Jason Abbott

Nontyphoidal Salmonella from Human Clinical Cases, Asymptomatic Children, and Raw Retail Meats in Yucatan, Mexico

BACKGROUND We report the results of a 3-year Salmonella surveillance study of persons with diarrhea; asymptomatic children; and retail pork, poultry, and beef in Yucatan, Mexico. METHODS Isolates were characterized according to serotype, antimicrobial susceptibility, and genetic relatedness with pulsed-field gel electrophoresis. RESULTS Salmonella Typhimurium was the most common serotype found in ill humans (21.8% of isolates), followed by Salmonella Agona (21% of isolates). Salmonella Enteritidis was a minor serotype (4.2% of isolates). Asymptomatic children carried S. Agona (12.1% of isolates), Salmonella Meleagridis (11.6% of isolates), Salmonella Anatum (8% of isolates) and S. Enteritidis (5.8% of isolates). A high percentage of retail meat samples contained Salmonella; it was most commonly found in pork (58.1% of samples), followed by beef (54% of samples) and poultry (39.7% of samples). Resistance to oral drugs used for the treatment of salmonellosis was observed for ampicillin (14.6% of isolates were resistant), chloramphenicol (14.0% of isolates), and trimethoprim-sulfamethoxazole (19.7% of isolates). Resistance to ceftriaxone emerged in 2002 and was limited to the serotype S. Typhimurium. Twenty-seven percent of the isolates were resistant to nalidixic acid, and none were resistant to ciprofloxacin. Multidrug resistance was most common among isolates of serotypes S. Typhimurium and S. Anatum. Pulsed-field gel electrophoresis showed that strains found in retail meats were genetically identical to strains found in both asymptomatic children and ill patients. CONCLUSIONS Our study found a high prevalence of Salmonella in retail meats and persons with enteric infection; many of these isolates were resistant to clinically important antimicrobials. A random selection of isolates from people and retail meat showed genetic relatedness, which suggests that, in Yucatan, considerable transfer of Salmonella occurs through the food chain.

Characterization of Antimicrobial-Resistant Salmonella Isolated from Imported Foods

Two-hundred eight Salmonella isolates recovered from over 5,000 imported foods entering the United States in 2001 were tested for antimicrobial susceptibilities and further characterized for quinolone resistance mechanisms, integron carriage, and genetic relatedness. Salmonella Weltevreden (20%), Salmonella Newport (6%), Salmonella Lexington (5%), and Salmonella Thompson (4%) were the four most common serotypes recovered. Twenty-three (11%) isolates were resistant to at least one antimicrobial, and seven (3.4%) to three or more antimicrobials. Resistance was most often observed to tetracycline (9%), followed by sulfamethoxazole (5%), streptomycin (4%), nalidixic acid (3%), and trimethoprim/sulfamethoxazole (2%). One Salmonella Schwarzengrund isolate recovered from squid imported from Taiwan exhibited resistance to eight antimicrobials, including ampicillin, chloramphenicol, gentamicin, kanamycin, nalidixic acid, sulfamethoxazole, tetracycline, and trimethoprim/sulfamethoxazole. Six isolates (Salmonella Bareilly, Salmonella Derby, Salmonella Ohio and three Salmonella Schwarzengrund) contained class 1 integrons, which carried several resistance genes including dhfrI/dhfrXII, aadA, pse-1, and sat1, conferring resistance to trimethoprim/sulfamethoxazole, streptomycin, ampicillin, and streptothricin, respectively. Five of six nalidixic acid-resistant isolates possessed DNA point mutations at either Ser83 or Asp87 in DNA gyrase. One ciprofloxacin-resistant isolate possessed double mutations in DNA gyrase at positions Ser83 and Asp87 as well as a single mutation at Ser80 in parC. The top three serotypes identified, Salmonella Weltevreden (n = 41), Salmonella Newport (n = 13), and Salmonella Lexington (n = 11), were further characterized for genetic relatedness by pulsed-field gel electrophoresis. Fifty-five distinct pulsed-field gel electrophoresis patterns were observed among the 65 isolates, indicating extensive genetic diversity among these Salmonella serotypes contaminating imported foods.

Integrated Food Chain Surveillance System for Salmonella spp. in Mexico 1

This system effectively identified major public health priorities.

