Global growth continues in diagnostic and clinical microbiology. However, do regional solutions attempt to address universal problems?
Vol. 20 • Issue 12 • Page 42
Remarkable global growth continues in diagnostic and clinical microbiology. It is fortunate (and almost a requirement), given the global nature of infectious diseases, continued impact of climate change and unrelenting impact of global transportation. The authors’ recent travels in Asia Pacific, Australia and New Zealand have emphasized how universal our problems are, yet our solutions are regional and the impact significant.
Here, we emphasize five items that have had a particular importance in the managerial aspects of infectious diseases and the laboratory in 2011:
- global resistance and the “revenge” of the gram-negative rods,
- global surveillance of antibiotic resistance and real-time tracking of infectious diseases,
- newer tests for classic diseases,
- normal flora stewardship and
- newer disease recognition and potential intervention.
Global Resistance and Gram-negative Rods
Often fostered by public opinion, the emphasis in the last 10 years has dealt with the Gram positives, particularly Methicillin-resistant Staphylococcus aureus (MRSA). The smoldering and continuing global evolution of Gram-negative resistance has only recently reached public opinion. It continues to be the focus for international tracking, although clearly Gram-negative rods have developed unique mechanisms of resistance, stretching the capabilities of antimicrobial therapy and ultimately requiring alternative interventions (such as Probiotics).
Table 1 highlights the “alphabet soup” of these emerging resistance mechanisms. All are variants of extended spectrum beta-lactamases (ESBLs), first described in the 1970s by David N Livermore, PhD, of England. The Table highlights the nomenclature, or mechanism, of the organisms involved, and the extent of the global occurrence. Clinically, you are more than twice as likely to die if you have an ESBL compared to a non-ESBL isolate.1
A number of key points can be highlighted:
- CTX-M leaked from Klebsiella to E. coli then Enterobacter, and so on. In the U.S., the most prevalent form is CTX-M-15; in Spain it’s CTX-M-14; and in South America and Israel CTX-M-2. Diversity equals survival for microbes.
- In 2005, 50% of Greece’s Klebsiella bacteremias were resistant to carbapenems with VIM strains dominant from 2005- 2008, but since 2008, KPC became the dominant force.
- Acquired carbapenemase-class B-NDM strain linked to healthcare in India/Pakistan is sensitive to Colistin, and may be sensitive to tigecycline and/or fosfomycin except for urinary tract infections.
- Acquired carbapenemase-class C (Enterobacteracae) were found in outbreaks in Africa, London, India and South America; but, interestingly, still susceptible to cephalosporins (first generation) but resistant to carbapenems (third generation).
These variants of ESBL are found increasingly in long-term and/or nursing home environments in the U.S. Colonization does not predict disease, but clearly the potential of gene transfer and mechanisms of resistance limiting traditional therapeutics is a significant problem. It is interesting how the older transitional antimicrobials, off the therapeutic environment, may have significant impact in the era of these new microorganisms, called “Multi-Drug Resistant Organisms” (MDROs). A more complete discussion can be found in Dr. Arias’ manuscript.2
To address these MDROs, regulatory bodies-the FDA, CLSI and NIH-have collaborated to evaluate the necessity for changing the methods of laboratory reporting. Laboratory “breakpoints” for establishing the resistance of an isolate were based on organisms prevalent in the community several years ago. With the
emerging global nature and the change of the mechanisms of resistance, it is time to upgrade laboratory methods. Newer changes will be forthcoming in the next CLSI January 2012. It is imperative that laboratory directors continue to upgrade and reflect methods of reporting consistent with the global resistance.
As well, there’s another problem: The mechanisms of resistance may not be detected by automated systems generally used in large laboratories. The problem with automation is often not measuring the resistance, but having concentrations low enough to measure “susceptible” strains versus “intermediate” resistance. Validation of newer antimicrobials is considerably more difficult now and the FDA has published suggestions for validating testing. These new breakpoints are focused on the Gram-negative organisms predictably and particularly Pseudomonas aeruginosa and Enterobacteriaceae and are directed toward the cephalosporins and carbapenems.
