News Scan for Jul 09, 2018

News brief

Study of H5N1 avian flu genetic changes in Egypt finds potential hot spots

A new analysis of a decade's worth of highly pathogenic H5N1 avian flu virus genetic sequences collected from poultry and wild birds in Egypt found 39 distinct substitutions with the possible ability to increase the pandemic potential of the virus, with spatial clustering that focused on two governorates—Alexandria and Beheira—that are located in the northwestern Nile Delta.

Egypt is the country with by far the most human H5N1 infections, and aside from commercial poultry farms, about 4 million to 5 million families raise backyard poultry. The study is the first spatial analysis of key genetic substitutions (KS)—changes that alter the host specificity, virulence replication, transmissibility, or drug susceptibility that make the virus a greater threat to humans. The US-based group published its findings Jul 6 in BMC Infectious Diseases.

The team looked at sequences from 925 viral samples from poultry and wild birds collected from 2005 to 2015 that were in the Influenza Virus Sequence Database hosted by the national Center for Biotechnology Information. They geocoded the isolates and mapped them to identify clusters where rates of KS were high.

Of the 39 distinct KS, 17 had not be previously reported in Egypt. Most involved the surface hemagglutinin and neuraminidase proteins, as well as the interior nonstructural 1 protein. The most frequent types were linked to increased viral binding to mammalian cells and virulence. Samples with high KS detection rates clustered in the two northwestern Nile Delta governorates, which appeared to be hot spots.

The team said the report serves as a helpful baseline for distribution and clustering of KS in Egypt, adding that the high detection rates in the cluster areas raise concerns about the possibility of a pandemic strain developing in the region. "Better geographic data and improved genetic surveillance are necessary to properly evaluate and monitor this potential threat to global public health," they wrote.
Jul 6 BMC Infect Dis study

Experiments track pandemic potential of recent H3N2v viruses

Lab tests and animal studies to assess the threat from variant H3N2 (H3N2v) viruses isolated from people from 2011 through 2016 found that they grow well in human epithelial airway cells, but vary in their ability to replicate throughout the respiratory tract and transmit among ferrets, researchers from the US Centers for Disease Control and Prevention reported in the July issue of the Journal of Virology.

A large outbreak of H3N2v occurred in 2011 and 2012 in the United States, mostly in children who were exposed to pigs at county fairs. Though cases have declined since then, scientists continue to monitor the threat. So far this summer, one H3N2v case has been reported, involving an Indiana resident who was exposed to pigs at a county fair.

The researchers in today's study said that, because of the continuous evolution and cocirculation of diverse H3N2 viruses in US swine, it's challenging to predict which ones may transmit to humans. To help understand the pandemic potential of the viruses, the team examined H3N2v replication in cell and animals studies and tested how well the four different samples transmitted through the airborne route in ferrets.

All four viruses showed similar or enhanced replication in human bronchial cells. In experimentally infected mice, the H3N2v viruses were mildly virulent and replicated with different degrees of efficiency. Ferrets infected with the virus had moderate disease with comparable upper airway involvement, but only two of the four viruses replicated in the lower respiratory tract.

In co-housed ferrets, transmission was efficient, but recently isolated H3N2v varied considerably in their ability to spread by respiratory droplets.

The team concluded that efficient droplet transmission shown by some of the viruses, combined with low population immunity against the virus in young children and older adults, underscores the pandemic potential of H3N2v. "Extensive surveillance and risk assessment of H3N2v viruses should continue to be an essential component of our pandemic preparedness strategy," they wrote.
Jul J Virol abstract
Jul 2 CIDRAP News scan on most recent H3N2v case

Stewardship / Resistance Scan for Jul 09, 2018

News brief

Israeli program sees CRE rates cut in half during 7-year period

Israeli long-term care facilities (LTCFs) saw a 50% reduction in carbapenem-resistant Enterobacteriaceae (CRE) during a 7-year national intervention program, according to a study today in Clinical Infectious Diseases.

The Israeli National Center for Infection Control (NCIC) led the program, which included implementation of population-tailored contact precautions, and early detection of carriers. NCIC started the program and enhanced surveillance in 2008, 2 years after the introduction of CRE into Israeli hospitals.

The program targeted Israel's 15 post-acute care hospitals (PACHs), 15 skilled nursing facilities (SNFs), and 300 nursing homes (NHs). Within 3 years of launching the program CRE acquisition rates dropped steadily, reaching 50% of baseline values by 2015. The incidence of CRE acquisition declined between 2009 and 2015 in all facility types, as expressed by an incidence rate ratio (IRR) of less than 1 per year (PACHs, 0.90; SNFs, 0.87; NHs, 0.93).

The number of these LTCFs reporting 5 or more CRE acquisitions annually (defined by the authors as an outbreak) decreased from 35 to 11 from 2012 to 2015, as well.

"We demonstrated that a comprehensive, multimodal, nationwide strategy effort focusing on improved infection control, early carrier detection and contact isolation succeeded in reducing CRE incidence in LTCFs by over 50%, and almost eliminating CRE prevalence 8 years into implementation," the authors concluded.
Jul 9 Clin Infect Dis study

Study: Many neonatal infections have no known cause

Late last week The Lancet published the findings of the Aetiology of Neonatal Infection in South Asia (ANISA) study, which surveyed neonatal possible serious bacterial infections (pSBIs) among pregnant women in India, Bangladesh, and Pakistan, and noted a possible antibiotic stewardship connection.

The prospective study included 6,022 pSBI episodes among 63,114 babies, identified by community health care workers from 2011 to 2014 between days 0 through 59 post-birth. The workers found that 28% of episodes (16% bacterial and 12% viral) could be attributed to a known pathogen. Mean incidence of bacterial infections was 13.2 (95% credible interval [CrI], 11.2-15.6) per 1,000 livebirths and of viral infections was 10.1 (9.4-11.6) per 1,000 livebirths.

According to the study, among fatal infections, causes were attributed in 46% of pSBI episodes, among which 92% were bacterial. The vast majority (83%) of 102 blood culture isolates were susceptible to penicillin, ampicillin, gentamicin, or a combination of these drugs.

Respiratory syncytial virus (RSV) was the most commonly identified pathogen, represented in 5.4 per 1,000 livebirths.

The lack of a cause in a high proportion of cases suggests that pSBI episodes might not be due to bacterial infection, and subsequently, antibiotics may be overused in this patient population.

In an accompanying commentary, Anna Seale, MD, and Ramesh Agarwal, PhD, write, "Of 6,022 pSBI episodes, only 16% had attributed bacterial causes, and 102 (2%) of 4859 tested blood samples had clinically significant pathogens isolated by culture." Seal and Argawal said this information should shape antibiotic use among this patient population.
Jul 6 Lancet study
Jul 6 Lancet commentary