The leading infectious cause of death in children worldwide is lower acute respiratory infection (LARI), particularly pneumonia. We enrolled a total of 538 acute respiratory infection (ARI) cases according to WHO criteria and age-sex matched 514 controls in the Forcibly Displaced Myanmar National (FDMN) refugee camps in Cox’s Bazar, Bangladesh, between June 2018 and March 2020 to investigate the role of bacteria, viruses, and their co-infection patterns and observe Streptococcus pneumoniae (S. pneumoniae) serotype distribution. According to the etiological findings, children ≤5 years of age have a higher bacterial positivity (90%) and viral positivity (34%) in nasopharyngeal samples (NPS) compared to those >5 years of age, in both ARI cases as well as for the control group. Among the bacteria, S. pneumoniae was predominant in both cases and controls (85% and 88%). Adenovirus (ADV)(34), influenza virus A and B (IFV-A, B)(32,23), and respiratory syncytial virus (RSV)(26) were detected as the highest number among the viruses tested for the ARI cases. The total number of viruses was also found higher in ≤5 years of age group. Within this group, positive correlation was observed between bacteria and viruses but negative correlation was observed between bacteria. Both single and co-infection for viruses were found higher in the case group than the control group. However, co-infection was significantly high for Streptococcus aureus (S. aureus) and Haemophilus influenzae b (H. influenza b) (p<0.05). Additionally, semi-quantitative bacterial and viral load was found higher for the ARI cases over control considering Cycle threshold (Ct)≤30. Pathogen identification from blood specimens was higher by qRT-PCR than blood culture (16% vs 5%, p<0.05). In the S. pneumoniae serotype distribution, the predominant serotypes in ARI cases were 23F, 19A, 16F, 35B, 15A, 20 and 10F, while 11A, 10A, 34, 35A and 13 serotypes were predominant in the control group. Pathogen correlation analysis showed RSV positively correlated with human metapneumovirus (HMPV), S. aureus and H. influenza b while S. pneumoniae was negatively correlated with other pathogens in ≤5 years age group of ARI cases. However, in >5 years age group, S. aureus and H. influenza b were positively correlated with IFVs, and S. pneumoniae was positively correlated with HMPV and ADV. Logistic regression data for viruses suggested among the respondents in cases were about 4 times more likely to be RSV positive than the control. Serotype distribution showed 30% for PCV10 serotypes, 41% for PCV13 and 59% for other serotypes. Also, among the 40 serotypes of S. pneumoniae tested, the serotypes 22F, Sg24, 9V, 38, 8, and 1 showed strong positive correlation with viruses in the case group whereas in the control group, it was predominant for serotypes 14, 38, 17F and 39 ARI cases were prevalent mostly in monsoon, post-monsoon, and winter periods, and peaked in September and October. Overall these region-specific etiological data and findings, particularly for crisis settings representing the FDMNs in Cox’s Bazar, Bangladesh, is crucial for disease management and disease prevention control as well as immunization strategies more generally in humanitarian crisis settings.

Introduction Forcibly Displaced Myanmar Nationals fled into Cox’s Bazar, Bangladesh due to internal conflict. Considering the public health situation, a surveillance network was established to identify the enteric pathogens and early detection of cholera epidemics. Purpose of this manuscript is to report the clinical, epidemiological determinants of cholera and other enteric pathogens among hospitalized diarrhoeal patients from FDMNs and host community. Methodology A total of 11 sentinel surveillance sites were established around the camps in Ukhia and Teknaf Upazila, Cox’s Bazar. Rapid diagnostic testing was conducted for immediate detection of cholera cases. Stool samples were transferred to the icddr,b laboratory for culture. Result A total of 8134 participants with diarrhea were enrolled from 2017- 2019: 4881 were FDMNs and 3253 from the Bangladeshi host community. Among the FDMNs, the proportion of V. cholerae 0.7%, ETEC 4.9% and Shigella 1.5%. The distributions from host community were 1.2% V. cholerae, 1.8% ETEC and 1.1% Shigella. Similar risk factors have been identified for the diarrhoeal pathogens for both communities. Conclusion This surveillance helped to monitor the situation of diarrheal diseases including cholera in refugee camps as well as in the neighboring host community. These findings lead policy makers to take immediate preventive measures.

