Api system

Manufactured by bioMérieux

Sourced in France, Italy, United Kingdom

The API system is a manual identification system for the biochemical characterization of microorganisms. It provides a standardized, standardized, and simplified approach to the identification of a wide range of bacterial and yeast species.

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41 protocols using api system

Enumeration of Foodborne Pathogens

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– Food specimens were subjected to Bacillus cereus and CPS enumeration using standards UNI EN ISO 7932:2005 (UNI, 2005 ) and UNI EN ISO 6888-2:2004 (UNI, 2004 ), respectively. Enumeration of Clostridium perfringens was performed with an in-house method, using Tryptose Sulfite Cycloserine agar medium (TSC; Oxoid, Basingstoke, United Kingdom) for the anaerobic growth of sulfite-reducing bacteria and the API^® systems (bioMérieux) for identifying the isolates.
– The environmental samples included three swabs collected from the surfaces of two kitchen tables and from a cold room shelf, respectively. These samples were investigated only for CPS enumeration according to the UNI EN ISO 6888-2:2004 protocol.
– CPS strains isolated from food and environmental samples were analyzed for the presence of S. aureus, by inoculating them onto 5% sheep blood agar plates (Oxoid) and identifying them using API systems (BioMérieux). The human swabs were streaked onto Mannitol Salt Agar plates (MSA; Oxoid). After 18–24 h incubation, typical yellow colonies on MSA were subcultured onto 5% sheep blood agar plates, and presumptive S. aureus isolates were identified using the catalase and coagulase tests (Han et al., 2007 (link)).

Ercoli L., Gallina S., Nia Y., Auvray F., Primavilla S., Guidi F., Pierucci B., Graziotti C., Decastelli L, & Scuota S. (2017). Investigation of a Staphylococcal Food Poisoning Outbreak from a Chantilly Cream Dessert, in Umbria (Italy). Foodborne Pathogens and Disease, 14(7), 407-413.

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Identification of Bacterial Isolates

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Gram positive cocci isolates were identified as S. aureus by traditional biochemical tests, including catalase, coagulase, and acid production from D-mannitol (10 ). Identification of Gram negative bacteria at the species level was performed using conventional biochemical methods and tests incorporated in the API system (bio Merieux SA, Marcy-1, Etoile, France) (10 ).

Poorabbas B., Mardaneh J., Rezaei Z., Kalani M., Pouladfar G., Alami M.H., Soltani J., Shamsi-Zadeh A., Abdoli-Oskooi S., Saffar M.J, & Alborzi A. (2015). Nosocomial Infections: Multicenter surveillance of antimicrobial resistance profile of Staphylococcus aureus and Gram negative rods isolated from blood and other sterile body fluids in Iran. Iranian Journal of Microbiology, 7(3), 127-135.

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Fecal microbiome profiling protocol

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The homogenates fecal specimens were serially diluted with both half-strength Wilkins-Chalgren Anaerobe Broth (WCAB) and Buffered Peptone Water (ThermoScientific-Oxoid, UK). Dilutions in duplicate were plated on MacConkey agar (Merck, Germany) for Enterobacteriaceae, Perfringens agar Base (OPSP) (Oxoid, UK) for C. perfringens, vancomycin and bromocresol green (LAMVAB) agar (Hartemink and Rombouts, 1999 (link)) for lactobacilli, and Azide maltose agar (Biolife, Italy) for enterococci counts. MacConkey agar and Azide maltose agar plates were incubated aerobically at 37°C for 24 and 48 h, respectively. Other media were incubated anaerobically at 37°C for 48-72 h. The taxonomy of colonies isolated random on selective media were determined at genus and species level by API System (Bio-Merieux, Italy) to verify the reliability of the media utilized.

Sabbioni A., Ferrario C., Milani C., Mancabelli L., Riccardi E., Di Ianni F., Beretti V., Superchi P, & Ossiprandi M.C. (2016). Modulation of the Bifidobacterial Communities of the Dog Microbiota by Zeolite. Frontiers in Microbiology, 7, 1491.

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Retrospective Study of Osteomyelitis in Patients

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Patients appearing in hospital records as having diagnosis of OM between January 1, 2007 and December 31, 2010 were reviewed. Patients with implant-related OM were excluded from the study. The clinical records and radiographs of every patient were retrospectively studied using a predefined protocol, which included age, sex, site of infection, and response to treatment. These variables were all compared. A summary of the findings is shown in Table 1.
Diagnosis of OM was based on the assessment of the Infectious Disease Department of the hospital, taking into account both clinical assessment and physical examination, along with wound or blood cultures, histology, and radiographic examinations.
During the studied period, cultures from different samples were performed according to commonly accepted techniques. Isolated microorganisms were identified by common biochemical tests (coagulase and oxidase) and commercial identification kits (API System, bioMérieux, Marcy L'Etoile, France). Susceptibility testing was performed using a disc-plate assay according to the EUCAST protocols.18) The study was approved by the Ethics Research Committee of the hospital.

