Rare bacterial outbreak
in the Midwest

Published April 03 2017

In November 2015, a deadly outbreak of a rare bacterial species began in the U.S. Midwest. The affected states included Wisconsin, Illinois and Michigan. The outbreak led to 20 deaths of elderly or immunocompromised persons; it remains unclear whether the bacterial infection alone or a combination of the infection and pre-existing health conditions was the cause of death. The culprit was a little-known bacterial species called Elizabethkingia anophelis.

A group of researchers from Peter Hoyt’s laboratory at Oklahoma State University now are reporting on the transposon genome rearrangements that are unique to the Elizabethkingia strains from the outbreak.

According to the Centers for Disease Control and Prevention, the outbreak was a rare occurrence, as only a few cases of E. anophelis typically are confirmed in the U.S. every year.

From November 2015 to January 2016, 67 cases were reported to the Wisconsin Division of Public Health; of those, 63 were confirmed. With the outbreak spreading across state lines, the CDC began an investigation last year to understand the outbreak better. They found that the median age of the patients infected was 72 years old, and 47 percent were female. The infections presented predominantly in the blood. They resulted in sepsis and were highly resistant to several antibiotics.

To this day, the source of the outbreak remains unknown. There is no evidence to link the outbreak to contamination in health-care products, food, water or patient-to-patient transmission.

Starting research on Elizabethkingia

The genus of Elizabethkingia first was described in 1959 by bacteriologist Elizabeth O. King while she was working at the CDC; the bacteria were named in her honor. Elizabethkingia are Gram-negative bacteria commonly found in soil and water. The strain responsible for the outbreak, E. anophelis, first was isolated in the midgut of the Anopheles gambiae mosquito from the McCarthy Islands in Gambia in 2011. Before that time, only two other species of Elizabethkingia had been proposed based on 16S rRNA sequence similarity studies, E. meningoseptica and E. miricola. In 2011, another species, E. endophytica, was reported in some specimens of sweet corn. All Elizabethkingia strains isolated to date are resistant to many common antibiotics.

The Hoyt lab was interested in Elizabethkingia years before the outbreak. Hoyt explains his department head, John Gustafson, got him interested in these bacteria. At the time, the Gustafson group was isolating bacteria that cause mastitis in dairy cows. The Hoyt lab was interested in trying to separate the different species of Elizabethkingia; it’s still unknown how many species may exist in the genus.

Hoyt says that he found the genomes of Elizabethkingia intriguing. According to him, the bacterial genes effectively move like “liquid;” they are highly mobile and able to rearrange rapidly.

Petri dish wih Elizabethkingia anophelis growing on it IMAGE COURTESY OF PETER HOYT

Studying the outbreak strains

Hoyt explains that he and his colleagues read about the outbreak and knew that the CDC would get involved. Gustafson contacted the CDC and was put in touch with Ainsley Nicholson, a microbiologist, who had been working on sequencing the outbreak strains and looking for underlying genetic clues as to what caused the outbreak. Nicholson provided the Hoyt laboratory with some of the outbreak strains.

Rita Flores, a graduate student in the Hoyt lab, and colleagues identified a homologous double transposon region in a few of the strains from the outbreak. Their data suggested that these DNA rearrangements were recent genetic events. The conserved homologous region was about 63 kilobases in length and was flanked by typical mobile genetic elements.

Further, there was variation in the length of the conserved region depending on the strain. For example, the shortest conserved region was found in the E. anophelis PW2809 strain, while the longest was found in E. anophelis NUHP-1, miricola ATCC and the four strains from the outbreak. Importantly, the location of these transposons in the CDC outbreak strains was different from other strains. The affected genetic location occurs in a gene coding for an A/G-specific adenine glycosylase, which is much like the E. coli MutY that is involved in DNA repair. This genetic change in the outbreak strains could have resulted in aberrant glycolytic function or increased mutagenic potential.

Additionally, Flores and colleagues identified a toxin–antitoxin complex unique to the strains given to them by the CDC. This toxin–antitoxin, along with the disruption in the adenine glycosylase function, could have increased the survival of E. anophelis, possibly underlying the phenotypic changes associated with the outbreak strains.

The aftermath of the outbreak

Hoyt explains that some event, such as altered gene expression or the acquisition of new toxins, enabled the bacteria to mutagenize rapidly. Further, Hoyt notes that Elizabethkingia are essentially “reservoirs of antibiotic resistance” for other bacteria, as most bacteria have the ability readily to take up DNA from other bacteria in their surrounding environment. The relatively ubiquitous presence of Elizabethkingia, coupled with their ability easily to rearrange their genome, provide the first clues regarding how E. anophelis caused the recent outbreak. Using high-throughput sequencing, the CDC was the first to confirm in patient samples that the E. anophelis strain was responsible for the outbreak occurring in the Midwest.

The Hoyt laboratory now is interested in understanding more about the evolutionary mechanisms of the bacteria that allow them to recombine so frequently. By analysing the sequences of the bacteria, the investigators found a high frequency of antibiotic-resistance genes as well as genes involved in creation of mobile genetic elements. These features could afford the bacteria increased opportunities for recombination and may have driven the observed cases from the outbreak.

Flores notes that no cases have been reported since last June and that the outbreak appears to have subsided. Despite these advances in understanding Elizabethkingia, it still is not understood how or where the bacteria were able to infect their immunocompromised hosts. But the work in Hoyt’s and other laboratories is helping researchers better understand how bacteria like Elizabethkingia drive deadly outbreaks.

The researchers will present their results at the 2017 ASBMB Annual Meeting at the 1:15 p.m. poster session on April 23 in McCormick Place in Chicago.

Hailey Gahlon Hailey Gahlon is a Marie Curie postdoctoral research fellow at Imperial College London.