Ci a ion: Ga aiza , J.; Lao den, L.
Bac e ial Genomics and
Epidemiology. Mic oo ganisms 2023,
11, 1428. h ps://doi.o g/10.3390/
mic oo ganisms11061428
Recei ed: 9 Ma ch 2023
Re ised: 24 May 2023
Accep ed: 25 May 2023
Published: 29 May 2023
Copy igh : © 2023 by he au ho s.
Licensee MDPI, Basel, Swi ze land.
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mic oo ganisms
Edi o ial
Bac e ial Genomics and Epidemiology
Ja ie Ga aiza * and Lo ena Lao den
Mik oIke Resea ch G oup, Depa men o Immunology, Mic obiology, and Pa asi ology, Facul y o Pha macy,
Uni e si y o he Basque Coun y UPV/EHU, 01006 Vi o ia-Gas eiz, Spain; lo ena.lao [email p o ec ed]
*Co espondence: ja ie [email p o ec ed]
Inno a i e echnologies o Whole-Genome Sequencing (WGS) help o imp o e ou
unde s anding o he epidemiology and pa hogenesis o bac e ial in ec ious diseases
and a e becoming a o dable o mos mic obiological labo a o ies [
1
]. These ecen
echnologies could be success ully applied o bac e ia isola ed om mul iple ese oi s
and habi a s, such as clinical, ood, animal, o en i onmen al ields [2]. The “One heal h”
concep encompasses in an in e disciplina y way he in e ela ion o human, animal, and
en i onmen al heal h [
3
]. This Special Issue o Mic oo ganisms collec s esea ch a icles
and a e iew on hese ields as examples o he aid p o ided by new genomic echniques
in he s udy o bac e ial in ec ion epidemiology.
G oup B S ep ococcus (GBS), o S ep ococcus agalac iae, is a majo cause o neona al
mo ali y. When colonizing he lowe geni al ac o p egnan women, GBS may cause
p ema u e and s illbi h. I ansmi ed o he newbo n, i may esul in li e- h ea ening
illnesses, including sepsis, meningi is, and pneumonia. Mo eo e , h ough con inuous
e olu ion, GBS can use i s o iginal s uc u e and unique ac o s o imp o e i s su i al
a e in he human body. The e iew by Liu and Liu [4] discusses he key i ulence ac o s
de e mined by WGS ha acili a e GBS in asion and coloniza ion and hei ela ed ac ion
mechanisms. A comp ehensi e unde s anding o he ole o i ulence ac o s in GBS
in ec ion is c ucial o de elop be e ea men op ions and sc een po en ial candida e
molecules o he de elopmen o a accine. In his sense, Shabayek e al. [
5
] p esen
genomic da a om a collec ion o colonizing GBS s ains om Ismailia, Egyp , ha we e
sequenced and cha ac e ized wi hin he global JUNO p ojec , esul ing in a conside able
p opo ion o se o ype VI ST14 s ains, a se o ype which is a ely ound in s ain collec ions
om he US and Eu ope and ypically no included in cu en accine o mula ions. The
molecula genomic epidemiology o hese s ains clea ly poin s o he A ican o igin wi h
he de ec ion o se e al sequence ypes ha ha e only been obse ed in A ica. Thei da a
unde line he impo ance o he con inuous molecula su eillance o he GBS popula ion
o u u e accine implemen a ions.
Salmonella en e ica is a leading cause o epidemic human gas oin es inal disease
wo ldwide. Gi en i s pe sis ence in aqua ic en i onmen s, González-López e al. [
6
]
examined he p e alence, le els, and geno ypic di e si y o Salmonella isola es eco e ed
om majo i e s in an impo an ag icul u al egion in no hwes e n Mexico. Du ing
a 13-mon h pe iod, a o al o 143 i e wa e samples we e collec ed and subjec ed o
size-exclusion ul a il a ion, ollowed by en ichmen , and selec i e media o he isola ion
and quan i a ion o Salmonella. The eco e ed isola es we e examined by nex -gene a ion
sequencing o genome cha ac e iza ion. Molecula sub yping e ealed ha O angebu g,
Ana um, and Sain paul we e he mos p edominan Salmonella se o a s. Single-nucleo ide
polymo phism (SNP)-based phylogeny e ealed ha he 27 dis inc se o a s de ec ed in
i e wa e clus e ed in wo majo clades. Mul iple nonsynonymous SNPs we e de ec ed in
s iA,si H, and a A genes equi ed o Salmonella’s i ness and su i al, and hese indings
iden i ied ele an ma ke s o po en ially de elop imp o ed me hods o cha ac e izing
his pa hogen.