Presence and Characterization of Shiga Toxin-Producing Escherichia coli and Other Potentially Diarrheagenic E. coli Strains in Retail Meats

ABSTRACT To determine the presence of Shiga toxin-producing Escherichia coli (STEC) and other potentially diarrheagenic E. coli strains in retail meats, 7,258 E. coli isolates collected by the U.S. National Antimicrobial Resistance Monitoring System (NARMS) retail meat program from 2002 to 2007 were screened for Shiga toxin genes. In addition, 1,275 of the E. coli isolates recovered in 2006 were examined for virulence genes specific for other diarrheagenic E. coli strains. Seventeen isolates (16 from ground beef and 1 from a pork chop) were positive for stx genes, including 5 positive for both stx1 and stx2, 2 positive for stx1, and 10 positive for stx2. The 17 STEC strains belonged to 10 serotypes: O83:H8, O8:H16, O15:H16, O15:H17, O88:H38, ONT:H51, ONT:H2, ONT:H10, ONT:H7, and ONT:H46. None of the STEC isolates contained eae, whereas seven carried enterohemorrhagic E. coli (EHEC) hlyA. All except one STEC isolate exhibited toxic effects on Vero cells. DNA sequence analysis showed that the stx2 genes from five STEC isolates encoded mucus-activatable Stx2d. Subtyping of the 17 STEC isolates by pulsed-field gel electrophoresis (PFGE) yielded 14 distinct restriction patterns. Among the 1,275 isolates from 2006, 11 atypical enteropathogenic E. coli (EPEC) isolates were identified in addition to 3 STEC isolates. This study demonstrated that retail meats, mainly ground beef, were contaminated with diverse STEC strains. The presence of atypical EPEC strains in retail meat is also of concern due to their potential to cause human infections.

Antimicrobial resistance, virulence, and genotypic profile comparison of Campylobacter jejuni and Campylobacter coli isolated from humans and retail meats.

A total of 360 spatially and temporally related Campylobacter isolates, including 168 from clinical human cases (Campylobacter jejuni n = 148; Campylobacter coli n = 20) and 192 from retail meats (C. jejuni n = 114; C. coli n = 78), were analyzed for antimicrobial susceptibilities, virulence, and genotypic profiles. Ciprofloxacin-resistant C. jejuni was observed in 13.5% and 19% of the isolates from humans and retail chicken breasts, respectively. Antimicrobial resistance to ciprofloxacin and erythromycin was detected in C. coli isolates recovered from 29% and 16.6% of retail meats and 15% and 5% humans, respectively. Overall, virulence determinants were more prevalent in Campylobacter isolates recovered from retail meats than from humans. C. jejuni isolates from humans were significantly associated with the rakR, dnaJ, and pld genes, whereas C. coli isolates from retail meats were associated with the dnaJ, pld, and virB11 virulence genes. Genotyping of 262 C. jejuni isolates using pulsed-field gel electrophoresis revealed a total of 186 unique SmaI patterns, with 14% of patterns composed of isolates recovered from retail meats and ill humans. All unique groups with indistinguishable SmaI patterns were further analyzed by a second restriction enzyme (KpnI), which revealed limited overlap between isolates from different sources. Significant association between doxycycline-resistant C. jejuni strains recovered from humans and different virulence genes (e.g., cdtB) was identified at the statistical level but not at the genotypic level. In conclusion, significant differences observed in the distribution of antimicrobial resistance profiles, virulence determinants, and genotypic diversity among C. jejuni and C. coli isolates indicate that there are sources other than retail meats that may also contribute to human Campylobacter infections.

Retrospective Analysis of Salmonella, Campylobacter, Escherichia coli, and Enterococcus in Animal Feed Ingredients

