Acceso abierto

Comparison of automatic methods MALDI-TOF, VITEK2 and manual methods for the identification of intestinal microbial communities on the example of samples from alpacas (Vicugna pacos)

Joanna Pławińska-Czarnak
Joanna Pławińska-Czarnak
, 
Karolina Wódz
Karolina Wódz
, 
Zuzanna Strzałkowska
Zuzanna Strzałkowska
, 
Monika Żychska
Monika Żychska
, 
Tomasz Nowak
Tomasz Nowak
, 
Adam Kwieciński
Adam Kwieciński
, 
Piotr Kwieciński
Piotr Kwieciński
, 
Wojciech Bielecki
Wojciech Bielecki
, 
Anna Rodo
Anna Rodo
, 
Magdalena Rzewuska
Magdalena Rzewuska
, 
Daria Kłosińska
Daria Kłosińska
, 
Krzysztof Anusz
Krzysztof Anusz
 y 
Blanka Orłowska
Blanka Orłowska
   | 20 sept 2023
Journal of Veterinary Research's Cover Image
Acerca de este artículo
Artículo anterior
Artículo siguiente
Cite
Publicado en línea: 20 sept 2023
Páginas: 361 - 372
Recibido: 23 mar 2023
Aceptado: 22 ago 2023
DOI: https://doi.org/10.2478/jvetres-2023-0051
Palabras clave
© 2023 Joanna Pławińska-Czarnak et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Fig. 1a.

Bacillus “anthraci” presented aerobic growth of dull grey colonies with a raw matted surface with surrounding β-haemolysis on Columbia agar with 5% sheep blood as classical Bacillus cereus
Bacillus “anthraci” presented aerobic growth of dull grey colonies with a raw matted surface with surrounding β-haemolysis on Columbia agar with 5% sheep blood as classical Bacillus cereus

Fig. 1b.

Bacillus cereus created classical rough and dry with a bright pink colonies with egg yolk precipitation halo on MYP agar
Bacillus cereus created classical rough and dry with a bright pink colonies with egg yolk precipitation halo on MYP agar

Fig. 2.

Complexity of microbial communities in small intestine 1A – the first alpaca; 2A – the second alpaca; AH – healthy alpaca
Complexity of microbial communities in small intestine 1A – the first alpaca; 2A – the second alpaca; AH – healthy alpaca

Fig. 3.

Complexity of microbial communities in colon 1A – first (male) neglected alpaca; 2A – second (male) neglected alpaca; AH – third (male) healthy alpaca
Complexity of microbial communities in colon 1A – first (male) neglected alpaca; 2A – second (male) neglected alpaca; AH – third (male) healthy alpaca

Fig. 4.

Complexity of microbial communities in rectum 1A – first (male) neglected alpaca; 2A – second (female) neglected alpaca; AH – third (male) healthy alpaca
Complexity of microbial communities in rectum 1A – first (male) neglected alpaca; 2A – second (female) neglected alpaca; AH – third (male) healthy alpaca

Results of identification using matrix-assisted laser desorption/ionisation–time-of-flight mass spectrometry (MALDI-TOF MS) and VITEK2 Corynebacterium (CBC) fluorogenic and analytical profile index for Coryneform bacteria (API CORYNE) tests for Corynebacterium spp. isolated from one fallen alpaca

Sample source MALDI-TOF MS (score) VITEK2 CBC (% probability) API Coryne
colon (1A) Candida lipolytica Corynebacterium diphtheriae (91) Corynebacterium diphtheriae (95)
small intestine (1A) Corynebacterium stationis (9.560) Corynebacterium sp. (97) Corynebacterium diphtheriae (97)
small intestine (1A) Corynebacterium stationis (9.465) Corynebacterium minutissimum (96) Corynebacterium sp. (89)
colon (1A) Corynebacterium stationis (9.376) Corynebacterium minutissimum (95) Corynebacterium sp. (82)
colon (1A) Corynebacterium stationis (8.985) Corynebacterium minutissimum (93) Corynebacterium sp. (91)
colon (1A) Corynebacterium stationis (9.167) Corynebacterium minutissimum (97) Corynebacterium sp. (89)
small intestine (1A) Corynebacterium xerosis (9.440) Corynebacterium xerosis (98) Corynebacterium sp. (85)

