Title GENSKA ANALIZA IZOLATA
STREPTOKOKA IZ UZORAKA
KRAVLJEGA MLIJEKA Title (english) STREPTOCOCCAL GEN SEQUENCE
ANALYSES FROM MILK SAMPLES IN
DAIRY COWS Author Tihana Fumić Mentor Miroslav Benić (mentor)Mentor Nino Maćešić (komentor)Committee member Goran Bačić (predsjednik povjerenstva)Committee member Silvijo Vince (član povjerenstva)Committee member Boris Habrun (član povjerenstva)Granter University of Zagreb Defense date and country 2021-01-25, Croatia Scientific / art field, BIOMEDICINE AND HEALTHCARE Universal decimal classificationUDC ) 61 - Medical sciences Abstract Mastitis je multikauzalna bolest uzrokovana interakcijama između
mikroorganizma, domaćina i okoliša. Najznačajniji uzročnici mastitisa krava su
bakterije iz rodova Streptococcus, Staphylococcus, Echerichia i drugi koliformni
mikroorganizmi. U većini kliničkih laboratorija, identifikacija streptokoka temelji se na
biokemijskim testovima. S obzirom da niti jedan klasifikacijski sustav nije potpuno
točan, razvoj i primjena metoda genskih analiza unaprijedio je identifikaciju
streptokoka.
... More Ciljevi ovog istraživanja bili su dobiti detaljniji uvid u zastupljenost
pojedinih vrsta streptokoka u etiologiji mastitisa krava, kao i u javno-zdravstveno
značenje infekcija mliječne žlijezde prouzročenih streptokokima, te u podudarnost
rezultata klasične mikrobiološke pretrage i identifikacije streptokoka molekulatnim
metodama.
Mikrobiološka pretraga provedena je u skladu s opće prihvaćenim preporukama
opisanima u Laboratory handbook on bovine mastitis Primarno izdvajanje i
identifikaciju streptokoka provedeno je korištenjem podloge eskulin krvni agar. Nakon
identifikacije sojeve smo do daljnjih pretraga čuvali na glicerin bujonu na temperaturi
od -20 °C. Zamrznute sojeve revitalizirali smo ponovnim nacjepljivanjem na eskulin
krvni agar. Za potrebe genotipizacije koristili smo izdvajanje pomoću kitova na
automatiziranom uređaju za izdvajanje DNK. Pri molekularnoj identifikaciji vrste
Streptococcus sp koristili smo početnice pA i pH. Tipizacija sljedova za više lokusa
(Multi-locus sequence typing, MLST) vrlo je diskriminatorna tehnika, jer se zasniva na
tipiziranju sljedova veličine približno 500 bp unutar fragmenata 7 tzv. ''housekeeping'' gena. Proučavali smo četiri različite vrste Streptococcus sp. te je za svaku
pojedinu vrstu korišten drugačiji skup lokusa. Primjerice, za S. agalactiae (adhP,
pheS, atr, glnA, sdhA, glcK i tkt), za S. uberis (gki, recP, ddl, tdk, arcC, tpi, i yqiL), za
S. canis (gki, gtr, murl, mutS, recP, Xptgc i yqiZ), a za S. dysgalactiae (gki, gtr, murl,
mutS, recP, xpt I atoB). Kombinacija alela na svakom lokusu sačinjava sedmeročlani
brojčani kod koje smo međusobno uspoređivali na osnovu kategoričkog koeficijenta i prosječne udaljenosti dva klastera ( eng. unweighted pair group method with
arithmetic mean).
Molekularnom identifikacijom streptokoka pretražena su 54 izolata soja
bakterija iz uzoraka mlijeka, a za 47 sojeva je potvrđeno da pripadaju rodu
Streptococcus, i to 6 S. agalactiae, 10 S. dysgalactiae, 2 S. canis i 31 S. uberis, dok
su 3 soja pripadalii vrsti Enterococcus faecalis, a 4 su soja pripadali vrsti Lactococcus
lactis. Sve smo sojeve uspjeli tipizirati MLST tehnikom. U tipiziranim uzorcima S.
agalactiae definirali smo 4, u S. dysgalactiae 7, u S. canis 1 , a u S. uberis 22
različita alelna profila. Najzasupljeniji alelni profil u S. agalactiae bio je ST314.
Najpolimorfniji lokusi su atr i glcK s Hunter-Gaston indeksom raznolikosti (HGDI) od
0,73. Slijede adhP, glnA, sdhA i tkt, s HGDI indeksom od 0,60. Najmanje polimorfan
bio je pheS s HGDI indeksom od 0,33. Alelni profil ST305 bio je zastupljen u
najvećem broju uzoraka S. dysgalactiae. Najpolimorfniji lokus bio je mutS s HGDI
indeksom 0,86. Slijede gki i xpt s HGDI indeksom od 0,71 odnosno 0,64 te gtr, recP i
atoB s indeksom 0,46. Najmanje polimorfan bio je murI s HGDI indeksom od 0,25. Za
dva izdvojena soja S. canis bio je određen identični alelni profil ST9. HGDI indeks na
svim lokusima jednak je 0, jer nema polimorfizma s obzirom da je na dva soja
idemtificiran isti ST. Svi alelni tipovi S. uberis bili su do sada nepoznati u bazi
podataka. Najzastupljeniji ST je ST1203 s 9 uzoraka. ST1210 utvrđen je u dva
uzorka dok su ostali ST u uzorcima zastupljeni s jednim uzorkom za pojedini alelni
profil. Najpolimorfniji lokusi su tdk i arcC s HGDI indeksima 0,85, odnosno 0,82.
