Sameera M. Al Johani

Molecular Characterization of Carbapenemase-Producing Escherichia coli and Klebsiella pneumoniae in the Countries of the Gulf Cooperation Council: Dominance of OXA-48 and NDM Producers

ABSTRACT The molecular epidemiology and mechanisms of resistance of carbapenem-resistant Enterobacteriaceae (CRE) were determined in hospitals in the countries of the Gulf Cooperation Council (GCC), namely, Saudi Arabia, United Arab Emirates, Oman, Qatar, Bahrain, and Kuwait. Isolates were subjected to PCR-based detection of antibiotic-resistant genes and repetitive sequence-based PCR (rep-PCR) assessments of clonality. Sixty-two isolates which screened positive for potential carbapenemase production were assessed, and 45 were found to produce carbapenemase. The most common carbapenemases were of the OXA-48 (35 isolates) and NDM (16 isolates) types; 6 isolates were found to coproduce the OXA-48 and NDM types. No KPC-type, VIM-type, or IMP-type producers were detected. Multiple clones were detected with seven clusters of clonally related Klebsiella pneumoniae. Awareness of CRE in GCC countries has important implications for controlling the spread of CRE in the Middle East and in hospitals accommodating patients transferred from the region.

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Isolates in the Gulf Cooperation Council States: Dominance of OXA-23-Type Producers

ABSTRACT The molecular epidemiology and mechanisms of resistance of carbapenem-resistant Acinetobacter baumannii (CRAB) were determined in hospitals in the states of the Cooperation Council for the Arab States of the Gulf (Gulf Cooperation Council [GCC]), namely, Saudi Arabia, United Arab Emirates, Oman, Qatar, Bahrain, and Kuwait. Isolates were subjected to PCR-based detection of antibiotic resistance genes and repetitive sequence-based PCR (rep-PCR) assessments of clonality. Selected isolates were subjected to multilocus sequence typing (MLST). We investigated 117 isolates resistant to carbapenem antibiotics (either imipenem or meropenem). All isolates were positive for OXA-51. The most common carbapenemases were the OXA-23-type, found in 107 isolates, followed by OXA-40-type (OXA-24-type), found in 5 isolates; 3 isolates carried the ISAba1 element upstream of bla OXA-51-type. No OXA-58-type, NDM-type, VIM-type, or IMP-type producers were detected. Multiple clones were detected with 16 clusters of clonally related CRAB. Some clusters involved hospitals in different states. MLST analysis of 15 representative isolates from different clusters identified seven different sequence types (ST195, ST208, ST229, ST436, ST450, ST452, and ST499), as well as three novel STs. The vast majority (84%) of the isolates in this study were associated with health care exposure. Awareness of multidrug-resistant organisms in GCC states has important implications for optimizing infection control practices; establishing antimicrobial stewardship programs within hospital, community, and agricultural settings; and emphasizing the need for establishing regional active surveillance systems. This will help to control the spread of CRAB in the Middle East and in hospitals accommodating transferred patients from this region.

Severe neurologic syndrome associated with Middle East respiratory syndrome corona virus (MERS-CoV).

BackgroundSince the identification of the first case of infection with the Middle East respiratory syndrome corona virus (MERS-CoV) in Saudi Arabia in June 2012, the number of laboratory-confirmed cases has exceeded 941 cases globally, of which 347 died. The disease presents as severe respiratory infection often with shock, acute kidney injury, and coagulopathy. Recently, we observed three cases who presented with neurologic symptoms. These are so far the first reported cases of neurologic injury associated with MERS-CoV infection.MethodsData was retrospectively collected from three patients admitted with MERS-CoV infection to Intensive Care unit (ICU) at King Abdulaziz Medical City, Riyadh. They were managed separately in three different wards prior to their admission to ICU.FindingThe three patients presented with severe neurologic syndrome which included altered level of consciousness ranging from confusion to coma, ataxia, and focal motor deficit. Brain MRI revealed striking changes characterized by widespread, bilateral hyperintense lesions on T2-weighted imaging within the white matter and subcortical areas of the frontal, temporal, and parietal lobes, the basal ganglia, and corpus callosum. None of the lesions showed gadolinium enhancement.InterpretationCNS involvement should be considered in patients with MERS-CoV and progressive neurological disease, and further elucidation of the pathophysiology of this virus is needed.

