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Biological Hazard – Antibiotic resistant Mutant Superbug (Klebsiella pneumoniae): prolific urban distribution | Houston, Texas


Published Date: 2017-05-22 22:45:34
Subject: PRO/EDR> Antibiotic resistance (03): USA (TX) MDR K. pneumoniae, CG307 predominant clone
Archive Number: 20170522.5055025

Date: Wed 17 May 2017 3:58 PM ET
Source: NBC News [edited]

A dangerous strain of antibiotic-resistant bacteria is far more common in Houston than anyone knew and shows signs it can spread prolifically, researchers reported [Tue 16 May 2017].

It’s a specific strain of bacteria known as _Klebsiella pneumoniae_. The superbug is showing a special talent for picking up genes that give it the ability to resist a broad range of antibiotics, the team at Houston Methodist hospital system said. “It causes very serious infection in hospitalized patients,” said Dr James Musser, who led the study team. “What we discovered, surprisingly, is one of the major strains causing infection in our patients in Houston is genetically distinct from strains of this same germ causing human infections [elsewhere] in the United States,” Musser added.

Doctors and public health officials have been warning for years about the rise of drug-resistant superbugs. They are especially dangerous to patients in the hospital for extended periods of time but they can also be found in people with ordinary infections such as cystitis and pneumonia.

There have been some nightmarish outbreaks — like one in 2011 at the flagship National Institutes of Health’s clinical center in Bethesda, Maryland, that killed 7 people. That outbreak was caused by a strain of _Klebsiella_ resistant to a major class of antibiotics called carbapenems. Officials eventually discovered it was breeding in the hospital’s sinks. And just this past January [2017], doctors reported on the case of a Nevada woman who had traveled to India and died from a rare superbug that could not be killed by any antibiotic available in the U.S.

Musser’s team did an extended genetic analysis of 1777 _Klebsiella_ samples taken from patients at the 2000-bed Houston Methodist hospital system between 2011 and 2015. They found all sorts of tricks the bacteria had developed to resist antibiotics. That included plasmids — little cassette-like pieces of genetic material that different species of bacteria can swap. They are a very quick and easy way for bacteria to acquire resistance genes and are very worrying to infectious disease experts.

“We identified 15 strains expressing the New Delhi metallo-beta-lactamase-1 (NDM-1) enzyme that confers broad resistance to nearly all beta-lactam antibiotics,” the team reported in the journal mBio, published by the American Society for Microbiology [1].

These extended-spectrum beta-lactamase (ESBL) genes are especially dangerous and often kill patients. A once-rare strain of ESBL _Klebsiella_ called CG307 was unusually common, they found. That may mean there’s more to come, the team warned. “Our results may portend the emergence of an especially successful clonal group of antibiotic-resistant _K. pneumoniae_,” they concluded.

In other words, bacteria are actively trading a toolkit that makes them both deadly and resistant to treatment. The discovery in Houston, a diverse city of 6 million people that’s also a popular destination for people seeking medical treatment, is especially troubling, the researchers noted. The superbug is still around, by the way. “We confirmed that CG307 strains continue to be an abundant cause of infections in our hospital system by sequencing an additional 96 ESBL-producing _K. pneumoniae_ strains recovered in 2017,” the team wrote.

“Currently, unfortunately, there is no approved human vaccine against _Klebsiella pneumoniae_,” Musser said. “We desperately need to have a human vaccine.”

[Byline: Maggie Fox]

[1. Long SW, Olsen RJ, Todd N. Eagara TN, et al. Population Genomic Analysis of 1777 Extended-Spectrum Beta-Lactamase-Producing _Klebsiella pneumoniae_ Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307. mBIO 2017; 8(3). Published 16 May 2017. Available online at: ]

Communicated by:

[The following is the edited abstract from the journal article referenced in the news report above:

_Klebsiella pneumoniae_ is a major human pathogen responsible for high morbidity and mortality rates. The emergence and spread of strains resistant to multiple antimicrobial agents and documented large nosocomial outbreaks are especially concerning. To develop new therapeutic strategies for _K. pneumoniae_, it is imperative to understand the population genomic structure of strains causing human infections.

To address this knowledge gap, we sequenced the genomes of 1777 extended-spectrum beta-lactamase-producing _K. pneumoniae_ strains cultured from patients in the 2000-bed Houston Methodist Hospital system between September 2011 and May 2015, representing a comprehensive, population-based strain sample. Strains of largely uncharacterized clonal group 307 (CG307) caused more infections than those of well-studied epidemic CG258. Strains varied markedly in gene content and had an extensive array of small and very large plasmids, often containing antimicrobial resistance genes. Some patients with multiple strains cultured over time were infected with genetically distinct clones.

We identified 15 strains expressing the New Delhi metallo-beta-lactamase 1 (NDM-1) enzyme that confers broad resistance to nearly all beta-lactam antibiotics. Transcriptome sequencing analysis of 10 phylogenetically diverse strains showed that the global transcriptome of each strain was unique and highly variable.

Experimental mouse infection provided new information about immunological parameters of host-pathogen interaction. We exploited the large data set to develop whole-genome sequence-based classifiers that accurately predict clinical antimicrobial resistance for 12 of the 16 antibiotics tested. We conclude that analysis of large, comprehensive, population-based strain samples can assist understanding of the molecular diversity of these organisms and contribute to enhanced translational research.