Mic oo ganisms 2023,11, 1428. h ps://doi.o g/10.3390/mic oo ganisms11061428 h ps://www.mdpi.com/jou nal/mic oo ganisms
Mic oo ganisms 2023,11, 1428 2 o 2
Finally, despi e he innume able ad an ages o using WGS, se e al d awbacks con-
ce ning da a analysis, da a managemen and exchange, and he lack o alida ion, hinde
i s in eg a ion in o ou ine use in na ional e e ence cen e s o labo a o ies. In small o
less-de eloped coun ies, he in eg a ion o WGS is pa icula ly oublesome, as hey do
no always ha e equal access o esou ces compa ed o public heal h agencies o la ge
labo a o ies. Da a analysis also ep esen s a bo leneck, and is becoming a se ious hu dle
o o e come as i ypically consis s o a s epwise p ocess ha is complex and edious o
non-expe s. A xae andio-Landa e al. [
7
] p opose a bioin o ma ics wo k low o (Illumina)
WGS da a o bac e ial cha ac e iza ion, including genome anno a ion, species iden i ica-
ion, se o ype p edic ion, an imic obial esis ance p edic ion, i ulence- ela ed gene and
plasmid eplicon de ec ion, and co e-genome-based o single nucleo ide polymo phism
(SNP)-based phylogene ic clus e ing and sequence yping. This bioin o ma ics wo k low
can be ailo ed o o he pa hogens o in e es , and is eely a ailable o academic and
non-p o i use as i in ol es an uploadable ile o he Galaxy pla o m ha does no equi e
he use o complex in o ma ic commands.
Acknowledgmen s:
Thanks o all he au ho s and e iewe s o hei excellen con ibu ions o his
Special Issue. Addi ional hanks o he Mic oo ganisms Edi o ial O ice o hei p o essional assis ance
and con inuous suppo .
Con lic s o In e es : The edi o s decla e no con lic o in e es .
Re e ences
1.
Hahm, C.; Chung, H.S.; Lee, M. Whole-genome sequencing o he cha ac e iza ion o esis ance mechanisms and epidemiology
o colis in- esis an Acine obac e baumannii.PLoS ONE 2022,17, e0264335. [C ossRe ] [PubMed]
2.
Rossen, J.W.A.; F ied ich, A.W.; Mo an-Gilad, J.; ESCMID S udy G oup o Genomic and Molecula Diagnos ics (ESGMD).
P ac ical issues in implemen ing whole-genome-sequencing in ou ine diagnos ic mic obiology. Clin. Mic obiol. In ec .
2018
,24,
355–360. [C ossRe ] [PubMed]
3.
FAO; UNEP; WHO; WOAH. One Heal h Join Plan o Ac ion (2022–2026): Wo king Toge he o he Heal h o Humans, Animals, Plan s
and he En i onmen ; FAO: Rome, I aly, 2022. [C ossRe ]
4.
Liu, Y.; Liu, J. G oup B S ep ococcus: Vi ulence Fac o s and Pa hogenic Mechanism. Mic oo ganisms
2022
,10, 2483. [C ossRe ]
[PubMed]
5.
Shabayek, S.; Vogel, V.; Jam ozy, D.; Ben ley, S.D.; Spelle be g, B. Molecula Epidemiology o G oup B S ep ococcus Coloniza ion
in Egyp ian Women. Mic oo ganisms 2023,11, 38. [C ossRe ] [PubMed]
6.
González-López, I.; Med ano-Félix, J.A.; Cas o-del Campo, N.; López-Cue as, O.; González-Gómez, J.P.; Valdez-To es, J.B.;
Agui e-Sánchez, J.R.; Ma ínez-U aza, J.; Gómez-Gil, B.; Lee, B.G.; e al. P e alence and Genomic Di e si y o Salmonella en e ica
Reco e ed om Ri e Wa e in a Majo Ag icul u al Region in No hwes e n Mexico. Mic oo ganisms 2022,10, 1214. [C ossRe ]
[PubMed]
7.
A xae andio-Landa, A.; A ie a-Gisasola, A.; Lao den, L.; Bikandi, J.; Ga aiza , J.; Ma inez-Malaxe xeba ia, I.; Ma inez-
Balles e os, I. A P ac ical Bioin o ma ics Wo k low o Rou ine Analysis o Bac e ial WGS Da a. Mic oo ganisms
2022
,10, 2364.
[C ossRe ] [PubMed]
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