Prieto-Pérez L., Pérez-Tanoira R., Petkova-Saiz E., Pérez-Jorge C., Lopez-Rodriguez C., Alvarez-Alvarez B., Polo-Sabau J, & Esteban J. (2014). Osteomyelitis: A Descriptive Study. Clinics in Orthopedic Surgery, 6(1), 20-25.

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Epidemiology of Shigella sonnei in Jiangsu

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A total of 340 S. sonnei were collected between 2002 and 2011 from outpatients and inpatients in hospitals throughout Jiangsu Province. Jiangsu Province, a populous and prosperous province in China, was divided into three regions comprised of 13 provincial cities, the South (Nanjing, Suzhou, Wuxi, Changzhou and Zhenjiang), the Centre (Yangzhou, Taizhou and Nantong) and the North (Xuzhou, Suqian, Huai’an, Yancheng and Lianyungang). As shown in Table 1, South Jiangsu exhibited the highest isolation rate of S. sonnei (186/340; 54.7%), followed by the Centre (84/340; 24.7%) and the North (70/340; 20.6%).Table 1

Source of Shigella sonnei strains (n = 340), by year and by city, 2002–2011.

Table 1

Characteristic	No. of strains	%
Year
2002	6	1.8
2003	2	0.6
2004	6	1.8
2005	7	2.1
2006	19	5.6
2007	48	14.1
2008	89	26.2
2009	98	28.8
2010	33	9.7
2011	32	9.4

City
Changzhou	75	22.1
Huai’an	15	4.4
Lianyungang	21	6.2
Nanjing	36	10.6
Nantong	63	18.5
Suqian	0	0.0
Suzhou	22	6.5
Taizhou	4	1.2
Wuxi	28	8.2
Xuzhou	27	7.9
Yancheng	7	2.1
Yangzhou	17	5.0
Zhenjiang	25	7.4

All strains were identified by API system (bioMérieux, Marcy-l’Étoile, France) and were confirmed as S. sonnei by slide agglutination with Shigella antisera (Lanzhou Institute of Biological Products, Lanzhou, China).

Gu B., Xu T., Kang H., Xu Y., Liu G., Pan S., Qian H, & Ma P. (2017). A 10-year surveillance of antimicrobial susceptibility patterns in Shigella sonnei isolates circulating in Jiangsu Province, China. Journal of Global Antimicrobial Resistance, 10, 29-34.

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Prevalence of ESBL-producing Enterobacterales

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Between July 2018 and June 2019, a total of 2134 clinical samples (wound, respiratory tract specimens, blood and body fluids) received in the Microbiology laboratory, Government Medical College and Hospital, Badaun, India were analyzed for ESBL producing strains of Enterobacterales. This hospital laboratory receives samples from two civil hospitals and three primary health care centers that are attached to it. Among the total samples analyzed (N = 2134), a total of 186 non-repetitive phenotypically confirmed ESBL producing Enterobacterales isolates (one organism per patient was included to avoid duplication) were obtained. All the isolates were identified by manual API^® system (BioMérieux, Durham, NC, USA) and the results interpreted as recommended by the manufacturer. The strains included were K. pneumoniae (N = 74), E. coli (N = 58), P. mirabilis (N = 15), C. freundii (N = 13), K. oxytoca (N = 11), E. cloacae (N = 9), P. vulgaris (N = 3) and M. morganii (N = 3). All the clinical isolates were identified by standard laboratory procedure [11 ]. All the bacterial isolates were stored at −80 °C in glycerol for future use.

Shinu P., Bareja R., Nair A.B., Mishra V., Hussain S., Venugopala K.N., Sreeharsha N., Attimarad M, & Rasool S.T. (2020). Monitoring of Non-β-Lactam Antibiotic Resistance-Associated Genes in ESBL Producing Enterobacterales Isolates. Antibiotics, 9(12), 884.

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Blood Culture Protocol for Bacteremia Detection

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At fever onset, 2 blood samples were collected at 1 h interval from the central intravenous line; otherwise, at least one blood sample was collected from a peripheral vein. Blood samples were processed by an automated blood system for detection of bacteraemia, the BacT/ALERT system (bioMérieux, Marcy l'Etoile, France), with an incubation of five days [21 ]. Bacterial isolates were identified by routine phenotypical tests using the API system (bioMérieux). When phenotypical testing failed to identify bacterial isolates, a 16S rRNA gene sequencing was performed as previously described [22 (link)] because of its particularly good accuracy for species designation. Bacteraemia was defined as ≥1 positive blood culture for bacteria other than coagulase-negative Staphylococcus (CNS), Micrococcus, Corynebacterium (other than jeikeium species), and Bacillus spp., for which ≥2 positive blood cultures were required.