Multi-drug carbapenem-resistant Klebsiella pneumoniae infection carrying the OXA-48 gene and showing variations in outer membrane protein 36 causing an outbreak in a tertiary care hospital in Riyadh, Saudi Arabia

OBJECTIVES To investigate the genes of antibiotic resistance among isolates from the first reported carbapenem-resistant Klebsiella pneumoniae (CRKP) outbreak in a tertiary care hospital, Riyadh, Saudi Arabia. METHODS Antimicrobial susceptibility testing was performed on bacterial isolates using the Microscan Walkaway system (Siemens, Germany) and was confirmed by Etest (AB Biodisk, Sweden). bla-CTX-M, -SHV, -TEM, -OXA-48, OXA-A,B,C,D, -KPC, -NDM, -VIM, -IMP, integron 1, and outer membrane proteins(Omp)-35 and Omp-36 were investigated by PCR amplification and direct sequencing of PCR products. Isolates were sequence-typed by multilocus sequence typing (MLST). RESULTS All isolates were resistant to cefotaxime, ceftazidime, cefepime, ciprofloxacin, and piperacillin-tazobactam, and 91% (21 out of 23) were resistant to amikacin and gentamicin. All isolates except two from a single patient were resistant to one of the carbapenems. CTX-M and SHV genes were detected in all isolates, CTX-M-15 and SHV-1 types being predominant among these extended-spectrum beta-lactamases (ESBLs). TEM-1 was found in all except one isolate (isolate 3). Significantly, the OXA-48 gene was also found in all isolates. OXA-D-gene was found in three out of 23 isolates. KPC, NDM, OXA-A, -B, -C, VIM, and IMP genes were absent in all isolates. Disruption of the Omp-36 gene due to insertion of transposon IS903 and/or IS4 was detected in four out of 23 isolates, and some unique variations were also observed in this gene, including an insertion of two amino acids in the L3 region of Omp-36 in one isolate (isolate 3) and a mutation resulting in a premature stop codon in another isolate (isolate 25). MLST revealed ST29 to be the predominant sequence type (17 out of 23 isolates, 74%). Three were ST709 and one each was ST37 and ST111; one isolate had an unknown ST. CONCLUSIONS This is probably the first reported outbreak of multidrug/carbapenem-resistant Klebsiella infection involving the OXA-48 gene from Saudi Arabia. Although the presence of ESBLs such as OXA, CTX-M, TEM, and SHV are predictable reasons for resistance, variations in the Omp-36 gene might also have precipitated this phenomenon. Disruption of the Omp-36 sequence by large insertional elements, the insertion of two amino acids in a very crucial part of this protein, and the presence of a premature stop codon in one isolate might have rendered this protein incomplete and non-functional. The study also demonstrated that more than one type of clone was responsible for this reported apparent outbreak and that ST29, a clone not reported from this region before, was the major clone responsible.

Feasibility of Using Convalescent Plasma Immunotherapy for MERS-CoV Infection, Saudi Arabia.

Efficacy testing will be challenging because of the small pool of donors with sufficiently high antibody titers.

Description of a Hospital Outbreak of Middle East Respiratory Syndrome in a Large Tertiary Care Hospital in Saudi Arabia.

BACKGROUND Since the first isolation of Middle East respiratory syndrome coronavirus (MERS-CoV) in Saudi Arabia in 2012, sporadic cases, clusters, and sometimes large outbreaks have been reported. OBJECTIVE To describe the recent (2015) MERS-CoV outbreak at a large tertiary care hospital in Riyadh, Saudi Arabia. METHODS We conducted an epidemiologic outbreak investigation, including case finding and contact tracing and screening. MERS-CoV cases were categorized as suspected, probable, and confirmed. A confirmed case was defined as positive reverse transcription polymerase chain reaction test for MERS-CoV. RESULTS Of the 130 suspected cases, 81 (62%) were confirmed and 49 (38%) were probable. These included 87 patients (67%) and 43 healthcare workers (33%). Older age (mean [SD], 64.4 [18.3] vs 40.1 [11.3] years, P<.001), symptoms (97% vs 58%, P<.001), and comorbidity (99% vs 42%, P<.001) were more common in patients than healthcare workers. Almost all patients (97%) were hospitalized whereas most healthcare workers (72%) were home isolated. Among 96 hospitalized cases, 63 (66%) required intensive care unit management and 60 (63%) required mechanical ventilation. Among all 130 cases, 51 (39%) died; all were patients (51 [59%]) with no deaths among healthcare workers. More than half (54%) of infections were believed to be caught at the emergency department. Strict infection control measures, including isolation and closure of the emergency department, were implemented to interrupt the chain of transmission and end the outbreak. CONCLUSION MERS-CoV remains a major healthcare threat. Early recognition of cases and rapid implementation of infection control measures are necessary. Infect Control Hosp Epidemiol 2016;1–9

Antibiotic-resistant ST38, ST131 and ST405 strains are the leading uropathogenic Escherichia coli clones in Riyadh, Saudi Arabia