Conditions for bacteria incubation on individual solid media

Type of solid media Incubation atmosphere Temperature/time Comment
Baird-Parker aerobic 37°C for 24 ± 2 h The reading was made after 24h and after 48 h
OCLA aerobic 37°C for 24 ± 2 h Negative plates were read again after 48 h
Yersinia CIN agar aerobic 3O°C/24h The reading was made after 24h and after 48 h
Columbia agar with 5% sheep blood aerobic 37°C/24h +/− 2h
Columbia agar with 5% sheep blood anaerobic 37°C/24h +/− 2h
mCCD agar anaerobic 42°C/48h Negative plates was read again after 48 h
CHROMagar Campylobacter anaerobic 42°C/48h Negative plates was read again after 72 h
Chapman aerobic 37°C/24h +/− 2h
MYP Agar aerobic 37°C/24h Negative plates was read again after 48 h
MacConkey’s agar aerobic 37°C/24h +/− 2h
CNA aerobic 37°C/24h +/− 2h

Results of identification using matrix-assisted laser desorption/ionisation–time-of-flight mass spectrometry (MALDI-TOF MS) and VITEK2 BCL test for Bacillus isolated from two alpacas

Sample source MALDI-TOF (score) VITEK2 BCL (% probability)
rectum (2A) Bacillus aeolinus (5.139) Bacillus subtilis/Bacillus amyloliquefaciens/Bacillus atrophaeus (97)
small intestine (2A) Bacillus altitudinis (8.713) Bacillus subtilis/Bacillus amyloliquefaciens/Bacillus atrophaeus (95)
rectum (2A) Bacillus anthraci 6.295) Bacillus cereus (98)
colon (2A) Bacillus cereus (9.279) Bacillus cereus (98)
colon (2A) Bacillus sp. (7.835) Bacillus cereus (99)
colon (2A) Bacillus cecembensis (5.993) Bacillus pumilus (93)
colon (2A) Bacillus flexus (5.375) unidentified
small intestine (2A) Bacillus licheniformis (9.476) Bacillus licheniformis (99)
small intestine (2A) Bacillus licheniformis (8.525) Bacillus licheniformis (99)
colon (2A) Bacillus licheniformis (4.744) Bacillus licheniformis (91)
colon (2A) Bacillus licheniformis (9.253) Bacillus licheniformis (99)
rectum (2A) Bacillus licheniformis (7.233) Bacillus licheniformis (99)
small intestine (AH) Bacillus pumilus (9.157) Bacillus pumilus (92)
colon (2A) Bacillus pumilus (9.547) Bacillus pumilus (98)
colon (2A) Bacillus pumilus (6.156) Bacillus pumilus (96)
colon (2A) Bacillus pumilus (8.884) Bacillus pumilus (98)
colon (2A) Bacillus subtilis (7.181) Bacillus subtilis (98)
colon (2A) Bacillus subtilis (6.428) Bacillus subtilis (95)

Results of identification using matrix-assisted laser desorption/ionisation–time-of-flight mass spectrometry (MALDI-TOF MS) and VITEK2 Anaerobic and Corynebacterium (ANC) fluorogenic test for Clostridium perfringens isolated from an alpaca which was healthy until its death (AH)

Sample source MALDI-TOF MS (score) VITEK2 ANC (% probability)
small intestine (AH) Clostridium perfringens (9.635) Clostridium perfringens (95)
small intestine (AH) Clostridium perfringens (9.665) Clostridium perfringens (92)
colon (AH) Clostridium perfringens (9.619) Clostridium perfringens (95)
colon (AH) Clostridium perfringens (9.664) Clostridium perfringens (98)

Results of identification using matrix-assisted laser desorption/ionisation–time-of-flight mass spectrometry (MALDI-TOF MS) and VITEK2 Gram-positive (GP) and analytical profile index for Staphylococcus (API Staph) tests for Gram-positive cocci isolated from three alpacas

