each urine culture were randomly picked and subtyped by ERIC2-PCR assay, as described previously (18, 19). Single colonies on tryptic soy agar plates were selected and inoculated into 2 ml of tryptic soy broth and incubated in a shaking incubator for 15 h at 37°C. The 2-ml aliquots of grown cultures were centrifuged, and the pellets were resuspended in a test tube with 350 μl of distilled water, boiled for 10 min in a water bath, and then cooled on ice for 2 min. The samples were centrifuged for 2 min at 13,000 rpm, and the supernatants were stored at −20°C before they were subjected to PCR tests.
The five colonies that had identical ERIC2 electrophoretic banding patterns by visual inspection were considered to belong to the same clonal group, and one of them was selected for further analysis by multilocus sequence typing (MLST). All E. coli isolates were genotyped by MLST based on the seven-gene scheme described at the PubMLST website (https://pubmlst.org/bigsdb?db=pubmlst_mlst_seqdef) (10). The allelic number and the corresponding genotype number were assigned by the curator of the MLST website. E. coli genotypes ST10, ST69, ST73, ST95, ST127, and ST131 were considered major genotypes since they account for more than 50% of ExPEC infections worldwide (12–14, 20). The other genotypes were considered minor genotypes.
Beta-lactamase gene identification.
Ampicillin-resistant E. coli isolates were examined for beta-lactamase gene families by multiplex PCRs as described previously (21, 22). These beta-lactamase gene families included the following: TEM variants (blaTEM-1 and blaTEM-2), an SHV variant (blaSHV-1), CTX-M group 1 (blaCTX-M-1, blaCTX-M-3, and blaCTX-M-15), CTX-M group 2 (blaCTX-M-2), CTX-M group 9 (blaCTX-M-9 and blaCTX-M-14), CTX-M group 8/25 (blaCTX-M-8, blaCTX-M-25, blaCTX-M-26, and blaCTX-M-39 to blaCTX-M-41), OXA variants (blaOXA-1, blaOXA-4, and blaOXA-30), and AmpC types (blaMOX-1, blaMOX-2, blaCMY-1, blaCMY-8 to blaCMY-11, blaLAT-1 to blaLAT-4, blaCMY-2 to blaCMY-7, blaBIL-1, blaDHA-1, blaDHA-2, blaACC, blaMIR-1T, blaACT-1, and blaFOX-1 to blaFOX-5b). To detect the plasmid-mediated AmpC β-lactamase genes, we performed six types of multiplex PCR as described previously (22).
Comparison to E. coli isolates obtained from 1999 to 2000.
Between September 1999 and January 2000, E. coli isolates were obtained from urine samples consecutively collected from patients with symptoms of UTI at the Northern California university campus health service, as described by Manges et al. (6). E. coli samples were stored in sterile 15% glycerol at −80°C. Aliquots of the stored samples were incubated at 37°C on tryptic soy agar plates overnight, and single colonies were selected and reinoculated into 2 ml tryptic soy broth and incubated in a shaking incubator for 15 h at 37°C. The bacterial DNA was extracted by the freeze-boil method as described above. We conducted antimicrobial drug susceptibility testing and MLST analysis on the isolates as described above.
Statistical analysis.
The difference in the prevalences of the E. coli genotypes and the drug resistance data between the two sampling periods was assessed by two-sided Fisher's exact test. Statistical significance was defined as a P value of less than 0.05. All analyses were performed by the use of R-Studio version 3.4.2.
RESULTS
Study isolates.
Between 19 September 2016 and 4 May 2017, we collected 1,087 nonduplicate urine samples from the university health service. Among those samples, 788 tested negative by culture, 56 grew lactose-negative bacteria, and 13 grew lactose-positive and indole-negative bacteria; 230 (21%) contained E. coli. From the study conducted by Manges et al. in 1999 to 2000 (6), 231 stored E. coli isolates were available for testing, and 225 of those E. coli isolates were recultured and genotyped by MLST.
Distribution of MLST genotypes.