El Maaroufi H., Goubard A., Redjoul R., Legrand P., Pautas C., Mikdame M., Doghmi K., Toma A., Maury S., Schwarzinger M, & Cordonnier C. (2015). Risk Factors and Scoring System for Predicting Bacterial Resistance to Cefepime as Used Empirically in Haematology Wards. BioMed Research International, 2015, 945769.

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Blood Culture Identification and Antibiotic Susceptibility

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Blood samples were collected in a set of an aerobic and an anaerobic bottles which were incubated in a BacT/ALERT 3D (bioMérieux, Marcy l’étoile, France) automated blood culture system for 5 days. Bottles that showed a positive signal in the BacT/ALERT 3D system were routinely subjected to Gram staining and subcultured at least on blood agar plates and upon results of Gram on Drigalski agar or on chocolate agar. Colonies were identified using the API system (bioMérieux) and, since 2013, MALDI-TOF MS Microflex LT (Bruker Daltonics GmbH, Bremen, Germany) according to the manufacturer’s recommendation. Antimicrobial susceptibility testing was performed in accordance with the EUCAST disk diffusion test methodology, as recommended [11 ].

Courjon J., Demonchy E., Degand N., Risso K., Ruimy R, & Roger P.M. (2017). Patients with community-acquired bacteremia of unknown origin: clinical characteristics and usefulness of microbiological results for therapeutic issues: a single-center cohort study. Annals of Clinical Microbiology and Antimicrobials, 16, 40.

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Isolation and Identification of E. coli

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Organ samples were streaked on MacConkey agar (Thermo Scientific, Milan, Italy) for the semi-quantitative evaluation of the presence of E. coli and incubated at 37 ± 1 °C for 24 h [27 (link)]. Single colonies showing characteristic E. coli morphology were selected from each plate, inoculated in a Brain Heart Infusion Broth (BHI, Thermo Scientific) and incubated at 37 ± 1 °C for 24 h. Pure cultures were stocked and stored at −80 °C with 10% of glycerol until further use. Following, each stock culture was submitted to biochemical tests with the API system (BioMérieux, Marcy L’Etoile, Lyon, France) for species confirmation. A total of 179 E. coli isolates were selected, all belonging to different sampled organs and distributed as follows: 52 from Farm A, 70 from Farm B and 57 from Farm C. The assigned ID was built on two numbers: the first number representing the day of sampling at one of the three farms and the second related to the animal.

Pasquali F., Crippa C., Parisi A., Lucchi A., Gambi L., Merlotti A., Remondini D., Stonfer M, & Manfreda G. (2023). Genetic Diversity and Antimicrobial Resistance of Extraintestinal E. coli Populations Pre- and Post-Antimicrobial Therapy on Broilers Affected by Colisepticemia. Animals : an Open Access Journal from MDPI, 13(16), 2590.

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Isolation and Identification of K. pneumoniae

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After the samples were isolated and placed in test tubes containing normal saline, the gut homogenate was kept in buffered peptone water, after which the samples were inoculated on blood agar and Mac-Conkey agar (MCA), then incubated for 24 hours at 37°C. For the growth of gram-negative bacteria such as K. pneumonia, BPW was used that was inoculated in seven primary media (Sheep Blood Agar, Chocolate Agar, Mac-Conkey, Deoxycholate Citrate Agar, SS agar, Mannitol Salt Agar, and Xylose Lysine Deoxycholate). In addition, identification of gram-negative bacteria was achieved by use of standard methods (API System; bioMerieux, Marcy-l'Étoile, France). The biochemical reagents and test used to identify K. pneumoniae included triple sugar iron agar, simmons citrate, indole, urease, motility, and H₂S. The biochemical characteristics of K. pneumoniae identified were as follows: positive citrate utilization test, negative methyl red test, negative indole test, positive urease test, positive Voges–Proskauer test, sucrose, acid and abundant gas production from glucose, lactose, mannitol sugar fermentation tests, and maltose.

Doosti A., Pourabbas M., Arshi A., Chehelgerdi M, & Kabiri H. (2014). TEM and SHV Genes in Klebsiella pneumoniae Isolated from Cockroaches and Their Antimicrobial Resistance Pattern. Osong Public Health and Research Perspectives, 6(1), 3-8.

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