Characterization of antimicrobial resistance among Escherichia coli O111 isolates of animal and human origin

Multidrug resistance, biofilm formation and detection of bla CTX-M and bla VIM genes in E. coli and Salmonella isolates from chutney served at the street-food stalls of Bharatpur, Nepal

Antimicrobial resistance (AMR) amid the bacteria found in ready-to-eat foods is a grave concern today warranting an immediate intervention. The current study was undertaken to explore the status of AMR in E. coli and Salmonella species in ready-to-eat Chutney samples (n = 150) served at the street food stalls in Bharatpur, Nepal, with a major focus on detecting extended-spectrum β-lactamase (ESBL) and metallo β-lactamase (MBL) genes along with biofilm formation. Average viable counts, coliform counts, and Salmonella Shigella counts were 1.33 × 10⁶±141481.4, 1.83 × 10⁵±91303.6, and 1.24 × 10⁵±63933.19 respectively. Out of 150 samples, 41 (27.33%) harbored E. coli, of which 7 were E. coli O157:H7; whereas Salmonella spp. were found in 31 (20.67%) samples. Bacterial contamination of Chutney by E. coli and Salmonella and ESBL-production were both found significantly affected by different sources of water used, personal hygiene and literacy rate of the vendors as well as by the type of cleaning materials used to wash knives and chopping boards (P < 0.05). Antibiotic susceptibility testing revealed that imipenem was the most effective drug against both types of bacterial isolates. Additionally, 14 (45.16%) Salmonella isolates and 27 (65.85%) E. coli isolates were found to be multi-drug resistant (MDR). Total ESBL (bla _CTX-M) producers reported were 4 (12.90%) Salmonella spp. and 9 (21.95%) E. coli. Only 1 (3.23%) Salmonella spp. and 2 (4.88%) E. coli isolates were bla _VIM gene carriers. Dissemination of knowledge of personal hygiene amongst the street vendors and consumer awareness regarding ready-to-eat foods are crucial factors that can be suggested to curtail the emergence and transmission of food-borne pathogens.

Clonality and virulence traits of Escherichia coli associated with haemorrhagic septicaemia in turkeys

Fifty-five clinical isolates of avian pathogenic Escherichia coli (APEC) from seven outbreaks of acute haemorrhagic septicaemia in turkeys were characterized by serotyping, plasmid profiling including restriction analysis with HindIII, ribotyping with EcoRI and HindIII, multilocus sequence typing (MLST) and virulence profiling. A clonal relationship was demonstrated for each outbreak according to serotype, plasmid profiling, ribotyping, and MLST. In addition, isolates demonstrated highly similar virulence profiles, as all isolates were positive for F11 pili and possessed genes encoding aerobactin (iucD), increased serum survival (iss), temperature-sensitive haemagglutinin (tsh) and colicin V plasmid operon genes (cva/cvi). However, only 20% of the isolates produced colicin V and 42% exhibited serum resistance. All strains with O group O111 and a single O18ac strain (demonstrating non-clonal DNA profiles) were positive for enteroaggregative heat-stabile toxin (EAST1), while isolates of a single outbreak all possessed the enteroaggregative toxin gene (astA). All isolates were negative for genes encoding verocytotoxins (vtx/stx), iron-repressible protein (irp2), P-fimbria (papC), invasion plasmid antigen (ipaH), attaching and effacing gene (eae), enterohaemolysin (ehxA), and enterotoxins LT, STIa (ST(p)) and STIb (ST(h)). In conclusion, highly similar virulence profiles were demonstrated for isolates of E. coli associated with a single well-defined lesion type of colibacillosis in turkeys; acute haemorrhagic septicaemia. The isolates obtained, however, demonstrated a different phylogenetic background, underlining the importance of using well-defined strain collections for characterization of APEC pathotypes.

Related antimicrobial resistance genes detected in different bacterial species co-isolated from swine fecal samples

A potential factor leading to the spread of antimicrobial resistance (AR) in bacteria is the horizontal transfer of resistance genes between bacteria in animals or their environment. To investigate this, swine fecal samples were collected on-farm and cultured for Escherichia coli, Salmonella enterica, Campylobacter spp., and Enterococcus spp. which are all commonly found in swine. Forty-nine of the samples from which all four bacteria were recovered were selected yielding a total of 196 isolates for analysis. Isolates were tested for antimicrobial susceptibility followed by hybridization to a DNA microarray designed to detect 775 AR-related genes. E. coli and Salmonella isolated from the same fecal sample had the most AR genes in common among the four bacteria. Genes detected encoded resistance to aminoglycosides (aac(3), aadA1, aadB, and strAB), β-lactams (ampC, ampR, and bla(TEM)), chloramphenicols (cat and floR), sulfanillic acid (sul1/sulI), tetracyclines (tet(A), tet(D), tet(C), tet(G), and tet(R)), and trimethoprim (dfrA1 and dfh). Campylobacter coli and Enterococcus isolated from the same sample frequently had tet(O) and aphA-3 genes detected in common. Almost half (47%) of E. coli and Salmonella isolated from the same fecal sample shared resistance genes at a significant level (χ², p < 0.0000001). These data suggest that there may have been horizontal exchange of AR genes between these bacteria or there may be a common source of AR genes in the swine environment for E. coli and Salmonella.