In 2016 to 2017, 227 of 230 samples contained one E. coli ST each and three contained two STs. Therefore, 233 E. coli isolates were analyzed; 225 E. coli isolates were assigned to 61 unique STs, whereas 8 could not be assigned an ST designation (Table 1). Among 225 E. coli isolates collected in 1999 to 2000, 216 were assigned to 63 unique STs whereas 9 could not be assigned an ST designation (Table 1). Five genotypes (ST95, ST127, ST73, ST69, and ST131) were composed of more than 10 isolates each in 2016 to 2017, whereas 51 (83.6%) genotypes had a frequency of fewer than three isolates each. The most common genotypes among UPEC strains in 2016 to 2017 (ST95, ST127, ST73, ST69, ST131, and ST10) were the same as the genotypes found in the UPEC strains from 1999 to 2000 (Table 2). In 2016 to 2017, the most common genotypes were ST95 (16.7%) and ST127 (15.9%); in 1999 to 2000, ST95 (15.1%) and ST69 (11.6%) were the most common. Between the two periods, the proportion of UPEC genotypes ST95, ST127, ST69, ST73, and ST131 increased from 50.7% to 60.9% (P = 0.03); however, there was no significant change in ST10 frequency during the two study periods. Of 61 genotypes identified in 2016 to 2017, 44 were not found in 1999 to 2000, and of 63 genotypes in 1999 to 2000, 46 were not found in 2016 to 2017 (Table 1).
TABLE 1.
Multilocus sequence types of uropathogenic E. coli isolates obtained from patients with urinary tract infection in a Northern California college community during 1999 to 2000 and 2016 to 2017
| Genotype | 1999–2000 | 2016–2017 |
|---|---|---|
| 95 | 34 | 39 |
| 127 | 24 | 37 |
| 73 | 23 | 32 |
| 69 | 26 | 22 |
| 131 | 7 | 12 |
| 10 | 11 | 6 |
| 12 | 2 | 6 |
| 141 | 2 | 6 |
| 420 | 9 | 4 |
| 2628 | 0 | 3 |
| 28 | 0 | 2 |
| 88 | 4 | 2 |
| 569 | 0 | 2 |
| 998 | 4 | 2 |
| 1948 | 0 | 2 |
| 2261 | 0 | 2 |
| 6767 | 0 | 2 |
| 13 | 0 | 1 |
| 34 | 0 | 1 |
| 38 | 1 | 1 |
| 59 | 1 | 1 |
| 80 | 1 | 1 |
| 83 | 0 | 1 |
| 91 | 0 | 1 |
| 101 | 0 | 1 |
| 117 | 2 | 1 |
| 200 | 0 | 1 |
| 224 | 0 | 1 |
| 280 | 0 | 1 |
| 345 | 0 | 1 |
| 363 | 0 | 1 |
| 372 | 1 | 1 |
| 379 | 0 | 1 |
| 416 | 0 | 1 |
| 472 | 0 | 1 |
| 550 | 0 | 1 |
| 636 | 1 | 1 |
| 746 | 0 | 1 |
| 906 | 0 | 1 |
| 929 | 0 | 1 |
| 945 | 0 | 1 |
| 964 | 0 | 1 |
| 989 | 0 | 1 |
| 1380 | 0 | 1 |
| 1643 | 0 | 1 |
| 1670 | 0 | 1 |
| 1844 | 0 | 1 |
| 1873 | 0 | 1 |
| 2003 | 0 | 1 |
| 2015 | 0 | 1 |
| 2165 | 0 | 1 |
| 2562 | 0 | 1 |
| 2646 | 0 | 1 |
| 2813 | 0 | 1 |
| 2831 | 0 | 1 |
| 3018 | 0 | 1 |
| 5016 | 0 | 1 |
| 5135 | 0 | 1 |
| 5150 | 0 | 1 |
| 5552 | 0 | 1 |
| 6143 | 0 | 1 |
| 14 | 2 | 0 |
| 58 | 2 | 0 |
| 62 | 3 | 0 |
| 65 | 1 | 0 |
| 93 | 2 | 0 |
| 130 | 1 | 0 |
| 135 | 1 | 0 |
| 155 | 1 | 0 |
| 218 | 1 | 0 |
| 226 | 1 | 0 |
| 295 | 3 | 0 |
| 297 | 1 | 0 |
| 349 | 1 | 0 |
| 355 | 1 | 0 |
| 358 | 1 | 0 |
| 362 | 1 | 0 |
| 404 | 1 | 0 |
| 405 | 1 | 0 |
| 410 | 1 | 0 |
| 446 | 1 | 0 |
| 448 | 1 | 0 |
| 453 | 3 | 0 |
| 484 | 1 | 0 |
| 491 | 1 | 0 |
| 522 | 1 | 0 |
| 538 | 2 | 0 |
| 544 | 3 | 0 |
| 547 | 1 | 0 |
| 555 | 4 | 0 |
| 706 | 1 | 0 |
| 847 | 1 | 0 |
| 867 | 1 | 0 |
| 1039 | 1 | 0 |
| 1064 | 1 | 0 |
| 1119 | 1 | 0 |
| 1170 | 3 | 0 |
| 1312 | 1 | 0 |
| 1465 | 1 | 0 |
| 1735 | 1 | 0 |
| 1867 | 1 | 0 |
| 2554 | 1 | 0 |
| 3386 | 1 | 0 |
| 4377 | 1 | 0 |
| 4774 | 1 | 0 |
| 5463 | 1 | 0 |
| 6439 | 1 | 0 |
| Total | 216 | 225 |
TABLE 2.