This should not detract from the fact that these problems are associated with planktonic or free-floating organisms. Biofilms play a significant role in sepsis and chronic infections, and colonization resistance is another form of resistance. The impact of multiple organisms growing in a community covered by a glycocalyx is another reason for continuing failure of antimicrobial stewardship and/or methods that have historically had success against planktonic organisms.
The growing awareness of MDROs and the importance of tracking their movement globally have increased the significance of global tracking and surveillance. Table 2 highlights two of these, which we have found to be very helpful and beneficial in the global and national sense.
In tracking infectious diseases and the significance of recent outbreaks, Google’s Health Map (www.healthmap.org) is unparalleled. It highlights reported outbreaks to a community and relates the potential consequence. It is updated on a frequent basis and allows one to continually “zero in” on a particular global region and newer occurrences.
GIDEON (Global Infectious Diseases and Epidemiology Network) has a particular benefit because it not only tracks infectious diseases, but incorporates world literature review classified into four specific sections: 1) diagnoses (Dx), 2) pharmacology (Rx), 3) identification and 4) control. Although we have used this primarily as a means of recognizing international disease (not readily seen in our own environment), the capacity to reach a potential diagnosis is remarkable. This system is a wealth of education and clinical data summarized on a regular basis in a single place-www.gideon.com.
MALDI-TOF, BARDOT and WASP apply to the emerging methods of rapid microbial detection well beyond traditional cultures, PCR and microarray. In fact, these are significantly different, which adds to their uniqueness and ability to be incorporated into a traditional workflow without altering the lab procedure. Table 3 highlights these newer methods focusing on some of the benefits and costs.
MALDI-TOF, which stands for Matrix Assisted Laser Desorption/Ionization-Time of Flight, is based on mass spectrometry and computational analysis.It has been available in the European market for the last five years with well over 300 laboratories utilizing this strategy. Although there is a significant outlay for initial purchase, its cost per assays is reduced, approximately $0.05 U.S. dollars; as well, it has the potential of analyzing approximately 96 organisms in a two-hour time frame.
BARDOT, which stands for Bacterial Rapid Detection using Optical scattered Technology, was originally designed by scientists and investigators at Purdue University and applied to rapid detection of microbes in food and food poisoning. It is the most unique, based on laser scatter patterns and amplification of those patterns mathematically from a laser diffraction of the colony on a plate. We became involved as a test site for evaluating its usefulness in bioterrorism and homeland security, but found its clinical application well beyond the original expectations; its use is appropriate for classifying wound isolates, their status as to “early” versus “late” and the potential of recognizing certain classes of antibiotic resistance.
One company (COPAN Diagnostics Inc.) has addressed the need for automating the early phases of specimen preparation and plate inoculation, utilizing robotics in a unique collection of stations, each with specific functions. It is called the WASP (Walk Away Specimen Processing) and is advertised as a revolutionary approach for frontline processing in the microbiology laboratory. It automates the processes involved in plating and streaking, as well as Gram stain preparation and inoculation. With WASP-2 Spiral Plater, as a compliment, colony counts can be addressed simultaneously. Its uniqueness is based on its volume capacity, reproducibility and time reduction given the instrumentations, organization and stratification.
Newer Tests for Classic Diseases
Ventilator Associated Pneumonia (VAP) continues to be a global focus given its costs and resource utilization in the ICU. Recent studies by Morrow3 and others highlight the growing awareness and impact in medical practice of probiotics. The Figure highlights the present use of antibiotics, its globalization and the reality that different parts of that globe utilize probiotics directed toward different disease. There are really three distinct areas as highlighted in the Figure, but the potential for economic impact is similar and significant. It is estimated, for example, that probiotic purchases that will occur between now and the year 2015 will be $87.7 billion U.S. dollars (www.who.int/about/regions/em/index/html).
