News Scan for Apr 18, 2018

News brief

WHO: Pockets of activity remain at end of flu season

Flu is dropping to off-season levels in most of the Northern Hemisphere, except Eastern Europe, according to the latest global flu update from the World Health Organization (WHO).

As has been seen in the last several weeks, circulating influenza strains are almost evenly divided among types A and B, with 52.3% of laboratory specimens typed as influenza A and 47.7% as influenza B. Of the sub-typed influenza A viruses, 62.7% were influenza 2009 H1N1 and 37.3% were influenza H3N2. Of the characterized B viruses, 91% belonged to the Yamagata lineage and 9% to the Victoria lineage.

Flu declined in the United States, Canada, and Mexico. North Africa, Western Asia, and Central Asia all described waning flu, except for activity in Egypt, Qatar, and Kazakhstan.

The WHO said flu was still circulating widely throughout much of Europe, and parts of Eastern Europe, including Latvia and Russia, continued to report high flu activity.
Apr 16 WHO update

Lassa outbreaks continue in Nigeria, Liberia

The Nigerian Centre for Disease Control (NCDC) confirmed five new cases of Lassa fever last week, including three deaths. This is the lowest weekly case count the NCDC has reported since the outbreak began in January.

From Jan 1 to Apr 15, the NCDC has confirmed 413 cases of Lassa fever, including 105 deaths. The case-fatality rate is 25.4%. No new healthcare workers have been infected in the last week, keeping the total number of healthcare workers who've contracted Lassa at 27.

The NCDC said there are only eight patients currently being treated in centers throughout the country, the lowest number since the outbreak began. Lassa fever is endemic in Nigeria, and is transmitted mostly by rats. Human transmission can occur when a person comes into contact with infected bodily fluids.

Earlier this week, Liberia also reported 25 new suspected cases of Lassa fever, bringing the country's total since January to 67 suspected cases, including 19 deaths (case-fatality rate, 28.4%), according to a weekly WHO bulletin.
Apr 15 NCDC report
Apr 13 WHO bulletin

Stewardship / Resistance Scan for Apr 18, 2018

News brief

New colistin resistance gene identified in Chinese poultry

Chinese scientists have discovered another colistin resistance gene in bacteria isolated from chickens, according to a study yesterday in the Journal of Antimicrobial Chemotherapy.

The plasmid-mediated gene was detected among 183 Klebsiella pneumoniae isolates collected from 2010 to 2015 from chickens in 13 Chinese provinces. Of the 10 colistin-resistant isolates detected, polymerase chain reaction (PCR) screening identified the MCR-1 gene in seven; the other three were negative for known colistin resistance genes. Whole-genome sequencing of one of the isolates identified a novel colistin resistance gene, dubbed MCR-7.1, in an Inc12-type plasmid that also harbored the blaCTX-M-55 beta-lactam resistance gene. Subsequent PCR screening showed that the other two K pneumoniae isolates also carried the MCR-7.1 gene. Conjugation experiments showed that the plasmid can successfully be transferred from K pneumoniae to E coli.

The researchers report that the amino acid sequence of MCR-7.1 shares a 70% similarity with MCR-3, and that the gene may have originated from Aeromonas species. They recommend screening bacteria in animals, humans, and the environment to understand dissemination of the gene throughout the world.

Before this discovery, various research groups had described MCR-1 though MCR-6 genes.
Apr 17 J Antimicrob Chemother abstract

Chinese study finds low MCR-1 prevalence in clinical isolates

In another study yesterday in the Journal of Antimicrobial Chemotherapy, a separate group of Chinese researchers report that the prevalence of MCR-1 among clinical isolates of E coli and K pneumoniae is low, but that MCR-1–positive E coli strains were highly resistant to other antibiotics.

The researchers from Peking University First Hospital and China Agricultural University analyzed 6,424 clinical E coli and K pneumoniae isolates collected from patients in Chinese hospitals from 2007 through 2016. Overall, 34 E coli isolates and 5 K pneumoniae isolates were positive for MCR-1. Multilocus sequence typing revealed high clonal diversity, identifying three different sequence types (STs) among the K pneumoniae isolates, and 28 distinct STs among the E coli isolates.

All the MCR-1–positive isolates were resistant to colistin, and MCR-1–positive E coli also displayed high levels of resistance to tetracycline, ciprofloxacin, and some cephalosporins. In addition, the researchers noted extremely significant difference in the rates of resistance to piperacillin, amikacin, nitrofurantoin, and fosfomycin between MCR-1–negative E coli and MCR-1–positive E coli. This finding, they suggest, indicates that infections caused by MCR-1–postive E coli strains should be treated differently than those caused by MCR-1–negative E coli.

All but six of the MCR-1–positive isolates (84.6%) were also extended-spectrum beta-lactamase producers, and 36 of the 39 (92.3%) were multidrug-resistant.
Apr 17 J Antimicrob Chemother abstract

High level of Shiga toxin-producing E coli found in Iranian dairy products

Iranian researchers report a high prevalence of Shiga toxin–producing Escherichia coli (STEC) with high levels of antibiotic resistance in raw milk and traditional dairy products.

In the study, published in Antimicrobial Resistance and Infection Control, the researchers collected 600 raw milk and traditional dairy product samples from producers in Isfahan province from March 2015 to March 2016, then cultured all the samples and isolated E coli strains. PCR was used to identify virulence factors, O-serogroups, and antibiotic resistance genes, and antibiotic resistance patterns were determined by disk diffusion.

Of the 600 samples tested, 181 (30.16%) were positive for E coli strains, with cheese (80%) and raw buffalo milk (50%) having the highest prevalence. Sixty-four of the E coli isolates were determined to be STEC strains, with O157 (43.75%) and O26 (37.5%) the most frequently identified serogroups.

Stx, eae, and ehly were the most commonly identified virulence factors in the STEC strains, and Aac(3)-IV, CITM, and tetA were the most commonly detected resistance genes. STEC strains harbored the highest prevalence of resistance against ampicillin (100%), gentamicin (100%), and tetracyclines (96.87%), and all of the STEC strains were resistant to at least one antibiotic. In addition, 43.75% were resistant to seven or more antibiotics.

The authors suggest that Iranian ranchers' use of their hands and traditional milking equipment could partially explain the high prevalence of E coli and STEC strains, as could keeping raw milk samples at temperatures that allow bacteria to proliferate and survive and using unpasteurized milk for production of dairy products. They also cite illegal and inaccurate use of antibiotics in veterinary medicine as the main reason for the high prevalence of antibiotic resistance in the STEC strains.
Apr 16 Antimicrob Resist Infect Control study