PMID- 36194132
OWN - NLM
STAT- MEDLINE
DCOM- 20221028
LR  - 20230103
IS  - 2165-0497 (Electronic)
IS  - 2165-0497 (Linking)
VI  - 10
IP  - 5
DP  - 2022 Oct 26
TI  - Comprehensive Assessment of Subtyping Methods for Improved Surveillance of 
      Foodborne Salmonella.
PG  - e0247922
LID - 10.1128/spectrum.02479-22 [doi]
LID - e02479-22
AB  - High-resolution and efficient typing for the bacterial pathogen is essential for 
      tracking the sources, detecting or diagnosing variants, and conducting a risk 
      assessment. However, a systematic in-field investigation of Salmonella along the 
      food chain has not been documented. This study assessed 12 typing methods, such 
      as antimicrobial-resistance (AMR) gene profile typing, Core Genome Multilocus 
      Sequence Typing (cgMLST), and CRISPR multi-virulence locus sequence typing 
      (CRISPR-MVLST), to evaluate their effectiveness for use in routine monitoring of 
      foodborne Salmonella transmission along the poultry production chain. During 
      2015-16, a total of 1,064 samples were collected from poultry production chain, 
      starting from breeding farms and slaughterhouses to the markets of Zhejiang 
      province in China. A total of 61 consecutive unique Salmonella isolates recovered 
      from these samples were selected for genome sequencing and further comparative 
      typing analysis. Traditional typing methods, including serotyping, AMR 
      phenotype-based typing, as well as modern genotyping approaches, were evaluated 
      and compared by their discrimination index (DI). The results showed that the 
      serotyping method identified nine serovars. The gold standard cgMLST method 
      indicated only 18 different types (DI = 0.8541), while the CRISPR-MVLST method 
      detected 30 types (DI = 0.9628), with a higher DI than all examined 
      medium-resolution WGS-based genotyping methods. We demonstrate that the 
      CRISPR-MVLST might be used as a tool with high discriminatory power, comparable 
      ease of use, ability of tracking the source of Salmonella strains along the food 
      chain and indication of genetic features especially virulence genes. The 
      available methods with different purposes and laboratory expertise were also 
      illustrated to assist in rational implementation. IMPORTANCE In public health 
      field, high-resolution and efficient typing of the bacterial pathogen is 
      essential, considering source-tracking and risk assessment are fundamental 
      issues. Currently, there are no recommendations for applying molecular 
      characterization methods for Salmonella along the food chain, and a systematic 
      in-field investigation comparing subtyping methods in the context of routine 
      surveillance was partially addressed. Using 1,064 samples along a poultry 
      production chain with a considerable level of Salmonella contamination, we 
      collected representative isolates for genome sequencing and comparative analysis 
      by using 12 typing techniques, particularly with whole-genome sequence (WGS) 
      based methods and a recently invented CRISPR multi-virulence locus sequence 
      typing (CRISPR-MVLST) method. CRISPR-MVLST is identified as a tool with higher 
      discriminatory power compared with medium-resolution WGS-based typing methods, 
      comparable ease of use and proven ability of tracking Salmonella isolates. 
      Besides, we also offer recommendations for rational choice of subtyping methods 
      to assist in better implementation schemes.
FAU - Pan, Hang
AU  - Pan H
AD  - Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, 
      Zhejiang Universitygrid.13402.34 College of Animal Sciences, Hangzhou, China.
AD  - Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, 
      China.
FAU - Jia, Chenghao
AU  - Jia C
AD  - Hainan Institute of Zhejiang Universitygrid.13402.34, Sanya, China.
FAU - Paudyal, Narayan
AU  - Paudyal N
AD  - Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, 
      Zhejiang Universitygrid.13402.34 College of Animal Sciences, Hangzhou, China.
FAU - Li, Fang
AU  - Li F
AD  - Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, 
      Zhejiang Universitygrid.13402.34 College of Animal Sciences, Hangzhou, China.
FAU - Mao, Junyong
AU  - Mao J
AD  - Hainan Institute of Zhejiang Universitygrid.13402.34, Sanya, China.
FAU - Liu, Xi
AU  - Liu X
AD  - Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, 
      Zhejiang Universitygrid.13402.34 College of Animal Sciences, Hangzhou, China.
FAU - Dong, Chenghang
AU  - Dong C
AD  - Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, 
      Zhejiang Universitygrid.13402.34 College of Animal Sciences, Hangzhou, China.
FAU - Zhou, Kun
AU  - Zhou K
AD  - Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, 
      Zhejiang Universitygrid.13402.34 College of Animal Sciences, Hangzhou, China.
FAU - Liao, Xiayi
AU  - Liao X
AD  - Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, 
      Zhejiang Universitygrid.13402.34 College of Animal Sciences, Hangzhou, China.
FAU - Gong, Jiansen
AU  - Gong J
AD  - Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, China.
FAU - Fang, Weihuan
AU  - Fang W
AUID- ORCID: 0000-0002-2460-0743
AD  - Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, 
      Zhejiang Universitygrid.13402.34 College of Animal Sciences, Hangzhou, China.
AD  - Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, 
      China.
FAU - Li, Xiaoliang
AU  - Li X
AUID- ORCID: 0000-0002-2058-7764
AD  - Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, 
      Zhejiang Universitygrid.13402.34 College of Animal Sciences, Hangzhou, China.
AD  - Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, 
      China.
FAU - Kehrenberg, Corinna
AU  - Kehrenberg C
AUID- ORCID: 0000-0001-8556-4080
AD  - Institute for Veterinary Food Science, Justus Liebig University Giessen, Giessen, 
      Germany.
FAU - Yue, Min
AU  - Yue M
AUID- ORCID: 0000-0002-6787-0794
AD  - Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, 
      Zhejiang Universitygrid.13402.34 College of Animal Sciences, Hangzhou, China.
AD  - Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, 
      China.
AD  - Hainan Institute of Zhejiang Universitygrid.13402.34, Sanya, China.
AD  - State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National 
      Clinical Research Center for Infectious Diseases, National Medical Center for 
      Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang 
      University, Hangzhou, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20221004
PL  - United States
TA  - Microbiol Spectr
JT  - Microbiology spectrum
JID - 101634614
SB  - IM
MH  - *Salmonella/genetics
MH  - Multilocus Sequence Typing/methods
MH  - Serogroup
MH  - Sequence Analysis, DNA
MH  - *Clustered Regularly Interspaced Short Palindromic Repeats
PMC - PMC9602514
OTO - NOTNLM
OT  - CRISPR-MVLST
OT  - CoreSNP
OT  - Salmonella
OT  - antimicrobial resistance
OT  - cgMLST
OT  - poultry production chain
OT  - typing method
COIS- The authors declare no conflict of interest.
EDAT- 2022/10/05 06:00
MHDA- 2022/10/29 06:00
PMCR- 2022/10/04
CRDT- 2022/10/04 10:11
PHST- 2022/10/05 06:00 [pubmed]
PHST- 2022/10/29 06:00 [medline]
PHST- 2022/10/04 10:11 [entrez]
PHST- 2022/10/04 00:00 [pmc-release]
AID - 02479-22 [pii]
AID - spectrum.02479-22 [pii]
AID - 10.1128/spectrum.02479-22 [doi]
PST - ppublish
SO  - Microbiol Spectr. 2022 Oct 26;10(5):e0247922. doi: 10.1128/spectrum.02479-22. 
      Epub 2022 Oct 4.