Six major multilocus sequence types of uropathogenic E. coli strains obtained in a Northern California college community during 1999 to 2000 and 2016 to 2017a
| Lineage category and ST | No. (%) of isolates typed |
P value | |
|---|---|---|---|
| 1999–2000 (n = 225) | 2016–2017 (n = 233) | ||
| Major | |||
| ST95 | 34 (15.1) | 39 (16.7) | 0.70 |
| ST127 | 24 (10.7) | 37 (15.9) | 0.12 |
| ST73 | 23 (10.2) | 32 (13.7) | 0.25 |
| ST69 | 26 (11.6) | 22 (9.4) | 0.54 |
| ST131 | 7 (3.1) | 12 (5.2) | 0.35 |
| ST10 | 11 (9.0) | 6 (4.0) | 0.22 |
| Total | 125 (55.6) | 148 (63.5) | 0.08 |
| Minor | 100 (45.8) | 85 (36.5) | 0.08 |
Multilocus sequence typing was performed according to the PubMLST website (https://pubmlst.org/bigsdb?db=pubmlst_mlst_seqdef). ST, sequence type. P values are based on Fisher's exact test for categorical variables.
Changes in prevalence of ampicillin, trimethoprim-sulfamethoxazole, and ciprofloxacin resistance.
In 2016 to 2017, 97 (41.6%) E. coli isolates were resistant to ampicillin, compared with 55 (24.4%) in 1999 to 2000 (P < 0.001) (Table 3). Between 1999 to 2000 and 2016 to 2017, ampicillin resistance increased from 26.4% to 44.6% (P = 0.002) among the six major genotypes and increased from 22.0% to 36.4% (P = 0.03) among the minor genotypes. ST95, ST127, ST73, and ST131 comprised 46.4% of the ampicillin-resistant isolates in 2016 to 2017 but only 21.8% in 1999 to 2000 (P = 0.0004). Strikingly, only four of the six major STs (ST95, ST127, ST73, and ST131) contributed to 78.6% of the increase in ampicillin resistance.
TABLE 3.
