Dataset Information

Molecular detection of colistin resistance genes (mcr-1, mcr-2 and mcr-3) in nasal/oropharyngeal and anal/cloacal swabs from pigs and poultry.

ABSTRACT: Antimicrobial resistance against colistin has emerged worldwide and is threatening the efficacy of colistin treatment of multi-resistant Gram-negative bacteria. In this study, PCRs were used to detect mcr genes (mcr-1, mcr-2, mcr-3) in 213 anal and 1,339 nasal swabs from pigs (n?=?1,454) in nine provinces of China, and 1,696 cloacal and 1,647 oropharyngeal samples from poultry (n?=?1,836) at live-bird markets in 24 provinces. The mcr-1 prevalences in pigs (79.2%) and geese (71.7%) were significantly higher than in chickens (31.8%), ducks (34.6%) and pigeons (13.1%). The mcr-2 prevalence in pigs was 56.3%, significantly higher than in chickens (5.5%), ducks (2.3%), geese (5.5%) and pigeons (0%). The mcr-3 prevalences in pigs (18.7%), ducks (13.8%) and geese (11.9%) were significantly higher than in chickens (5.2%) and pigeons (5.1%). In total, 173 pigs and three chickens were positive for all three mcr genes. The prevalences of the mcr were significantly higher in nasal/oropharyngeal swabs than in the anal /cloacal swabs. Phylogenetic studies identified 33 new mcr-2 variants and 12 new mcr-3 variants. This study demonstrates high prevalences of mcr in pigs and poultry in China, and indicates there is need for more thorough surveillance and control programs to prevent further selection of colistin resistance.

SUBMITTER: Zhang J

PROVIDER: S-EPMC5829079 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Molecular detection of colistin resistance genes (mcr-1, mcr-2 and mcr-3) in nasal/oropharyngeal and anal/cloacal swabs from pigs and poultry.

Zhang Jilei J Chen Li L Wang Jiawei J Yassin Afrah Kamal AK Butaye Patrick P Kelly Patrick P Gong Jiansen J Guo Weina W Li Jing J Li Min M Yang Feng F Feng Zhixing Z Jiang Ping P Song Chunlian C Wang Yaoyao Y You Jinfeng J Yang Yi Y Price Stuart S Qi Kezong K Kang Yuan Y Wang Chengming C

Scientific reports 20180227 1

Antimicrobial resistance against colistin has emerged worldwide and is threatening the efficacy of colistin treatment of multi-resistant Gram-negative bacteria. In this study, PCRs were used to detect mcr genes (mcr-1, mcr-2, mcr-3) in 213 anal and 1,339 nasal swabs from pigs (n = 1,454) in nine provinces of China, and 1,696 cloacal and 1,647 oropharyngeal samples from poultry (n = 1,836) at live-bird markets in 24 provinces. The mcr-1 prevalences in pigs (79.2%) and geese (71.7%) were significa ...[more]

PMID: 29487327

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Project description:BackgroundRecent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. Currently, there are no guidelines recommending HPV oral cavity screening as a mandatory test, and it remains unknown which HPV types should be included in HPV screening programs. Our goal was to assess HPV prevalence in oropharyngeal, anal, and cervical swabs using different sets of primers,which are able to amplify α, β, γ HPV types.MethodsWe analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. All untyped strains were genetically characterized through PCR amplification and direct sequencing of partial L1 region, and the resulting sequences were classified through phylogenetic analysis.ResultsHPV prevalence was 20.9% in 124 oropharyngeal swab samples, including infections with multiple HPV types (5.6%). HPV prevalence in this anatomical site was significantly associated with serostatus: 63.3%in HIV positive and 36.3% in HIV negative patients (p < 0.05). Unclassified types were detected in 6 specimens. In our analysis, we did not observe any difference in HPV (α, β, γ) prevalence between men and women. Overall, β species were the most frequently detected 69.7%. When using anal swabs, for HIV positive patients, β genus prevalence was 1% and γ genus was 3.7% including 6 unclassified types. In cervical samples from 43 HIV positive women (18 HPV negative and 25 positive by MY09/11 PCR), only one sample was positivite for β1 species (2.4%) using FAP primers. Six of the untyped strains clustered with sequences from species 7, 9, 10, 8,12 of γ genus. Four sequences remained unclassified. Finally, β and γ HPV prevalence was significantly lower than their respective HPV prevalence as identified by the Luminex system in all anatomical sites that were analyzed in previous studies.ConclusionThis study provides new information about viral isolates present in oropharyngeal site and it will contribute to improve the monitoring of HPV infection.

Project description:Introduction The porcine reproductive and respiratory syndrome virus (PRRSV) continues to challenge swine production in the US and most parts of the world. Effective PRRSV surveillance in swine herds can be challenging, especially because the virus can persist and sustain a very low prevalence. Although weaning-age pigs are a strategic subpopulation in the surveillance of PRRSV in breeding herds, very few sample types have been validated and characterized for surveillance of this subpopulation. The objectives of this study, therefore, were to compare PRRSV RNA detection rates in serum, oral swabs (OS), nasal swabs (NS), ear-vein blood swabs (ES), and family oral fluids (FOF) obtained from weaning-age pigs and to assess the effect of litter-level pooling on the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detection of PRRSV RNA. Methods Three eligible PRRSV-positive herds in the Midwestern USA were selected for this study. 666 pigs across 55 litters were sampled for serum, NS, ES, OS, and FOF. RT-qPCR tests were done on these samples individually and on the litter-level pools of the swabs. Litter-level pools of each swab sample type were made by combining equal volumes of each swab taken from the pigs within a litter. Results Ninety-six piglets distributed across 22 litters were positive by PRRSV RT-qPCR on serum, 80 piglets distributed across 15 litters were positive on ES, 80 piglets distributed across 17 litters were positive on OS, and 72 piglets distributed across 14 litters were positive on NS. Cohen's kappa analyses showed near-perfect agreement between all paired ES, OS, NS, and serum comparisons (). The serum RT-qPCR cycle threshold values (Ct) strongly predicted PRRSV detection in swab samples. There was a ≥ 95% probability of PRRSV detection in ES-, OS-, and NS pools when the proportion of positive swab samples was ≥ 23%, ≥ 27%, and ≥ 26%, respectively. Discussion ES, NS, and OS can be used as surveillance samples for detecting PRRSV RNA by RT-qPCR in weaning-age pigs. The minimum number of piglets to be sampled by serum, ES, OS, and NS to be 95% confident of detecting ≥ 1 infected piglet when PRRSV prevalence is ≥ 10% is 30, 36, 36, and 40, respectively.

Dataset Information

Molecular detection of colistin resistance genes (mcr-1, mcr-2 and mcr-3) in nasal/oropharyngeal and anal/cloacal swabs from pigs and poultry.

Publications

Molecular detection of colistin resistance genes (mcr-1, mcr-2 and mcr-3) in nasal/oropharyngeal and anal/cloacal swabs from pigs and poultry.

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