Molecular typing of antimicrobial-resistant Shiga-toxin-producing Escherichia coli strains (STEC) in Brazil

Antimicrobial resistance patterns and molecular characteristics were determined in thirty-two Shiga-toxin-producing Escherichia coli (STEC) strains previously identified in São Paulo State associated with human infections (n = 21) and in cattle feces (n = 11). The highest resistance rates were identified for tetracycline (100%), streptomycin (78%) and trimethoprim-sulfamethoxazole (56%). Eleven STEC strains showed resistance to ampicillin and carried bla(TEM) that was confirmed as bla(TEM-1) in one representative isolate. The class 1 integrase gene (intI1) was detected in seven (22%) strains, and most of them belonged to the O111:H8 serotype. The class 1 integron was located on plasmids in five of the seven STEC strains, and conjugation assays confirmed the plasmid support of those resistant determinants. STEC strains were genetically classified into the B1 group, and PFGE analysis showed that most of the strains in each serogroup were grouped into the same cluster (80-97% similarity). The presence of a class 1 integron and bla(TEM-1) genes is described for the first time among STEC isolates in Brazil and clearly represents a public health concern.

Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry

Salmonella enterica, a leading cause of food-borne gastroenteritis worldwide, may be found in any raw food of animal, vegetable, or fruit origin. Salmonella serovars differ in distribution, virulence, and host specificity. Salmonella enterica serovar Kentucky, though often found in the food supply, is less commonly isolated from ill humans. The multidrug-resistant isolate S. Kentucky CVM29188, isolated from a chicken breast sample in 2003, contains three plasmids (146,811 bp, 101,461 bp, and 46,121 bp), two of which carry resistance determinants (pCVM29188_146 [strAB and tetRA] and pCVM29188_101 [bla(CMY-2) and sugE]). Both resistance plasmids were transferable by conjugation, alone or in combination, to S. Kentucky, Salmonella enterica serovar Newport, and Escherichia coli recipients. pCVM29188_146 shares a highly conserved plasmid backbone of 106 kb (>90% nucleotide identity) with two virulence plasmids from avian pathogenic Escherichia coli strains (pAPEC-O1-ColBM and pAPEC-O2-ColV). Shared avian pathogenic E. coli (APEC) virulence factors include iutA iucABCD, sitABCD, etsABC, iss, and iroBCDEN. PCR analyses of recent (1997 to 2005) S. Kentucky isolates from food animal, retail meat, and human sources revealed that 172 (60%) contained similar APEC-like plasmid backbones. Notably, though rare in human- and cattle-derived isolates, this plasmid backbone was found at a high frequency (50 to 100%) among S. Kentucky isolates from chickens within the same time span. Ninety-four percent of the APEC-positive isolates showed resistance to tetracycline and streptomycin. Together, our findings of a resistance-conferring APEC virulence plasmid in a poultry-derived S. Kentucky isolate and of similar resistance/virulence plasmids in most recent S. Kentucky isolates from chickens and, to lesser degree, from humans and cattle highlight the need for additional research in order to examine the prevalence and spread of combined virulence and resistance plasmids in bacteria in agricultural, environmental, and clinical settings.

Antimicrobial resistance patterns of Shiga toxin-producing Escherichia coli O157:H7 and O157:H7- from different origins

