In the wake of H5N1 avian flu detections in wild birds and poultry in South America over the past few months, Ecuador's health ministry yesterday reported the country's first human infection involving H5 avian influenza.

The patient is a 9-year-old girl from Bolivar province, an Andes Mountain area in the central part of the country, according to a ministry statement translated and posted by Avian Flu Diary, an infectious disease news blog.

The report had few details about the case, but it said the girl presumably had contact with birds that carried the virus. So far, investigators haven't found any other human cases.

Her illness marks the world's seventh infection from the circulating H5 clade. The others were from the United Kingdom, the United States, Spain, Vietnam, and China. All involved exposure to sick poultry. Four of the cases were mild, but the ones from Vietnam and China were severe, according to a recent risk assessment from the World Health Organization, which said the overall threat remains low, but the virus bears close watch.

Three H9N2 cases in China

Meanwhile, China confirmed three more H9N2 avian flu cases in different provinces, according to a regular avian flu update from the Hong Kong Centre for Health Protection.

The illness onsets occurred in October and November. The patients include a 58-year-old man from Hunan province, a 5-year-old girl from Gansu province, and a 3-year-old boy from Anhui province.

H9N2 is known to circulate in poultry in parts of Asia, with most human cases reported in China. Infections are typically mild and affect children. The country's most recent cases involved two children, one from Guangdong province and the other from Gansu province, who became ill in August and September, respectively.

A systematic review and meta-analysis of studies published during the first 18 months of the COVID-19 pandemic provides further evidence that antibiotic use far exceeded the prevalence of bacterial co-infection, researchers reported this week in BMC Infectious Diseases.

The review included 85 studies, mostly from China (29) and the United States (16), involving more than 30,000 patients. Of the 70 studies that reported on the prevalence of bacterial co-infection, the meta-analysis showed an overall prevalence of bacterial co-infection of 12%. But among the 20 studies that gave a clear definition of bacterial co-infection, the overall prevalence was only 4%. Meta-analysis of the 52 studies that included data on antibiotic use showed that the overall antibiotic use rate was 60%, and the empiric antibiotic use rate was 62%.

The study authors note that the results are similar to other meta-analyses that have been conducted on antibiotic use and bacterial co-infections in COVID-19 patients, although their results showed a slightly lower rate of antibiotic use. They suggest this could reflect changes in empiric antibiotic use as clinicians gained more experience in managing COVID-19 and more data became available to inform evidence-based practice regarding antibiotic use. 

There is currently insufficient evidence to support the empirical use of antibiotics in most hospitalised patients with COVID-19.

"Our results show that there is currently insufficient evidence to support the use of empirical use of antibiotics in most hospitalised patients with COVID-19, as the overall proportion of bacterial co-infection in these patients is low," they wrote. "Furthermore, as the use of antibiotics in COVID-19 appears to have been largely empirical, it is necessary to identify clinical and laboratory markers and to formulate guidelines to promote more targeted administration of antibiotics in patients admitted to hospital with COVID-19."

The authors say they hope the study can help clinicians "reflect on and understand the initial response to a global pandemic of a novel respiratory virus."

Genomic analysis of extensively drug-resistant (XDR) typhoid isolates in Pakistan revealed numerous XDR variants circulating in the country, a team of Pakistani and US researchers reported this week in the American Journal of Tropical Medicine and Hygiene.

To get a better understanding of the genetic diversity of the sublineage of XDR Salmonella enterica serovar Typhi that emerged in Pakistan's Sindh Province in 2016 and has subsequently spread to other parts of the country, the researchers conducted whole-genome sequencing (WGS) on 58 XDR Salmonella Typhi isolates collected from November 2018 to December 2020.

XDR typhoid is defined as resistant to all recommended antibiotics for typhoid fever, including third-generation cephalosporins and fluoroquinolones. Susceptibility testing showed all isolates were resistant to ampicillin and ceftriaxone, and 54 of 58 were resistant to ciprofloxacin.

WGS showed that all isolates were related to the outbreak strain that emerged in Sindh, that multiple XDR variants exist, and that nearly one third of the isolates had integrated the plasmid containing the extended-spectrum beta-lactamase (ESBL) gene blaCTX-M-15 into the chromosome, which could enable them to acquire additional drug resistance and virulence genes.

"Our results reveal there are many circulating typhoid variants in Pakistan that have lost the IncY plasmid after integrating the ESBL into the chromosome," the study authors wrote. "These could acquire new plasmids to make them resistant to the few antibiotics to which it is susceptible (pan-resistant)."

These could acquire new plasmids to make them resistant to the few antibiotics to which it is susceptible (pan-resistant).

More than 15,000 cases of XDR typhoid have been reported in Pakistan since 2016. XDR strains have also been identified in Southeast Asia and eastern and southern Africa, and have been introduced into the United Kingdom, Canada, and the United States by travelers.

The authors say that, given the continued spread of XDR typhoid and the associated genomic diversity, countries need to take steps to reduce the burden of typhoid, which is transmitted by contaminated food and water and person-to-person contact and tends to spread in areas with poor sanitation. Among the steps they recommend are improving vaccination rates and the quality of drinking water and promoting good hygiene.