Ongoing diarrheal disease surveillance throughout Bangladesh over the last decade has revealed seasonal localised cholera outbreaks in Cox’s Bazar, where both Bangladeshi Nationals and Forcibly Displaced Myanmar Nationals (FDMNs) reside in densely populated settlements. FDMNs were recently targeted for the largest cholera vaccination campaign in decades. We aimed to infer the epidemic risk of circulating Vibrio cholerae strains by determining if isolates linked to the ongoing global cholera pandemic (“7PET” lineage) were responsible for outbreaks in Cox’s Bazar. We found two sublineages of 7PET in this setting during the study period; one with global distribution, and a second lineage restricted to Asia and the Middle East. These subclades were associated with different disease patterns that could be partially explained by genomic differences. Here we show that as the pandemic V. cholerae lineage circulates in this vulnerable population, without a vaccine intervention, the risk of an epidemic was very high.

Background: Over 700,000 Myanmar nationals known as the ‘Rohingyas’ fled into Cox’s Bazar, Bangladesh, in late 2017. Due to this huge displacement into unhygienic areas, these people became vulnerable to communicable diseases including cholera. Assessing the risk, the Government of Bangladesh (GoB), with the help of the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B) and other international partners, decided to take preventive measures, one of which is the execution of oral cholera vaccination (OCV) campaigns. This paper describes the implementation and delivery of OCV campaigns during humanitarian crises in Bangladesh. Methods: Seven rounds of OCV campaigns were conducted between October 2017 and December 2021. The OCV campaigns were conducted by applying different strategies. Results: Approximately 900,000 Rohingya Myanmar nationals (RMNs) and the host population (amounting to 528,297) received OCV across seven campaigns. In total, 4,661,187 doses of OCVs were administered, which included 765,499 doses for RMNs, and 895,688 doses for the host community. The vaccine was well accepted, and as a result, a high level of coverage was achieved, ranging from 87% to 108% in different campaigns. Conclusions: After successful pre-emptive campaigns in Cox’s Bazar humanitarian camps, no cholera outbreaks were detected either in the RMN or host communities.

Over the last decade, the influx of Forcibly Displaced Myanmar Nationals (FDMNs) into Bangladesh has increased the population of Cox’s Bazar. Due to the already high population density coupled with poor living conditions, FDMNs and the host population of Bangladeshi Nationals (BGDNs) were at heightened risk of diarrhoeal disease outbreaks. Due to this, a nationwide sentinel surveillance programme was established, which revealed that there were seasonal localised sporadic cholera outbreaks in Cox’s Bazar. In this study, we aimed to infer the epidemic risk of the Vibrio cholerae strains circulating in the FDMN and BGDN populations, by determining if isolates linked to the current cholera pandemic were responsible for these outbreaks. Further, to better understand the dynamics of cholera before and during the mass oral cholera vaccination campaign conducted in Cox’s Bazar – the largest in the last decades – we also wanted to understand the links between these circulating strains and the current radiation of lineages causing disease in Haiti and Yemen – places in which reactive vaccination campaigns were conducted in response to outbreaks following humanitarian crises. To do this, we sequenced 223 V. cholerae isolates obtained from stool collected from ten intra-district surveillance sites in Cox’s Bazar, sampling both the FDMN and BGDN subpopulations over a period spanning the pre-and post-vaccination campaign (2014–2019). Phylogenetic analysis of these genomes showed that all isolates belonged to the epidemic “7PET” lineage – responsible for the current cholera pandemic – branching alongside V. cholerae that were circulating in Dhaka and Kolkata between 2014 and 2018. Two distinct sublineages of V. cholerae were present in Cox’s Bazar during the study period; one lineage (PG 1.3) that had radiated globally, and another lineage (PG 1.5) that was restricted to Asia and the Middle East. PG 1.3 was associated with a shorter duration of diarrhoea and lower relative risk of rice watery stool compared to PG 1.5. Given the nature and diversity of the V. cholerae isolated from the BGDN and FDMN subpopulations in Cox’s Bazar, without a vaccine intervention, the risk of local or widespread epidemics or even a pandemic was very high.