Shiga toxin-producing Escherichia coli (STEC) serotypes including O157:H7 (n = 129) from dairy cows, cull dairy cow feces, cider, salami, human feces, ground beef, bulk tank milk, bovine feces, and lettuce; and O157:H7- (n = 24) isolated from bovine dairy and bovine feedlot cows were evaluated for antimicrobial resistance against 26 antimicrobials and the presence of antimicrobial resistance genes (tetA, tetB, tetC, tetD, tetE, tetG, floR, cmlA, strA, strB, sulI, sulII, and ampC). All E. coli exhibited resistance to five or more antimicrobial agents, and the majority of isolates carried one or more target antimicrobial resistance gene(s) in different combinations. The majority of E. coli showed resistance to ampicillin, aztreonam, cefaclor, cephalothin, cinoxacin, and nalidixic acid, and all isolates were susceptible to chloramphenicol and florfenicol. Many STEC O157:H7 and O157:H7-isolates were susceptible to amikacin, carbenicillin, ceftriaxone, cefuroxime, ciprofloxacin, fosfomycin, moxalactam, norfloxacin, streptomycin, tobramycin, trimethoprim, and tetracycline. The majority of STEC O157:H7 (79.8%) and O157:H7- (91.7%) carried one or more antimicrobial resistance gene(s) regardless of whether phenotypically resistant or susceptible. Four tetracycline resistant STEC O157:H7 isolates carried both tetA and tetC. Other tetracycline resistance genes (tetB, tetD, tetE, and tetG) were not detected in any of the isolates. Among nine streptomycin resistant STEC O157:H7 isolates, eight carried strA-strB along with aadA, whereas the other isolate carried aadA alone. However, the majority of tetracycline and streptomycin susceptible STEC isolates also carried tetA and aadA genes, respectively. Most ampicillin resistant E. coli of both serotypes carried ampC genes. Among sulfonamide resistance genes, sulII was detected only in STEC O157:H7 (4 of 80 sulfonamide-resistant isolates) and sulI was detected in O157:H7- (1 of 16 sulfonamide resistant isolates). The emergence and dissemination of multidrug resistance in STEC can serve as a reservoir for different antimicrobial resistance genes. Dissemination of antimicrobial resistance genes to commensal and pathogenic bacteria could occur through any one of the horizontal gene transfer mechanisms adopted by the bacteria.

Impact of hospitalization and antimicrobial drug administration on antimicrobial susceptibility patterns of commensalEscherichia coliisolated from the feces of horses

Objective-To evaluate antimicrobial susceptibility of commensal Escherichia coli strains isolated from the feces of horses and investigate relationships with hospitalization and antimicrobial drug (AMD) administration. Design-Observational study. Animals-68 hospitalized horses that had been treated with AMDs for at least 3 days (HOSP-AMD group), 63 hospitalized horses that had not received AMDs for at least 4 days (HOSP-NOAMD group), and 85 healthy horses that had not been hospitalized or treated with AMDs (community group). Procedures-Fecal samples were submitted for bacterial culture, and up to 3 E coli colonies were recovered from each sample. Antimicrobial susceptibility of 724 isolates was evaluated. Prevalence of resistance was compared among groups by use of log-linear modeling. Results-For 12 of the 15 AMDs evaluated, prevalence of antimicrobial resistance differed significantly among groups, with prevalence being highest among isolates from the HOSP-AMD group and lowest among isolates from the community group. Isolates recovered from the HOSP-AMD and HOSP-NOAMD groups were also significantly more likely to be resistant to multiple AMDs. Resistance to sulfamethoxazole and resistance to trimethoprim-sulfamethoxazole were most common, followed by resistance to gentamicin and resistance to tetracycline. Use of a potentiated sulfonamide, aminoglycosides, cephalosporins, or metronidazole was positively associated with resistance to 1 or more AMDs, but use of penicillins was not associated with increased risk of resistance to AMDs. Conclusion and Clinical Relevance-Results suggest that both hospitalization and AMD administration were associated with prevalence of antimicrobial resistance among E coli strains isolated from the feces of horses.

Stxgenotypes and antimicrobial resistance profiles of Shiga toxin-producingEscherichia colistrains isolated from human infections, cattle and foods in Brazil

A total of 107 Shiga toxin-producing Escherichia coli strains (STEC) isolated from different origins in São Paulo, Brazil, and belonging to different serotypes were characterized regarding stx subtypes and susceptibility to antimicrobial agents. Most of the human STEC strains harbored stx1 (85.7%), while stx2, associated or not to stx1, was identified preferentially in the animal and food strains. None of the STEC strains carried stx1c. Some genotypes occurred exclusively among strains of bovine origin as stx2c, stx1+2+2c (16.5% each), and stx2d (0.9%), whereas stx2+2c2vha) was only identified among the O157:H7 human strains. Moreover, the stx(2c2vhb) subtype was found more frequently among bovine than human strains (39% vs. 4.8%). The highest frequencies of susceptibility to antimicrobial agents were observed among bovine (87%) and food (100%) STEC strains, while 47.6% of the human isolates were resistant to at least one drug. Multiresistance occurred among O111 STEC strains from human and bovine origin. The antimicrobials to which resistance was most frequently observed were tetracycline (90%) and streptomycin (75%) among human strains, and also sulphazotrin (88%) in animal strains. A few serotypes were commonly identified among STEC strains isolated from diverse sources in Brazil, but in general the strains presented distinct stx subtypes and/or antimicrobial resistance profiles.