The presence and antimicrobial susceptibility of foodborne pathogens and indicator organisms in animal feed are not well understood. In this study, a total of 201 feed ingredient samples (animal byproducts, n=122; plant byproducts, n=79) were collected in 2002 and 2003 from representative rendering plants and the oilseed (or cereal grain) industry across the United States. The occurrence and antimicrobial susceptibility of four bacterial genera (Salmonella, Campylobacter, Escherichia coli, and Enterococcus) were determined. Salmonella isolates were further characterized by serotyping and pulsed-field gel electrophoresis (PFGE). None of the samples yielded Campylobacter or E. coli O157:H7, whereas Salmonella, generic E. coli, and Enterococcus were present in 22.9%, 39.3%, and 86.6% of samples, respectively. A large percentage (47.8%) of Salmonella-positive samples harbored two serovars, and the vast majority (88.4%) of Enterococcus isolates were E. faecium. Animal byproducts had a significantly higher Salmonella contamination rate (34.4%) than plant byproducts (5.1%) (p<0.05). Among 74 Salmonella isolates recovered, 27 serovars and 55 PFGE patterns were identified; all were pan-susceptible to 17 antimicrobials tested. E. coli isolates (n=131) demonstrated similar susceptibility to these antimicrobials except for tetracycline (15.3% resistance), sulfamethoxazole (7.6%), streptomycin (4.6%), ampicillin (3.8%), and nalidixic acid (1.5%). Enterococcus isolates (n=362) were also resistant to five of 17 antimicrobials tested, ranging from 1.1% to penicillin to 14.6% to tetracycline. Resistance rates were generally higher among isolates recovered from animal byproducts. Taken together, our findings suggest that diverse populations of Salmonella, E. coli, and Enterococcus are commonly present in animal feed ingredients, but antimicrobial resistance is not common. Future large-scale studies to monitor these pathogenic and indicator organisms in feed commodities is warranted.

Antimicrobial resistance and molecular subtyping of Campylobacter jejuni and Campylobacter coli from retail meats.

Campylobacter isolates (n = 297; 202 C. jejuni and 95 C. coli isolates) recovered from 2,513 retail meat samples (chicken breasts, ground turkey, ground beef, and pork chops) were examined for antimicrobial susceptibility. The isolates were further analyzed for genetic relatedness by pulsed-field gel electrophoresis (PFGE) using SmaI and KpnI restriction enzymes, and a subset of isolates (n = 174) were subtyped by multilocus sequence typing (MLST). The resistance most frequently observed was that to doxycycline (27.6%), followed by ciprofloxacin (13.8%) and erythromycin (6.4%). All isolates were susceptible to gentamicin and meropenem. C. coli showed higher resistance to doxycycline than did C. jejuni (42.1 versus 20.8%) and lower resistance to ciprofloxacin than did C. jejuni (10.5 versus 15.3%). Erythromycin resistance was only observed in C. coli. PFGE using SmaI plus KpnI digestion generated 168 clusters from 297 isolates: 115 from C. jejuni and 53 from C. coli. MLST revealed 44 sequence types (STs) under 10 clonal complexes from 120 C. jejuni and 27 STs under two clonal complexes from 54 C. coli. There was a positive association between PFGE and STs; however, PFGE showed greater discriminatory power than MLST. Subtyping data did not correlate with antimicrobial resistance phenotypes.

Molecular Subtyping and Source Attribution of Campylobacter Isolated from Food Animals

Campylobacter spp. commonly cause gastrointestinal illness in humans. Poultry meats have long been considered the predominant source of these infections, but few in-depth Campylobacter source attribution studies have been completed. We analyzed more than 1,300 Campylobacter isolates recovered from a number of animal and food sources, including dairy and beef cattle, pigs, poultry, and retail poultry meat, and compared them with Campylobacter isolates recovered from human clinical samples. Each isolate was subtyped using pulsed-field gel electrophoresis (PFGE) with SmaI and queried against the Centers for Disease Control and Prevention PulseNet database to identify human isolates with indistinguishable patterns. Half (49.5%) of the PFGE patterns from poultry animal and retail meat isolates were indistinguishable from patterns of at least one human isolate. Among the isolates from beef and dairy cows, 56.6 and 65.0%, respectively, of their PFGE patterns were indistinguishable from those of human isolates. Only a small portion of the PFGE patterns of Campylobacter isolated from pigs (9.5%) were found to have PFGE patterns in common with human isolates. These data imply that cattle may be larger contributors to Campylobacter infections than previously recognized and help further our understanding of potential sources of human campylobacteriosis.

Whole-genome sequencing of Salmonella enterica subsp. enterica serovar Cubana strains isolated from agricultural sources

ABSTRACT We report the draft genomes of Salmonella enterica subsp. enterica serovar Cubana strain CVM42234, isolated from chick feed in 2012, and S. Cubana strain 76814, isolated from swine in 2004. The genome sizes are 4,975,046 and 4,936,251 bp, respectively.