Frequency of ampicillin, trimethoprim-sulfamethoxazole, and ciprofloxacin resistance of uropathogenic E. coli during 1999 to 2000 and 2016 to 2017
| Lineage category and ST | No. of isolates with indicated result/total no. of isolates typed (% of isolates with indicated result)a |
||||||||
|---|---|---|---|---|---|---|---|---|---|
| Ampicillin resistance |
Trimethoprim-sulfamethoxazole resistance |
Ciprofloxacin resistance |
|||||||
| 1999–2000 | 2016–2017 | P value | 1999–2000 | 2016–2017 | P value | 1999–2000 | 2016–2017 | P value | |
| Major | |||||||||
| ST95 | 1/34 (2.9) | 8/39 (20.5) | 0.03 | 1/34 (2.9) | 1/39 (2.6) | 1.00 | 0/34 (0.0) | 0/39 (0.0) | 1.00 |
| ST127 | 3/24 (12.5) | 8/37 (21.6) | 0.51 | 1/24 (4.2) | 2/37 (5.4) | 1.00 | 0/24 (0.0) | 0/37 (0.0) | 1.00 |
| ST73 | 6/23 (26.1) | 20/32 (62.5) | 0.01 | 1/23 (4.3) | 7/32 (21.9) | 0.12 | 0/23 (0.0) | 0/32 (0.0) | 1.00 |
| ST69 | 19/26 (73.1) | 17/22 (77.3) | 1.00 | 17/26 (65.4) | 15/22 (68.2) | 1.00 | 0/26 (0.0) | 1/22 (4.5) | 0.46 |
| ST131 | 2/7 (28.6) | 9/12 (75.0) | 0.07 | 1/7 (14.3) | 3/12 (25.0) | 1.00 | 0/7 (0.0) | 7/12 (58.3) | 0.01 |
| ST10 | 2/11 (18.2) | 4/6 (66.7) | 0.10 | 2/11 (18.2) | 1/6 (16.7) | 1.00 | 0/11 (0.0) | 0/6 (0.0) | 1.00 |
| Total | 33/125 (26.4) | 66/148 (44.6) | 0.002 | 23/125 (18.4) | 29/148 (19.6) | 0.88 | 0/125 (0.0) | 8/148 (5.4) | 0.009 |
| Minor | 22/100 (22.0) | 31/85 (36.4) | 0.03 | 15/100 (15.0) | 11/85 (12.9) | 0.83 | 1/100 (0.10) | 4/85 (4.7) | 0.18 |
| Total | 55/225 (24.4) | 97/233 (41.6) | <0.001 | 38/225 (16.9) | 40/233 (17.1) | 0.80 | 1/225 (0.9) | 12/233 (5.1) | 0.003 |
Numbers in parentheses represent the percentages of isolates within one genotype in each sampling period. P values are based on Fisher's exact test for categorical variables.
Unlike the ampicillin resistance results, there was no significant change in TMP-SMZ resistance during the two study periods (Table 3). During both study periods, TMP-SMZ resistance was 17%, and the proportion of TMP-SMZ-resistant isolates was highest among the strains belonging to ST69 (65% in 1999 to 2000 and 68% in 2016 to 2017) (6). In 1999 to 2000, ST69 accounted for 44.7% of all TMP-SMZ-resistant isolates, while in 2016 to 2017, it accounted for 37.5%. During the two study periods, the proportions of ST73 and ST131 isolates that were resistant to TMP-SMZ increased from 4.3% to 21.9% and from 14.3% to 25.0%, respectively; they accounted for 25% of all TMP-SMZ-resistant isolates in 2016 to 2017 (P = 0.02) and 5.3% in 1999 to 2000.
In 2016 to 2017, 12 (5.1%) E. coli isolates were resistant to ciprofloxacin compared with only 1 (0.9%) in 1999 to 2000 (P = 0.003) (Table 3). ST131 accounted for more than half (58%) of 12 isolates from 2016 to 2017.
β-Lactamase gene types among ampicillin resistance strains.
Among 55 ampicillin-resistant E. coli isolates collected in 1999 to 2000, β-lactamase TEM variants were detected in 49 (89%), 2 of which had OXA variants. No CTX-M group, SHV variant, or AmpC-type gene was found (Fig. 1). Among 97 ampicillin-resistant E. coli isolates collected in 2016 to 2017, the percentage of isolates possessing only TEM variants decreased to 64.9% (P < 0.01). One isolate had CTX-M group 1; two isolates had OXA variants; two isolates had TEM variants and CTX-M group 1; two isolates had TEM variants and CTX-M group 9; one isolate had a TEM variant, CTX-M group 1, and OXA variants; four isolates had TEM variants and OXA variants; and one isolate had SHV variants. The E. coli isolates possessing CTX-M groups, OXA variants, and SHV variants accounted for 13.4% in 2016 to 2017 (Fig. 1); the major genotypes were responsible for 70% of the CTX-M-carrying strains (Table 4). During the two study periods, there was no isolate with an AmpC-type gene. Six (10.9%) and 21 (21.6%) of ampicillin-resistant isolates in the two study periods, respectively, did not have any TEM variants, CTX-M groups, OXA variants, SHV variants, or AmpC-type genes.
FIG 1.
