BackgroundSalmonella Typhimurium ST213 was first detected in the Mexican Typhimurium population in 2001. It is associated with a multi-drug resistance phenotype and a plasmid-borne blaCMY-2 gene conferring resistance to extended-spectrum cephalosporins. The objective of the current study was to examine the association between the ST213 genotype and blaCMY-2 plasmids.ResultsThe blaCMY-2 gene was carried by an IncA/C plasmid. ST213 strains lacking the blaCMY-2 gene carried a different IncA/C plasmid. PCR analysis of seven DNA regions distributed throughout the plasmids showed that these IncA/C plasmids were related, but the presence and absence of DNA stretches produced two divergent types I and II. A class 1 integron (dfrA12, orfF and aadA2) was detected in most of the type I plasmids. Type I contained all the plasmids carrying the blaCMY-2 gene and a subset of plasmids lacking blaCMY-2. Type II included all of the remaining blaCMY-2-negative plasmids. A sequence comparison of the seven DNA regions showed that both types were closely related to IncA/C plasmids found in Escherichia, Salmonella, Yersinia, Photobacterium, Vibrio and Aeromonas. Analysis of our Typhimurium strains showed that the region containing the blaCMY-2 gene is inserted between traA and traC as a single copy, like in the E. coli plasmid pAR060302. The floR allele was identical to that of Newport pSN254, suggesting a mosaic pattern of ancestry with plasmids from other Salmonella serovars and E. coli. Only one of the tested strains was able to conjugate the IncA/C plasmid at very low frequencies (10-7 to 10-9). The lack of conjugation ability of our IncA/C plasmids agrees with the clonal dissemination trend suggested by the chromosomal backgrounds and plasmid pattern associations.ConclusionsThe ecological success of the newly emerging Typhimurium ST213 genotype in Mexico may be related to the carriage of IncA/C plasmids. We conclude that types I and II of IncA/C plasmids originated from a common ancestor and that the insertion and deletion of DNA stretches have shaped their evolutionary histories.

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Background: Salmonella and Shigella cause significant morbidity and mortality among children worldwide. Increased antimicrobial resistance results in greater burden of disease.Materials and Methods: From 2005 to 2011, Salmonella and Shigella isolates collected from ill children at a major hospital in Yucatan, Mexico, were subjected to serotyping and antimicrobial susceptibility testing by disk diffusion and agar dilution. The identification of blaCTX, blaCMY, blaSHV, blaTEM, and blaOXA and qnr resistance genes was conducted by PCR and sequencing.Results: Among 2344 children with acute gastroenteritis, salmonellosis decreased from 17.7% in 2005 to 11.2% in 2011 (p < 0.001). In contrast, shigellosis increased from 8.3% in 2010 to 12.1% in 2011. Compared to children with Salmonella, those with Shigella had significantly more bloody stools (59 vs 36%, p < 0.001), dehydration (27 vs 15%, p = 0.031), and seizures (11 vs 3%, p = 0.03). In Salmonella (n = 365), there was a significant decrease in resistance to ampicillin (43 to 16%, p < 0.001), trimethoprim–sulfamethoxazole (44 to 26%, p = 0.014), and extended-spectrum cephalosporins (27 to 10%, p = 0.009). Reduced susceptibility to ciprofloxacin in Salmonella rose from 30 to 41% (p < 0.001). All ceftriaxone-resistant isolates harbored the blaCMY-2 gene. qnr genes were found in 42 (36%) of the 117 Salmonella isolates with a ciprofloxacin MIC ≥ 0.125 μg/ml. Four were qnrA1 and 38 were qnrB19. Resistance to ampicillin (40%) and trimethoprim–sulfamethoxazole (58%) was common in Shigella (n = 218), but isolates remained fully susceptible to ceftriaxone and ciprofloxacin.Conclusion: Illness from Salmonella has decreased while severe Shigella infections have increased among children with gastroenteritis in the Yucatan Peninsula. While Shigella resistance to clinically important antibiotics remained unchanged, resistance to most of these, except ciprofloxacin, declined in Salmonella. blaCMY-2 and qnr genes are common in Salmonella isolates.

We describe prevalence and antimicrobial susceptibility results for thermophilic Campylobacter isolates collected from humans, food, and food-animals in an integrated food chain surveillance network in Mexico. From 2003 to 2006, stool samples were collected from children with diarrhea at state sentinel hospitals. Concurrently, fecal samples from asymptomatic children in kindergartens, as well as raw chicken, pork and beef from retail outlets, and food-animal intestines from slaughterhouses were all collected in 65 cities from four different states. C. jejuni was identified with a standardized hippurate test. Hippurate negative, indoxyl acetate positive isolates were classified as Campylobacter spp. Susceptibility testing was performed by agar dilution according to Clinical and Laboratory Standards Institute guidelines. A total of 1,259 C. jejuni and 1,797 Campylobacter spp. isolates were recovered from 11,811 samples. Chicken was significantly more contaminated for both intestinal samples (93.6%) and meat products (58.3%), compared with swine (71.4%)/pork (14.6%) samples, and cattle (25.1%)/beef (5.3%) samples (p<0.001). Campylobacter was recovered from 5.1% of children with diarrhea and from 3.2% of asymptomatic children. Chicken was significantly more likely to harbor ciprofloxacin-resistant C. jejuni (85.8%) than swine (62.5%, OR=3.6), cattle (39.8%, OR=9.3), or humans (58.2%, OR=4.4). No significant differences were found for ciprofloxacin-resistant Campylobacter spp. among food-animals, but the rate in food-animals was significantly higher than in humans (84% vs. 56.7%, OR=4.0). Swine was significantly more likely to harbor erythromycin-resistant C. jejuni (14.8%) than chicken (3.5%, OR=4.9), cattle (1.8%, OR=9.3), or humans (3.0%, OR=5.7), and was associated with higher rates of erythromycin-resistant Campylobacter spp. (41.9%) than chicken (10.5%, OR=6.1) and humans (11.9%, OR=5.3). The high resistance rates to ciprofloxacin preclude the use of fluoroquinolones for treatment of campylobacteriosis in Mexico. Our results emphasize the need for ongoing and integrated surveillance of antimicrobial usage and antimicrobial susceptibility in humans and animals.

Globally, diarrheal diseases are a leading cause of death in children under five and disproportionately affect children in developing countries. Children who contract diarrheal diseases are rarely screened to identify the etiologic agent due to time and cost considerations associated with pathogen-specific screening and hence pathogen-directed therapy is uncommon. The development of biomarkers to rapidly identify underlying pathogens could improve treatment options and clinical outcomes in childhood diarrheal diseases. Here, we perform RNA sequencing on blood samples collected from children evaluated in an emergency room setting with diarrheal disease where the pathogen(s) present are known. We determine host response gene signatures specific to Salmonella, Shigella and rotavirus, but not E. coli, infections that distinguish them from each other and from healthy controls. Specifically, we observed differential expression of genes related to chemokine receptors or inflammasome signaling in Shigella cases, such as CCR3, CXCR8, and NLRC4, and interferon response genes, such as IFI44 and OASL, in rotavirus cases. Our findings add insight into the host peripheral immune response to these pathogens, and suggest strategies and limitations for the use host response transcript signatures for diagnosing the etiologic agent of childhood diarrheal diseases.