Phenotypic and genotypic changes over time and across facilities of serial colonizing and infecting Escherichia coli isolates recovered from injured service members

Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in critical care patients

Colonization with multidrug-resistant Escherichia coli strains causes a substantial health burden in hospitalized patients. We performed a longitudinal genomics study to investigate the colonization of resistant E. coli strains in critically ill patients and to identify evolutionary changes and strain replacement events within patients. Patients were admitted to the intensive care unit and hematology wards at a major hospital in Lebanon. Perianal swabs were collected from participants on admission and during hospitalization, which were screened for extended-spectrum beta-lactamases and carbapenem-resistant Enterobacterales. We performed whole-genome sequencing and analysis on E. coli strains isolated from patients at multiple time points. The E. coli isolates were genetically diverse, with 11 sequence types (STs) identified among 22 isolates sequenced. Five patients were colonized by E. coli sequence type 131 (ST131)-encoding CTX-M-27, an emerging clone not previously observed in clinical samples from Lebanon. Among the eight patients whose resident E. coli strains were tracked over time, five harbored the same E. coli strain with relatively few mutations over the 5 to 10 days of hospitalization. The other three patients were colonized by different E. coli strains over time. Our study provides evidence of strain diversity within patients during their hospitalization. While strains varied in their antimicrobial resistance profiles, the number of resistance genes did not increase over time. We also show that ST131-encoding CTX-M-27, which appears to be emerging as a globally important multidrug-resistant E. coli strain, is also prevalent among critical care patients and deserves further monitoring.IMPORTANCEUnderstanding the evolution of bacteria over time in hospitalized patients is of utmost significance in the field of infectious diseases. While numerous studies have surveyed genetic diversity and resistance mechanisms in nosocomial infections, time series of within-patient dynamics are rare, and high-income countries are over-represented, leaving low- and middle-income countries understudied. Our study aims to bridge these research gaps by conducting a longitudinal survey of critically ill patients in Lebanon. This allowed us to track Escherichia coli evolution and strain replacements within individual patients over extended periods. Through whole-genome sequencing, we found extensive strain diversity, including the first evidence of the emerging E. coli sequence type 131 clone encoding the CTX-M-27 beta-lactamase in a clinical sample from Lebanon, as well as likely strain replacement events during hospitalization.

Multidrug-Resistant and Virulent Organisms Trauma Infections: Trauma Infectious Disease Outcomes Study Initiative

INTRODUCTION

During the wars in Iraq and Afghanistan, increased incidence of multidrug-resistant (MDR) organisms, as well as polymicrobial wounds and infections, complicated the management of combat trauma-related infections. Multidrug resistance and wound microbiology are a research focus of the Trauma Infectious Disease Outcomes Study (TIDOS), an Infectious Disease Clinical Research Program, Uniformed Services University, research protocol. To conduct comprehensive microbiological research with the goal of improving the understanding of the complicated etiology of wound infections, the TIDOS MDR and Virulent Organisms Trauma Infections Initiative (MDR/VO Initiative) was established as a collaborative effort with the Brooke Army Medical Center, Naval Medical Research Center, U.S. Army Institute of Surgical Research, and Walter Reed Army Institute of Research. We provide a review of the TIDOS MDR/VO Initiative and summarize published findings.

METHODS

Antagonism and biofilm formation of commonly isolated wound bacteria (e.g., ESKAPE pathogens-Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), antimicrobial susceptibility patterns, and clinical outcomes are being examined. Isolates collected from admission surveillance swabs, as part of infection control policy, and clinical infection workups were retained in the TIDOS Microbiological Repository and associated clinical data in the TIDOS database.

RESULTS

Over the TIDOS study period (June 2009 to December 2014), more than 8,300 colonizing and infecting isolates were collected from military personnel injured with nearly one-third of isolates classified as MDR. At admission to participating U.S. military hospitals, 12% of wounded warriors were colonized with MDR Gram-negative bacilli. Furthermore, 27% of 913 combat casualties with ≥1 infection during their trauma hospitalization had MDR Gram-negative bacterial infections. Among 335 confirmed combat-related extremity wound infections (2009-2012), 61% were polymicrobial and comprised various combinations of Gram-negative and Gram-positive bacteria, yeast, fungi, and anaerobes. Escherichia coli was the most common Gram-negative bacilli isolated from clinical workups, as well as the most common colonizing MDR secondary to extended-spectrum β-lactamase resistance. Assessment of 479 E. coli isolates collected from wounded warriors found 188 pulsed-field types (PFTs) from colonizing isolates and 54 PFTs from infecting isolates without significant overlap across combat theaters, military hospitals, and study years. A minority of patients with colonizing E. coli isolates developed subsequent infections with the same E. coli strain. Enterococcus spp. were most commonly isolated from polymicrobial wound infections (53% of 204 polymicrobial cultures). Patients with Enterococcus infections were severely injured with a high proportion of lower extremity amputations and genitourinary injuries. Approximately 65% of polymicrobial Enterococcus infections had other ESKAPE organisms isolated. As biofilms have been suggested as a cause of delayed wound healing, wound infections with persistent recovery of bacteria (isolates of same organism collected ≥14 days apart) and nonrecurrent bacterial isolates were assessed. Biofilm production was significantly associated with recurrent bacteria isolation (97% vs. 59% with nonrecurrent isolates; P < 0.001); however, further analysis is needed to confirm biofilm formation as a predictor of persistent wound infections.