Distribution of β-lactamase gene types among ampicillin-resistant isolates from 1999 to 2000 and 2016 to 2017.
TABLE 4.
Genotypes of uropathogenic E. coli isolates possessing β-lactamase genes other than TEM variants
| Lineage category and sequence type | β-Lactamase gene type(s) (no. of isolates)a |
|---|---|
| Major | |
| ST69 | blaTEM type + blaCTX-M group 1 (1) |
| ST127 | blaCTX-M group 1 (1) |
| ST131 | blaCTX-M group 1 + blaOXA type (4) |
| blaTEM type + blaCTX-M group 9 (1) | |
| blaOXA type (1) | |
| Minor | |
| ST59 | blaOXA type (1) |
| ST280 | blaTEM type + blaCTX-M group 1 + blaOXA type (1) |
| ST2003 | blaTEM type + blaCTX-M group 9 (1) |
| ST2261 | blaSHV-1 (1) |
| Unknown | blaTEM type + blaCTX-M group 1 (1) |
blaTEM type, blaTEM-1 and blaTEM-2; blaSHV type, blaSHV-1; blaCTX-M group 1, blaCTX-M-1, blaCTX-M-3, and blaCTX-M-15; blaCTX-M group 2, blaCTX-M-2; blaCTX-M group 9, blaCTX-M-9 and blaCTX-M-14; blaCTX-M group 8/25, blaCTX-M-8, blaCTX-M-25, blaCTX-M-26, and blaCTX-M-39 to blaCTX-M-41; blaOXA type, blaOXA-1, blaOXA-4, and blaOXA-30. Numbers in parentheses following gene designations represent the percentages of isolates possessing CTX-M groups or SHV variants among the E. coli isolates obtained in 2016 to 2017.
Association of MLST genotypes with antibiotic susceptibility.
To assess the association of MLST genotypes with resistance to different antibiotic classes, we tested the susceptibility of all six major ST isolates to six additional antimicrobial agents. Most E. coli isolates from the six major STs in the 1999–2000 study were susceptible to cephalosporins (cefotaxime, cefoxitin, and ceftazidime), nitrofurantoin, fosfomycin, and gentamicin; resistance to fosfomycin and gentamicin was found in only two ST95 strains. In contrast, in 2016 to 2017, nine (6.1%) isolates from the six major lineages were resistant to gentamicin; seven (4.7%) were extended-spectrum-β-lactamase (ESBL)-producing strains. All ESBL-producing strains of ST69, ST131, and ST10 were MDR. Resistance to nitrofurantoin and fosfomycin was found in only one strain each of ST73 and ST69, respectively.
DISCUSSION
In this university community, the six most common genotypes accounted for more than half (63%) of all the UPEC isolates in 2016 to 2017. These genotypes were also the most common genotypes in a collection of UPEC isolates obtained 17 years earlier in the same community, although the compositions of the minor genotypes had completely changed. These six major genotypes accounted for nearly 80% of the increase in ampicillin resistance and 73% of the increase in resistance to ciprofloxacin. The other genotypes accounted for only 21% and 27% of the increases in ampicillin and ciprofloxacin resistance, respectively. The proportions of isolates with TMP-SMZ resistance did not differ significantly between the periods separated by 17 years. These results indicate that the prevalence of resistant CA-UTI in this population is largely influenced by a few circulating dominant E. coli lineages.
In this study, MLST was used to genotype E. coli isolates. Although conventional 7-locus MLST is based on a small set of housekeeping genes of a bacterial genome, phylogenic classification based on this MLST scheme of E. coli isolates closely matches that based on their whole-genome sequences (23–25). The observation that a small set of dominant evolutionarily related UPEC lineages persisted to cause UTI in the same community 17 years apart suggests the existence of common-source reservoirs.
Interestingly, these same genotypes (ST95, ST127, ST73, ST69, ST131, and ST10) account for a large proportion of both CA-UTI and bloodstream infections (BSI) in many other communities around the world (12–14, 26–28). The predominance of these major genotypes varies geographically. For example, ST127, the second-most-common genotype in our study, is less frequently reported in studies from Europe, Canada, or Japan (12–14, 27, 28), but it was the third-most-common genotype in the Seattle region (26). The predominance of ST127 in the West Coast cities in the United States is not explained. However, these types of observations suggest that most cases of CA-UTI occur as outbreaks and that the dominant genotypes may be spread by contaminated vehicles distributed locally, regionally, or globally. It also suggests that the selective pressure of antimicrobial use exerts differential effects on ExPEC genotypes such that certain genotypes become progressively more resistant.
