Development of a method for identification and genotyping of Pasteurella multocida and Mannheimia haemolytica bacteria using polymerase chain reaction and phylogenetic analysis of bacterial cultures isolated from cattle

Nefedchenko, A.V.; Shikov, A. N.; Глотов, А.Г.; Glotova, T.I.; Ternovoy, V. A.; Агафонов, А. П.; Сергеев, А. Н.; Donchenko, N. A.

doi:10.3103/s0891416816020063

Cited by 5 publications

(7 citation statements)

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“…All studies included primer/probe sequence data or clearly referenced cited studies. All articles included both analytical sensitivity and specificity and only one study included diagnostic sensitivity and specificity ( Andres-Lasheras et al, 2020 ); ten studies reported on PCR optimization ( Horwood and Mahony, 2011 ; Thonur et al, 2012 ; Nefedchenko et al, 2016 ; Fan et al, 2017 ; Zhang et al, 2017 ; Loy et al, 2018 ; Thanthrige-Don et al, 2018 ; Liu et al, 2019 ; Andres-Lasheras et al, 2020 ; Xie et al, 2021 ) and three studies reported the use of quantitative PCR methods; qPCR ( Andres-Lasheras et al, 2020 ), Multiplex qRT-PCR ( Goto et al, 2020 ) and RT-qPCR ( Xie et al, 2021 ). Quantitative values were not reported in any of the studies included in this analysis ( Table 3 ).…”

Section: Resultsmentioning

confidence: 99%

“…Of the 14 studies included in this review, 8 reported on the use of PCR for the detection of bacterial organisms associated with BRD ( Szacawa et al, 2015 ; Nefedchenko et al, 2016 ; Kishimoto et al, 2017 ; Zhang et al, 2017 ; Loy et al, 2018 ; Thanthrige-Don et al, 2018 ; Andres-Lasheras et al, 2020 ; Goto et al, 2020 ). A total of 63 primer/probe sequences were extracted (probes n = 9, forward primers n = 27, reverse primers n = 27) and analysed using BLASTn ( Madden, 2003 ) and Primer-Blast ( Ye et al, 2012 ) ( Table 6 ).…”

Section: Resultsmentioning

confidence: 99%

“…The primers and probe targeting the 16s-rRNA gene of H. somni ( Kishimoto et al, 2017 ) all had significantly more results for non-target genes than that target ( Figure 3 ). While the primers targeting the tbpB gene of M. haemolytica ( Thanthrige-Don et al, 2018 ), Pm0762 ( Thanthrige-Don et al, 2018 ), dcbF ( Nefedchenko et al, 2016 ) and ecbJ ( Nefedchenko et al, 2016 ) genes of P. multocida , and plo gene of T. pyogenes ( Zhang et al, 2017 ) all returned significantly more results for non-targets than the target ( Figure 3 ).…”

Section: Resultsmentioning

confidence: 99%

“…Analysis of bacterial primer sets identified a number of primer pairs that showed 100% specificity for their intended target; specifically H. somni 16S rDNA ( Thanthrige-Don et al, 2018 ); M. haemolytica tbpB and nmaA ( Thanthrige-Don et al, 2018 ) and sodA ( Nefedchenko et al, 2016 ); M. bovis oppD ( Kishimoto et al, 2017 ; Loy et al, 2018 ; Goto et al, 2020 ); P. multocida Pm0762 ( Thanthrige-Don et al, 2018 ), kmt-1 ( Zhang et al, 2017 ), kmt-1, dcbF and bcbD ( Nefedchenko et al, 2016 ); T. pyogenes plo-Pyolysin ( Kishimoto et al, 2017 ) and plo ( Zhang et al, 2017 ). Conversely, the primer pair targeting the P. multocida Pm1231 gene ( Loy et al, 2018 ; Goto et al, 2020 ) reported no search results from Primer-Blast analysis ( Supplementary Table S4 ).…”

Section: Resultsmentioning

confidence: 99%

“…Of the 27 primer sets analysed, 81.4% returned a higher number of target-specific results than non-target sequences whilst four primer pairs returned a significantly higher number of non-target hits than target-specific sequences ( Supplementary Table S4 ). All non-target sequences identified that were either same genus and species as target but different strain, or a different genus but same target species (bovine) but a different bacterial species had product lengths below 1,000, potentially resulting in non-specifically amplification.Where primer pairs were identifying organisms of a completely different genus and species to the intended target, which was the case for reported sequences for M. haemolytica LktD ( Loy et al, 2018 ; Goto et al, 2020 ), LktA ( Thanthrige-Don et al, 2018 ) and artJ-lktC ( Zhang et al, 2017 ); M. bovis uvrC ( Andres-Lasheras et al, 2020 ) and UvrC ( Szacawa et al, 2015 ); P. multocida kmt-1 ( Kishimoto et al, 2017 ), hyaD ( Nefedchenko et al, 2016 ), ecbJ ( Nefedchenko et al, 2016 ) and fcbD ( Nefedchenko et al, 2016 ) all non-target products had lengths above 1,000 and therefore would be unlikely to results in non-specific amplification ( Supplementary Table S4 ) if the differential target was present in a mixed clinical sample.…”

Section: Resultsmentioning

confidence: 99%

See 4 more Smart Citations

Meta-Analysis of qPCR for Bovine Respiratory Disease Based on MIQE Guidelines

Marsh

Quinn

2022

Front. Mol. Biosci.