CONCLUSIONS

The TIDOS MDR/VO Initiative provides comprehensive and detailed data of major microbial threats associated with combat-related wound infections to further the understanding of wound etiology and potentially identify infectious disease countermeasures, which may lead to improvements in combat casualty care.

Clinical Characteristics and Resistance Patterns of Pseudomonas aeruginosa Isolated From Combat Casualties

INTRODUCTION

Multidrug-resistant (MDR) Gram-negative infections complicate care of combat casualties. We describe the clinical characteristics, resistance patterns, and outcomes of Pseudomonas aeruginosa infections in combat casualties.

METHODS

Combat casualties included in the Trauma Infectious Disease Outcomes Study with infections with and without P. aeruginosa isolation during initial hospitalization were compared. Pseudomonas aeruginosa from initial wound, blood, and serial isolates (≥7 days from previous isolate) collected from June 2009 through February 2014 was subjected to antimicrobial susceptibility testing, pulsed-field gel electrophoresis, and whole genome sequencing for assessing clonality. Multidrug resistance was determined using the CDC National Healthcare Safety Network definition.

RESULTS

Of 829 combat casualties with infections diagnosed during initial hospitalization, 143 (17%) had P. aeruginosa isolated. Those with P. aeruginosa were more severely injured (median Injury Severity Score 33 [interquartile range (IQR) 27-45] vs 30 [IQR 18.5-42]; P < .001), had longer hospitalizations (median 58.5 [IQR 43-95] vs 38 [IQR 26-56] days; P < .001), and higher mortality (6.9% vs 1.5%; P < .001) than those with other organisms. Thirty-nine patients had serial P. aeruginosa isolation (median 2 subsequent isolates; IQR: 1-5), with decreasing antimicrobial susceptibility. Ten percent of P. aeruginosa isolates were MDR, associated with prior exposure to antipseudomonal antibiotics (P = .002), with amikacin and colistin remaining the most effective antimicrobials. Novel antimicrobials targeting MDR Gram-negative organisms were also examined, and 100% of the MDR P. aeruginosa isolates were resistant to imipenem/relabactam, while ceftazidime/avibactam and ceftolozane/tazobactam were active against 35% and 56% of the isolates, respectively. We identified two previously unrecognized P. aeruginosa outbreaks involving 13 patients.

CONCLUSIONS

Pseudomonas aeruginosa continues to be a major cause of morbidity, affecting severely injured combat casualties, with emergent antimicrobial resistance upon serial isolation. Among MDR P. aeruginosa, active antimicrobials remain the oldest and most toxic. Despite ongoing efforts, outbreaks are still noted, reinforcing the crucial role of antimicrobial stewardship and infection control.

Emerging Infectious Diseases and Antimicrobial Resistance (EIDAR)

Introduction

The Infectious Disease Clinical Research Program’s (IDCRP) Emerging Infectious Diseases and Antimicrobial Resistance (EIDAR) Research Area is a Department of Defense (DoD) clinical research capability that is responsive and adaptive to emerging infectious disease (EID) threats to US military readiness. Among active-duty and other Military Health System (MHS) beneficiaries, EIDAR research is largely focused on evaluating the incidence, risk factors, and acute- and long-term health effects of military-relevant EIDs, especially those caused by high-consequence pathogens or are responsible for outbreaks among US military populations. The EIDAR efforts also address Force Health Protection concerns associated with antimicrobial resistance and antimicrobial stewardship practices within the MHS.

Methods

The EIDAR studies utilize the approach of: (1) Preparing for emergent conditions to systematically collect clinical specimens and data and conduct clinical trials to assist the military with a scientifically appropriate response; and (2) Evaluating burden of emergent military-relevant infectious diseases and assessing risks for exposure and development of post-infectious complications and overall impact on military readiness.