Recently, several epidemiological studies have resulted in reports that E. coli causing UTI may be transmitted by contaminated food products (27, 29–35). A case-control study suggested that antimicrobial-resistant UPEC could have a food reservoir, possibly in poultry or pork (34). E. coli genotypes identified on the basis of ERIC2-PCR and pulsed-field gel electrophoresis (PFGE) results that were shared between CA-UTI isolates and retail meat concurrently obtained from the same geographic region have been observed (31, 33, 35). However, despite those studies suggesting foodborne transmission of UTI, the reservoir of these common lineages, how they are introduced into the food chain, and why only these lineages predominate in human populations remain unclear.
In the mid-2000s in the United States, fluoroquinolones replaced TMP-SMZ as the most widely prescribed antimicrobial agent for treatment of uncomplicated UTI (36). In 2016 to 2017, we found 12 ciprofloxacin-resistant strains, of which more than half were due to ST131, whereas, in 1999 to 2000, only 1 was identified. In early 2000, the university health service replaced TMP-SMZ with ciprofloxacin as the first-line empirical drug used to treat UTI. Despite this change, fluoroquinolone resistance occurred in only one genotype during the ensuing 17 years. Dominant genotypes ST95 and ST127 remained susceptible to most antimicrobial agents, while others, such as ST131, evolved to become MDR during the same period. ST131 is well recognized globally as an extensively resistant ExPEC clonal group (37–40). During the two study periods, ST95 was the most common dominant genotype, and the prevalence of ST127 increased from 11% to 16%. Drug resistance does not seem to be the driving force responsible for a UPEC genotype becoming dominant, as indicated by the ST95 and ST127 data.
A similar observation was made in a population dynamics analysis of ExPEC lineages in England over an 11-year period, which found ST73 to be the most common lineage among pandemic strains ST69, ST95, and ST131 (14). ST73 was consistently susceptible to most antibiotics, and it was suggested that drug resistance was not the main reason for the prevalence of E. coli lineages in this population (14). The community dominance of these lineages may be due to their intrinsic biological fitness together with epidemiologic factors that contribute to their global dissemination.
Limitations of this study included a lack of patient clinical and exposure history in both study periods. While the UTI subjects were largely women attending a Northern California university, we do not have information about their previous use of antimicrobial agents; such use could have influenced the resistance status of their UTI episodes and thus the differences in the prevalences of resistant UTI in the two periods. However, such a factor would not explain the dominance of a small set of UPEC genotypes in the two study periods.
We observed that six UPEC genotypes were persistently dominant in all CA-UTI cases at one university community in Northern California during two study periods separated by 17 years. These findings suggest that the community prevalence of drug-resistant CA-UTI is largely determined by the number and proportion of dominant UPEC genotypes circulating in that community. Antimicrobial agents may select for drug-resistant strains, but they do not appear to exert their effect equally on all UPEC strains. Control of drug-resistant CA-UTI will likely require new interventions in addition to antibiotic stewardship programs in outpatient clinical settings. Further studies are needed to elucidate the mechanisms by which these common lineages disseminate and prevail within a community.
ACKNOWLEDGMENTS
We thank Holly Berryman Stern and the other staff members of the Tang Center of University of California, Berkeley (UC Berkeley)-affiliated health care service for their time and support of this project. We are grateful to Amee Manges for providing us with the data for antimicrobial susceptibility to ciprofloxacin and trimethoprim-sulfamethoxazole for E. coli isolates in 1999 to 2000. We also thank all the members of the Riley laboratory for fruitful discussion and their contributions to this study.
This work was supported by Centers for Disease Control and Prevention investments to combat antibiotic resistance under BAA 200-2016-91939. The contents of this work are solely the responsibility of the authors and do not necessarily represent the official views of the Centers for Disease Control and Prevention. The funder of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. The corresponding author had full access to all the data in the study and had final responsibility for the decision to submit for publication.
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