Slijede gki, ddl, rec i tpi lokusi s HGDI indeksima 0,79; 0,57 i 0,55. Najmanje
polimorfan bio je yqiL s HGDI indeksom od 0,30.
Dobiveni rezultati sekvenciranjem gena omogućili su usporedbu genskih
odsječaka streptokoka s odsječcima streptokoka analiziranim drugdje u svijetu.
Provedeno istraživanje otvara put daljnjim istraživanjima molekularne epidemiologije
streptokoknih uzročnika mastitisa. Naime, zaključili smo da bi za neke vrste
streptokoka laboratorijske postupke treba proširiti radi uvrđivanja njihove zoonotske
naravi. Less Abstract (english) Objectives: Mastitis is the most expensive disease in dairy cows. It is of multicausal
etiology as the result of interactions among microorganisms, the host and the
environment. The most important pathogens of bovine mastitis are Streptococcus,
Staphylococcus, Escherichia coli and the other coliform microorganisms. Numerous
Streptococcus species are important pathogens in animals and humans. Among the
streptococci that are the main pathogens of bovine hosts are species such as S.
... More agalactiae, S. uberis and S. dysgalactiae, which are also the most common mastitis
pathogens in dairy cows. In the most clinical laboratories, the identification of
streptococci is based on biochemical tests, and. in this way, up to 10-15% of isolated
strains are misidentified. The strains within a particular species may differ in the
same property, whereas the same strain may show biochemical variability. Since
there is no classification system ompletely accurate, the development and application
of genetic analysis methods improved the identification of streptococci. The aim of
this research was to establish a detailed insight into the presence of certain types of
streptococci in the etiology of the mastitis in dairy cows, to recognize public health
significance of mammary gland infections caused by streptococci and to determine
compliance of the results obtained by the classic microbiological analyses with those
obtained by identification of the causative agents using molecular methods.
Materials and Methods: The samples taken for bacteriological culture, prior regular
milking, were collected aseptically in sterile 10 mL tubes, without additives, according
to the National Mastitis Council recommendations and kept at 4 oC during transport.
The samples were analyzed within 12 hours following the collection. The described
microbiological testing was performed in accordance with generally approved
recommendations as described in the Laboratory Handbook on Bovine Mastitis. The
primary streptoccci isolation and identification were performed using aesculin blood
agar. After identification, the strains were stored in glycerol broth at the temperature of - 20 oC. The frozen strains were revitalized by repeated inoculations on aesculin blood agar. During storage, the vitality of the strains was examined using random
selection method. Isolation of DNA from the selected strains for species confirmation
by genes detection and sequencing were carried using the so-called “cultural”
isolation method. The DNA for further analyses was isolated with commercial kits and
automated device. For molecular identification of Streptococcus sp. was used
method based on gene sequencing and coding for 16S RNA, and comparison of
sequences with sequences in the available databases. The primers used for
molecular identification of species were pA and pH. The obtained amplification
products were sequenced using the Sanger method in Macrogen Europe B. V.,
Amsterdam, The Netherland. The obtained sequences were compared with the
sequences listed in the internationally available database NCBI (National Center for
Biotechnology Information) and RDP (Ribosomal database Project) througu
BioNumeric 7.6.3 software.
The multilocus sequence typing (MLST) is a method based on determining DNA
fragment sequences of approximately 450 bp size in seven housekeeping genes of
S. agalactiae (adhP, pheS, atr, glnA, sdhA, glcK and tkt), S. uberis (gki, recP, ddl,
tdk, arcC, tpi, and yqiL), S. canis (gki, gtr, murl, mutS, recP, Xptgc and yqiZ) and S.
dysgalactiae (gki, gtr, murl, mutS, recP, xpt and atoB). Obtained type of sequences,
i.e. allele profiles represent the SequenceType (ST). The obtained amplification
products were sequenced using the Sanger method in Macrogen Europe B. V.,
Amsterdam, Netherland. The obtained nucleotide sequences were aligned, verified
and compared using the BioNumerics software (version 7.6; applied Maths, Kortrijk,
Belgium). Allele and ST are determined using Streptococcus MLST
http://pubmlst.org/ database that can be loaded and used via BioNumerics software.
Each species of Streptococcus sp. has a separate database. The combination of
alleles on each locus consists of seven-member numerical code in which we
compared each other based on the categorical coefficient and unweighted pair group
method with arithmetic mean.