Sample source MALDI-TOF (score) VITEK2 GP (% probability) API Staph (% probability)
colon (1A) Staphylococcus aureus (9.380) Staphylococcus aureus (97) Staphylococcus aureus (94)
rectum (1A) Staphylococcus aureus (9.410) Staphylococcus aureus (99) Staphylococcus aureus (96)
colon (1A) Staphylococcus equorum (9.001) Staphylococcus equorum (92) Staphylococcus intermedius (90)
colon (1A) Staphylococcus lentus (9.457) Staphylococcus lentus (96) Staphylococcus lentus (96)
rectum (2A) Staphylococcus pseudintermedius (7.247) Staphylococcus pseudintermedius (98) Staphylococcus simulans (82)
small intestine (2A) Staphylococcus sciuri (9.111) Staphylococcus sciuri (86) Staphylococcus sciuri (92)
small intestine (2A) Staphylococcus sciuri (9,428) Staphylococcus sciuri (95) Staphylococcus sciuri (92)
small intestine (2A) Staphylococcus sciuri (9.471) Staphylococcus sciuri (95) Staphylococcus sciuri (96)
colon (1A) Staphylococcus sciuri (8.228) Staphylococcus sciuri (95) Staphylococcus sciuri (97)
colon (1A) Staphylococcus sciuri (9.120) Staphylococcus sciuri (95) Staphylococcus sciuri (97)
colon (1A) Staphylococcus sciuri (9.345) Staphylococcus sciuri (95) Staphylococcus sciuri (97)
colon (1A) Staphylococcus sciuri (9.528) Staphylococcus sciuri (97) Staphylococcus sciuri (97)
colon (1A) Staphylococcus sciuri (9.513) Staphylococcus sciuri (95) Staphylococcus sciuri (97)
colon (1A) Staphylococcus sciuri (9.405) Staphylococcus sciuri (95) Staphylococcus sciuri (94)
colon (1A) Staphylococcus sciuri (9.571) Staphylococcus sciuri (87) Staphylococcus sciuri (89)
colon (1A) Staphylococcus sciuri (9.385) Staphylococcus sciuri (88) Staphylococcus sciuri (89)
rectum (2A) Micrococcus luteus (9.169) unidentified Micrococcus sp. (77)
rectum (AH) Lactococcus lactis subsp. cremoris (9.041) Lactococcus lactis subsp. cremoris (9.041) unidentified

Results of identification using matrix-assisted laser desorption/ionisation–time-of-flight mass spectrometry (MALDI-TOF MS) and VITEK2 Gram-negative (GN) fluorogenic, analytical profile index for 20 Enterobacteriaceae (API 20E), and RapID ONE tests for Gram-negative Yersiniaceae, Morganellaceae and Pseudomonadaceae isolated from three alpacas

Sample source MALDI-TOF MS (score) VITEK2 GN (% probability) API 20E (% probability) rapID ONE (% probability)
Yersiniaceae
small intestine (2A) Serratia odorifera (9.285) Serratia odorifera (99) Serratia odorifera 1 (97) Serratia odorifera 1,2 (97)
colon (2A) Serratia liquefaciens (9.098) Serratia odorifera (97) Serratia liquefaciens (99) Serratia liquefaciens (98)
rectum (2A) Serratia odorifera (9.606) Serratia odorifera (99) Serratia odorifera 1 (99) Serratia odorifera 1,2 (97)
faeces (2A) Serratia odorifera (9.654) Serratia odorifera (98) Serratia odorifera 1 (96) Serratia odorifera 1,2 (97)
faeces (1A) no spectrum Serratia marcescens (99) Serratia marcescens (97) Serratia marcescens (98)
Morganellaceae
rectum (AH) Morganella morganii (9.362) Morganella morganii subsp. morganii (99) Morganella morganii (99) Morganella morganii (99)
rectum (AH) Morganella morganii (9.480) Morganella morganii subsp. morganii (99) Morganella morganii (98) Morganella morganii (98)
small intestine (AH) Providencia alcalifaciens (9.589) Providencia alcalifaciens (97) Providencia alcalifaciens/rustigianii (98) Providencia alcalifaciens (98)
rectum (AH) Providencia alcalifaciens (9.067) Providencia alcalifaciens (98) Providencia alcalifaciens/rustigianii (98) Providencia alcalifaciens (99)
rectum (AH) Providencia alcalifaciens (9.611) Providencia alcalifaciens (98) Providencia alcalifaciens/rustigianii (99) Providencia alcalifaciens (96)
Pseudomonadaceae
small intestine (1A) Pseudomonas aeruginosa (8.239) Pseudomonas aeruginosa (99) Pseudomonas aeruginosa (99) Pseudomonas aeruginosa (99)
rectum (1A) Pseudomonas aeruginosa (8.856) Pseudomonas aeruginosa (98) Pseudomonas aeruginosa (98) Pseudomonas aeruginosa (98)

Results of identification using matrix-assisted laser desorption/ionisation–time-of-flight mass spectrometry (MALDI-TOF MS), VITEK2 Gram-positive (GP) for Gram-positive Enterococcaceae isolated from three alpacas

