Genomic characterisation of Escherichia coli isolated from poultry at retail through Sink Surveillance in Dhaka, Bangladesh reveals high levels of multi-drug resistance.

The surveillance of antimicrobial resistance (AMR) in commensal Escherichia coli from livestock at slaughter is widely employed to assess the potential for risk to humans. There is currently a limited understanding of AMR in Bangladesh poultry at retail in live bird markets, with studies focussing solely on phenotypic characterisation of resistance. To address this evidence gap we performed antimicrobial susceptibility testing and whole genome sequencing on E. coli obtained from chickens from live bird markets in Dhaka in 2018 (n = 38) and 2020 (n = 45). E. coli were isolated from caeca samples following ISO guidelines and sequenced using short and long read methods. Multidrug resistance was extremely common (n = 77) and there was excellent concordance between AMR phenotype and the presence of corresponding AMR genes or mutations. There was considerable genomic diversity, with 43 different sequence types detected. Public health considerations included the high occurrence of resistance to ciprofloxacin (n = 75) associated with plasmid-residing qnrS or mutations in the gyrA and parC chromosomal genes; and the detection of a tigecycline resistant isolate harbouring tet(X4) on an IncHI1A/B-IncFIA mosaic plasmid. Thirty-nine isolates were resistant to azithromycin and harboured mphA, with a significant increase in the incidence of resistance between 2018 and 2020. Although azithromycin is banned for veterinary use in Bangladesh it remains an important treatment option for humans. Interestingly, mphA confers high-level resistance to azithromycin and erythromycin, and the latter is commonly used on poultry farms in Bangladesh. Seven isolates were colistin resistant and carried mcr1. For two isolates hybrid assemblies revealed that mcr1 resided on a highly conserved IncHI2 plasmid that had 93% nucleotide identity to a plasmid from the published genome of an E. coli isolate of Bangladeshi human origin. Six isolates had resistance to third generation cephalosporins, associated with plasmid-residing bla CTX-M-55, bla CTX-M-65, or bla DHA-1. By employing phenotypic and genomic approaches for AMR surveillance we have provided new insights into the potential for One Health AMR linkages in Bangladesh. Employing similar approaches in human and environmental sectors will help inform the One Health approach to addressing AMR, and generate evidence to support mitigation measures such as improved antimicrobial stewardship.

Effect of parboiling conditions on zinc and iron retention in biofortified and non-biofortified milled rice.

BACKGROUND: Zinc-biofortified rice could contribute to zinc intake in deficient populations, but processing it into parboiled rice could affect this potential benefit. Zinc and iron true retention (TR) in milled rice produced under conditions resembling household and commercial parboiled methods was evaluated. Zinc and iron TR in milled rice obtained from biofortified and non-biofortified rice subjected to different soaking temperatures during parboiling was also evaluated. RESULTS: Conditions resembling commercial parboiling methods resulted in 52.2-59.7% zinc TR and 55.4-79.1% iron TR, whereas those used for household parboiling resulted in 70.7-79.6% zinc TR and 78.2-119.8% iron TR. Zinc TR in milled (8-16% bran removal) biofortified and non-biofortified parboiled rice was 50.6-66.8% when soaking rough rice at 20 °C and 29.9-56.0% when soaking rough rice at 65 °C; both had lower zinc TR than non-parboiled rice (58.0-80.6%). Iron TR was generally similar between milled non-parboiled and parboiled rice (26.2-67.6%) and between parboiled biofortified and non-biofortified milled rice. CONCLUSION: Parboiling conditions used to obtain milled rice targeted for own household consumption resulted in higher zinc and iron TR compared to parboiling conditions used for milled rice targeted for markets. More zinc from the inner endosperm moved towards the outer layers at high soaking temperature, resulting in lower zinc TR for milled parboiled rice soaked in hotter water. Parboiled rice soaked at temperatures used in households could provide more zinc to diets compared to rice soaked in hotter water commonly used in large rice mills, especially when rice is extensively milled. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Efficacy of two vaccines against recent emergent antigenic variants of clade 2.3.2.1a highly pathogenic avian influenza viruses in Bangladesh.

H5N1 highly pathogenic avian influenza viruses (HPAIVs) have caused outbreaks in poultry in Bangladesh since 2007. While clade 2.2.2 and 2.3.4.2 HPAIVs have not been detected since 2012, clade 2.3.2.1a viruses have caused continuous outbreaks since 2012 despite the use of vaccines. In this study, we evaluated the efficacy of two H5 vaccines licensed in Bangladesh, RE-6 inactivated vaccine, and a recombinant herpesvirus of turkeys vaccine with an H5 insert (rHVT-H5), for protection against recent field viruses in chickens. We selected three viruses for efficacy tests (A/chicken/Bangladesh/NRL-AI-3237/2017, A/crow/Bangladesh/NRL-AI-8471/2017 and A/chicken/Bangladesh/NRL-AI-8323/2017) from 36 H5 viruses isolated from Bangladesh between 2016 and 2018 by comparing the amino acid sequences at five antigenic sites (A-E) and analyzing hemagglutination inhibition (HI) titers with reference antisera. The RE-6 and rHVT-H5 vaccines both conferred 80-100% clinical protection (i.e. reduced morbidity and mortality) against the three challenge viruses with no significant differences in protection. In addition, both vaccines significantly decreased viral shedding from infected chickens as compared to challenge control chickens. Based on these metrics, the current licensed H5 vaccines protected chickens against the recent field viruses. However, the A/crow/Bangladesh/NRL-AI-8471/2017 virus exhibited antigenic divergence including: several unique amino acid changes in antigenic epitope sites A and B and was a serological outlier in cross HI tests as visualized on the antigenic map. The continuing emergence of such antigenic variants which could alter the dominant antigenicity of field viruses should be continuously monitored and vaccines should be updated if field efficacy declines.

Qualitative risk assessment of transmission pathways of highly pathogenic avian influenza (HPAI) virus at live poultry markets in Dhaka city, Bangladesh.

Analysis of environmental samples obtained from the Live Poultry Markets (LPMs) of Dhaka City, Bangladesh, has revealed that the highest degree of prevalence of highly pathogenic avian influenza A (HPAI, H5N1), besides other subtypes of the LPAI virus, poses the plausible risk of transmission of these viruses between human and poultry species. The present study was conducted using the OIE risk analysis framework to assess the risk level of each pathway successively. The estimated risk parameters were integrated towards to obtain the overall risk level for each specific HPAI transmission pathway using the matrix adapted by Cristobel Zepeda accompanying other expert consultations. The relevant data obtained from published and unpublished sources, together with survey data of field observations, were used to formulate and confirm the risk pathways and their associated risks. The results revealed that the risk of the release of the HPAI virus was medium when exposure was high. Additionally, the consequence would be considered very high with a medium degree of uncertainty for all parameters. Ultimately, the overall risk for transmission was estimated as medium with a medium degree of uncertainty. The findings of this study reveal that there is a significant threat that HPAI virus transmission could occur among poultry and humans and effectively sustain within the environment of the LPMs. Our findings are primarily focused on public health considerations, the hygienic slaughter of poultry and the relevant cleaning and sanitation practices conducted in the LPMs to support evidence-based decision-making processes. The findings of the study have the potential to be used to formulate effective risk reduction measures and can be further adapted in low-resource settings without major infrastructural changes required of the LPMs. All of which would reduce the risk of HPAI virus release and further lessen the degree of exposure and transmission in established LPMs.