Antimicrobial resistance in Irish isolates of verocytotoxigenic Escherichia coli (E. coli)—VTEC

This study compared the antimicrobial resistance profiles of Escherichia coli O157:H7 isolates (n=257) recovered from bovine hides, minced beef and human clinical samples in Ireland, to those profiles of a range of Irish non-O157 E. coli (O111 and O26) isolates (n=31) from a variety of clinical and veterinary sources. Four multi-drug resistant (MDR) E. coli O157:H7 food isolates were identified, with resistance to 10 (1 isolate), 6 (1 isolate) and 4 (2 isolates) antimicrobial agents, respectively. Two of these isolates (resistant to 7 and 4 antimicrobial classes) were characterised further by molecular methods and found to contain class 1 integrons along with a beta-lactamase-encoding tem-1 gene. Transfer of antimicrobial resistance (ampicillin, streptomycin and sulphonamides), the tem-1 gene and markers (int1, qacEDelta1, sul1) characteristic of class 1 integrons were evident in one MDR isolate (resistant to 4 antimicrobial classes) when conjugation and transformation experiments were performed. A clinical isolate and a veterinary isolate of the O111 serotype were MDR and resistant to 4 and 3 antimicrobial classes, respectively. These data suggest that the prevalence of antimicrobial resistance among the three VTEC serotypes examined in this study is low. However, these organisms may become a public health risk should they enter the food chain.

Prevalence of class 1 integrons and antimicrobial resistance gene cassettes among enteric bacteria found in multisite group-level cohorts of humans and swine

The prevalence of antimicrobial resistance genotypic characteristics (class 1 integrons and antimicrobial resistance gene cassettes) among commensal Escherichia coli isolated from humans and swine in a semiclosed, integrated farrow-to-fork population was evaluated in a cross-sectional study. The objective of this study was to establish baseline antimicrobial resistance patterns of enteric bacteria from animals and humans within the study population; specifically, genotypic traits both unique and common to commensal E. coli derived from the different sources were evaluated. There were significant differences between host species; swine isolates were more likely to harbor integrons (odds ratio = 2.33, P = 0.0487). No significant differences were found for facility location, facility type, human housing cohort, or time of day (P > 0.05). There were significant differences (P = 0.006) among swine production groups (fecal samples from boars, dry sows, finishers, growers, intake boars, lactating sows, the lagoon, nursery piglets, influent, and piglets); the grower group was less likely than the nursery group to harbor a class 1 integron (nursery as referent: odds ratio = 0.22, P = 0.04). Among all isolates with an integron present, human isolates were more likely to harbor an antimicrobial resistance gene cassette (odds ratio = 6.36, P = 0.003). When isolates that possessed gene cassettes coding for resistance to specific antimicrobials were compared, no significant differences between host species (P > 0.05) were observed.

Patterns of antimicrobial resistance among commensal Escherichia coli isolated from integrated multi-site housing and worker cohorts of humans and swine

We examined antimicrobial resistance (AR) phenotypes among commensal Escherichia coli isolated from fecal matter of humans and swine housed in a semi-closed and uniquely integrated multi-site farrow-to-plate operation. Aggregate cohorts of humans consisted of (1) "control" groups of consumers, (2) groups of swine workers, and (3) groups of slaughter-plant workers. Analyses of cross-sectional AR data from 472 human and 376 swine isolates are presented. AR phenotypes among these isolates were compared by (1) host species, (2) facility location, (3) facility type, (4) housing (human) or production (swine) cohort, and (5) sample collection period and time of day. There were significant (p < 0.05) differences in isolates among host-species with swine uniformly at greater risk for (1) AR to four specific antimicrobials (kanamycin, streptomycin, sulfamethoxazole, tetracycline), and (2) multiple resistance phenotypes (p < 0.0001). Facility type and unit location were more often associated with AR differences among swine isolates than among human isolates. Swine production group was significantly associated with AR prevalence (p < 0.05) for nine antimicrobials; in general, purchased boars, suckling piglets, weaned piglets, and lactating sows were at higher risk of AR. There was no significant (p > 0.05) association of human occupational/consumer cohort with AR prevalence. Several unique AR phenotypes were detected in each of the human- and swine-intake groups. These data establish baseline characteristics for an on-going 3-year longitudinal study designed to further characterize AR phenotype and genotype in this population. Host-, facility-, and cohort-specific data demonstrate that sufficient prevalence differences exist to permit the future quantification of AR transmission, should it occur. Based on these cross-sectional data, occupational exposure to either swine-rearing or swine-slaughter facilities does not appear to be associated with the prevalence of phenotypic resistance among the commensal fecal E. coli isolated from this integrated system.