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Qualitative and quantitative PCR-based tests are widely used in both diagnostics and research to assess the prevalence of disease-causing pathogens in veterinary medicine. The efficacy of these tests, usually measured in terms of sensitivity and specificity, is critical in confirming or excluding a clinical diagnosis. We undertook a meta-analysis to assess the inherent value of published PCR diagnostic approaches used to confirm and quantify bacteria and viruses associated with bovine respiratory disease (BRD) in cattle. This review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A thorough search of nine electronic databases (Web of Science, EBSCOhost, Cambridge journals online, ProQuest, PubMed, Sage journals online, ScienceDirect, Wiley online library and MEDLINE) was undertaken to find studies that had reported on the use of PCR and/or qPCR for the detection and/or quantification of BRD associated organisms. All studies meeting the inclusion criteria for reporting quantitative PCR for identification of BRD associated microorganisms were included in the analysis. Studies were then assessed on the applications of the Minimum Information for Publication of Quantitative Real-Time PCR Experiment (MIQE) and PCR primer/probe sequences were extracted and tested for in silico specificity using a high level of stringency. Fourteen full-text articles were included in this study. Of these, 79% of the analysed articles did not report the application of the MIQE guidelines in their study. High stringency in silico testing of 144 previously published PCR primer/probe sequences found many to have questionable specificity. This review identified a high occurrence of primer/probe sequences with a variable in silico specificity such that this may have implications for the accuracy of reporting. Although this analysis was only applied to one specific disease state, identification of animals suspected to be suffering from bovine respiratory disease, there appears to be more broadly a need for veterinary diagnostic studies to adopt international best practice for reporting of quantitative PCR diagnostic data to be both accurate and comparable between studies and methodologies.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 3 more Smart Citations

Meta-Analysis of qPCR for Bovine Respiratory Disease Based on MIQE Guidelines

Marsh

Quinn

2022

Front. Mol. Biosci.

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Prevalence of different OmpH-types among Pasteurella multocida isolated from lungs of calves with respiratory problems

Nefedchenko

Glotova

Глотов

et al. 2017

Microbial Pathogenesis

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Identification of serotypes of Mannheimia haemolytica and Pasteurella multocida from pneumonic cases of sheep and goats and their antimicrobial sensitivity profiles in Borana and Arsi zones, Ethiopia

Girma

Getachew

Beyene

et al. 2023

Sci Rep

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Respiratory diseases caused by Mannheimia haemolytica (M. haemolytica) and Pasteurella multocida (P. multocida) have been known to result in a considerable loss due to mortality and reduced production. This study aimed at isolation and identification of M. haemolytica and P. multocida associated with pneumonic pasteurellosis in sheep and goats using bacteriological and molecular techniques. Identification of serotypes of M. haemolytica and P. multocida was done using indirect haemagglutination test. The in vitro antimicrobial sensitivity profiles of the M. haemolytica were tested using standard disk diffusion method. A total of 52 and 78 nasal swabs were collected from pneumonic cases for bacterial isolation and identification in Borana and Arsi zone, respectively. Four hundred sera samples were collected for identification of serotypes. The results showed that 17 of 52 (32.69%; 95% CI 20.33, 47.11) nasal swabs collected from pneumonic animals in Borana yielded positive results for Pasteurella/Mannheimia species, 13 (25.00%; 95% CI 14.03, 38.95) of which were M. haemolytica. None of the samples yielded P. multocida. Twenty-three of 78 (29.49%; 95% CI 19.69, 40.89) nasal swabs collected at Arsi from pneumonic animals yielded positive results for M. haemolytica (17) and P. multocida (6). Secondary biochemical characterization revealed that 14 of the 17 isolates conform to M. haemolytica whereas none of the 6 isolates suspected to be P. mutocida were confirmed. Eleven (84.62%) isolates from Borana and 4 (28.57%) from Arsi were confirmed to be M. haemolytica using PCR targeting the Rpt2 genes. Assay for M. haemolytica serotype A1 revealed all belong to A1. None of the isolates with cultural and morphological features of P. multocida gave positive results by molecular assay. Serological assay identified three serotypes of M. haemolytica namely A1, A2 and A7 almost in all of the samples whereas P. multocida serotype A was detected in 78.75% of the samples. The M. haemolytica isolates tested for susceptibility to antibiotics showed resistance against Bacitracin (83.33%) and Penicillin (50.00%) while they were found susceptible to Gentamycin (100%), Chloramphenicol (100%) and Sulfamethoxazole (100%) and Tetracycline (83.33%). In conclusion, the results of the present study revealed the association of M. haemolytica with pneumonic pasteurellosis in sheep and goats and can be of use in vaccine development in Ethiopia. Nevertheless, further investigations and continuous monitoring of antimicrobial resistance and appropriate selection and prudent use of antimicrobials in livestock sector are required.

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Development of a method for identification and genotyping of Pasteurella multocida and Mannheimia haemolytica bacteria using polymerase chain reaction and phylogenetic analysis of bacterial cultures isolated from cattle

Cited by 5 publications

References 5 publications

Meta-Analysis of qPCR for Bovine Respiratory Disease Based on MIQE Guidelines

Meta-Analysis of qPCR for Bovine Respiratory Disease Based on MIQE Guidelines

Prevalence of different OmpH-types among Pasteurella multocida isolated from lungs of calves with respiratory problems

Identification of serotypes of Mannheimia haemolytica and Pasteurella multocida from pneumonic cases of sheep and goats and their antimicrobial sensitivity profiles in Borana and Arsi zones, Ethiopia

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