Results

In response to the Ebola virus epidemic in West Africa, the IDCRP partnered with the National Institutes of Health in developing a multicenter, randomized safety and efficacy study of investigational therapeutics in Ebola patients. Subsequently, the EIDAR team developed a protocol to serve as a contingency plan (EpICC-EID) to allow clinical research activities to occur during future outbreaks of viral hemorrhagic fever and severe acute respiratory infections among MHS patients. The EIDAR portfolio recently expanded to include studies to understand exposure risks and impact on military readiness for a diversity of EIDs, such as seroincidence of non-Lyme disease borreliosis and Coccidioides fungal infections among high-risk military populations. The team also launched a new prospective study in response to the recent Zika epidemic to conduct surveillance for Zika and other related viruses among MHS beneficiaries in Puerto Rico. Another new study will prospectively follow U.S. Marines via an online health assessment survey to assess long-term health effects following the largest DoD Shiga Toxin-Producing Escherichia coli outbreak at the U.S. Marine Corps Recruit Depot-San Diego. In cooperation with the Trauma-Related Infections Research Area, the EIDAR Research Area is also involved with the Multidrug-Resistant and Virulent Organisms Trauma Infections Initiative, which is a collaborative effort across DoD laboratories to characterize bacterial and fungal isolates infecting combat-related extremity wounds and link lab findings to clinical outcomes. Furthermore, the EIDAR team has developed an Antimicrobial Resistance and Stewardship Collaborative Clinical Research Consortium, comprised of Infectious Disease and Pharmacy specialists.

Conclusions

The EIDAR Research Area is responsive to military-relevant infectious disease threats that are also frequently global public health concerns. Several new EIDAR efforts are underway that will provide Combatant Command Surgeons, Infectious Diseases Service Chiefs, and other Force Health Protection stakeholders with epidemiological information to mitigate the impact of EIDs and antimicrobial resistance on the health of U.S. military service members and their dependents.

On the Etiological Relevance of Escherichia coli and Staphylococcus aureus in Superficial and Deep Infections - A Hypothesis-Forming, Retrospective Assessment

Introduction

Escherichia coli and Staphylococcus aureus are important causes of severe diseases like blood stream infections. This study comparatively assessed potential differences in their impact on disease severity in local and systemic infections.

Methods

Over a 5-year interval, patients in whom either E. coli or S. aureus was detected in superficial or primary sterile compartments were assessed for the primary endpoint death during hospital stay and the secondary endpoints duration of hospital stay and infectious disease as the main diagnosis.

Results

Significance was achieved for the impacts as follows: Superficial infection with S. aureus was associated with an odds ratio of 0.27 regarding the risk of death and of 1.42 regarding infectious disease as main diagnosis. Superficial infection with E. coli was associated with a reduced duration of hospital stay by –2.46 days and a reduced odds ratio of infectious diseases as main diagnosis of 0.04. The hospital stay of patients with E. coli was increased due to third-generation cephalosporin and ciprofloxacin resistance, and in the case of patients with S. aureus due to tetracycline and fusidic acid resistance.

Conclusions

Reduced disease severity of superficial infections due to both E. coli and S. aureus and resistance-driven prolonged stays in hospital were confirmed, while other outcome parameters were comparable.

High acquisition rate of extended-spectrum β-lactamase-producing Enterobacteriaceae among French military personnel on mission abroad, without evidence of inter-individual transmission

OBJECTIVES

Acquisition of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) by Europeans travelling individually in high-endemicity countries is common. However, how the different ESBL-E strains circulate in groups of travellers has not been studied. We investigated ESBL-E transmission within several groups of French military personnel serving overseas for 4-6 months.

METHODS

We conducted a prospective study among French military personnel assigned to Afghanistan, French Guiana or Côte d'Ivoire for 4-6 months. Faecal samples provided by volunteers before leaving and after returning were screened for ESBL-E isolates. ESBL Escherichia coli from each military group was characterized by repetitive element palindromic polymerase chain reaction (rep-PCR) fingerprinting followed, in the Afghanistan group, by whole-genome sequencing (WGS) if similarity was ≥97%.

RESULTS

Among the 189 volunteers whose samples were negative before departure, 72 (38%) were positive after return. The highest acquisition rates were observed in the Afghanistan (29/33, 88%) and Côte d'Ivoire (39/80, 49%) groups. Acquisition rates on return from French Guiana were much lower (4/76, 5%). WGS of the 20 strains from the Afghanistan group that clustered by rep-PCR identified differences in sequence type, serotype, resistance genes and plasmid replicons. Moreover, single-nucleotide polymorphism (SNP) differences across acquired strains from a given cluster ranged from 30 to 3641, suggesting absence of direct transmission.

CONCLUSIONS

ESBL-E. coli acquisition was common among military personnel posted overseas. Many strains clustered by rep-PCR but differed by WGS and SNP analysis, suggesting acquisition from common external sources rather than direct person-to-person transmission.

