Vitek system

The isolation, culture, and species identification of C. parapsilosis were performed using standard methods in the mycology laboratory of Hospital USM. Blood was drawn simultaneously from the catheter and a peripheral vein, and separate blood culture bottles were inoculated with an equal amount of each blood sample. The incubation of the blood cultures took place in an automated system (BACTEC 9000 system™, Becton Dickinson, USA) and positive blood bottles were subcultured on Sabouraud Dextrose Agar (SDA, Oxoid, UK) plates. Commercially available identification systems, namely, API 20C AUX® or ID 32C® biochemical identification kit (BioMérieux, Marcy I'Etoile, France) or VITEK® system (BioMérieux, Marcy I'Etoile, France) (last 2 years), have been used for the identification of Candida to species level. Molecular identification by the internal-transcribed spacer (ITS) region of ribosomal DNA sequencing was also performed in selected cases.

During the period from April 2017 to November 2018, ready-to-eat raw vegetables were collected from fixed and mobile food service establishments, in Puebla, Mexico (19.03 N, -98.20 W). A total of 183 samples were obtained from 82 establishments with lettuce (21%), tomato (17%), onion with coriander (13%), cucumber (12%), onion (9%), carrot (6%), radish (6%), coriander (5%), brussels sprouts (3%), red onion (3%), celery (1%), spinach (1%), a mix of tomato, onion and coriander (1%), squash (1%), and green bell pepper (1%). All samples were stored at 4°C and processed within 24 h. For bacterial isolation, 10g of food were inoculated in 20 mL of sodium lauryl sulfate broth (BD Bioxon ®) and incubated at 37°C with shaking at 30 rpm for 24 h. Subsequently, the cultures were streaked onto MacConkey agar plates (BD Bioxon) supplemented with cefotaxime (CTX) (2ug/ml). Colonies were picked from the selective plates, subcultured and streaked to obtain pure cultures. Putative strains were identified according to biochemical tests with Vitek system (bioMérieux, France) following the schemes in MacFaddin’s Manual of Biochemical Tests for the Identification of Clinically Important Bacteria (MacFaddin, 2003 ). Also, E. coli-specific ybbW and uidA genes were used to confirm their identity by PCR (Silkie et al., 2008 (link); Walker et al., 2017 (link)).

From each animal slaughterhouse, fresh fecal swabs were randomly collected from different individual animals, and transported in an ice box to our laboratory within 6 h for further bacteriological analysis. Each swab sample was added into 50 mL buffered peptone water (BPW) and was incubated at 37°C for 16 to 18 h. After that, 0.1 mL of the BPW suspensions was sub-cultured in 10 mL subpackaged Rappaport-Vassiliadis (RV) broth at 42°C for 24 h. One loopful of each RV broth culture was then plated onto xylose lysine tergitol 4 agar plates, and was incubated at 37°C for 24 to 48 h (Yan et al., 2010 (link)). Presumptive Salmonella colonies were identified using both the VITEK system (BioMerieux, Marcy 1'Etoile, France) and polymerase chain reaction (PCR) amplification of the inherent gene invA (Malorny et al., 2003 (link)).
All Salmonella isolates were serotyped according to the Kauffmann-White scheme by slide agglutination with O and H antigen-specific sera (Tianrun Bio-Pharmaceutical, Ningbo, China) (Grimont and Weill, 2007 ).

The study period was from January 1, 2009, through December 31, 2010. All samples were collected from the Southwest Hospital, which is one of the largest teaching hospitals in Chongqing, China, with approximately 3000 beds. The bacterial isolates were identified in the clinical microbiology laboratory using standard biochemical tests and the Vitek system (BioMérieux, Hazelwood, MO). If the meropenem inhibition zone was ≤ 22 mm, an attempt was made to amplify the NDM-1 gene from the strain, and the strain was evaluated with the modified Hodge test (MHT) [5 (link)]. The MHT has been widely used to screen for carbapenemase activity because it directly analyzes this activity. If the sample was either MHT-positive or NDM-1-positive, the medical records and laboratory data for the associated patient were retrospectively reviewed using records available from the Southwest Hospital information system and from the microbiology laboratory. In this study, each isolate was collected from a different patient. This study was approved by the Ethics Committee of the Third Military Medical University (Approval number, KY200508).