The numbers of mechanically ventilated patients with VAP has not decreased, and the consequences of long-term ventilation with resistance and development of C. difficile has been unrelenting. Morrow3 focused on a limited number of selected patients for a 5-year study; patients received a probiotic twice daily as a slurry and/or NG tube. Inoculum comprised of 2×109 CFUs of a well-established probiotic Lactobacillus rhamnosusGC. Patients on probiotics had fewer complications, did not cascade to VAP in 50% of the cases and had a concomitant reduction in antibiotic usage with a significant reduction in C. difficile infections.3
Another disease that will not go away is Mycobacterium tuberculosis, particularly with recent reemphasis on global Rifampin resistance. The World Health Organization (Table 4) has endorsed a new method (C-GEME X, MTB/RIF) with results available within two hours. Published reports indicated that its usefulness, particularly in HIV positive patients where multi-drug resistance TB can be a problem, were beneficial.
Clostridium difficile continues to fend off attempts to resolve its growing significance. Newer tests reflect altered physiologic response with earlier warnings. Lactoferrin production and GDH have all become useful biomarkers for C. difficile; additionally, several updated PCR detection systems have emerged.
Normal Flora Stewardship
Normal flora of Homo sapiens is, in fact, one of its best defense mechanisms. It limits invasion of exogenous flora/pathogens via the traditional concept of occupying space, but our endogenous flora may be a biomarker and individual signature for disease and/or health. There is a growing awareness that our microbial signature can define an individual’s health and perhaps be predictive of who we are, such as a standard A, B, O blood type. Arumugam4 described three Entero-types of the human gut flora; these were distinct for selected populations and reflective of a physiologic stability within the GI tract defined by the microbial population. Simultaneously, a group from Cleveland5 established (at the other end of the GI tract) that the oral fungal mycobiome in healthy individuals is considerably more complex than we had recognized. Hence, it too may be part of this evolving recognition of a human microbial signature that is defining who we are and our status with health equal to the iris and fingerprint definition. This group defined 20 healthy individuals and looked at the 18-SRNA consistent with mycologic detection.5 Out of 74 recovered fungal organisms, each individual carried between nine and 23 species of oral fungi, with Candida (75%) the most frequent.
This enhances our recognition that we live in a microbial world but is not new. In 2002, Dr. Steward Levy had already described the concerns that he had with the overuse of antimicrobials.6 He pointed out that “we began the antibiotic era with a full-fledged assault on bacteria; it was a battle misconceived and of which we cannot be the winner, we cannot destroy the microbial world in which we evolve. The best solution now is to make a broader view of the microbial world while focusing on the pathogens. Our efforts should act in ways that impact fewer commensal flora.”
Our microbial world-the human microbiota and mycobiota-is equivalent to an organ system. It has functions and capacities consistent with the functions of our traditional six-organ system; hence, in contrast to stewardship of antibiotics, stewardship of our normal flora should be paramount in managing an infectious disease.
- Schwaber MJ, Carmeli Y. Mortality and delay in effective therapy associated with extended-spectrum beta-lactamase production in Enterobacteriaceae bacteraemia: A systematic review and meta-analysis. The Journal of antimicrobial chemotherapy. J Antimicrob Chemother.2007 Nov; 60(5):913-20. Epub 2007 Sep 11.
- Arias CA, Murray BE. Antibiotic-resistant bugs in the 21st century – A clinical super-challenge. N Engl J Med.2009 Jan 29;360(5):439-43.
- Morrow LE, Kollef MH, Casale TB. Probiotic prophylaxis of ventilator-associated pneumonia: a blinded, randomized, controlled trial. Am J Respir Crit Care Med. 2010 Oct 15;182(8):1058-64.
- Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature. 2011 May 12; 473(7346):174-80.
- 5. Ghannoum MA, Jurevic RJ, Mukherjee PK, et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog. 2010 Jan 8;6(1):e1000713.
- 6. Levy SB. Factors impacting on the problem of antibiotic resistance. J Antimicrob Chemother. 2002 Jan;49(1):25-30.