Antimicrobial resistance of Shiga toxin (verotoxin)-producing Escherichia coli O157:H7 and non-O157 strains isolated from humans, cattle, sheep and food in Spain

A total of 722 Shiga toxin-producing Escherichia coli (STEC) isolates recovered from humans, cattle, ovines and food during the period from 1992 to 1999 in Spain were examined to determine antimicrobial resistance profiles and their association with serotypes, phage types and virulence genes. Fifty-eight (41%) out of 141 STEC O157:H7 strains and 240 (41%) out of 581 non-O157 STEC strains showed resistance to at least one of the 26 antimicrobial agents tested. STEC O157:H7 showed a higher percentage of resistant strains recovered from bovine (53%) and beef meat (57%) than from human (23%) and ovine (20%) sources, whereas the highest prevalence of antimicrobial resistance in non-O157 STEC was found among isolates recovered from beef meat (55%) and human patients (47%). Sulfisoxazole (36%) had the most common antimicrobial resistance, followed by tetracycline (32%), streptomycin (29%), ampicillin (10%), trimethoprim (8%), cotrimoxazole (8%), chloramphenicol (7%), kanamycin (7%), piperacillin (6%), and neomycin (5%). The multiple resistance pattern most often observed was that of streptomycin, sulfisoxazole, and tetracycline. Ten (7%) STEC O157:H7 and 71 (12%) non-O157 strains were resistant to five or more antimicrobial agents. Most strains showing resistance to five or more antimicrobial agents belonged to serotypes O4:H4 (4 strains), O8:H21 (3 strains), O20:H19 (6 strains), O26:H11 (8 strains eae-beta1), O111:H- (3 strains eae-gamma2), O118:H- (2 strains eae-beta1), O118:H16 (5 strains eae-beta1), O128:H- (2 strains), O145:H8 or O145:H- (2 strains eae-gamma1), O157:H7 (10 strains eae-gamma1), O171:H25 (3 strains), O177:H11 (5 strains eae-beta1), ONT:H- (3 strains/1 eae-beta1) and ONT:H21 (2 strains). Interestingly, most of these serotypes, i.e., those indicated in bold) were found among human STEC strains isolated from patients with hemolytic uremic-syndrome (HUS) reported in previous studies. We also detected, among non-O157 strains, an association between a higher level of multiple resistance to antibiotics and the presence of the virulence genes eae and stx(1). Moreover, STEC O157:H7, showed an association between certain phage types, PT21/28 (90%), PT23 (75%), PT34 (75%), and PT2 (54%), with a higher number of resistant strains. We conclude that the high prevalence of antimicrobial resistance detected in our study is a source of concern, and cautious use of antibiotics in animals is highly recommended.

Isolation and characterization of Escherichia coli recovered from Maryland apple cider and the cider production environment

Contaminated apple cider has been implicated in several Escherichia coli O157:H7 outbreaks. In an attempt to investigate sources and modes of entry of E. coli into apple cider, samples of fresh apple, pomace, and cider and equipment and mill floor swabs were analyzed for standard plate counts (SPC), total coliforms (TC), fecal coliforms (FC), and E. coli. E. coli was isolated from 14 (33%) of 42 samples of bottled fresh cider, from food equipment in 6 (67%) of 9 mills, and from apples, pomace, or cider in 7 (78%) of 9 mills. Seventy-five E. coli isolates were further characterized for Shiga toxin-producing E. coli (STEC)-associated virulence factors, antimicrobial susceptibility, and pulsed-field gel electrophoresis (PFGE) type. No E. coli O157:H7 or other STEC was identified. Serotyping and PFGE revealed 64 distinct profiles, suggesting that recovered E. coli arose from multiple independent sources. However, on one occasion, E. coli isolated from the source apple sample was closely related to the E. coli identified in the finished cider sample. E. coli isolates were further tested for antimicrobial susceptibility to 17 antimicrobial agents of human and veterinary importance. Fourteen (19%) of the 75 isolates were resistant to at least one of the antimicrobial agents tested, and 9 (12%) were resistant to at least two of these agents. Of the resistant isolates recovered, 64% were resistant to tetracycline and 57% were resistant to streptomycin. Overall, the level of E. coli contamination in source apple samples did not differ significantly from those in samples of pomace, cider at the press, and cider entering the bottling tank; therefore, source apples cannot be dismissed as a potential contributor of E. coli to the cider-making process.