Early Infections Complicating the Care of Combat Casualties from Iraq and Afghanistan

BACKGROUND

During the conflicts in Iraq and Afghanistan, more than 52,000 U.S. military members were wounded in action. The battlefield mortality rate was lower than in past conflicts, however, those surviving often had complex soft tissue and bone injuries requiring multiple surgeries. This report describes the rates, types, and risks of infections complicating the care of combat casualties.

PATIENTS AND METHODS

Infection and microbiology data obtained from the Trauma Infectious Disease Outcomes Study (TIDOS), a prospective observational study of infections complicating deployment-related injuries, were used to determine the proportion of infection, types, and associated organisms. Injury and surgical information were collected from the Department of Defense Trauma Registry. Multivariable Cox proportional hazards and logistic regression models were used to evaluate potential factors associated with infection.

RESULTS

From 2009-2012, 1,807 combat casualties were evacuated to U.S. TIDOS-participating hospitals. Among the 1,807 patients, the proportion of overall infections from time of injury through initial U.S. hospitalization was 34% with half being skin, soft tissue, or bone infections. Infected wounds most commonly grew Enterococcus faecium, Pseudomonas aeruginosa, Acinetobacter spp. or Escherichia coli. In the multivariable model, amputation, blood transfusions, intensive care unit admission, injury severity scores, mechanical ventilation, and mechanism of injury were associated with risk of infection.

CONCLUSIONS

One-third of combat casualties from Iraq and Afghanistan develop infections during their initial hospitalization. Amputations, blood transfusions, and overall injury severity are associated with risk of infection, whereas more easily modifiable factors such as early operative intervention or antibiotic administration are not.

Low Prevalence of carbapenem-resistant Enterobacteriaceae among wounded military personnel

Multidrug-resistant organisms (MDROs) are a global health problem that affect both civilian and military populations. Among wounded warriors, MDROs further complicate the care of trauma-related infections, resulting in extended duration of hospitalization, as well as increased morbidity and mortality. During the wars in Iraq and Afghanistan, extended spectrum β-lactamase-producing Enterobacteriaceae were frequently isolated from wounded warriors. The potential emergence of difficult-to-treat carbapenem-resistant Enterobacteriaceae represented a serious challenge for clinicians. We examined carbapenem-resistant Enterobacteriaceae prevalence among wounded military personnel over a 6-year period (2009-2015). Among 4090 Enterobacteriaceae isolates collected, 16 (0.4%) were carbapenem-resistant, of which the majority was Enterobacter aerogenes (44%) followed by Klebsiella pneumoniae (37%), and Escherichia coli (19%). Five isolates (31%) collected from 2 patients were carbapenemase-producers with one associated with an infection. All 5 carbapenemase-producing isolates were resistant to all tested carbapenems and each carried one carbapenemase gene (4 with blaKPC-3 and 1 with blaNDM-1). Overall, although a large number of Enterobacteriaceae isolates were collected, only a small proportion was carbapenem-resistant and data indicate a lack of a cluster. Due to these limited numbers, it is difficult to make any conclusions regarding the association between carbapenem resistance, antibiotic exposure, and clinical outcomes.

Resistance patterns and clinical significance of Candida colonization and infection in combat-related injured patients from iraq and afghanistan

BACKGROUND

Penetrating wounds with environmental contamination are associated with a range of infectious complications, including fungus. This is the first study to examine the epidemiology, resistance patterns, and outcomes of Candida infections and colonization in United States military patients injured in Iraq and Afghanistan.

METHODS

Clinical information associated with initial unique and serial Candida isolates collected from patients (June 2009-October 2013) through the Trauma Infectious Disease Outcomes Study (TIDOS) was evaluated. Susceptibilities were performed using Sensititre YeastOne (YO-9) plates and interpreted by Clinical Laboratory and Standards Institute (CLSI) and adjusted-European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria.

RESULTS

The analysis included 127 patients with 131 unique Candida isolates, of which 102 were Candida albicans and 29 non-albicans Candida spp. Overall, 99% of patients were male with a median age of 23 and an injury severity score of 22. Injuries were primarily due to blasts (77%) and sustained among personnel serving in Afghanistan (89%). There was a median of 7 days from injury to Candida isolation, and 74 isolates were associated with infection. In the multivariate analysis, non-albicans Candida spp were associated with prior antifungal exposure, blood isolates, and wound isolates (P < .01). Nonsusceptibility by CLSI and EUCAST criteria was associated with non-albicans Candida spp (P < .05). Patients with Candida isolation had a 7.1% mortality rate, compared with 1.4% from the overall TIDOS population.

CONCLUSIONS

Candida isolation from patients with penetrating war injuries may identify a population at higher risk for death. Prospective studies are needed to determine whether targeted antifungals and surgical management will affect this mortality rate.