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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  bla  CTX ,  bla  CMY ,  bla  SHV ,  bla  TEM , and  bla  OXA  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  bla  CMY-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 .  bla  CMY-2  and  qnr  genes are common in  Salmonella  isolates.

Incidence, clinical presentation, and antimicrobial resistance trends in Salmonella and Shigella infections from children in Yucatan, Mexico