Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen

Since 2016, Yemen has been experiencing the largest cholera outbreak in modern history. Multidrug resistance (MDR) emerged among Vibrio cholerae isolates from cholera patients in 2018. Here, to characterize circulating genotypes, we analysed 260 isolates sampled in Yemen between 2018 and 2019. Eighty-four percent of V. cholerae isolates were serogroup O1 belonging to the seventh pandemic El Tor (7PET) lineage, sub-lineage T13, whereas 16% were non-toxigenic, from divergent non-7PET lineages. Treatment of severe cholera with macrolides between 2016 and 2019 coincided with the emergence and dominance of T13 subclones carrying an incompatibility type C (IncC) plasmid harbouring an MDR pseudo-compound transposon. MDR plasmid detection also in endemic non-7PET V. cholerae lineages suggested genetic exchange with 7PET epidemic strains. Stable co-occurrence of the IncC plasmid with the SXT family of integrative and conjugative element in the 7PET background has major implications for cholera control, highlighting the importance of genomic epidemiological surveillance to limit MDR spread.

Circulating vaccine derived polio virus type 1 outbreak, Saadah governorate, Yemen, 2020

Background

Yemen has faced one of the worst humanitarian crises in the world since the start of the war in 2015. In 2020; 30 Vaccine Derived Polio Virus type 1 (VDPV1) isolates were detected in Saadah governorate. The aims are to characterize the outbreak and address the gaps predisposing the emergence and circulation of VDPV1 in Saadah governorate, Yemen.

Method

A retrospective descriptive study of confirmed cases of VDPV1 between January and December 2020 was performed. Surveillance staff collected data from patient cases, contacts, as well as stool specimens that shipped to WHO accredited polio labs. Data of population immunity was also reviewed. The difference in days between the date of sample collection, shipment, and receiving lab result was used to calculate the average of delayed days for lab confirmation.

Results

From January to December 2020, a total of 114 cases of acute flaccid paralysis (AFP) were reported from 87% (13/15) districts, and cVDPV1 was confirmed among 26% (30) AFP cases. 75% (21) were < 5 years, 73% (20) had zero doses of Oral Polio Vaccine (OPV). The first confirmed case (3%) was from Saadah city, with paralysis onset at the end of January 2020 followed by 5 cases (17%) in March from another four districts, 8 cases (27%) in April, and 13 (43%) up to December 2020 were from the same five districts in addition to 3 (10%) form three new districts. The lab confirmation was received after an average of 126 days (71–196) from sample collection. The isolates differ from the Sabin 1 type by 17- 30 VP1 nucleotides (nt) and were linked to VDPV1 with 13 (nt) divergence that isolated in July 2020 from stool specimens collected before one year from contacts of an inadequate AFP case reported from Sahar district.

Conclusion

The new emerging VDPV1 was retrospectively confirmed after one year of sample collection from Sahar district. Delayed lab confirmation, as well as the response and low immunization profile of children against polio, were the main predisposing factors for cVDPV1 outbreak. This outbreak highlights the need to maintain regular biweekly shipments to referral polio labs in the short-term, and the exploration of other options in the longer-term to enable the Yemen National Lab to fully process national samples itself.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07397-0.

Influenza circulating viruses, positivity rate and risk factors for influenza associated severe acute respiratory infection during 2018/2019 winter season, Yemen

BACKGROUND

The burden of seasonal influenza in conflict counties is exacerbated due to limited resource and collapse of health system. During 2018 /2019 season, two-fold increase in the incidence of influenza was reported in Yemen with 22% case fatality of severe acute respiratory infection (SARI). The aims are to analyze the influenza circulating viruses, positivity rate and risk factors for hospitalizing influenza associated-SARI.

METHODOLOGY

We used a retrospective analytical study based on surveillance data. All reported patients during 2018/2019 season, fulfilling the WHO cases definition for SARI or influenza like illness (ILI), and had laboratory result from the National Laboratory were included. Influenza positivity rate was calculated, all SARI and ILI patients with positive influenza were included for further analysis by univariate and multivariate binary logistic regression. Crude and adjusted Odds ratio (AOR), 95% confidence interval and P-value < 0.05 were used for statistically significant.

RESULTS

Out of 2186 patients enrolled, 768 patients were tested for influenza viruses,: 19% were children < 15 years, 15% were ≥ 65 years, 69% males and 18% had co-morbidity with chronic diseases. Patients with SARI were 37% and 63% were ILI patients. Influenza viruses were detected in 411 (53.5%), 68% were influenza A subtype (H1N1)pdm09, 27% influenza B and 5% was influenza A not subtyped. The influenza positivity was significantly higher in SARI compared to ILI for patients < 15 years (95% vs, 66%, p < 0.001), and patients ≥ 65 years (83% vs. 56%, p < 0.002), respectively. The highest positivity for influenza type A and B reached 44% and 33% for patients ≥ 65 years and < 15 years, respectively. The risk factors for influenza-associated SARI in multivariate analysis included age < 5 [AOR 2.8] and ≥ 65 years old [AOR 3.1] compared to age 5- < 25 years, diabetes [AOR 4.7], heart diseases [AOR 3.1] and chronic respiratory diseases [AOR 5.0].

CONCLUSION

The influenza positivity during 2018/2019 winter season was high in Yemen and varied by age distribution. Influenza subtype A (H1N1) pdm09 was the predominant and co circulated with influenza B. An influenza vaccination program for the risk group is necessary. Strengthening lab capacity to detect respiratory pathogens and further prospective study for more comprehensive picture are recommended.