Resistance to third-generation cephalosporins in non-typhoidal Salmonella (NTS) is emerging worldwide. We report the occurrence of extended-spectrum beta-lactamase (ESBL) phenotypes in 53.4 % of NTS isolated over a period of nine years from gastroenteritis cases. ESBL and AmpC co-production was observed in 21 % of the isolates. Occurrence of blaCTX-M-15 and blaCMY-2 resistance genes was observed in 11.6 % and 37 % of the isolates respectively. Overall, Salmonella enterica serovar Senftenberg was the predominant serovar carrying blaCTX-M-15 and blaCMY-2 resistance genes. We report for the first time from India, one isolate each of S. enterica serovar Thompson, S. enterica serovar Infantis and S. enterica serovar Newport, carrying the blaCTX-M-15 gene. We also report for the first time from India, a case of gastroenteritis due to S. enterica serovar Thompson.

The sequences generated in this study are available from the European Nucleotide Archive under the study accession number PRJEB30273. Data statement: All supporting data, code and protocols have been provided within the article or through supplementary data files. Two supplementary tables are available with the online version of this article.

Elizabethkingia miricola (E. miricola) is a gram-negative non-fermentative bacterium which is rarely encountered. It is usually misidentified or considered as a contaminant in routine microbiology laboratories due to the limitations in conventional biochemical techniques. However, with the advent of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), the identification of non-fermenters has become easy and this has led to enhanced understanding of the clinical significance of these uncommonly isolated microorganisms. The genus Elizabethkingia has only two species E. meningoseptica and E. miricola. Both of these organisms are known to be multi-drug resistant and therefore, their accurate identification and antimicrobial susceptibility testing are necessary prior to the initiation of appropriate therapy. In the world literature till date, only 3 cases of sepsis caused by E. miricola have been reported. We present the first case of E. miricola association with urinary tract infection.

The study is the first from India to show high CRE carriage in patients admitted to a tertiary care centre and emphasises the need of strict antimicrobial stewardship implementation in hospitals to prevent dissemination of multidrug-resistant CRE.

Enteroaggregative Escherichia coli (EAEC) is an evolving enteric pathogen that causes acute and chronic diarrhea in developed and industrialized nations in children. EAEC epidemiology and the importance of atypical EAEC (aEAEC) isolation in childhood diarrhea are not well documented in the Indian setting. A comparative analysis was undertaken to evaluate virulence, phylogeny, and antibiotic sensitivity among typical tEAEC versus aEAEC. A total of 171 EAEC isolates were extracted from a broad surveillance sample of diarrheal (N = 1210) and healthy children (N = 550) across North India. Polymerase chain reaction (PCR) for the aggR gene (master regulator gene) was conducted to differentiate tEAEC and aEAEC. For 21 virulence genes, we used multiplex PCR to classify possible virulence factors among these strains. Phylogenetic classes were identified by a multiplex PCR for chuA, yjaA, and a cryptic DNA fragment, TspE4C2. Antibiotic susceptibility was conducted by the disc diffusion method as per CLSI guidelines. EAEC was associated with moderate to severe diarrhea in children. The prevalence of EAEC infection (11.4%) was higher than any other DEC group (p = 0.002). tEAEC occurrence in the diarrheal group was higher than in the control group (p = 0.0001). tEAEC strain harbored more virulence genes than aEAEC. astA, aap, and aggR genes were most frequently found in the EAEC from the diarrheal population. Within tEAEC, this gene combination was present in more than 50% of strains. Also, 75.8% of EAEC strains were multidrug-resistant (MDR). Phylogroup D (43.9%) and B1 (39.4%) were most prevalent in the diarrheal and control group, respectively. Genetic analysis revealed EAEC variability; the comparison of tEAEC and aEAEC allowed us to better understand the EAEC virulence repertoire. Further microbiological and epidemiological research is required to examine the pathogenicity of not only typical but also atypical EAEC.