Sample source MALDI-TOF (score) VITEK2 GP (% probability)
small intestine (1A) Enterococcus faecium (9.721) Enterococcus faecium (99)
rectum (1A) Enterococcus gallinarum (9.705) Enterococcus gallinarum (99)
small intestine (1A) Enterococcus hirae (9.686) Enterococcus hirae (99)
colon (2A) Enterococcus hirae (9.618) Enterococcus hirae (99)
colon (2A) Enterococcus hirae (9.697) Enterococcus hirae (99)
colon (2A) Enterococcus hirae (9.670) Enterococcus hirae (99)
rectum (2A) Enterococcus hirae (9.591) Enterococcus hirae (99)
rectum (2A) Enterococcus hirae (9.694) Enterococcus hirae (99)
small intestine (AH) Enterococcus casseliflavus (9.616) Enterococcus casseliflavus (98)
colon (2A) Enterococcus casseliflavus (9.615) Enterococcus casseliflavus (98)
rectum (2A) Enterococcus casseliflavus (8.198) Enterococcus casseliflavus (99)
rectum (AH) Enterococcus casseliflavus (9.637) Enterococcus casseliflavus (99)
rectum (AH) Enterococcus casseliflavus (9.539) Enterococcus casseliflavus (99)

Results of identification using matrix-assisted laser desorption/ionisation–time-of-flight mass spectrometry (MALDI-TOF MS), VITEK2 Gram-negative (GN) fluorogenic, VITEK2 Gram-positive (GP), analytical profile index for 20 Enterobacteriaceae (API 20E), analytical profile index for 20 non-Enterobacteriaceae (API 20NE) and RapID NF Plus tests for different bacteria isolated from two alpacas

Sample source Gram-negative MALDI-TOF MS (score) VITEK2 GN (% probability) API 20E/API 20NE RapID NF Plus
colon (1A) Stenotrophomonas spp. (Xanthomonadaceae), (9.158) Stenotrophomonas maltophilia (96%) Stenotrophomonas maltophilia (99%) unidentified
small intestine (2A) Moraxella osloensis (Moraxellaceae), (9.365) Moraxella group, (94) GN Moraxella spp. (94) Moraxella osloensis (97)
small intestine (2A) Arcticiflavibacter luteus (Flavobacteriaceae), (5.436) unidentified unidentified unidentified
colon (2A) Leeuwenhoekiella nanhaiensis (Flavobacteriaceae), (5.259) unidentified unidentified unidentified
small intestine (1A) Ochrobactrum intermedium (9.574) (Brucellaceae) Ochrobactrum anthropi (82) Ochrobactrum anthropi (97) Ochrobactrum anthropi (97)
colon (2A) Sphingobacterium anhuiense (Sphingobacteriaceae) (9.158) unidentified unidentified unidentified
colon (2A) Thalassolituus oleivorans (5.545), (Oceanospirillaceae) unidentified unidentified unidentified
Sample source Gram-positive MALDI-TOF (score) VITEK2 GP (probability %) API STAPH
rectum (2A) Cellulosimicrobium cellulans (8.475) (Promicromonosporaceae) unidentified unidentified
colon (2A) Paenibacillus amylolyticus (6.065) (Paenibacillaceae) Paenibacillus amylolyticus, BCL (93) unidentified
colon (1A) Brachybacterium conglomeratum (7.247) unidentified unidentified
rectum (2A) Leuconostoc citreum (4.426) Leuconostoc mesenteroides (97) unidentified

Results of identification using matrix-assisted laser desorption/ionisation–time-of-flight mass spectrometry (MALDI-TOF MS) and VITEK2 yeast (YST) fluorogenic test for Candida isolated from two alpacas

Sample source MALDI-TOF MS (score) VITEK2 YST (% probability)
small intestine (1A) Candida albicans (8.982) Candida albicans (96)
small intestine (1A) Candida albicans (6.608) Candida albicans (98)
small intestine (1A) Candida albicans (7.777) Candida albicans (97)
small intestine (1A) Candida albicans (5.434) Candida albicans (91)
colon (1A) Candida albicans (7.651) Candida albicans (91)
colon (2A) Candida haemulonii (4.777) Candida haemulonii (95)
colon (1A) Candida lipolytica (4.495) Corynebacterium diphtheriae (91)
colon (1A) Candida metapsilosis (4.683) Candida ciferrii (89)

