The University Hospital Città della Salute e della Scienza di Torino is a tertiary-care teaching hospital in Turin, North-western Italy. Four national hospitals (San Giovanni Battista Molinette General Hospital; CTO Trauma Orthopaedic Hospital; Regina Margherita Paediatric Hospital and Sant’Anna Maternity Hospital) belong to this facility, which counts over 2.300 beds and approximately 80,000 admissions per year. Here, a proactive surveillance program to detect intestinal colonization by CPE and carbapenem-resistant Gram-negative (CR-GN) organisms among Enterobacterales, P. aeruginosa and Acinetobacter baumannii isolates has been adopted in acute and chronic care facilities for new admissions and for inpatients on a weekly basis. Rectal swabs are collected using the FecalSwab™ system (Copan, Brescia, Italy) and inoculated on a chromogenic screening plate (Chromatic CRE medium, Liofilchem, Roseto degli Abruzzi, Italy) by automated direct plating using the WASP® instrument (Copan, Brescia, Italy). Overnight colonies are identified by MALDI-TOF MS analysis (Bruker Daltonics GmbH, Bremen, Germany), and carbapenemase production in Enterobacterales isolates is investigated by genotypic testing (Xpert Carba-R assay; Cepheid Sunnyvale, CA) and/or lateral flow immunoassay (NG-test CARBA 5; NG Biotech, Guipry, France).
Fecalswab system
Manufactured by Copan
Sourced in Italy
The FecalSwab system is a collection device for the transportation and preservation of fecal samples. It is designed to collect, stabilize, and transport fecal specimens for microbiological analysis.
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Lab products found in correlation
5 protocols using fecalswab system
1
Surveillance of Carbapenem-Resistant Gram-Negatives
2
Bat Fecal Samples Collected During Wildfires
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Bat faecal samples (n = 155) were collected from pups at three locations in New South Wales (Sydney, Shoalhaven and Bega) and one location in South Australia (Adelaide) (Supplementary Data 1 ). Bat pups in Shoalhaven and Bega were sampled once (during one birthing season), and pups in Adelaide and Sydney were sampled twice (during two different birthing seasons) (Supplementary Data 1 ). Relative to the 2019–2020 wildfires, the 155 samples were classified as pre-fire samples (n = 77, collected October 2018 to April 2019), fire-affected samples (n = 48, collected November 2019 to February 2020), and post-fire samples (n = 30, collected January 2021) (Supplementary Data 1 ). Most of the sampled bat pups were in-care (118 of 155) and the remaining were wild (37 of 155) (Supplementary Data 1 ). The FecalSwab™ system (COPAN, Brescia, Italy) was used to collect all faecal samples, which included faecal deposits from 116 live bat pups and faecal material from the intestines of 39 deceased pups that had been stored at -20˚C until necropsy. Metadata is provided for all individual bat pups (Supplementary Data 1 ). FaecalSwab samples were frozen at -30˚C until processing. DNA was extracted from FecalSwab media using the ISOLATE II Fecal DNA Kit (Bioline, London, UK) and stored at -30˚C.
3
Surveillance of Carbapenem-Resistant Enterobacterales
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Bacterial strains investigated in this work included all the available CRE isolates (n=38) obtained from surveillance cultures (rectal swabs) of colonized patients from the SBI ward of the Don Carlo Gnocchi Foundation LTCRF of Florence (Italy), during 2016. Each isolate was from a different patient. The studied isolates represented approximately half of the total cases of carriage (n=74) observed in the SBI ward during 2016, and had been isolated throughout the whole study period (1–5 per month).
Rectal swabs were collected using the FecalSwab system (Copan). The specimens (in 10 µl medium) were cultured on ChromID CARBA SMART plates (bioMérieux) to screen for CRE, within 48 h of collection. Plates were inspected for growth after 18–24 h incubation at 35±2 °C. Colonies grown on the selective medium were identified using the MALDI-TOF MS Vitek 2 system (bioMérieux). Suspect CRE isolates with a meropenem minimum inhibitory concentration >0.125 mg l−1 were included in the study.
Rectal swabs were collected using the FecalSwab system (Copan). The specimens (in 10 µl medium) were cultured on ChromID CARBA SMART plates (bioMérieux) to screen for CRE, within 48 h of collection. Plates were inspected for growth after 18–24 h incubation at 35±2 °C. Colonies grown on the selective medium were identified using the MALDI-TOF MS Vitek 2 system (bioMérieux). Suspect CRE isolates with a meropenem minimum inhibitory concentration >0.125 mg l−1 were included in the study.
4
Gut Microbiome of Wild and Captive GHFF
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A total of 318 faecal samples from wild GHFF (n=287) and captive GHFF (n=31) were used in this study. Captive GHFF were injured or sick flying foxes (from wild colonies) undergoing rehabilitation. Samples representing wild GHFF were obtained from three locations: Sydney, New South Wales (NSW) (n=61); Lake Macquarie, NSW (n=121); and Adelaide, South Australia (SA) (n=104). Captive GHFF samples were obtained via two wildlife rehabilitation organizations: Fauna Rescue of South Australia (SA) (n=19) and Wildlife Information, Rescue and Education Service NSW (WIRES) (n=12). The captive GHFF in SA were recovering from heat stress and did not receive antimicrobial therapy and veterinary treatment records were unavailable for the NSW captive GHFF.
Faecal samples were acquired either directly from individual GHFF or opportunistically under roosting flying foxes. Using a FecalSwab system (COPAN), discrete faecal samples were collected from plastic drop sheets placed under roosting flying foxes (n=194), via a rectal swab (n=94; Adelaide) or collected aseptically from the intestine at necropsy (n=30; Adelaide and Sydney). Euthanized and freshly deceased GHFF were frozen at −20 °C and thawed for necropsy and sampling within 4–8 weeks. FecalSwab samples were stored at 4 °C and cultured within 72 h of collection.
Faecal samples were acquired either directly from individual GHFF or opportunistically under roosting flying foxes. Using a FecalSwab system (COPAN), discrete faecal samples were collected from plastic drop sheets placed under roosting flying foxes (n=194), via a rectal swab (n=94; Adelaide) or collected aseptically from the intestine at necropsy (n=30; Adelaide and Sydney). Euthanized and freshly deceased GHFF were frozen at −20 °C and thawed for necropsy and sampling within 4–8 weeks. FecalSwab samples were stored at 4 °C and cultured within 72 h of collection.
5
Rectal Swabs for Carbapenem-Resistant Enterobacteriaceae
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Rectal swabs were collected using the FecalSwab system (Copan, Brescia, Italy) containing 2 mL of modified Cary-Blair medium, and processed by an external laboratory (Synlab Toscana, Sesto Fiorentino, Italy). The specimens (10 mL of medium) were cultured on chromID CARBA SMART plates (bio-Me ´rieux, Marcy L'Etoile, France) to screen for CRE, and on McConkey agar (as a quality control of the rectal swab), within 48 h of collection. Plates were inspected for growth after 18e24 h of incubation at 35AE2 C. Colonies representative of different morphologies grown on the selective medium were identified using the Vitek 2 system (bioMe ´rieux). Phenotypic characterization of carbapenemase production was investigated according to the EUCAST guidelines for detection of mechanisms [24] . In accordance with routine laboratory protocol, blood cultures were performed at the same external laboratory as rectal swab cultures using the BACTEC FX instrument (Becton Dickinson, Franklin Lakes, NJ, USA), and bacterial identification and susceptibility testing were performed using the Vitek 2 system (bioMe ´rieux).
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