[The above was extracted from the full article, which is available at the source URL. – Mod.ML]

_Klebsiella pneumoniae_ are Gram-negative bacteria that can cause healthcare-associated infections, including pneumonia, urinary tract infections, bloodstream infections, wound or surgical site infections, and meningitis. They spread from patient to patient via contact with the contaminated hands of healthcare personnel or contaminated environmental surfaces. Patients at most risk are those who require mechanical ventilators or intravenous catheters, and patients who are taking long courses of antibiotics.

_K. pneumoniae_ have become increasingly multidrug resistant. The development of multiple-drug resistance allows _K. pneumoniae_ to persist in the hospital environment, in which antibiotic usage is widespread. Multidrug-resistant (MDR) _K. pneumoniae_ isolates frequently produce extended-spectrum β-lactamases (ESBLs) and/or carbapenemases in combination with quinolone and aminoglycoside resistance.

ESBLs are frequently plasmid-encoded beta-lactamases that hydrolyze extended-spectrum cephalosporins with an oxyimino side chain (cefotaxime, ceftriaxone, and ceftazidime), as well as the oxyimino-monobactam aztreonam. ESBLs also confer resistance to penicillins and older cephalosporins, but do not confer resistance to the carbapenems. However, _K. pneumoniae_ have also developed resistance to carbapenem antibiotics by the acquisition of certain transmissible plasmid-encoded beta-lactamases (carbapenemases) that destroys the carbapenems, as well as most other beta-lactam antibiotics. These organisms are named Klebsiella pneumoniae carbapenemase (KPC)-producers.

Because transmissible resistance plasmids can be shared between _Klebsiella_ spp. and other pathogens, these enzymes now been identified in several other species in the Enterobacteriaceae family and are called carbapenem-resistant Enterobacteriaceae or CRE.

Molecular typing procedures, such as multilocus sequence typing (MLST) and whole genome sequencing, have been used to classify _K. pneumoniae_ into ST and clonal groups (CG). The above investigation sequenced the genomes of 1777 ESBL-producing _K. pneumoniae_ strains cultured from patients in the 2000-bed Houston Methodist Hospital system between September 2011 and May 2015. The study found that CG307, an otherwise unusual clonal group caused more infections, for unknown reasons, in the Houston, Texas region throughout the study period (between September 2011 and May 2015), as well as in 2017, than CG258 that predominates elsewhere in the U.S. ( The study also found that 64.6 percent of the CG258 strains compared to 34.3 percent of the CG307 strains were KPC-producers and CG307 strains causing infections in Houston appeared to be as virulent as CG258 strains. – Mod.ML

A HealthMap/ProMED-mail map can be accessed at:]

See Also

Antibiotic resistance (02): WHO, priority pathogens 20170301.4871299
Antibiotic resistance (01): China: colistin, MCR-1 clin. Enterobacteriaceae isolates 20170129.4799871

Carbapenem-resistant Enterobacteriaceae – Ireland: (LK) nosocomial, fatal, 2009-2015 20161124.4652418
Antibiotic resistance (04): India, China, environmental pollution 20161020.4574059
Antibiotic resistance (03): India (TG) environmental pollution 20161010.4548738
Antibiotic -resistant Enterobacteriaceae – USA: (CA) reportable 20161008.4545844
Gonococcal disease – USA (05): (HI) ceftriaxone plus azithromycin resistance 20160924.4513277
Antibiotic resistance (02): UN General Assembly 2016, WHO Global Action Plan 20160923.4511617
Antibiotic resistance: International Journal of Infectious Diseases, editorial 20160918.4497194
Antibiotic resistance – USA (06): ESBL, FQ, E. coli, UTI 20160918.4496481
Antibiotic resistance – France: non-MCR-1, colistin/carbapenem, 2014 20160916.4492825
Antibiotic resistance – USA (05): colistin, MCR-1, E. coli, new case, contacts 20160911.4479863
Gonococcal disease – UK (02): azithromycin resistance, spread, MSM, RFI 20160910.4479782
Antibiotic resistance, Salmonella – USA: NARMS, 2014 20160910.4478868
Antibiotic resistance – USA (04): (NJ) colistin/carbapenem, MCR-1, E. coli, human 20160902.4459453
Antibiotic resistance – Europe, Canada: colistin, MCR-1, E. coli, bovine, human 20160808.4400601
Antibiotic resistance – Germany: colistin, MCR-1, E. coli, poultry, 2010 – 2015 20160728.4374873
Gonococcal disease – USA (03): increasing azithromycin resistance, 2014 20160716.4349791
Antibiotic resistance – Belgium: colistin, MCR-2, plasmid, E. coli, pigs, calves 20160709.4335297
Antibiotic resistance – Portugal: colistin, MCR-1, Salmonella, Cu tolerance 20160703.4323241
Antibiotic resistance – USA (03): (NY) colistin, MCR-1, E. coli, human 20160630.4317770
Antibiotic resistance – multicountry: colistin, MCR-1, E. coli, gull 20160630.4313655
Antibiotic resistance, Salmonella – Africa: (sub-Saharan) fluoroquinolones 20160617.4293589
Antibiotic resistance – USA (02): colistin, MCR-1, E. coli, pig 20160616.4290293
Antibiotic resistance – USA: colistin, MCR-1, E. coli, human, pig 20160528.4251552
Antibiotic resistance – Denmark: AR genes, archived soil, 1923-2010 20160224.4047676
Antibiotic resistance – Italy: colistin, MCR-1, E. coli, turkeys, 2014 20160113.3933461
Antibiotic resistance – Canada: colistin, MCR-1, E. coli, grd. beef, human, 2010 20160106.3915891
Gonococcal disease – UK: (England) azithromycin monotherapy resistance, RFI 20160103.3907866

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