Results of identification using matrix-assisted laser desorption/ionisation–time-of-flight mass spectrometry (MALDI-TOF MS) and VITEK2 Gram-negative (GN) fluorogenic, analytical profile index for 20 Enterobacteriaceae (API 20E), and RapID ONE tests for Gram-negative Enterobacteriaceae isolated from three alpacas

Sample source MALDI-TOF MS (score) VITEK2 GN (% probability) API 20E (% probability) RapID ONE (% probability)
small intestine (1A) Citrobacter braakii (9.003) Citrobacter braakii (97) Citrobacter freundii (94) Citrobacter freundii (94)
colon (1A) Citrobacter braakii (8.770) Citrobacter braakii (89) Citrobacter freundii (92) Citrobacter freundii (90)
rectum (1A) No spectrum Citrobacter freundii (95) Citrobacter freundii (98) Citrobacter freundii (96)
rectum (1A) Citrobacter freundii (9.617) Citrobacter freundii (95) Citrobacter freundii (92) Citrobacter freundii (95)
faeces (1A) Citrobacter freundii (9.533) Citrobacter braakii (89) Citrobacter braakii (92) Citrobacter freundii (90)
faeces (2A) Citrobacter freundii (8.771) Citrobacter freundii (95) Citrobacter freundii (95) Citrobacter freundii (95)
colon (1A) Enterobacter cloacae (9.440) Enterobacter cloacae complex (95) Enterobacter cloacae (97) Enterobacter cloacae (92)
colon (1A) Enterobacter cloacae (9.607) Enterobacter cloacae complex (97) Enterobacter cloacae (96) Enterobacter cloacae (93)
colon (1A) Enterobacter cloacae (9.543) Enterobacter cloacae complex (96) Enterobacter cloacae (97) Enterobacter cloacae (96)
colon (1A) Enterobacter cloacae (9.010) Enterobacter cloacae complex (95) Enterobacter cloacae (96) Enterobacter cloacae (95)
rectum (2A) Enterobacter cloacae (9.539) Enterobacter cloacae complex (96) Enterobacter cloacae (98) Enterobacter cloacae (95)
faeces (2A) Enterobacter cloacae (9.573) Enterobacter cloacae complex (97) Enterobacter cloacae (96) Enterobacter cloacae (97)
small intestine (2A) Enterobacter gergoviae (9.170) Enterobacter cloacae complex (94) Enterobacter gergoviae (99) Enterobacter gergoviae (99)
colon (2A) Enterobacter hormaechei (9.617) Enterobacter cloacae complex (94) Enterobacter cloacae (91) Enterobacter cloacae (89)
rectum (1A) Enterobacter ludwigii (9.042) Enterobacter cloacae complex (94) Enterobacter cloacae (94) Enterobacter cloacae (86)
small intestine (1A) Escherichia coli (9.691) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
small intestine (1A) Escherichia coli (9.679) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
colon (1A) Escherichia coli (9.646) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
colon (1A) Escherichia coli (9.088) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
rectum (1A) Escherichia coli (9.613) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
rectum (1A) Escherichia coli (9.550) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
small intestine (AH) Escherichia coli (9.616) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
small intestine (AH) Escherichia coli (9.509) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
small intestine (AH) Escherichia coli (9.587) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
small intestine (AH) Escherichia coli (9.594) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
small intestine (AH) Escherichia coli (9.578) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
small intestine (AH) Escherichia coli (9.649) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
small intestine (AH) Escherichia coli (9.603) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
small intestine (AH) Escherichia coli (9.568) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
colon (AH) Escherichia coli (9.568) Escherichia coli (99) Escherichia coli (99) Escherichia coli (99)
colon (AH) Klebsiella pneumoniae (9.132) Klebsiella pneumoniae subsp. pneumoniae (96) Klebsiella pneumoniae subsp. pneumoniae (97) Klebsiella pneumoniae (98)
colon (AH) Klebsiella pneumoniae subsp. pneumoniae (9.063) Klebsiella pneumoniae subsp. pneumoniae (99) Klebsiella pneumoniae subsp. pneumoniae (96) Klebsiella pneumoniae (98)
eISSN:
2450-8608
Idioma:
Inglés
Calendario de la edición:
4 veces al año
Temas de la revista:
Life Sciences, Molecular Biology, Microbiology and Virology, other, Medicine, Veterinary Medicine
RSS Feed de revista