OBJECTIVES We investigated the molecular epidemiology of uropathogenic Escherichia coli (UPEC) from a tertiary care hospital in Riyadh, Saudi Arabia, revealing, for the first time, the population structure of UPEC in the region. METHODS A total of 202 UPEC isolates were recovered from hospital and community patients with urinary tract infection in December 2012 and January 2013. Strains were characterized by MLST, antibiotic susceptibility determination and virulence gene detection. RESULTS The most common lineages were ST131 (17.3%), ST73 (11.4%), ST38 (7.4%), ST69 (7.4%), ST10 (6.4%), ST127 (5.9%), ST95 (5.4%), ST12 (3.5%), ST998 (3.5%) and ST405 (3%). ST131 and ST405 isolates were significantly associated with high levels of antibiotic resistance (60% of ST131 carried CTX-M-14 or CTX-M-15 and 66.7% of ST405 isolates carried CTX-M-15). ST131, CTX-M-15-positive isolates were predominantly of the fimH30/clade C group, resistant to fluoroquinolones; members of this sub-group were more likely to carry a high number of genes encoding selected virulence determinants. The relatively high proportion of ST38 was notable and four of these isolates harboured aggR. CONCLUSIONS Our findings highlight the presence of MDR, CTX-M-positive ST38, ST131 and ST405 UPEC in Saudi Arabia. The high proportion of isolates with CTX-M is a particular concern. We suggest that ST38 UPEC warrant further study.

Recovery from the Middle East respiratory syndrome is associated with antibody and T cell responses

MERS-CoV T cell responses can be detected in MERS survivors in the absence of detectable virus-specific antibody. Breaking the camel virus’s back Middle East respiratory syndrome coronavirus (MERS-CoV) causes a potentially lethal zoonotic pneumonia that can transfer between individuals after initial exposure to an infected camel. Now, Zhao et al. dig deeper into the immune response in MERS-CoV survivors. They found that neutralizing antibody titers could predict protection in an animal model but that antibody levels were often transient. Moreover, both CD4+ and CD8+ T cells were induced after MERS-CoV infection, and these cells could be detected even in the absence of virus-specific antibody. These data suggest that T cells may be useful in detecting mild or subclinical infection and that epitopes recognized by these T cells may form the basis for future vaccine design and immunotherapy. The Middle East respiratory syndrome coronavirus (MERS-CoV) causes a highly lethal pneumonia. MERS was recently identified as a candidate for vaccine development, but most efforts focus on antibody responses, which are often transient after CoV infections. CoV-specific T cells are generally long-lived, but the virus-specific T cell response has not been addressed in MERS patients. We obtained peripheral blood mononuclear cells and/or sera from 21 MERS survivors. We detected MERS-CoV–specific CD4+ and CD8+ T cell responses in all MERS survivors and demonstrated functionality by measuring cytokine expression after peptide stimulation. Neutralizing (PRNT50) antibody titers measured in vitro predicted serum protective ability in infected mice and correlated with CD4+ but not CD8+ T cell responses; patients with higher PRNT50 and CD4+ T cell responses had longer intensive care unit stays and prolonged virus shedding and required ventilation. Survivors with undetectable MERS-CoV–specific antibody responses mounted CD8+ T cell responses comparable with those of the whole cohort. There were no correlations between age, disease severity, comorbidities, and virus-specific CD8+ T cell responses. In conclusion, measurements of MERS-CoV–specific T cell responses may be useful for predicting prognosis, monitoring vaccine efficacy, and identifying MERS patients with mild disease in epidemiological studies and will complement virus-specific antibody measurements.

The strategic plan for combating antimicrobial resistance in Gulf Cooperation Council States.

The Gulf Cooperation Council Center for Infection Control (GCC-IC) has placed the emergence of antimicrobial resistance (AMR) on the top of its agenda for the past four years. The board members have developed the initial draft for the GCC strategic plan for combating AMR in 2014. The strategic plan stems from the WHO mandate to combat AMR at all levels. The need for engaging a large number of stakeholders has prompted the GCC-IC to engage a wider core of professionals in finalizing the plan. A multi-disciplinary group of more than 40 experts were then identified. And a workshop was conducted in Riyadh January 2015 and included, for the first time, representation of relevant ministries and agencies as well as international experts in the field. Participants worked over a period of two and a half days in different groups. International experts shared the global experiences and challenges in addressing human, food, animal, and environmental aspects of controlling AMR. Participants were then divided into 4 groups each to address the human, animal, microbiological and diagnostic, or the environmental aspect of AMR. At the end of the workshop, the strategic plan was revised and endorsed by all participants. The GCC-IC board members then approved it as the strategic plan for AMR. The document produced here is the first GCC strategic plan addressing AMR, which shall be adopted by GCC countries to develop country-based plans and related key performance indicators (KPIs). It is now the role of each country to identify the body that will be accountable for implementing the plan at the country level.

Middle East respiratory syndrome coronavirus on inanimate surfaces: A risk for health care transmission

The Middle East Respiratory syndrome coronavirus (MERS-CoV) has been responsible for multiple health care–associated outbreaks. We investigated whether high-touch surfaces in 3 rooms of laboratory-confirmed MERS-CoV patients were contaminated with MERS-CoV RNA. We found 2 out of 51 surfaces were contaminated with MERS-CoV viral genetic material. Hence, environmental contamination may be a potential source of health care transmission and outbreaks. Meticulous environmental cleaning may be important in preventing transmission within the health care setting.