Results: In the study, 54 strains of bacteria isolated from milk samples from udder
quarters of dairy cows with subclinical mastitis were examined using molecular
methods. By conventional microbiological examination, the strains were identified to
the species (S. agalactiae, S. dysgalactiae i S. uberis) or to the genus (Streptococcus
spp.) without final identification of the species. Out of 54 examined bacterial strains, 47 of them were confirmed to belong to the genus Streptococcus spp., 6 strains of
Streptococcus agalactiae, 10 strains of Streptococcus dysgalactiae, 2 of
Streptococcus canis and 31 strain of Streptococcus uberis, while 3 strains belonged
to Enterococcus faecalis and 4 strains to the species Lactococcus lactis. All 47
Streptococcus sp. strains were typed using the MLST technique. The MLST is a
highly discriminating technique because it is based on typing sequences of
approximately 500 bp size within fragments of 7 so-called „house-keeping“ genes.
Each different sequence of genes represents another allele. The combination of
alleles to seven loci is an allele profile or ST. Since it is possible to have a large
number of alleles in each locus, the samples do not have the same profile randomly.
In this research we have studied four different species of Streptococcus sp. and a
different set of loci was used for each species.
In typed samples of S. agalactiae 4 different allele profiles were defined. The most
common ST was ST314. The other STs were represented in the samples with one
sample for each allelic profile. Allele profiles were examined at 7 loci: adhP, pheS,
atr, glnA, sdhA, glcK, and tkt. The most polymorphic loci were atr and glcK with the
Hunter-Gaston discriminatory index (HGDI) of 0.73. It is followed by adhP, glnA,
sdhA and tkt with the HGDI index of 0.60. The least polymorphic was pheS with the
HGDI index of 0.33. Using the eBURST algorithm, we defined that there were no
allelic profiles form a group, i. e. that they were "singletons". No local distribution of
allelic profiles was visible from the Minimum spanning tree (MST) view. In the
samples of S. dygalactiae were defined 7 different allele profiles. The most common
ST was ST305. Allelic profiles were examined at 7 loci: gki, gtr, murI, mutS, recP, xpt,
and atoB.The most polymorphic locus was mutS with the HGDI index of 0.86. It is
followed by gki and xpt with the HGDI index of 0.71 and 0.64, respectively, and gtr,
recP and atoB with an index of 0.46. The least polymorphic was murI with the HGDI
index of 0.25. Using the eBURST algorythm, we have defined only one cluster to
which ST305 and ST453 belong. The regional grouping of the samples from our
research was clearly visible from the MST presentation. In the typed S. canis
samples, we have defined one allelic profile. An identical ST9 allele profile was
determined for the two isolated strains. Allelic profiles were examined at 7 loci: gki,
gtr, murI, mutS, recP, xpt, and yqiZ. The HGDI at all loci was equal to 0 because
there is no polymorphism since the same ST was identified on two strains. There is no grouping using the eBURST algorythm. From the MST presentation it is clear that
Streptococcus canis strains identified in our research belong to one of the most
represented groups in the Europe, ST9 which very likely, forms a clonal cluster in
which ST9 is even a carrier. In the S. uberis samples, we have defined 22 different
allelic profiles. All allelic types have so far been unknown in the database. The most
common ST was ST1203 with 9 samples. ST1210 was determined in 2 samples
while the other STs were represented with one sample for each allelic profile. The
allelic profiles of S. uberis were examined at 7 loci: arcC, ddl, gki, recP, tdk, tpi and
yqiL. The most polymorphic loci were tdk and arcC with the the the HGDI indices of
0.85 and 0.82, respectively. It is followed by gki, ddl, rec and tpi with HGDI indices of
0.79; 0.57 and 0.55. The least polymorphic was yqiL with the HGDI index of 0.30.
Using the eBURST algorythm, we have defined one group of three allelic profiles:
ST1212, ST1224 and ST1228. No significant regional grouping of allelic profiles was
visible from the MST view. Nevertheless, it should be noted that we conducted the
study on 31 samples of which the vast majority have newly-identified STs. Allelic
profiles are original due to new alleles at the arcC locus.
Conclusion: In conclusion, the concordance of the conventional microbiological
identification to the genus level with molecular identification was high (87%). The
identification of the species by conventional microbiological procedures mostly
coincides with S. uberis molecular identification and least for S. agalactiae. The
research paves the way for further molecular epidemiology studies of streptococcal
mastitis pathogens, because for some streptococcus strains laboratory procedures
should be extended to determine their zoonotic nature and potential. Less Keywords
mastitis
Streptococcus sp.
mikrobiološka pretraga
molekularna pretraga
house keeping geni
MLST
Keywords (english)
mastitis
Streptococcus sp.
MLST
microbiological analyses
molecular analyses
house-keeping genes
Language croatian URN:NBN urn:nbn:hr:178:211485 Promotion 2021-01-25 Study programme Title: Doctoral Study Programme - Veterinary Sciences Type of resource Text File origin Born digital Access conditions Open access Terms of use Created on 2022-09-05 08:16:29
